CDS 66 - 452
  /gene="1"
  /product="gp1"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_1"
    /note=Original Glimmer call @bp 66 has strength 14.04; Genemark calls start at 66
    /note=SSC: 66-452 CP: no SCS: both ST: NI BLAST-Start:  GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.936, -2.5594668560256912, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 
    /note=
    /note=Glimmer and Genemark both call the gene and the same start site.
    /note=RBS: Best Z-score and final score. 
    /note=Coding potential: Start site includes all coding potential. 
    /note=Starterator: Only this gene and another gene in DunneganBoMo are part of the Pham. Identical genes
    /note=
    /note=Function: 
    /note=
    /note=No matches in NCBI, PhagesDB, Conserved domain database, or HHPred (JP)
    /note=No transmembrane domains based on DeepTMHMM
    /note=
    /note=Reviewed: HA, TH, TM

CDS complement (624 - 833)
  /gene="2"
  /product="gp2"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_2"
    /note=
    /note=SSC: 833-624 CP: no SCS: neither ST: NI BLAST-Start:  GAP: 43 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.827, -4.996372795139552, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=there is some coding potential but not a great deal. Neither Glimmer nor Genemark call it a gene. It does seem to have some coding potential and match on some level to proteins of known structure. This start site gives the best z and final score. There are no NCBI BLAST matches and no HHpred matches over 90% so hypothetical protein

CDS complement (877 - 2373)
  /gene="3"
  /product="gp3"
  /function="ParB-N-terminal-like domain"
  /locus tag="DunneganBoMo_3"
    /note=Original Glimmer call @bp 2373 has strength 11.06; Genemark calls start at 2373
    /note=SSC: 2373-877 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_103 [Arthrobacter phage Atuin]],,NCBI, q2:s3 99.7992% 0.0 GAP: 236 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.748, -3.6146798363680817, yes F: ParB-N-terminal-like domain SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_103 [Arthrobacter phage Atuin]],,UDL16697,92.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start Site:
    /note=
    /note=Good Coding potential.
    /note=Glimmer and Genemark both call the gene and the same start site that includes all coding potential.
    /note=Starterator: Only this gene and one other from DunneganBoMo (275) have this start site. All other commonly called start sites are missing from this gene.
    /note=RBS: Best Raw score and Z-Score
    /note=
    /note=Function:
    /note=The protein sequence alignment with two other phages in the pham both of which called this function. Due to update in the SEA PHAGES approved function list the function has been changed (JP)
    /note=
    /note=Reviewed: TM

CDS 2610 - 2822
  /gene="4"
  /product="gp4"
  /function="RNA binding protein"
  /locus tag="DunneganBoMo_4"
    /note=Original Glimmer call @bp 2610 has strength 3.96; Genemark calls start at 2610
    /note=SSC: 2610-2822 CP: no SCS: both ST: NI BLAST-Start:  GAP: 236 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.909, -5.40983604789782, yes F: RNA binding protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start Site:
    /note=RBS: Best Z-score and final score
    /note=Covers all coding potential
    /note=Glimmer and GeneMark both call the start site 
    /note=
    /note=Function:
    /note= - No BLAST matches, Several matches on HHpred to a KOW domain which is a RNA binding domain
    /note=
    /note=Reviewed: HA, TM

CDS 2969 - 3316
  /gene="5"
  /product="gp5"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_5"
    /note=Genemark calls start at 2969
    /note=SSC: 2969-3316 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_104 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.68286E-56 GAP: 146 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.473, -5.15706299163995, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_104 [Arthrobacter phage Atuin]],,UDL16698,84.3478,1.68286E-56 SIF-HHPRED:  SIF-Syn: 
    /note=Start site:
    /note=Called only by GeneMark
    /note=Best Z-score and final score
    /note=Starterator - most likely start site, not many genes had this start site
    /note=
    /note=Function: 
    /note=hypothetical protein in the most similar proteins, No significant HHPred matches
    /note=
    /note=Reviewed: TM

CDS 3436 - 3834
  /gene="6"
  /product="gp6"
  /function="membrane protein"
  /locus tag="DunneganBoMo_6"
    /note=Original Glimmer call @bp 3436 has strength 6.75; Genemark calls start at 3436
    /note=SSC: 3436-3834 CP: no SCS: both ST: NI BLAST-Start:  GAP: 119 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.748, -3.0425830684175623, yes F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start Site:
    /note=RBS: Best Z-score and final score
    /note=Covers all coding potential
    /note=Glimmer and GeneMark both call the start site 
    /note=Starterator calls this start site when present
    /note=
    /note=Function:
    /note=hypothetical protein - No BLAST matches, no significant hits on HHpred, no conserved domains, one transmembrane domain
    /note=
    /note=Reviewed: TM

CDS 3916 - 4239
  /gene="7"
  /product="gp7"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_7"
    /note=Original Glimmer call @bp 3916 has strength 8.52; Genemark calls start at 3916
    /note=SSC: 3916-4239 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_107 [Arthrobacter phage Atuin]],,NCBI, q1:s1 61.6822% 6.28927E-11 GAP: 81 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_107 [Arthrobacter phage Atuin]],,UDL16701,36.7521,6.28927E-11 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 3916
    /note=RBS: Final Score and Z-Score
    /note=Starterator: No additional Genes (other than a duplicated gene in this genome) same as gene 280
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=
    /note=Reviewed: TM
    /note=Checked: C.A.R

CDS 4327 - 4560
  /gene="8"
  /product="gp8"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_8"
    /note=Original Glimmer call @bp 4327 has strength 10.59; Genemark calls start at 4327
    /note=SSC: 4327-4560 CP: no SCS: both ST: NI BLAST-Start:  GAP: 87 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.145, -2.1123791669543204, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 4327
    /note=RBS: Final Score and Z-Score
    /note=Starterator: No additional Genes (other than a duplicated gene in this genome)
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=
    /note=Reviewed: TM
    /note=Checked: C.A.R

CDS 4570 - 4971
  /gene="9"
  /product="gp9"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_9"
    /note=Original Glimmer call @bp 4570 has strength 11.64; Genemark calls start at 4570
    /note=SSC: 4570-4971 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_100 [Arthrobacter phage Racecar]],,NCBI, q1:s1 92.4812% 7.46775E-31 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.35, -3.8137921535956054, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_100 [Arthrobacter phage Racecar]],,QFG12148,60.7407,7.46775E-31 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 4570
    /note=RBS: Final Score and Z-Score
    /note=Starterator: No additional Genes (other than a duplicated gene in this genome) same as gene 283
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=NCBI blast results show only hypothetical proteins
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=
    /note=Reviewed: TM
    /note=Checked: C.A.R

CDS 4955 - 5452
  /gene="10"
  /product="gp10"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_10"
    /note=Original Glimmer call @bp 5051 has strength 7.31; Genemark calls start at 5051
    /note=SSC: 4955-5452 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein [Butyricimonas sp. GBGM4] ],,NCBI, q84:s3 45.4545% 8.22742E-15 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.157, -5.8328603995233195, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Butyricimonas sp. GBGM4] ],,WP_306449729,60.2273,8.22742E-15 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential as shown by Genemark S. Start site is 4955, stop site is 5452. Hypothetical protein. there is coding potential that extends beyond the called start site. All others in the pham have two conserved start sites earlier with no manual annotations. I would err on the side of including the coding potential so I moved the start site earlier.
    /note=
    /note=No significant matches on HHpred, no matches on NCBI BLAST, no transmembrane domain.
    /note=
    /note=Checked: C.A.R
    /note=Checked: RR

CDS 5483 - 5767
  /gene="11"
  /product="gp11"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_11"
    /note=Genemark calls start at 5534
    /note=SSC: 5483-5767 CP: no SCS: genemark-cs ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_312 [Arthrobacter phage Atuin]],,NCBI, q4:s6 96.8085% 4.41904E-46 GAP: 30 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.106, -4.988391134024432, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_312 [Arthrobacter phage Atuin]],,WWQ87564,83.3333,4.41904E-46 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is 5483. the coding potential extends beyond the Genemark called start sites. This earlier start site is conserved in all members of the pham. Codes for a hypothetical protein. No significant hits on HHpred, No matches on NCBI BLAST, no transmembrane domains.
    /note=
    /note=Checked: C.A.R
    /note=Checked: R.R.

CDS 5838 - 5972
  /gene="12"
  /product="gp12"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_12"
    /note=Original Glimmer call @bp 5838 has strength 11.1; Genemark calls start at 5838
    /note=SSC: 5838-5972 CP: no SCS: both ST: NI BLAST-Start:  GAP: 70 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.451, -3.597563630176197, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 5838; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: There is no known function. 
    /note=
    /note=Checked: C.A.R; R.R.

CDS 5983 - 6465
  /gene="13"
  /product="gp13"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_13"
    /note=Original Glimmer call @bp 5983 has strength 15.4; Genemark calls start at 5983
    /note=SSC: 5983-6465 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_112 [Arthrobacter phage Atuin]],,NCBI, q3:s17 62.5% 3.42678E-22 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.245, -4.101388555093469, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_112 [Arthrobacter phage Atuin]],,UDL16706,37.9888,3.42678E-22 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : has coding potential based on GeneMark; Glimmer and GeneMark both call it. it has a start site
    /note=Start site? : 5983; this start includes all coding potential, It has the best Z-and final score that includes all coding potential; It is called by both Glimmer and GeneMark; Starterator is not much help because the only other gene is a duplicate from this genome (start site: 185395); Several more draft phages have been added since but all called the same start site (No manual annotations)
    /note=Function? : There are no significant matches on HHPred, the only BLAST match on NCBI is to a hypothetical protein, there are no transmembrane domains (DeepTMHMM)
    /note=
    /note=Checked: C.A.R;R.R

CDS 6558 - 6725
  /gene="14"
  /product="gp14"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_14"
    /note=Original Glimmer call @bp 6558 has strength 10.53; Genemark calls start at 6558
    /note=SSC: 6558-6725 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein [Prauserella muralis] ],,NCBI, q2:s59 94.5455% 8.02989E-8 GAP: 92 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prauserella muralis] ],,WP_112282550,35.7143,8.02989E-8 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 6558, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator is not very helpful because the only other gene in the pham is a duplicate of this gene in this genome. (start site 185970)
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM.
    /note=
    /note=Checked: R.R
    /note=
    /note=Checked: C.A.R

CDS 6813 - 7022
  /gene="15"
  /product="gp15"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_15"
    /note=Original Glimmer call @bp 6813 has strength 9.69; Genemark calls start at 6813
    /note=SSC: 6813-7022 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_115 [Arthrobacter phage Atuin]],,NCBI, q1:s1 98.5507% 7.6206E-40 GAP: 87 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_115 [Arthrobacter phage Atuin]],,UDL16709,100.0,7.6206E-40 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, Glimmer and GeneMark both call the gene. GeneMark does show coding potential for the gene. It has a start and stop site.
    /note=What is the start site?: 6813 - it is the only option. Glimmer and GeneMark both call the start site. It includes all coding potential for the gene. The Z-score and final score for the start site are good. The only other gene in the Pham has the same start site.
    /note=What is the function?: The protein is a hypothetical protein. The only match in phagesdb or NCBI are hypothetical proteins from phages in this cluster. There are no significant structural alignments on HHPred. No membrane domains. (JP)
    /note=Checked: JT; RR

CDS 7080 - 7361
  /gene="16"
  /product="gp16"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_16"
    /note=Original Glimmer call @bp 7080 has strength 8.51; Genemark calls start at 7080
    /note=SSC: 7080-7361 CP: no SCS: both ST: NI BLAST-Start:  GAP: 57 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.219, -2.033982896655645, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 7080, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator calls this site for all gene but they are all drafts. Now a couple of manual annotations that call this start site too. (start site 186492)
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM.
    /note=
    /note=Checked: JT; RR

CDS 7358 - 7777
  /gene="17"
  /product="gp17"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_17"
    /note=Original Glimmer call @bp 7358 has strength 7.41; Genemark calls start at 7358
    /note=SSC: 7358-7777 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_112 [Arthrobacter phage Atuin]],,NCBI, q85:s123 37.4101% 3.3186E-15 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.54, -3.5490877672587735, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_112 [Arthrobacter phage Atuin]],,UDL16706,22.905,3.3186E-15 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes. It has coding potential. Glimmer and GeneMark both call the gene. It has a start and stop site.
    /note=What is the start site?: 7358. It is the only gene (along with a duplicate gene in this phage) in the Pham. The start site includes all coding potential, has good Z- and final scores. Also has a -4 overlap with the previous gene.
    /note=What is the function?: Hypothetical protein. The matches on phagesdb and NCBI are not strong enough to consider calling a function other than hypothetical protein. The are no significant matches on HHPred. There is no membrane domain identified.(JP)
    /note=
    /note=Reviewed: HA, JT

CDS 7864 - 8193
  /gene="18"
  /product="gp18"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_18"
    /note=Original Glimmer call @bp 7864 has strength 17.66; Genemark calls start at 7864
    /note=SSC: 7864-8193 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_116 [Arthrobacter phage Racecar] ],,NCBI, q3:s10 95.4128% 3.52162E-21 GAP: 86 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_116 [Arthrobacter phage Racecar] ],,QFG12163,61.6071,3.52162E-21 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, It has coding potential. Glimmer and Genemark both call the start site. It has a start and stop site.
    /note=What is the start site?: 7864, Glimmer and GeneMark both call this start site. It includes all coding potential from GeneMark. It has the best Z- and final score, and other with good scores cut off a lot of coding potential. It is the only gene in this Pham with this start site. others have been added since but this gene does not have the manually annotated start sites (and this start is not conserved in the manual annotations)
    /note=What is the function?: hypothetical protein. PhagesDB and NCBI produced only significant matches hypothetical proteins. There were no significant matches in HHPred. There were no identified membrane domains. (JP)
    /note=
    /note=Checked: JT; RR

CDS 8362 - 8859
  /gene="19"
  /product="gp19"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_19"
    /note=Original Glimmer call @bp 8362 has strength 8.17; Genemark calls start at 8362
    /note=SSC: 8362-8859 CP: no SCS: both ST: NI BLAST-Start: [MAG: hypothetical protein DCC58_16935 [Chloroflexota bacterium]],,NCBI, q32:s16 76.9697% 1.00935E-4 GAP: 168 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.35, -3.8761054743559344, yes F: Hypothetical Protein SIF-BLAST: ,,[MAG: hypothetical protein DCC58_16935 [Chloroflexota bacterium]],,RIK38244,42.3358,1.00935E-4 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 8362, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and Final score for the start site candidates. The only other option that would include all coding potential has a much worse final score. This gene is the only one in the Pham with this start site and is missing the most frequently annotated start site. Others have been added with this start site now and autoannotate this start.
    /note=What is the function?: hypothetical protein, PhagesDB and NCBI only have significant matches to hypothetical proteins. There are no significant matches on HHPred. There is no predicted membrane domain. (JP) (KJ)
    /note=
    /note=Checked: JT
    /note=
    /note=No coding potential in the gap in front of this gene.

CDS 8952 - 9179
  /gene="20"
  /product="gp20"
  /function="membrane protein"
  /locus tag="DunneganBoMo_20"
    /note=Original Glimmer call @bp 8952 has strength 7.49; Genemark calls start at 8952
    /note=SSC: 8952-9179 CP: no SCS: both ST: NI BLAST-Start:  GAP: 92 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.466674028236667, yes F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 8952, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and Final score for the start site candidates. This gene is the only one in the Pham. Others have now been added and autoannotate the same start site
    /note=What is the function?: hypothetical protein, PhagesDB and NCBI only have significant matches to hypothetical proteins. There are no significant matches on HHPred. There is no predicted membrane domain. (JP)
    /note=
    /note=Reviewed: HA, KJ, 
    /note=I noticed a membrane protein on this one. JT

CDS 9227 - 9640
  /gene="21"
  /product="gp21"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_21"
    /note=Original Glimmer call @bp 9227 has strength 17.04; Genemark calls start at 9227
    /note=SSC: 9227-9640 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_132 [Arthrobacter phage Atuin]],,NCBI, q2:s3 48.9051% 4.32405E-4 GAP: 47 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_132 [Arthrobacter phage Atuin]],,UDL16726,60.0,4.32405E-4 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 9227, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator is not very helpful because the only other gene in the pham is a duplicate of this gene in this genome. (start site 188639). Other genes have now been added to starterator data. All autoannotate this start site as it is conserved in all members of the pham thus far. It includes all coding potential.
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM.
    /note=Reviewed: KJ, JT

CDS 9696 - 9902
  /gene="22"
  /product="gp22"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_22"
    /note=Original Glimmer call @bp 9696 has strength 8.67; Genemark calls start at 9696
    /note=SSC: 9696-9902 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_117 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.82247E-27 GAP: 55 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.745, -4.0178693334748665, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_117 [Arthrobacter phage Atuin]],,UDL16711,82.3529,2.82247E-27 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 9696, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator calls this start in all genes with this start site including two manually annotated genes. (start site 189108) It includes all coding potential; updated starterator data includes 10 manual annotations of this start site which is conserved in 36 members of the pham
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM.
    /note=Reviewed: KJ, JT

CDS 9944 - 10246
  /gene="23"
  /product="gp23"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_23"
    /note=Original Glimmer call @bp 9944 has strength 7.37; Genemark calls start at 9944
    /note=SSC: 9944-10246 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_118 [Arthrobacter phage Atuin]],,NCBI, q1:s1 96.0% 2.58335E-27 GAP: 41 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.156, -2.230514797657003, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_118 [Arthrobacter phage Atuin]],,UDL16712,67.3267,2.58335E-27 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 9944
    /note=GeneMark both call the same start site. It includes all coding potential. Phages within this pham that had this start cite called it 100% of the time with 10 manual annotations
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=Reviewed: KJ, JT

CDS 10343 - 10657
  /gene="24"
  /product="gp24"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_24"
    /note=Original Glimmer call @bp 10343 has strength 8.85; Genemark calls start at 10343
    /note=SSC: 10343-10657 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_120 [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.0385% 1.22698E-57 GAP: 96 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_120 [Arthrobacter phage Atuin]],,UDL16714,89.4231,1.22698E-57 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 10343
    /note=GeneMark both call the same start site. It includes all coding potential. Phages within this pham that had this start cite called it 100% of the time with 2 manual annotations.
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=
    /note=Reviewed: HA, KJ, JT

CDS 10807 - 11118
  /gene="25"
  /product="gp25"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_25"
    /note=Original Glimmer call @bp 10807 has strength 21.4; Genemark calls start at 10807
    /note=SSC: 10807-11118 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein RALTA_B0985 [Cupriavidus taiwanensis LMG 19424]],,NCBI, q52:s22 50.4854% 1.4088E-10 GAP: 149 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein RALTA_B0985 [Cupriavidus taiwanensis LMG 19424]],,CAQ71596,51.3889,1.4088E-10 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, this gene has a start site, end site, and coding potential based on genemark. it`s coding potential is at a higher probability
    /note=what is the start site? 10807 is the start site based on the information given from glimmer and genemark. the start sites are corresponding. only possible start site
    /note=what is the function? hypothetical protein based on NCBI blast; no significant matches on HHpred
    /note=
    /note=Did have a large gap before gene but there was no open reading frame so no gene was added, gap can be ignored. 
    /note=Reviewed: KJ, and CM

CDS 11393 - 11803
  /gene="26"
  /product="gp26"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_26"
    /note=Original Glimmer call @bp 11393 has strength 7.62; Genemark calls start at 11393
    /note=SSC: 11393-11803 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_124 [Arthrobacter phage Atuin]],,NCBI, q4:s3 83.0882% 7.03902E-33 GAP: 274 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.951, -4.669046746593814, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_124 [Arthrobacter phage Atuin]],,UDL16718,61.4173,7.03902E-33 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes. it has a start site, an end site, and majority coding potential
    /note=what is the start site? Glimmer and GeneMark both call this start site. Starterator indicates that this start site is called when present although there are no manual annotations. The Z and final scores are not as good as a couple of other sites but this includes all coding potential. (duplicated Gene 300), only start site in this gene with any manual annotations
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on phagesdb, the only significant matches on NCBI are to hypothetical proteins. No transmembrane domain on DeepTMHMM.
    /note=Reviewed: KJ and CM
    /note=
    /note=Gap before this gene does not have an open reading frame big enough to be a protein

CDS 11901 - 12164
  /gene="27"
  /product="gp27"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_27"
    /note=Original Glimmer call @bp 11946 has strength 12.23; Genemark calls start at 11946
    /note=SSC: 11901-12164 CP: no SCS: both-cs ST: NI BLAST-Start:  GAP: 97 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.089, -4.512860391142743, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Good coding potential
    /note=Start site - Glimmer and GeneMark agree; there is coding potential that extends beyond the called start sites, the z and final scores are better for those start sites; ther are a few genes in the starterator data but none contain this earlier start site
    /note=
    /note=Function: No matches on phagesDB or NCBI; no significant matches in HHPred
    /note=
    /note=Reviewed: HA, KJ

CDS 12222 - 12458
  /gene="28"
  /product="gp28"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_28"
    /note=Original Glimmer call @bp 12222 has strength 2.45; Genemark calls start at 12222
    /note=SSC: 12222-12458 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_126 [Arthrobacter phage Atuin]],,NCBI, q4:s3 96.1538% 8.21215E-39 GAP: 57 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.466674028236667, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_126 [Arthrobacter phage Atuin]],,UDL16720,88.3117,8.21215E-39 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 12222
    /note=RBS: Final Score and Z-Score
    /note=Starterator: No additional Genes (other than a duplicated gene in this genome) same as gene 302
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=a couple of significant HHPred matches but they are to functions that are not accepted phage functions
    /note=No called proteins in our cluster
    /note=
    /note=Reviewed: KJ and CM

CDS complement (12791 - 12949)
  /gene="29"
  /product="gp29"
  /function="RNA binding protein"
  /locus tag="DunneganBoMo_29"
    /note=Original Glimmer call @bp 12949 has strength 9.17; Genemark calls start at 12949
    /note=SSC: 12949-12791 CP: no SCS: both ST: NI BLAST-Start:  GAP: 17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.156, -2.0895162839948163, yes F: RNA binding protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 12949
    /note=RBS: Final Score and Z-Score
    /note=Starterator: No additional Genes (other than a duplicated gene in this genome) same as gene ending 192203; other genes have been added and all autoannotate the same start site (no manual annotations yet)
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=HHPred matches to a KOW motif of transcriptions factors which is a conserved RNA binding motif
    /note=No called proteins in our cluster
    /note=Checked by CM, TM

CDS complement (12967 - 13182)
  /gene="30"
  /product="gp30"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_30"
    /note=Original Glimmer call @bp 13182 has strength 2.59; Genemark calls start at 13182
    /note=SSC: 13182-12967 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_128 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.3861E-9 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.156, -2.741655139666096, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_128 [Arthrobacter phage Atuin]],,UDL16722,68.0556,2.3861E-9 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 13182
    /note=RBS: Final Score and Z-Score
    /note=Starterator: 30 genes in this pham and all have the same predicted start with 8 manual annotations
    /note=Glimmer and GeneMark both call the same start site
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=NCBI blast results yield a hypothetical protein
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=Checked by CM, TM

CDS complement (13266 - 13484)
  /gene="31"
  /product="gp31"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_31"
    /note=Genemark calls start at 13484
    /note=SSC: 13484-13266 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_129 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.86998E-27 GAP: 105 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.068, -2.2763497933341483, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_129 [Arthrobacter phage Atuin]],,UDL16723,84.0,1.86998E-27 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : yes. It has coding potential, a start and stop codon, called only by GeneMark
    /note=Start site:13484 - This includes all coding potential, is called by GeneMark, Has the best Z-score and final score. Starterator data indicates this start site is annotated when present 100% including 2 manual annotations
    /note=Function: Hypothetical protein: there are no significant matches on HHPred, The only BLAST match is for a hypothetical protein. There are no transmembrane domains and no conserved domains.
    /note=
    /note=Checked: RR

CDS complement (13590 - 13808)
  /gene="32"
  /product="gp32"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_32"
    /note=Original Glimmer call @bp 13808 has strength 6.65; Genemark calls start at 13808
    /note=SSC: 13808-13590 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein KBG_88 [Mycobacterium phage KBG] ],,NCBI, q8:s10 88.8889% 0.00109681 GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.84, -2.8454123590742793, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein KBG_88 [Mycobacterium phage KBG] ],,YP_001994546,55.8442,0.00109681 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 13808 because it includes all coding potential, and has the best z- score and final score. Starterator indicates that it does not contain the most commonly annotated start sites. Codes for a hypothetical protein. only hits on NCBI BLAST is to a hypothetical protein. HHpred only has hits to HIV proteins that are not on the approved list (and hits are only to a small portion of the protein)
    /note=Checked by CM, TM

CDS complement (13888 - 14079)
  /gene="33"
  /product="gp33"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_33"
    /note=Original Glimmer call @bp 14079 has strength 12.19; Genemark calls start at 14079
    /note=SSC: 14079-13888 CP: no SCS: both ST: NI BLAST-Start:  GAP: 91 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.101, -4.34663776219455, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene: yes, there is coding potential, it has a start and stop codon, glimmer and genemark both call it
    /note=Start: 14079, this start includes all coding potential possible, it is called by both glimmer and genemark, it has the best final score, this start site is indicated on starterator when present (no manual annotations though)
    /note=Function: Hypothetical protein, there are no significant matches on HHPred, Phages DB BLAST or NCBI Blast, There are no conserved domains or transmembrane domains
    /note=Checked by CM, TM

CDS complement (14171 - 14425)
  /gene="34"
  /product="gp34"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_34"
    /note=Original Glimmer call @bp 14425 has strength 6.82; Genemark calls start at 14425
    /note=SSC: 14425-14171 CP: no SCS: both ST: NI BLAST-Start:  GAP: 282 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.156, -2.1518296047551457, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : It has coding potential, a start site and a stop site, and is called by both glimmer and genemark
    /note=Start site?: 14425, called by both glimmer and genemark, it has the best Z- and final score, it includes all coding potential, while there are only 2 manual annotations in starterator all genes in the pham were auto-annotated to this start site (duplicate gene: start site 193837)
    /note=Function? : Hypothetical protein, there are no significant HHPred matches, there are no BLAST matches with a function assigned, there are no conserved domains or membrane domains.
    /note=
    /note=Checked:JT, TM
    /note=No significant ORFs in the gap before this gene

CDS complement (14708 - 14890)
  /gene="35"
  /product="gp35"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_35"
    /note=Genemark calls start at 14890
    /note=SSC: 14890-14708 CP: no SCS: genemark ST: NI BLAST-Start:  GAP: 135 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene is same as the gene ending at 194120
    /note=Gene? : It has coding potential, a start and stop site. Called by GeneMark
    /note=Start Site? : 14890 - Called by GeneMark; only start site that includes all coding potential; best Z- and final score; Starterator has several genes within this pham, this start site is called whenever it is present but no manual annotations
    /note=Function? : hypothetical protein; No matches in phages or NCBI BLAST; HHPred has no significant matches; No conserved domains; No transmembrane domains.

CDS complement (15026 - 15292)
  /gene="36"
  /product="gp36"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_36"
    /note=Genemark calls start at 15292
    /note=SSC: 15292-15026 CP: no SCS: genemark ST: NI BLAST-Start:  GAP: 213 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.684, -4.199347842547433, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Same as gene ending 194438
    /note=Gene? : It has coding potential; It has a start and stop site; call by GeneMark
    /note=Start Site? : 15292 - It has the best Z- and Final score that includes all coding potential; called by GeneMark; Starterator has a few other genes but most call another start site (no manual annotations). 
    /note=Function? : Hypothetical Protein - No phages or NCBI BLAST matches; no significant matches on HHPred; no conserved domains; no transmembrane domain

CDS complement (15506 - 16090)
  /gene="37"
  /product="gp37"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_37"
    /note=Original Glimmer call @bp 16090 has strength 13.62; Genemark calls start at 16090
    /note=SSC: 16090-15506 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_135 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.00783E-86 GAP: 448 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.698, -5.21028209587241, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_135 [Arthrobacter phage Atuin]],,UDL16729,80.1047,2.00783E-86 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 16090, (reverse gene) Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best final score that includes all the coding potential. This gene is the only one in the Pham with this start site. This gene does not have the most commonly called start site from other proteins in the pham.
    /note=What is the function?: membrane protein, PhagesDB and NCBI only have significant matches to hypothetical proteins. There are no significant matches on HHPred. There is a predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=Change to hypothetical protein. The membrane domain is a signal domain not a transmembrane domain.
    /note=
    /note=Reviewed: TM

CDS 16539 - 16700
  /gene="38"
  /product="gp38"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_38"
    /note=Original Glimmer call @bp 16539 has strength 2.65; Genemark calls start at 16503
    /note=SSC: 16539-16700 CP: no SCS: both-gl ST: NI BLAST-Start:  GAP: 448 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.291, -6.909353492036279, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 16539, Glimmer calls this start site and it includes all coding potential. GeneMark call a different start site. It includes the coding potential but does not have the best Z- or final score, although neither of those are very good for either potential start site. This gene is an orpham so there is no starterator data.
    /note=What is the function?: hypothetical protein, PhagesDB and NCBI have no matches to this protein. There are no significant matches on HHPred. There is no predicted membrane domain by DeepTMHMM via Phamerator. (JP)

CDS 16716 - 16919
  /gene="39"
  /product="gp39"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_39"
    /note=Original Glimmer call @bp 16716 has strength 6.07; Genemark calls start at 16716
    /note=SSC: 16716-16919 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_139 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.95802E-21 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.856, -5.523605800043125, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_139 [Arthrobacter phage Atuin]],,UDL16733,76.1194,2.95802E-21 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 16716, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score. This start site is called by the in the only other gene in the pham. 
    /note=What is the function?: hypothetical protein, PhagesDB and NCBI only have matches to hypothetical proteins. There are no significant matches on HHPred. There is no predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=
    /note=Reviewed: HA, TM

CDS 17038 - 17346
  /gene="40"
  /product="gp40"
  /function="membrane protein"
  /locus tag="DunneganBoMo_40"
    /note=Original Glimmer call @bp 17038 has strength 5.72; Genemark calls start at 17104
    /note=SSC: 17038-17346 CP: no SCS: both-gl ST: NI BLAST-Start: [tail needle protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 9.53793E-55 GAP: 118 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.665, -3.2017655760970833, no F: membrane protein SIF-BLAST: ,,[tail needle protein [Arthrobacter phage Atuin]],,UDL16734,86.6071,9.53793E-55 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 17038, This start site includes all coding potential. Glimmer calls this start site, GeneMark calls a later start site. The 17038 start site has good Z- and final scores (not the best) and includes all the coding potential. This is called in the genes that have manual annotations entered in this Pham.
    /note=What is the function?: membrane protein, PhagesDB only has significant matches to hypothetical proteins. The only other significant match on NCBI would not be a function for this type of phage. There are no significant matches on HHPred. There is a predicted membrane domain by DeepTMHMM via Phamerator. (JP)

CDS 17328 - 18251
  /gene="41"
  /product="gp41"
  /function="minor tail protein"
  /locus tag="DunneganBoMo_41"
    /note=Original Glimmer call @bp 17397 has strength 7.65; Genemark calls start at 17397
    /note=SSC: 17328-18251 CP: no SCS: both-cs ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 4.57757E-144 GAP: -19 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.684, -3.625316574819714, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Atuin]],,UDL16735,83.871,4.57757E-144 SIF-HHPRED:  SIF-Syn: 
    /note=Gene?: Yes, It has coding potential, Called by both Glimmer and GeneMark, Has a start and stop site
    /note=Start site?: 17328, This is not the site called by Glimmer and GeneMark but it has a better Z-score and final score. This start site also includes all coding potential, while the next start site leaves some out; On starterator the only manual annotation is for this start site on a very similar protein from a genome in our cluster.
    /note=Function? : Minor tail protein - no significant matches in HHPred; the matches in phagesdb are for draft proteins; On NCBI BLAST the match (to the very similar protein in our cluster) is annotated as a minor tail protein - both have a membrane domain and a collagen like domain as well

CDS 18265 - 18711
  /gene="42"
  /product="gp42"
  /function="membrane protein"
  /locus tag="DunneganBoMo_42"
    /note=Original Glimmer call @bp 18265 has strength 13.32; Genemark calls start at 18265
    /note=SSC: 18265-18711 CP: no SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 5.4038E-82 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.442961286954254, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Atuin]],,UDL16736,89.8649,5.4038E-82 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : It has coding potential, a start site and stope site. Called by both glimmer and genemark
    /note=Start site: 18265, only start site that includes all coding potential; glimmer and genemark both call the start site, best z- and final score, According to starterator the most common start site for this pham is not in our gene but this start site is auto-annotated when the most common site is not present
    /note=Function? : membrane protein is the most likely function; There are two transmembrane domains, there is a match to a holin in the HHPred matches but the other evidence to call the gene a holin is not present. The only match within out cluster is to a membrane protein as well.

CDS 18792 - 19100
  /gene="43"
  /product="gp43"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_43"
    /note=Original Glimmer call @bp 18792 has strength 14.41; Genemark calls start at 18792
    /note=SSC: 18792-19100 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_143 [Arthrobacter phage Atuin]],,NCBI, q9:s22 85.2941% 3.87472E-29 GAP: 80 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.689, -5.309117108752867, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_143 [Arthrobacter phage Atuin]],,UDL16737,59.633,3.87472E-29 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 18792
    /note=GeneMark both call the same start site. It includes all coding potential. Phages within this pham that had this start cite called it 100% of the time. 
    /note=
    /note=Function:
    /note=only NCBI blast results yield a hypothetical protein
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=
    /note=Reviewed: HA, TH

CDS 19093 - 19359
  /gene="44"
  /product="gp44"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_44"
    /note=Original Glimmer call @bp 19093 has strength 5.6; Genemark calls start at 19093
    /note=SSC: 19093-19359 CP: no SCS: both ST: NI BLAST-Start:  GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.016, -5.629327099143209, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 19093
    /note=GeneMark both call the same start site. It includes all coding potential. Phages within this pham that had this start cite called it 100% of the time. 
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=
    /note=Reviewed ML, TH

CDS 19356 - 19595
  /gene="45"
  /product="gp45"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_45"
    /note=Original Glimmer call @bp 19356 has strength 11.46; Genemark calls start at 19356
    /note=SSC: 19356-19595 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_146 [Arthrobacter phage Atuin]],,NCBI, q24:s13 68.3544% 1.40531E-6 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.156, -4.309437458116814, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_146 [Arthrobacter phage Atuin]],,UDL16740,58.7302,1.40531E-6 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, it has a start site and an end site and coding potential based on genemark
    /note=what is the start site? 19356 based on the corresponding start sites given by glimmer and genemark, -4 overlap with previous gene, Start site is called in all genes in the pham (1 MA)
    /note=what is the function? Likely hypothetical protein, nothing above 90 percent on HHpred, only NCBI BLAST match is to a hypothetical protein
    /note=
    /note=Reviewed SB, TH

CDS 19592 - 19885
  /gene="46"
  /product="gp46"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_46"
    /note=Original Glimmer call @bp 19592 has strength 15.47; Genemark calls start at 19592
    /note=SSC: 19592-19885 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_147 [Arthrobacter phage Atuin]],,NCBI, q5:s2 95.8763% 2.79633E-44 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.597, -3.364992052816827, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_147 [Arthrobacter phage Atuin]],,UDL16741,86.1702,2.79633E-44 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, it has a start site, an end site, and coding potential based on genemark
    /note=what is the start site? glimmer and genemark both claim 19592 as the start site; -4 overlap; best Z and final scores; start site is called 100% of the time when present but not well conserved in the pham
    /note=what is the function? this gene could be a hypothetical protein based on NCBI blast corresponding information alongside phagesbd blast`s unknown function of the same gene with a low e-value
    /note=
    /note=Reviewed SB, TH

CDS 19878 - 20036
  /gene="47"
  /product="gp47"
  /function="DNA binding protein"
  /locus tag="DunneganBoMo_47"
    /note=Original Glimmer call @bp 19878 has strength 3.11
    /note=SSC: 19878-20036 CP: no SCS: glimmer ST: NI BLAST-Start: [DNA binding protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.31048E-29 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.974, -3.1309088467834587, yes F: DNA binding protein SIF-BLAST: ,,[DNA binding protein [Arthrobacter phage Atuin]],,UDL16742,98.0769,1.31048E-29 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 19878
    /note=RBS: Final Score and Z-Score
    /note=Starterator: No additional Genes 
    /note=Glimmer called the gene but not GeneMark, but there is only one start site. There is coding potential for the gene
    /note=
    /note=Function:
    /note=
    /note=Agree with start site although GeneMark did not call the protein there is still some coding potential. I think the function could be a DNA binding protein - The first result from the NCBI BLAST is a protein from the same cluster and pham as this protein and almost 100% identity that has been identified as a DNA Binding Protein. HHpred also has many proteins that would include DNA binding as part of their function (JP)
    /note=
    /note=Checked: I also agree that this could very likely be a DNA binding protein because of the NCBI results, although the HHPred results does give results for an unknown function, it also gives quite a lot of other non-phage specific results and I am inclined to trust the NCBI results a bit more. -C.A.R

CDS 20036 - 20320
  /gene="48"
  /product="gp48"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_48"
    /note=Original Glimmer call @bp 20036 has strength 14.7; Genemark calls start at 20036
    /note=SSC: 20036-20320 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_149 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.11589E-47 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.369, -3.8362837638757656, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_149 [Arthrobacter phage Atuin]],,UDL16743,92.5532,1.11589E-47 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 20036
    /note=RBS: Final Score and Z-Score
    /note=Starterator: No additional Genes
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=-1 overlap
    /note=
    /note=Function:
    /note=only NCBI blast results are hypothetical proteins
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=
    /note=Checked: C.A.R, TH

CDS 20385 - 20645
  /gene="49"
  /product="gp49"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_49"
    /note=Original Glimmer call @bp 20385 has strength 14.62; Genemark calls start at 20385
    /note=SSC: 20385-20645 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_150 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.91067E-38 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.219, -1.953940808934884, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_150 [Arthrobacter phage Atuin]],,UDL16744,83.7209,1.91067E-38 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 20385
    /note=RBS: Final Score and Z-Score
    /note=Starterator: Start site is conserved in the pham  and called every time (4 MAs)
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=Onlt NCBI blast results are hypothetical proteins
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=
    /note=Checked: C.A.R, TH

CDS 20642 - 20809
  /gene="50"
  /product="gp50"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_50"
    /note=
    /note=SSC: 20642-20809 CP: no SCS: neither ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.785, -5.549643584778785, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? Not called by Glimmer or GeneMark but there is coding potential. Some hits to functional genes on HHpred but nothing to given a potential function
    /note=Start: 20642, only option, -4 overlap
    /note=Function: hypothetical protein, No 90% or greater matches on HHpred, no NCBI matches, no transmembrane domains

CDS 20816 - 21325
  /gene="51"
  /product="gp51"
  /function="ADP-ribosyltransferase"
  /locus tag="DunneganBoMo_51"
    /note=Original Glimmer call @bp 20816 has strength 10.7; Genemark calls start at 20816
    /note=SSC: 20816-21325 CP: no SCS: both ST: NI BLAST-Start: [ADP-ribosyltransferase [Arthrobacter phage Racecar] ],,NCBI, q1:s1 98.8166% 1.38697E-54 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.984, -3.5059859724959925, yes F: ADP-ribosyltransferase SIF-BLAST: ,,[ADP-ribosyltransferase [Arthrobacter phage Racecar] ],,QFG12192,77.9141,1.38697E-54 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene: yes, it has a start site, stop site and coding potential based on GeneMark.
    /note=
    /note=What is the start site? 20816, Glimmer and GeneMark both call this start site. It includes all coding potential from GeneMark. Phages within this pham that had this start site called this 100% of the time (4MAs).
    /note=
    /note=What is the function? PhagesDB blast - other similar genes in our cluster call this function; This function is called on NCBI; HHPred has matches to the ADP-ribosyltransferases (the macro domain specifically)
    /note=
    /note=Reviewed: HA, TH
    /note=
    /note=Checked: C.A.R

CDS 21360 - 21578
  /gene="52"
  /product="gp52"
  /function="membrane protein"
  /locus tag="DunneganBoMo_52"
    /note=Original Glimmer call @bp 21360 has strength 14.26; Genemark calls start at 21360
    /note=SSC: 21360-21578 CP: no SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 97.2222% 2.17458E-30 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.816, -3.9182746577281886, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Atuin]],,UDL16750,81.9444,2.17458E-30 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S but looks weird to me in context of the next gene. Not a gene.
    /note=
    /note=Gene? yes, It has coding potential. Called by both Glimmer and GeneMark
    /note=Start site? 21360 - called by both Glimmer and Genemark; Only option for this protein; has a good Z and final score; All proteins in the pham are in draft phages but all autoannotate the same start site
    /note=Function? membrane protein; No matches on HHPred of 90% or better; no matches in the NCBI or Phagesdb; Has a transmembrane domain per DeepTMHMM via phamerator
    /note=
    /note=Checked: I also agree that it does look quite weird in context of the next gene. Is it possible for a gene to get split up from the rest of it at some point? If that is not possible I am not sure why the coding potential goes straight through. However I am hesitant to say it is not a gene because the coding potential is so high.
    /note=Bacteriophage Atuin also has the same strange section in their GeneMark S for the corresponding gene, so I believe it may be something that FC phages do for this gene potentially. -C.A.R
    /note=
    /note=really not sure, but seems reasonable to call it as membrane protein for all above evidence. -TH

CDS 21579 - 22274
  /gene="53"
  /product="gp53"
  /function="endolysin"
  /locus tag="DunneganBoMo_53"
    /note=Original Glimmer call @bp 21579 has strength 7.98; Genemark calls start at 21579
    /note=SSC: 21579-22274 CP: no SCS: both ST: NI BLAST-Start: [endolysin [Arthrobacter phage Atuin]],,NCBI, q1:s1 87.4459% 4.6558E-85 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.156, -2.6167164030577963, yes F: endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Atuin]],,UDL16751,65.2893,4.6558E-85 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 21579. Includes all coding potential, start site is conserved in the pham and is called 100% of the time (1 MA). Codes for a hypothetical protein. There is a hit in HHpred for a GH24 family muramidase which breaks down bacterial cell walls like an endolysin. There is an endolysin hit in NCBI BLAST
    /note=
    /note=Checked: C.A.R, TH

CDS 22370 - 22930
  /gene="54"
  /product="gp54"
  /function="membrane protein"
  /locus tag="DunneganBoMo_54"
    /note=Original Glimmer call @bp 22370 has strength 10.37; Genemark calls start at 22370
    /note=SSC: 22370-22930 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_150 [Arthrobacter phage Racecar]],,NCBI, q1:s1 99.4624% 1.69032E-19 GAP: 95 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.896, -3.473611599459246, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_150 [Arthrobacter phage Racecar]],,QFG12196,48.1865,1.69032E-19 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 22370, includes all coding potential, good z and final scores, start site is called almost all the time in the pham (4 MAs). Codes for a hypothetical protein. No significant hits on HHpred, Only hypothetical proteins on NCBI BLAST. Does have a transmembrane domains
    /note=
    /note=Checked: C.A.R, JL

CDS 22938 - 23141
  /gene="55"
  /product="gp55"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_55"
    /note=Original Glimmer call @bp 22938 has strength 7.13; Genemark calls start at 22938
    /note=SSC: 22938-23141 CP: no SCS: both ST: NI BLAST-Start:  GAP: 7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.135, -2.9617282384803714, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 22938. Codes for a hypothetical protein.
    /note=
    /note=Checked: C.A.R, JL

CDS 23141 - 23371
  /gene="56"
  /product="gp56"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_56"
    /note=Original Glimmer call @bp 23141 has strength 7.98; Genemark calls start at 23141
    /note=SSC: 23141-23371 CP: no SCS: both ST: NI BLAST-Start:  GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.722, -5.238109312333945, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark both call. it has coding potential. 
    /note=Start: 23141, -1 overlap, good Z and final scores, includes all coding potential, does not have the most called start site but this only is called when it is present
    /note=Function: hypothetical protein, no hits on NCBI BLAST, no significant hits on HHpred, No transmembrane domain
    /note=
    /note=Checked: C.A.R, JL

CDS 23371 - 24288
  /gene="57"
  /product="gp57"
  /function="phosphoribosyltransferase"
  /locus tag="DunneganBoMo_57"
    /note=Original Glimmer call @bp 23371 has strength 10.64; Genemark calls start at 23371
    /note=SSC: 23371-24288 CP: no SCS: both ST: NI BLAST-Start: [phosphoribosyl transferase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 9.80139E-175 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.546, -5.000140566514435, yes F: phosphoribosyltransferase SIF-BLAST: ,,[phosphoribosyl transferase [Arthrobacter phage Atuin]],,UDL16755,89.1803,9.80139E-175 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark both call, has good z and final scores, -1 overlap, includes all coding potential, does not have the most annotated start site but this is called 100% of the time when present. Matches with phosphoribosyl transferase in HHpred and phagesdb and NCBI blast.
    /note=
    /note=Checked: C.A.R, JL

CDS 24288 - 24500
  /gene="58"
  /product="gp58"
  /function="membrane protein"
  /locus tag="DunneganBoMo_58"
    /note=Original Glimmer call @bp 24288 has strength 7.41; Genemark calls start at 24288
    /note=SSC: 24288-24500 CP: no SCS: both ST: NI BLAST-Start: [polysaccharide biosynthesis protein [Brevibacterium sp. UMB10442]],,NCBI, q4:s18 60.0% 0.0108327 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.796, -2.9392830384527056, yes F: membrane protein SIF-BLAST: ,,[polysaccharide biosynthesis protein [Brevibacterium sp. UMB10442]],,MDK7750298,4.48223,0.0108327 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark call, has good z and final score, -1 overlap, start site is conserved in the pham and called 100% of the time (3 MAs). Does not match with other proteins on HHpred and PhagesDB. has 2 transmembrane domains (AP)
    /note=Checked: JT, JL

CDS 24517 - 26040
  /gene="59"
  /product="gp59"
  /function="nicotinate ribosyltransferase"
  /locus tag="DunneganBoMo_59"
    /note=Original Glimmer call @bp 24517 has strength 11.66; Genemark calls start at 24517
    /note=SSC: 24517-26040 CP: no SCS: both ST: NI BLAST-Start: [nicotinate ribosyltransferase [Arthrobacter phage Racecar] ],,NCBI, q1:s11 100.0% 0.0 GAP: 16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.936, -2.6217801767860207, yes F: nicotinate ribosyltransferase SIF-BLAST: ,,[nicotinate ribosyltransferase [Arthrobacter phage Racecar] ],,QFG12199,96.7118,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark call, has good final and z-scores, does not have the most annotated start site but this is called 100% of the time when present (4 MAs). Matches almost exactly with other nicotinate ribosyltransferase on HHpred and NCBI.
    /note=Checked: JT, JL

CDS 26040 - 26195
  /gene="60"
  /product="gp60"
  /function="membrane protein"
  /locus tag="DunneganBoMo_60"
    /note=Original Glimmer call @bp 26040 has strength 10.78; Genemark calls start at 26040
    /note=SSC: 26040-26195 CP: no SCS: both ST: NI BLAST-Start:  GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.585, -3.3732766706951867, yes F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 26040, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score. There are 4 genes in the pham and all call this start site although no MAs. It also has a -1 overlap with the previous gene.
    /note=What is the function?: membrane protein, PhagesDB and NCBI no matches. There are no significant matches on HHPred. There is a predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=Checked: JT, JL

CDS 26196 - 26450
  /gene="61"
  /product="gp61"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_61"
    /note=Original Glimmer call @bp 26196 has strength 5.43; Genemark calls start at 26196
    /note=SSC: 26196-26450 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_163 [Arthrobacter phage Atuin]],,NCBI, q1:s1 79.7619% 0.00479493 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.775, -3.9548175877277774, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_163 [Arthrobacter phage Atuin]],,UDL16757,56.5217,0.00479493 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 26196, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score. This gene is called when present in other genes in the Pham based on starterator data (there is 1 MA). 
    /note=What is the function?: hypothetical protein, PhagesDB and NCBI have no significant matches. There are no significant matches on HHPred. There is no predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=
    /note=Reviewed: HA, JT, JL

CDS 26479 - 26973
  /gene="62"
  /product="gp62"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="DunneganBoMo_62"
    /note=Original Glimmer call @bp 26698 has strength 3.98; Genemark calls start at 26479
    /note=SSC: 26479-26973 CP: no SCS: both-gm ST: NI BLAST-Start: [helix-turn-helix DNA binding domain [Arthrobacter phage Atuin]],,NCBI, q2:s3 99.3902% 6.39049E-82 GAP: 28 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.451, -3.597563630176197, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain [Arthrobacter phage Atuin]],,UDL16759,84.8485,6.39049E-82 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 26479, Glimmer and GeneMark call different start sites. This start site includes all coding potential. It has the best Z- and final score. There is one other gene in the pham which has all the conserved start sites but this one has the best supporting data. 
    /note=What is the function?: Helix-turn-helix DNA binding domain, PhagesDB and NCBI have significant matches to this function including phages within this cluster. The matches on HHPred are for different types of DNA binding proteins. There is no predicted membrane domain by DeepTMHMM via Phamerator. (JP) AF3 does predict a structure that would be compatible with a HTH DNA binding domain
    /note=Checked: JT, JL

CDS 26966 - 27286
  /gene="63"
  /product="gp63"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_63"
    /note=Original Glimmer call @bp 26966 has strength 8.99; Genemark calls start at 26966
    /note=SSC: 26966-27286 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_166 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 3.84804E-37 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.402, -5.924300499696598, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_166 [Arthrobacter phage Atuin]],,UDL16760,74.5283,3.84804E-37 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 26966, Glimmer and GeneMark both call the same start site. It includes almost all the coding potential but to include more would mean a significant overlap with the previous gene. It has a -8 overlap with this start site. This start site is called when present in other genes in the Pham most of the time based on starterator data (5 manual annotations are available). 
    /note=What is the function?: hypothetical protein, PhagesDB and NCBI have no significant matches, other than hypothetical proteins. There are no significant matches on HHPred. There is no predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=Checked:JT, JL

CDS 27307 - 27516
  /gene="64"
  /product="gp64"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_64"
    /note=Original Glimmer call @bp 27307 has strength 9.66; Genemark calls start at 27307
    /note=SSC: 27307-27516 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_167 [Arthrobacter phage Atuin]],,NCBI, q1:s1 95.6522% 4.00125E-22 GAP: 20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -2.9845911214398755, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_167 [Arthrobacter phage Atuin]],,UDL16761,70.0,4.00125E-22 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark both call. includes all coding potential, has best z and final score, does not have the most annotated start site but this start site is called 100% of the time when present. (AP)
    /note=No significant hits on HHpred, only hypothetical proteins on NCBI BLAST, no transmembrane domain
    /note=Checked: Not a membrane protein JT, JL

CDS 27488 - 27772
  /gene="65"
  /product="gp65"
  /function="membrane protein"
  /locus tag="DunneganBoMo_65"
    /note=Original Glimmer call @bp 27488 has strength 9.19; Genemark calls start at 27488
    /note=SSC: 27488-27772 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_168 [Arthrobacter phage Atuin]],,NCBI, q2:s1 98.9362% 1.64862E-50 GAP: -29 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.377, -3.7560019881956337, no F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_168 [Arthrobacter phage Atuin]],,UDL16762,94.6237,1.64862E-50 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and glimmer call, has a good z value and final score. In called most of the time when present within the pham including 37 MAs. Doesn`t have a lot of coverage in HHpred other than a domain of unknown function, matches with hypothetical proteins in NCBI. (AP)
    /note=Checked: It has transmembrane domain for gene ending at 27488 on phamerator JT
    /note=Checked by TM

CDS 27824 - 29458
  /gene="66"
  /product="gp66"
  /function="portal protein"
  /locus tag="DunneganBoMo_66"
    /note=Original Glimmer call @bp 27884 has strength 7.51; Genemark calls start at 27884
    /note=SSC: 27824-29458 CP: no SCS: both-cs ST: NI BLAST-Start: [portal protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 51 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.377, -3.8183153089559627, no F: portal protein SIF-BLAST: ,,[portal protein [Arthrobacter phage Atuin]],,UDL16763,94.0959,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Checked: start site may instead be 27824 as the 27884 cuts off some coding potential, 27824 also has 9 MAs within the pham
    /note=The function could also be a portal protein as it has pretty good coverage and alignment on HHpred and NCBI Blast and others in the pham have named it such JT

CDS 29464 - 38886
  /gene="67"
  /product="gp67"
  /function="DNA helicase"
  /locus tag="DunneganBoMo_67"
    /note=Original Glimmer call @bp 29464 has strength 9.48; Genemark calls start at 29464
    /note=SSC: 29464-38886 CP: no SCS: both ST: NI BLAST-Start: [DNA helicase [Arthrobacter phage Atuin]],,NCBI, q1229:s1347 60.8917% 0.0 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.577, -4.234979229026771, no F: DNA helicase SIF-BLAST: ,,[DNA helicase [Arthrobacter phage Atuin]],,UDL16764,40.7645,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 29464
    /note=GeneMark both call the same start site. It includes all coding potential. Phages within this pham that had this start cite called it 100% of the time with 4 MAs. Has good z and final scores
    /note=
    /note=Function:
    /note=Multiple NCBI blast results that match a DNA helicase
    /note=Multiple HHPred matches to a DNA helicase
    /note=
    /note=
    /note=Reviewed: HA, JT

CDS 38867 - 39217
  /gene="68"
  /product="gp68"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_68"
    /note=Original Glimmer call @bp 38867 has strength 5.91; Genemark calls start at 38888
    /note=SSC: 38867-39217 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_171 [Arthrobacter phage Atuin]],,NCBI, q8:s1 87.931% 3.72713E-51 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.597, -3.6360588251033645, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_171 [Arthrobacter phage Atuin]],,UDL16765,84.6154,3.72713E-51 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene? Yes, it has a start and end site and coding potential based on genemark. 
    /note=what is the start site? Glimmer and GEnemark disagree on start site but the coding potential extends beyond the GeneMark start so the longer gene is better to include all coding potential; has a better z and final score
    /note=what is the function? ribosomal modulation factor is a highly probable function but it is not an approved function. the e-value and probability are in good ranges 
    /note=Checked by CM, TM

CDS 39225 - 39512
  /gene="69"
  /product="gp69"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_69"
    /note=Original Glimmer call @bp 39225 has strength 8.42; Genemark calls start at 39225
    /note=SSC: 39225-39512 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_172 [Arthrobacter phage Atuin]],,NCBI, q2:s1 98.9474% 2.49565E-29 GAP: 7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.057, -4.969381202708897, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_172 [Arthrobacter phage Atuin]],,UDL16766,76.8421,2.49565E-29 SIF-HHPRED: d.3.1.3 (A:) Calpain large subunit, catalytic domain (domain II) {Norway rat (Rattus norvegicus), M-type [TaxId: 10116]} | CLASS: Alpha and beta proteins (a+b), FOLD: Cysteine proteinases, SUPFAM: Cysteine proteinases, FAM: Calpain large subunit, catalytic domain (domain II),,,SCOP_d1mdwa_,49.4737,68.2 SIF-Syn: 
    /note=is it a gene? yes, it has a start an end site and coding potential 
    /note=what is the start site? according to glimmer and genemark the start site is 39225; all genes in the pham call this start site (1 MA); good Z and final scores
    /note=what is the function? no 90% or greater hits on HHpred; only NCBI BLAST hits are to hypothetical protein; no transmembrane domain
    /note=
    /note=Checked by CM
    /note=
    /note=TM: I think the function should be changed to hypothetical. There isn`t enough evidence to call it anything else.

CDS 39649 - 42015
  /gene="70"
  /product="gp70"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_70"
    /note=Original Glimmer call @bp 39649 has strength 7.47; Genemark calls start at 39622
    /note=SSC: 39649-42015 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_173 [Arthrobacter phage Atuin]],,NCBI, q1:s11 99.8731% 0.0 GAP: 136 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.001, -4.641378341780927, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_173 [Arthrobacter phage Atuin]],,UDL16767,85.607,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 39649
    /note=RBS: Final Score and Z-Score
    /note=Starterator: There are no manual annotations of this start site but several autoannotation
    /note=coding potential does not extend all the way to the Genemark called start site so the Glimmer call is better
    /note=
    /note=Function:
    /note=only hypothetical proteins match in NCBI BLAST
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=No transmembrane domain
    /note=
    /note=Checked by CM, TM
    /note=
    /note=No significant ORFs with coding potential in the gap before this gene

CDS 42015 - 43529
  /gene="71"
  /product="gp71"
  /function="capsid maturation protease"
  /locus tag="DunneganBoMo_71"
    /note=Original Glimmer call @bp 42015 has strength 7.5; Genemark calls start at 42015
    /note=SSC: 42015-43529 CP: no SCS: both ST: NI BLAST-Start: [capsid maturation protease [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.822, -3.6320499574786824, no F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease [Arthrobacter phage Atuin]],,UDL16768,94.0239,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 42,015, -1 overlap
    /note=RBS: Final Score and Z-Score are good
    /note=Starterator: No additional Genes 
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is included
    /note=
    /note=Function:
    /note=I think we can assign a function of capsid maturation protease (Top two result on NCBI BLAST). Both of those are from our cluster and one is in the same pham as our gene. Several HHpred hits are to proteases as well(JP)
    /note=Checked by CM

CDS 43679 - 45682
  /gene="72"
  /product="gp72"
  /function="major capsid protein"
  /locus tag="DunneganBoMo_72"
    /note=Original Glimmer call @bp 43679 has strength 9.61; Genemark calls start at 43679
    /note=SSC: 43679-45682 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_175 [Arthrobacter phage Atuin]],,NCBI, q147:s165 78.1109% 0.0 GAP: 149 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.23, -2.0111200136961407, yes F: major capsid protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_175 [Arthrobacter phage Atuin]],,UDL16769,71.4499,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 43,679
    /note=RBS: Final Score and Z-Score
    /note=Starterator: No additional Genes 
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=Ithink we can assign a function of major capsid protein based on similarities to Racecar (NCBI BLAST result number 2) and the conserved domain (MCP_Sipho) as identified in Phamerator. (JP)
    /note=Checked by CM
    /note=
    /note=No significant ORFs with coding potential in the gap before this gene

CDS 45738 - 46607
  /gene="73"
  /product="gp73"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_73"
    /note=Original Glimmer call @bp 45738 has strength 11.4; Genemark calls start at 45738
    /note=SSC: 45738-46607 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_176 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.03903E-180 GAP: 55 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.245, -4.180073747995326, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_176 [Arthrobacter phage Atuin]],,UDL16770,92.7586,1.03903E-180 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 45738, called by Glimmer and GeneMark, only start site that includes all coding potential, conserved in the pham and called 100% of the time (11 MAs)
    /note=Codes for a hypothetical protein. no significant hits on HHpred, only hypothetical proteins on NCBI BLAST, no transmembrane domain
    /note=Checked by CM, TM

CDS 46623 - 47267
  /gene="74"
  /product="gp74"
  /function="major tail protein"
  /locus tag="DunneganBoMo_74"
    /note=Original Glimmer call @bp 46623 has strength 6.42; Genemark calls start at 46623
    /note=SSC: 46623-47267 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_177 [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.5327% 9.23318E-140 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.219, -2.305049668942183, yes F: major tail protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_177 [Arthrobacter phage Atuin]],,UDL16771,96.7442,9.23318E-140 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 46623. Glimmer/GeneMark scores agree, includes maximum possible coding potential, good Z and final scores, start site called 100% of the time with 12 MAs
    /note=Codes for a major tail protein. There are also options for hypothetical protein presented by NCBI/PhagesDB BLAST and HHpred, but the presence of acceptable e-values partnered with Major tail protein 
    /note=Checked by CM, TM

CDS 47358 - 48047
  /gene="75"
  /product="gp75"
  /function="head-to-tail adaptor"
  /locus tag="DunneganBoMo_75"
    /note=Original Glimmer call @bp 47358 has strength 3.7; Genemark calls start at 47358
    /note=SSC: 47358-48047 CP: no SCS: both ST: NI BLAST-Start: [head-to-tail adaptor [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 4.7135E-129 GAP: 90 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.926, -4.801303705573801, no F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Arthrobacter phage Atuin]],,UDL16772,91.2664,4.7135E-129 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 47358. Both Glimmer and GeneMark agree that this is the start site. Along with this, this start site is the best due to the gap when considering how large the gaps are for the the other options. includes all coding potential, gene does not have the most commonly called start sites but this one is the best in this gene with 5 MAs
    /note=Codes for a head to tail adaptor protein. PhagesDB/NCBI BLAST provides the majority of the evidence for this claim, though HHpred`s findings also support this claim.
    /note=Checked by CM, TM

CDS 48044 - 48316
  /gene="76"
  /product="gp76"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_76"
    /note=Original Glimmer call @bp 48044 has strength 11.61; Genemark calls start at 48044
    /note=SSC: 48044-48316 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_179 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.22563E-16 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.068, -2.9284886490054283, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_179 [Arthrobacter phage Atuin]],,UDL16773,76.9231,1.22563E-16 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark call, has good z and raw scores. The -4 gap makes it clear that 48044 is the start site. High coding potential present in the called start site and end. called 100% of the time in the pham
    /note=Does not have good coverage in HHpred, matches with hypothetical proteins in NCBI. no transmembrane domains
    /note=Checked by CM, TM

CDS 48342 - 48875
  /gene="77"
  /product="gp77"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_77"
    /note=Original Glimmer call @bp 48339 has strength 6.64; Genemark calls start at 48339
    /note=SSC: 48342-48875 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_81 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.06854E-86 GAP: 25 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.748, -3.0425830684175623, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_81 [Arthrobacter phage Atuin]],,UDL16774,81.3559,1.06854E-86 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark both call 48339 but there are back-to-back start codons so the second on should be chosen. All members of the pham choose the first start codon unless both are present. Does not have good coverage in HHpred but has coverage in NCBI with hypothetical proteins. (AP)
    /note=Checked by CM, TM

CDS 48875 - 49255
  /gene="78"
  /product="gp78"
  /function="minor capsid protein"
  /locus tag="DunneganBoMo_78"
    /note=Original Glimmer call @bp 48911 has strength 2.21; Genemark calls start at 48911
    /note=SSC: 48875-49255 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_82 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 3.5882E-67 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.862, -6.99886075519778, no F: minor capsid protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_82 [Arthrobacter phage Atuin]],,UDL16775,88.0952,3.5882E-67 SIF-HHPRED:  SIF-Syn: 
    /note=Start site changed to 48875 due to -1 overlap and including all the coding potential. It also has more manual annotations.
    /note=Significant HHPred hit to several capsid related proteins in other phages. Best hit is to a minor capsid protein so that is the function chosen.
    /note=
    /note=Check by: JP
    /note=Checked by CM

CDS 49289 - 49633
  /gene="79"
  /product="gp79"
  /function="tail assembly chaperone"
  /locus tag="DunneganBoMo_79"
    /note=Original Glimmer call @bp 49289 has strength 12.42; Genemark calls start at 49289
    /note=SSC: 49289-49633 CP: no SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Arthrobacter phage Atuin]],,NCBI, q3:s2 98.2456% 2.60156E-62 GAP: 33 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.256, -4.016212351373635, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage Atuin]],,UDL16776,93.8053,2.60156E-62 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 49289, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score that includes all the coding potential. based on the starterator data this start site is called when it is present in this pham.
    /note=What is the function?: tail assembly chaperone, The best matches in phagesDB and NCBI are for tail assembly chaperone proteins. One of the significant matches on HHPred is for a tail assembly chaperone. There is not a predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=
    /note=Reviewed: HA, TM

CDS 49690 - 49992
  /gene="80"
  /product="gp80"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_80"
    /note=Original Glimmer call @bp 49690 has strength 10.7; Genemark calls start at 49711
    /note=SSC: 49690-49992 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_183 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.09045E-57 GAP: 56 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.087, -7.619117884189532, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_183 [Arthrobacter phage Atuin]],,UDL16777,96.0784,1.09045E-57 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 49690, Glimmer calls this start site. GeneMark calls a different start site. This start site includes almost all the coding potential. This start site is called when present in the pham. This likely is the second part of the tail assembly chaperone but the programmed translational frame shift cannot be identified.
    /note=What is the function?: hypothetical protein, PhagesDB and NCBI only have significant matches to hypothetical proteins. There are no significant matches on HHPred. There is not a predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=
    /note=Checked: C.A.R

CDS 50009 - 56788
  /gene="81"
  /product="gp81"
  /function="tape measure protein"
  /locus tag="DunneganBoMo_81"
    /note=Original Glimmer call @bp 50009 has strength 8.95; Genemark calls start at 50009
    /note=SSC: 50009-56788 CP: no SCS: both ST: NI BLAST-Start: [tape measure protein [Arthrobacter phage Atuin]],,NCBI, q1586:s1582 29.8362% 0.0 GAP: 16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.742, -3.036436186053076, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Arthrobacter phage Atuin]],,UDL16778,25.4658,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 50009, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best final score that includes all the coding potential. This start site is the most present in all members of the pham and called in all but one member including the only manual annotation.
    /note=What is the function?: tape measure protein, PhagesDB functiona frequency includes only tape measure proteins, as does a BLAST on phagesDB. NCBI has significant matches to tape measure proteins, including three in our cluster. There are no significant matches on HHPred. There is a predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=
    /note=Reviewed: HA, TM

CDS 56806 - 57657
  /gene="82"
  /product="gp82"
  /function="minor tail protein"
  /locus tag="DunneganBoMo_82"
    /note=Original Glimmer call @bp 56806 has strength 6.22; Genemark calls start at 56806
    /note=SSC: 56806-57657 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.78149E-149 GAP: 17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.245, -4.03907523433314, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Atuin]],,UDL16779,84.4523,1.78149E-149 SIF-HHPRED:  SIF-Syn: 
    /note=Start position has good scores, has coding potential. Matches with minor tail protein on NCBI and HHpred blasts.
    /note=
    /note=Checked by: JP, TM

CDS 57671 - 58597
  /gene="83"
  /product="gp83"
  /function="minor tail protein"
  /locus tag="DunneganBoMo_83"
    /note=Original Glimmer call @bp 57671 has strength 7.77; Genemark calls start at 57671
    /note=SSC: 57671-58597 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Racecar] ],,NCBI, q1:s1 99.6753% 3.37006E-167 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.984, -2.4559071081526747, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Racecar] ],,QFG12220,85.3896,3.37006E-167 SIF-HHPRED:  SIF-Syn: 
    /note=Start site has good scores, has coding potential. HHpred does not have good coverage, matches with minor tail protein NCBI.
    /note=
    /note=HHPred has a few good hits but not to proteins with an approved function but they are proteins associated with the tail; NCBI BLAST has multiple minor tail proteins listed
    /note=
    /note=Checked by: JP, TM

CDS 58597 - 59715
  /gene="84"
  /product="gp84"
  /function="minor tail protein"
  /locus tag="DunneganBoMo_84"
    /note=Original Glimmer call @bp 58597 has strength 4.28; Genemark calls start at 58597
    /note=SSC: 58597-59715 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.088, -4.454743937472115, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Atuin]],,UDL16781,92.2043,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=58597, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score. Only start site in the gene with a MA
    /note=
    /note=What is the function? 
    /note=Minor tail protein. Good matches on PhagesDB, NCBI, and HHpred.
    /note=
    /note=Start site: -1 overlap as well.
    /note=
    /note=Checked by: JP, RR

CDS 59721 - 72473
  /gene="85"
  /product="gp85"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_85"
    /note=Original Glimmer call @bp 59721 has strength 5.68; Genemark calls start at 59721
    /note=SSC: 59721-72473 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Atuin]],,NCBI, q1977:s1942 37.3176% 0.0 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.451, -4.5049749909507835, no F: Hypothetical Protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Atuin]],,UDL16782,28.1613,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=59721, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score.
    /note=
    /note=What is the function? 
    /note=hypothetical protein. No good matches between phagesDB, NCBI, and HHpred.
    /note=
    /note=All matches on HHpred are very small regions of the protein (3-5%). It could be a minor tail protein as many call it but insufficient evidence from my perspective.
    /note=
    /note=Checked by: JP; RR

CDS 72482 - 72817
  /gene="86"
  /product="gp86"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_86"
    /note=Original Glimmer call @bp 72482 has strength 6.15; Genemark calls start at 72482
    /note=SSC: 72482-72817 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_178 [Arthrobacter phage Racecar] ],,NCBI, q2:s3 98.1982% 7.49118E-45 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.135, -2.66069824281639, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_178 [Arthrobacter phage Racecar] ],,QFG12223,81.982,7.49118E-45 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=72482, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score. Most called start site in the pham with 41 MAs
    /note=
    /note=What is the function? 
    /note=hypothetical protein. No good matches between phagesDB, NCBI, and HHpred.
    /note=
    /note=Start site is also the most manually annotated start site on starterator.
    /note=
    /note=Checked by: JP

CDS 72889 - 73455
  /gene="87"
  /product="gp87"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_87"
    /note=Original Glimmer call @bp 72889 has strength 6.25; Genemark calls start at 72889
    /note=SSC: 72889-73455 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_190 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 7.88423E-107 GAP: 71 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.433, -5.776767086168905, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_190 [Arthrobacter phage Atuin]],,UDL16784,90.0524,7.88423E-107 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark. 
    /note=
    /note=What is the start site?
    /note=72889, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score.one of two start sites in the gene with a MA and this one includes more coding potential
    /note=
    /note=What is the function? 
    /note=hypothetical protein. No good matches between phagesDB, NCBI, and HHpred.
    /note=
    /note=Checked by: JP; RR

CDS 73516 - 74256
  /gene="88"
  /product="gp88"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_88"
    /note=Original Glimmer call @bp 73516 has strength 8.72; Genemark calls start at 73516
    /note=SSC: 73516-74256 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_191 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.44482E-105 GAP: 60 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.502, -3.5676719685030167, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_191 [Arthrobacter phage Atuin]],,UDL16785,81.7797,1.44482E-105 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=73516, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score. called 100% of the time when present (so present in all within this pham) with 5 MAs
    /note=
    /note=What is the function? 
    /note=hypothetical protein. No good matches between phagesDB, NCBI, and HHpred.
    /note=
    /note=Reviewed: TM; RR

CDS 74284 - 76077
  /gene="89"
  /product="gp89"
  /function="DNA polymerase I"
  /locus tag="DunneganBoMo_89"
    /note=Original Glimmer call @bp 74359 has strength 8.78; Genemark calls start at 74359
    /note=SSC: 74284-76077 CP: no SCS: both-cs ST: NI BLAST-Start: [DNA polymerase I [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.933, -4.769809638752346, no F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Arthrobacter phage Atuin]],,UDL16786,94.1374,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=74284, not the start site called by GLimmer and Genemark. the coding potential extends beyond their call. It includes all coding potential. It has the best final score and a good Z score. There are 4 MAs for this start site and none for the start called by Glimmer and Genemark
    /note=
    /note=What is the function? 
    /note=DNA polymerase 1. Good matches between phagesDB, NCBI, and HHpred. several conserved domain hits to DNA polymerase as well
    /note=
    /note=Reviewed: TM

CDS 76074 - 76526
  /gene="90"
  /product="gp90"
  /function="RuvC-like resolvase"
  /locus tag="DunneganBoMo_90"
    /note=Original Glimmer call @bp 76074 has strength 7.48; Genemark calls start at 76074
    /note=SSC: 76074-76526 CP: no SCS: both ST: NI BLAST-Start: [RuvC-like resolvase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 7.45792E-84 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.52, -5.589933576829573, no F: RuvC-like resolvase SIF-BLAST: ,,[RuvC-like resolvase [Arthrobacter phage Atuin]],,UDL16787,88.6667,7.45792E-84 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=76074, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score.-4 overlap as well
    /note=
    /note=What is the function? 
    /note=ruvC-like resolvase. Good matches between phagesDB, NCBI, and HHpred.
    /note=
    /note=Reviewed: TM; RR

CDS 76558 - 78402
  /gene="91"
  /product="gp91"
  /function="DNA helicase"
  /locus tag="DunneganBoMo_91"
    /note=Original Glimmer call @bp 76558 has strength 8.39; Genemark calls start at 76558
    /note=SSC: 76558-78402 CP: no SCS: both ST: NI BLAST-Start: [DNA helicase [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.6743% 0.0 GAP: 31 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.867, -4.989602575074527, no F: DNA helicase SIF-BLAST: ,,[DNA helicase [Arthrobacter phage Atuin]],,UDL16788,90.4531,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=76558, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score. this start site has the most MAs of those in the gene
    /note=
    /note=What is the function? 
    /note=DNA helicase. Good matches between phagesDB, NCBI, and HHpred.
    /note=
    /note=Reviewed: TM; RR

CDS 78412 - 79212
  /gene="92"
  /product="gp92"
  /function="ThyX-like thymidylate synthase"
  /locus tag="DunneganBoMo_92"
    /note=Original Glimmer call @bp 78412 has strength 8.69; Genemark calls start at 78412
    /note=SSC: 78412-79212 CP: no SCS: both ST: NI BLAST-Start: [ThyX-like thymidylate synthase [Arthrobacter phage Atuin]],,NCBI, q2:s9 99.6241% 0.0 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.017, -4.6062371647338365, no F: ThyX-like thymidylate synthase SIF-BLAST: ,,[ThyX-like thymidylate synthase [Arthrobacter phage Atuin]],,UDL16789,94.1392,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=78412, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score. This start site has 0 MAs but is auto-called 100% of the time when present
    /note=
    /note=What is the function? 
    /note=ThyX-like thymidylate synthase. Good matches between phagesDB, NCBI, and HHpred.
    /note=
    /note=Reviewed: TM; RR

CDS 79281 - 80207
  /gene="93"
  /product="gp93"
  /function="RecB-like exonuclease/helicase"
  /locus tag="DunneganBoMo_93"
    /note=Original Glimmer call @bp 79281 has strength 6.66; Genemark calls start at 79281
    /note=SSC: 79281-80207 CP: no SCS: both ST: NI BLAST-Start: [Cas4 family exonuclease [Arthrobacter phage Atuin]],,NCBI, q1:s16 100.0% 0.0 GAP: 68 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.745, -3.619929324802829, yes F: RecB-like exonuclease/helicase SIF-BLAST: ,,[Cas4 family exonuclease [Arthrobacter phage Atuin]],,UDL16790,93.1889,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=79281, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and final score. Only start site with a manual annotation in this gene
    /note=
    /note=What is the function? 
    /note=. Good matches between phagesDB, NCBI, and HHpred.
    /note=I`m calling a RecB-like exonuclease/helicase because there is a nuclease and helicase present. (AP)
    /note=
    /note=Reviewed: TM; RR

CDS 80225 - 81043
  /gene="94"
  /product="gp94"
  /function="ASCE ATPase"
  /locus tag="DunneganBoMo_94"
    /note=Original Glimmer call @bp 80225 has strength 8.25; Genemark calls start at 80252
    /note=SSC: 80225-81043 CP: no SCS: both-gl ST: NI BLAST-Start: [RecA-like DNA recombinase [Arthrobacter phage Atuin]],,NCBI, q1:s1 87.8676% 7.87747E-156 GAP: 17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.138, -4.79587683327015, no F: ASCE ATPase SIF-BLAST: ,,[RecA-like DNA recombinase [Arthrobacter phage Atuin]],,UDL16791,81.9495,7.87747E-156 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?
    /note=Yes, it has a start and stop site. It has coding potential and is called by both Glimmer and GeneMark.
    /note=
    /note=What is the start site?
    /note=80225, Glimmer calls this start site. It includes all coding potential. It has a good Z- and final score. This start site has 10 MAs (the one called by GeneMark has 0)
    /note=
    /note=What is the function? 
    /note=RecA-like DNA recombinase. Good matches between phagesDB, NCBI, and HHpred. I don`t see any matches to the C-terminal domain. Without this domain I believe the correct gene call is an ASCE ATPase
    /note=
    /note=Reviewed: TM KJ

CDS 81122 - 81781
  /gene="95"
  /product="gp95"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_95"
    /note=Original Glimmer call @bp 81122 has strength 9.13; Genemark calls start at 81122
    /note=SSC: 81122-81781 CP: no SCS: both ST: NI BLAST-Start: [ssDNA binding protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.5434% 8.42763E-97 GAP: 78 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.873, -4.9157003279346805, yes F: Hypothetical Protein SIF-BLAST: ,,[ssDNA binding protein [Arthrobacter phage Atuin]],,UDL16792,88.4444,8.42763E-97 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark S both agree on the start site. Has coding potential. Z score is decent and the Final score is okay. start site is called 100% of the time including 11 MAs. hypothetical protein, HHpred and NCBI BLAST hits to hypothetical proteins. no transmembrane domain
    /note=
    /note=Reviewed: TM KJ

CDS 81871 - 82482
  /gene="96"
  /product="gp96"
  /function="MazG-like nucleotide pyrophosphohydrolase"
  /locus tag="DunneganBoMo_96"
    /note=Original Glimmer call @bp 81871 has strength 12.64; Genemark calls start at 81871
    /note=SSC: 81871-82482 CP: no SCS: both ST: NI BLAST-Start: [MazG-like nucleotide pyrophosphohydrolase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 4.81012E-96 GAP: 89 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.502, -4.014829999845237, yes F: MazG-like nucleotide pyrophosphohydrolase SIF-BLAST: ,,[MazG-like nucleotide pyrophosphohydrolase [Arthrobacter phage Atuin]],,UDL16793,84.1584,4.81012E-96 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? yes, has coding potential; Glimmer and Genemark both call it
    /note=Start Site: 81871, Glimmer and genemark both agree; Starterator has another manual annotation of this start site within the pham (this gene does not have the most frequently called start site); Z-score and final score are good
    /note=Function? Mazg-like nucleotide pyrophosphohydrolase; Several matches in HHPred to nucleotide pyrophosphohydrolases; NCBI and PhagesDB so this function in almost all matches; also has hits in the CDD to a nucleotide triphosphate pyrophosphohydrolase
    /note=
    /note=Reviewed: TM KJ

CDS 82469 - 82903
  /gene="97"
  /product="gp97"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_97"
    /note=Original Glimmer call @bp 82463 has strength 5.03; Genemark calls start at 82463
    /note=SSC: 82469-82903 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_101 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 4.2429E-57 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.404, -6.189779885930021, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_101 [Arthrobacter phage Atuin]],,UDL16794,76.5101,4.2429E-57 SIF-HHPRED:  SIF-Syn: 
    /note=Gene: Yes, it has coding potential, Glimmer and GeneMark both call it
    /note=Start site: 82469, Includes all coding potential, it is the third of three start start codons so the third is the best choice, Pham has 3 MAs at this start site but not commonly called
    /note=Function: Hypothetical Protein; HHpred matches are to functions that are not approved; NCBI BLAST had only matches to hypothetical proteins
    /note=
    /note=Reviewed: KJ, TM

CDS 82929 - 83189
  /gene="98"
  /product="gp98"
  /function="NrdH-like glutaredoxin"
  /locus tag="DunneganBoMo_98"
    /note=Original Glimmer call @bp 82929 has strength 9.5; Genemark calls start at 82929
    /note=SSC: 82929-83189 CP: no SCS: both ST: NI BLAST-Start: [NrdH-like glutaredoxin [Arthrobacter phage Atuin]],,NCBI, q1:s1 97.6744% 2.24945E-46 GAP: 25 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.35, -3.893834241316366, no F: NrdH-like glutaredoxin SIF-BLAST: ,,[NrdH-like glutaredoxin [Arthrobacter phage Atuin]],,UDL16795,88.5057,2.24945E-46 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, according to genemark there is high coding potential for this specific gene 
    /note=what is the start site? according to Glimmer and GeneMark Start, the start site appears to be located at 82929, includes all coding potential, good z and final scores, only start site with MAs (23) in the gene
    /note=what is the function? It can be found that the function might exist as an NrdH-like glutaredoxin based on the majority agreement from the pham members in 185187 on phagesdb. On NCBI there are several hits to NrdH-like glutaredoxin; there is a couple of hits to consreved domains from glutaredoxins as well inlcuding an NrdH-like, however, the function may also work as a thioredoxin based on the 99.6% probability in HHPRED.
    /note=Reviewed: KJ; RR

CDS 83192 - 83581
  /gene="99"
  /product="gp99"
  /function="ribonucleotide reductase"
  /locus tag="DunneganBoMo_99"
    /note=Original Glimmer call @bp 83192 has strength 7.08; Genemark calls start at 83192
    /note=SSC: 83192-83581 CP: no SCS: both ST: NI BLAST-Start: [ribonucleotide reductase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.58692E-77 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.165, -6.4134324599936585, no F: ribonucleotide reductase SIF-BLAST: ,,[ribonucleotide reductase [Arthrobacter phage Atuin]],,UDL16796,92.2481,1.58692E-77 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, according to genemark there is coding potential for this particular gene 
    /note=what is the start site? the start site is set at 83192 according to glimmer and genemark. we can be sure that this is the start site because GeneMark Start shows that there should be a 2 nucleotide gap from the last gene and this one and that is reasonably seen in genemark; only start site in the gene with any manual annotations (6)
    /note=what is the function? HHPRED showsmultiple hits to a ribonucleotide reductase, NCBI blast shows multiple hits to a ribonucleotide reductase function, several conserved domains for ribonucleotide reductase as well
    /note=Reviewed: KJ; RR

CDS 83562 - 85703
  /gene="100"
  /product="gp100"
  /function="ribonucleotide reductase"
  /locus tag="DunneganBoMo_100"
    /note=Original Glimmer call @bp 83562 has strength 9.12; Genemark calls start at 83562
    /note=SSC: 83562-85703 CP: no SCS: both ST: NI BLAST-Start: [ribonucleotide reductase [Arthrobacter phage Racecar] ],,NCBI, q1:s1 100.0% 0.0 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.697, -3.4224590770118644, no F: ribonucleotide reductase SIF-BLAST: ,,[ribonucleotide reductase [Arthrobacter phage Racecar] ],,QFG12238,93.6798,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Gene: yes, it has coding potential and is called by Glimmer and GeneMark
    /note=Start: 83562, only start that includes all coding potential; glimmer and genemark both call it, this is not the most common start site but is called 100% of the time when present
    /note=Function: Multiple hits to ribonucleotide reductase on both HHpred and NCBI with good coverage. conserved domain data base has several matches as well
    /note=Reviewed: KJ; RR

CDS 85794 - 86744
  /gene="101"
  /product="gp101"
  /function="ribonucleotide reductase"
  /locus tag="DunneganBoMo_101"
    /note=Original Glimmer call @bp 85794 has strength 14.7; Genemark calls start at 85794
    /note=SSC: 85794-86744 CP: no SCS: both ST: NI BLAST-Start: [ribonucleotide reductase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 90 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.970161406017234, no F: ribonucleotide reductase SIF-BLAST: ,,[ribonucleotide reductase [Arthrobacter phage Atuin]],,UDL16798,93.6709,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 85,794; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: ribonucleotide reductase; Almost all phages within the pham called this function, Many phagesDB and NCBI BLAST hits to this function; HHPred predicted this result. Several conserved domain matches as well
    /note=Reviewed: KJ; RR

CDS 86744 - 86896
  /gene="102"
  /product="gp102"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_102"
    /note=Original Glimmer call @bp 86744 has strength 3.91
    /note=SSC: 86744-86896 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_205 [Arthrobacter phage Atuin]],,NCBI, q1:s1 92.0% 3.72847E-12 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.785, -3.7892872011995418, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_205 [Arthrobacter phage Atuin]],,UDL16799,72.0,3.72847E-12 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 86,744; it has good Z-score and final score; includes coding potential; and is called every time it is present in a gene.
    /note=What is the function?: There is no known function. no greater than 90% hits on HHpred, Only hypothetical proteins on NCBI, No conserved domains, no transmembrane domains
    /note=Reviewed: KJ; RR

CDS 86906 - 87319
  /gene="103"
  /product="gp103"
  /function="phosphatase"
  /locus tag="DunneganBoMo_103"
    /note=Original Glimmer call @bp 86906 has strength 9.6; Genemark calls start at 86906
    /note=SSC: 86906-87319 CP: no SCS: both ST: NI BLAST-Start: [phosphatase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.10774E-88 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.153, -6.437733311074659, no F: phosphatase SIF-BLAST: ,,[phosphatase [Arthrobacter phage Atuin]],,UDL16800,96.3504,1.10774E-88 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 86,906; Glimmer and GeneMark both called the same start site; includes all coding potential; and is called every time it is present in a gene which is every gene in the pham including two MAs
    /note=What is the function?: several good matches to phosphatases in HHpred, one match to a phosphatase in NCBI BLAST; 2 hits a disphosphate synthase in the Conserved domain database
    /note=Reviewed: KJ

tRNA 87420 - 87494
  /gene="104"
  /product="tRNA-Trp(cca)"
  /locus tag="DUNNEGANBOMO_104"
    /note=tRNA-Trp(cca)

tRNA 87548 - 87622
  /gene="105"
  /product="tRNA-Pro(tgg)"
  /locus tag="DUNNEGANBOMO_105"
    /note=tRNA-Pro(tgg)

tRNA 87740 - 87812
  /gene="106"
  /product="tRNA-Gly(tcc)"
  /locus tag="DUNNEGANBOMO_106"
    /note=tRNA-Gly(tcc)

CDS 87867 - 89492
  /gene="107"
  /product="gp107"
  /function="Ro-like RNA binding protein"
  /locus tag="DunneganBoMo_107"
    /note=Original Glimmer call @bp 87867 has strength 10.23; Genemark calls start at 87867
    /note=SSC: 87867-89492 CP: no SCS: both ST: NI BLAST-Start: [Ro-like RNA binding protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 547 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.701, -3.123974469270304, yes F: Ro-like RNA binding protein SIF-BLAST: ,,[Ro-like RNA binding protein [Arthrobacter phage Atuin]],,UDL16801,82.0841,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, it has a start site, an end site, and coding potential based on genemark
    /note=what is the start site? based on corresponding information from both glimmer and genemark, the start site is 87867; good Z and final scores; only start site in this gene with MAs (7)
    /note=what is the function? ro-like RNA binding protein based on HHpred descriptions and phagesdb and NCBI  blast, conserved domains to RNA binding proteins as well
    /note=Checked: RR, TM
    /note=
    /note=Gap has multiple tRNAs

tRNA 89677 - 89751
  /gene="108"
  /product="tRNA-Thr(tgt)"
  /locus tag="DUNNEGANBOMO_108"
    /note=tRNA-Thr(tgt)

tRNA 90178 - 90252
  /gene="109"
  /product="tRNA-Phe(gaa)"
  /locus tag="DUNNEGANBOMO_109"
    /note=tRNA-Phe(gaa)

tRNA 90265 - 90338
  /gene="110"
  /product="tRNA-Gln(ttg)"
  /locus tag="DUNNEGANBOMO_110"
    /note=tRNA-Gln(ttg)

CDS 90389 - 90562
  /gene="111"
  /product="gp111"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_111"
    /note=Original Glimmer call @bp 90389 has strength 7.7; Genemark calls start at 90389
    /note=SSC: 90389-90562 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_214 [Arthrobacter phage Atuin]],,NCBI, q1:s1 98.2456% 1.32919E-27 GAP: 896 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.35, -3.893834241316366, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_214 [Arthrobacter phage Atuin]],,UDL16802,92.8571,1.32919E-27 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, it has a start and end site and high coding potential based on genemark 
    /note=what is the start site? based on glimmer and genemark the start site is 90389; only start site with any manual annotations in the gene
    /note=what is the function? hypothetical protein based on no significant HHpred matches and only Hypothetical proteins on NCBI BLAST, no conserved domains, no transmembrane domains
    /note=Checked by TM
    /note=
    /note=Checked: RR

tRNA 90615 - 90686
  /gene="112"
  /product="tRNA-Gln(ctg)"
  /locus tag="DUNNEGANBOMO_112"
    /note=tRNA-Gln(ctg)

tRNA 90690 - 90763
  /gene="113"
  /product="tRNA-Ile(gat)"
  /locus tag="DUNNEGANBOMO_113"
    /note=tRNA-Ile(gat)

CDS 90797 - 90979
  /gene="114"
  /product="gp114"
  /function="hypothetical protein"
  /locus tag="DunneganBoMo_114"
    /note=Original Glimmer call @bp 90797 has strength 11.76; Genemark calls start at 90797
    /note=SSC: 90797-90979 CP: no SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 98.3333% 1.41376E-15 GAP: 234 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.826, -3.3213805070409657, yes F: hypothetical protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Atuin]],,UDL16803,78.3333,1.41376E-15 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, it has a start and end site and high coding potential based on genemark 
    /note=what is the start site? based on glimmer and genemark the start site is 90797, 
    /note=what is the function?  no significant hits on HHpred, based on findings from NCBI blast this may be a membrane protein but no transmembrane domain per DeepTMHMM
    /note=Checked: RR, JP
    /note=
    /note=No membrane domain predicted. Hypothetical Protein

tRNA 91006 - 91078
  /gene="115"
  /product="tRNA-Glu(ttc)"
  /locus tag="DUNNEGANBOMO_115"
    /note=tRNA-Glu(ttc)

tRNA 91082 - 91153
  /gene="116"
  /product="tRNA-Glu(ctc)"
  /locus tag="DUNNEGANBOMO_116"
    /note=tRNA-Glu(ctc)

tRNA 91213 - 91298
  /gene="117"
  /product="tRNA-Ser(tga)"
  /locus tag="DUNNEGANBOMO_117"
    /note=tRNA-Ser(tga)

tRNA 91363 - 91446
  /gene="118"
  /product="tRNA-Ser(gga)"
  /locus tag="DUNNEGANBOMO_118"
    /note=tRNA-Ser(gga)

tRNA 91499 - 91572
  /gene="119"
  /product="tRNA-Val(tac)"
  /locus tag="DUNNEGANBOMO_119"
    /note=tRNA-Val(tac)

tRNA 91620 - 91701
  /gene="120"
  /product="tRNA-Leu(caa)"
  /locus tag="DUNNEGANBOMO_120"
    /note=tRNA-Leu(caa)

tRNA 91702 - 91777
  /gene="121"
  /product="tRNA-Met(cat)"
  /locus tag="DUNNEGANBOMO_121"
    /note=tRNA-Met(cat)

tRNA 91780 - 91852
  /gene="122"
  /product="tRNA-Arg(acg)"
  /locus tag="DUNNEGANBOMO_122"
    /note=tRNA-Arg(acg)

CDS 91858 - 92328
  /gene="123"
  /product="gp123"
  /function="portal protein"
  /locus tag="DunneganBoMo_123"
    /note=Original Glimmer call @bp 91858 has strength 11.15; Genemark calls start at 91858
    /note=SSC: 91858-92328 CP: no SCS: both ST: NI BLAST-Start: [phage portal protein [Streptomyces sp. S1D4-14] ],,NCBI, q40:s203 74.359% 4.38091E-8 GAP: 878 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.213, -4.4583299492266635, yes F: portal protein SIF-BLAST: ,,[phage portal protein [Streptomyces sp. S1D4-14] ],,WP_143599366,11.2583,4.38091E-8 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree on start site. There is coding potential. Z and final scores are decent. includes all coding potential, no MAs in this pham and the start sites are not conserved. multiple hits to portal proteins on HHpred and NCBI BLAST.
    /note=
    /note=Reviewed: KJ

tRNA 92530 - 92614
  /gene="124"
  /product="tRNA-Leu(gag)"
  /locus tag="DUNNEGANBOMO_124"
    /note=tRNA-Leu(gag)

CDS 92587 - 92892
  /gene="125"
  /product="gp125"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_125"
    /note=Original Glimmer call @bp 92635 has strength 18.21; Genemark calls start at 92587
    /note=SSC: 92587-92892 CP: no SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_128 [Arthrobacter phage Atuin]],,NCBI, q17:s1 78.2178% 2.63692E-47 GAP: 258 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.791, -5.150794639099285, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_128 [Arthrobacter phage Atuin]],,UDL16804,89.6552,2.63692E-47 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 92587, Glimmer and GeneMark differ--GeneMark calls 92587. It has a worse Z-score and the best final score. Importantly, it aligns best with the gene`s coding potential. Start site is conserved and always called in the pham (5 MAs)
    /note=Function? : Hypothetical protein (PGDYG protein), only matches on HHPred we to PGDYG proteins, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM. (TH)
    /note=Reviewed: KJ - 92635

tRNA 92924 - 93006
  /gene="126"
  /product="tRNA-Leu(tag)"
  /locus tag="DUNNEGANBOMO_126"
    /note=tRNA-Leu(tag)

tRNA 93117 - 93190
  /gene="127"
  /product="tRNA-Arg(tct)"
  /locus tag="DUNNEGANBOMO_127"
    /note=tRNA-Arg(tct)

tRNA 93353 - 93436
  /gene="128"
  /product="tRNA-Tyr(gta)"
  /locus tag="DUNNEGANBOMO_128"
    /note=tRNA-Tyr(gta)

tRNA 93524 - 93598
  /gene="129"
  /product="tRNA-Lys(ctt)"
  /locus tag="DUNNEGANBOMO_129"
    /note=tRNA-Lys(ctt)

tRNA 93704 - 93779
  /gene="130"
  /product="tRNA-Lys(ttt)"
  /locus tag="DUNNEGANBOMO_130"
    /note=tRNA-Lys(ttt)

CDS 93823 - 94128
  /gene="131"
  /product="gp131"
  /function="membrane protein"
  /locus tag="DunneganBoMo_131"
    /note=Original Glimmer call @bp 93823 has strength 15.39; Genemark calls start at 93823
    /note=SSC: 93823-94128 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_MIMI_223 [Arthrobacter phage Mimi]],,NCBI, q1:s1 97.0297% 1.09651E-49 GAP: 930 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.4057176022952405, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein PBI_MIMI_223 [Arthrobacter phage Mimi]],,QFG12875,77.8761,1.09651E-49 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 93823, Glimmer and GeneMark both call this start site. It has the best Z-score and a good final score. Start site is annotated when present 100% of the time (3 MAs)
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, transmembrane domain on DeepTMHMM. (TH)
    /note=Reviewed: KJ changed membrane protein

CDS 94208 - 94384
  /gene="132"
  /product="gp132"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_132"
    /note=Original Glimmer call @bp 94214 has strength 9.19; Genemark calls start at 94214
    /note=SSC: 94208-94384 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_135 [Arthrobacter phage Atuin]],,NCBI, q1:s1 89.6552% 1.74563E-14 GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.826, -2.794180387977985, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_135 [Arthrobacter phage Atuin]],,UDL16806,72.8814,1.74563E-14 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 94208, neither Glimmer or GeneMark call this start site. It has the best Z-score and final score. Only start site in the gene with any Manual annotations (3)
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM. (TH)
    /note=Reviewed: KJ Start cite?

CDS 94412 - 94510
  /gene="133"
  /product="gp133"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_133"
    /note=
    /note=SSC: 94412-94510 CP: no SCS: neither ST: NI BLAST-Start:  GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.707, -5.252038504870807, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? there is some coding potential; not called by Glimmer or Genemark
    /note=Start site: 94412; only start that includes all the coding potential
    /note=Function: Hypothetical protein; No significant hits on HHpred or NCBI BLAST, No conserved domains; no transmembrane domains

CDS 94525 - 94944
  /gene="134"
  /product="gp134"
  /function="nuclease"
  /locus tag="DunneganBoMo_134"
    /note=Original Glimmer call @bp 94525 has strength 13.64; Genemark calls start at 94525
    /note=SSC: 94525-94944 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_229 [Arthrobacter phage Racecar] ],,NCBI, q1:s1 97.8417% 6.9242E-85 GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.519, -5.654416220050276, no F: nuclease SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_229 [Arthrobacter phage Racecar] ],,QFG12252,93.4307,6.9242E-85 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 94525, Glimmer and GeneMark both call this start site. only start site with any manual annotations in the gene (4); includes all conding potential
    /note=Function? : Multiple matches for nucleases on HHpred, NCBI BLAST and Conserved domain database. No transmembrane domain on DeepTMHMM. (TH)
    /note=Reviewed: KJ

CDS 95017 - 96927
  /gene="135"
  /product="gp135"
  /function="endolysin"
  /locus tag="DunneganBoMo_135"
    /note=Original Glimmer call @bp 95104 has strength 9.39; Genemark calls start at 95017
    /note=SSC: 95017-96927 CP: no SCS: both-gm ST: NI BLAST-Start: [endolysin [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 72 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.8, -5.0535707005373816, no F: endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Atuin]],,UDL16808,86.7299,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 95017. includes all coding potential; only start site in the gene with MAs called (2)
    /note=Based off of findings in NCBI and PhagesDB BLAST, this protein codes for an Endolysin.
    /note=Reviewed: KJ, TM

CDS 96989 - 97789
  /gene="136"
  /product="gp136"
  /function="peptidase"
  /locus tag="DunneganBoMo_136"
    /note=Original Glimmer call @bp 96989 has strength 9.35; Genemark calls start at 96995
    /note=SSC: 96989-97789 CP: no SCS: both-gl ST: NI BLAST-Start: [endolysin, protease domain [Arthrobacter phage Atuin]],,NCBI, q23:s1 91.3534% 2.42713E-102 GAP: 61 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.594, -5.511537306530897, no F: peptidase SIF-BLAST: ,,[endolysin, protease domain [Arthrobacter phage Atuin]],,UDL16809,79.1837,2.42713E-102 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 96989, inlcudes all coding potential, not the most called start site but only one that includes all coding potential, and this start is not present in most of the genes.  Codes for a peptidase enzyme. Conserved Domain on Phamerator called peptidase. several hits on HHpred to peptidases.
    /note=Reviewed: KJ

CDS 97943 - 98533
  /gene="137"
  /product="gp137"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_137"
    /note=Original Glimmer call @bp 97943 has strength 16.51; Genemark calls start at 97943
    /note=SSC: 97943-98533 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_235 [Arthrobacter phage Racecar]],,NCBI, q1:s1 96.9388% 1.17509E-101 GAP: 153 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.628, -5.422800743151544, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_235 [Arthrobacter phage Racecar]],,QFG12257,84.0206,1.17509E-101 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 97865.Good Z and Final scores, includes all coding potential, Called 100% of the time present in the pham with 91 MAs. Codes for a hypothetical protein. Many hits on HHpred to von-Willebrand domains, NCBI BLAST matches to hypothetical proteins
    /note=Reviewed: KJ

CDS 98540 - 99253
  /gene="138"
  /product="gp138"
  /function="DnaQ-like (DNA polymerase III subunit)"
  /locus tag="DunneganBoMo_138"
    /note=Original Glimmer call @bp 98540 has strength 10.13; Genemark calls start at 98540
    /note=SSC: 98540-99253 CP: no SCS: both ST: NI BLAST-Start: [DnaE-like DNA polymerase III (alpha) [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.06918E-160 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.016, -5.356325827079472, no F: DnaQ-like (DNA polymerase III subunit) SIF-BLAST: ,,[DnaE-like DNA polymerase III (alpha) [Arthrobacter phage Atuin]],,UDL16810,95.3587,1.06918E-160 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 98540, good Z and final scores, Called 100% of the time when present, includes all coding potential.  Codes for DNA Polymerase III subunit. several hit on HHpred to epsilon subunit of DNA polymerase III
    /note=Reviewed: KJ

CDS 99250 - 99582
  /gene="139"
  /product="gp139"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_139"
    /note=Original Glimmer call @bp 99250 has strength 13.74; Genemark calls start at 99250
    /note=SSC: 99250-99582 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_240 [Arthrobacter phage Atuin]],,NCBI, q3:s2 98.1818% 4.02765E-15 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.101, -4.87383788125753, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_240 [Arthrobacter phage Atuin]],,UDL16811,60.7143,4.02765E-15 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 99250, -4 overlap, includes all coding potential, called in both genes in the pham. Codes for a hypothetical protein. no significant hits on HHpred. Only NCBI hit is to a hypothetical protein, no conserved domains, no transmembrane domain

tRNA 99625 - 99701
  /gene="140"
  /product="tRNA-Met(cat)"
  /locus tag="DUNNEGANBOMO_140"
    /note=tRNA-Met(cat)

tRNA 99765 - 99839
  /gene="141"
  /product="tRNA-Asn(gtt)"
  /locus tag="DUNNEGANBOMO_141"
    /note=tRNA-Asn(gtt)

tRNA 99919 - 99992
  /gene="142"
  /product="tRNA-Ala(tgc)"
  /locus tag="DUNNEGANBOMO_142"
    /note=tRNA-Ala(tgc)

CDS 100033 - 100212
  /gene="143"
  /product="gp143"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_143"
    /note=Original Glimmer call @bp 100033 has strength 2.32
    /note=SSC: 100033-100212 CP: no SCS: glimmer ST: NI BLAST-Start:  GAP: 450 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.796, -3.3864410697949245, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=gene? Called by Glimmer; small amount of coding potential
    /note=Start: 100033, best Z and Final scores, includes all coding potential, only called start site in the pham (only 2 members)
    /note=Function: Hypothetical Protein, only on domain hit on HHpred, Nothing on NCBI or conserved domain, no transmembrane domain

tRNA 100222 - 100294
  /gene="144"
  /product="tRNA-Asp(gtc)"
  /locus tag="DUNNEGANBOMO_144"
    /note=tRNA-Asp(gtc)

CDS 100492 - 101259
  /gene="145"
  /product="gp145"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_145"
    /note=Original Glimmer call @bp 100492 has strength 12.11; Genemark calls start at 100492
    /note=SSC: 100492-101259 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_246 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.38555E-172 GAP: 279 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -3.206439871056232, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_246 [Arthrobacter phage Atuin]],,UDL16813,94.5098,2.38555E-172 SIF-HHPRED:  SIF-Syn: 
    /note=Has excellent coding potential. Glimmer score is good. Glimmer and genemark agree on start site. Starterator agrees on the call site. Z score is amazing and the final score is good. includes all coding potential. no Hits on HHpred over 90%, only hypothetical protein on NCBI, no conserved domains, no transmembrane domains

CDS 101261 - 101590
  /gene="146"
  /product="gp146"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_146"
    /note=Original Glimmer call @bp 101261 has strength 16.55; Genemark calls start at 101261
    /note=SSC: 101261-101590 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_247 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 8.00408E-20 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.502, -4.315859995509217, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_247 [Arthrobacter phage Atuin]],,UDL16814,67.2897,8.00408E-20 SIF-HHPRED:  SIF-Syn: 
    /note=Has excellent coding potential. Glimmer score is good. Glimmer and genemark agree on start site. Starterator agrees on the call site. Z score is amazing and the final score is good. only possible start site. JL
    /note=
    /note=No significant matches on HHpred, only hypothetical proteins in BLAST searches, no conserved domains, no transmembrane domains

CDS 101601 - 101942
  /gene="147"
  /product="gp147"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_147"
    /note=Original Glimmer call @bp 101601 has strength 12.43; Genemark calls start at 101601
    /note=SSC: 101601-101942 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_248 [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.115% 1.67685E-58 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.135, -2.13349812375341, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_248 [Arthrobacter phage Atuin]],,UDL16815,95.5357,1.67685E-58 SIF-HHPRED:  SIF-Syn: 
    /note=Has excellent coding potential. Glimmer score is good. Glimmer and genemark agree on start site. Starterator agrees on the call site. Z score is amazing and the final score is good. only possible start site. JL
    /note=
    /note=No significant matches on HHpred, only hypothetical proteins in BLAST searches, no conserved domains, no transmembrane domain.

CDS 101944 - 102327
  /gene="148"
  /product="gp148"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_148"
    /note=Original Glimmer call @bp 101944 has strength 12.62; Genemark calls start at 101944
    /note=SSC: 101944-102327 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PP457_gp069 [Streptomyces phage TunaTartare] ],,NCBI, q58:s29 51.1811% 1.40359E-5 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.369, -4.301170562178417, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PP457_gp069 [Streptomyces phage TunaTartare] ],,YP_010652030,45.0,1.40359E-5 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 101944, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best final score and Z-score. This gene is an orpham so there is no starterator data available. 
    /note=What is the function?: Hypothetical protein, The only significant matches on NCBI are to hypothetical proteins. there are no significant matches on HHPred.  There is not a predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=
    /note=Checked: C.A.R, TM

CDS 102327 - 102650
  /gene="149"
  /product="gp149"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_149"
    /note=Original Glimmer call @bp 102327 has strength 14.39; Genemark calls start at 102327
    /note=SSC: 102327-102650 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_250 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.43669E-68 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.294, -4.014494766727933, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_250 [Arthrobacter phage Atuin]],,UDL16817,100.0,1.43669E-68 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene? yes, it has a start and stop site, coding potential and Glimmer and GeneMark both call it.
    /note=What is the start site?: 102327, It has a -1 overlap with the previous gene and includes all coding potential. Other start site (with better Z- and final scores) would eliminate some coding potential. This start site is also called in the only other gene in the pham
    /note=What is the function?: Hypothetical Protein, only matches in phagesDB and NCBI BLASTs are to hypothetical proteins. No significant matches in HHPred. No transmembrane domains predicted by DeepTMHMM via Phamerator. (JP)
    /note=
    /note=Checked: C.A.R, TM

tRNA 102689 - 102763
  /gene="150"
  /product="tRNA-His(gtg)"
  /locus tag="DUNNEGANBOMO_150"
    /note=tRNA-His(gtg)

CDS 102838 - 103905
  /gene="151"
  /product="gp151"
  /function="UDP-glucose dehydrogenase"
  /locus tag="DunneganBoMo_151"
    /note=Original Glimmer call @bp 102838 has strength 9.57; Genemark calls start at 102838
    /note=SSC: 102838-103905 CP: no SCS: both ST: NI BLAST-Start: [UDP-glucose dehydrogenase [Arthrobacter phage Mimi]],,NCBI, q1:s1 100.0% 0.0 GAP: 187 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.867, -4.989602575074527, no F: UDP-glucose dehydrogenase SIF-BLAST: ,,[UDP-glucose dehydrogenase [Arthrobacter phage Mimi]],,QFG12888,96.6102,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, It has a start and stop site, coding potential and it is called by both Glimmer and GeneMark.
    /note=What is the start site?: 102838, It is called when present in almost all genes that have this start site (Starterator data) and the only other start site called by a member of the pham is not present in this gene. Glimmer and GeneMark both call this start site.
    /note=What is the function?: UDP-glucose dehydrogenase, All annotated proteins in this pham have this function called. There are several similar structures within the significant HHPred results. (JP)
    /note=
    /note=Checked: C.A.R, TM
    /note=
    /note=The gap in front of this gene has a tRNA

CDS 103979 - 106102
  /gene="152"
  /product="gp152"
  /function="rIIA-like protein"
  /locus tag="DunneganBoMo_152"
    /note=Original Glimmer call @bp 103979 has strength 10.96; Genemark calls start at 103979
    /note=SSC: 103979-106102 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_253 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 73 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.925, -2.9334385989924945, yes F: rIIA-like protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_253 [Arthrobacter phage Atuin]],,UDL16819,76.5867,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, It has a start site and stop site, coding potential and Glimmer and GeneMark both called it.
    /note=What is the start site?: 103979, Glimmer and GeneMark both call this start site, It has the best Z-score and final score, All members of the pham have this start site called. inlcudes the maximum possible coding potential
    /note=What is the function?: rIIA-Like protein; several matches on NCBI with this function. HHPred predicted this function using online HHpred searching the UniProt-SwissProt-viral database. (JP)
    /note=
    /note=Checked: C.A.R

CDS 106136 - 107074
  /gene="153"
  /product="gp153"
  /function="rIIB-like protein"
  /locus tag="DunneganBoMo_153"
    /note=Original Glimmer call @bp 106136 has strength 12.61; Genemark calls start at 106136
    /note=SSC: 106136-107074 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_254 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 33 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.701, -3.588861267572955, yes F: rIIB-like protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_254 [Arthrobacter phage Atuin]],,UDL16820,94.6372,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 106136, Glimmer and GeneMark both called the same start site, This start site has the best Z-score and final score, This start site includes all coding potential, This start site is called every time it is present in a gene.
    /note=What is the function?: rIIB-like protein; Almost all phages within the pham called this function, Many phagesDB and NCBI BLAST hits to this function; HHPred predicted this result using online HHpred searching the UniProt-SwissProt-viral database. (JP)
    /note=
    /note=Checked: C.A.R

CDS 107120 - 107278
  /gene="154"
  /product="gp154"
  /function="membrane protein"
  /locus tag="DunneganBoMo_154"
    /note=Original Glimmer call @bp 107120 has strength 6.1
    /note=SSC: 107120-107278 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein CUB19_gp34c [Stenotrophomonas phage CUB19]],,NCBI, q3:s17 84.6154% 3.50282E-9 GAP: 45 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.206, -4.263391326015678, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein CUB19_gp34c [Stenotrophomonas phage CUB19]],,UWJ04752,55.3846,3.50282E-9 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer shows a start site and there appears to be coding potential. There is however, a large gap that needs to be checked. The Z score is good and the final score is alright. The glimmer score is low. Could be potential for a Transmembrane protein. Needs Checked. JL
    /note=
    /note=Checked: Phamerator shows 2 transmembrane domains for this gene so I do believe it is a membrane protein. -C.A.R
    /note=
    /note=Only signifcant HHpred results are transmembrane proteins.

CDS 107323 - 107838
  /gene="155"
  /product="gp155"
  /function="phosphatase"
  /locus tag="DunneganBoMo_155"
    /note=Original Glimmer call @bp 107323 has strength 10.06; Genemark calls start at 107323
    /note=SSC: 107323-107838 CP: no SCS: both ST: NI BLAST-Start: [phosphatase [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.4152% 9.40658E-106 GAP: 44 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.748, -4.01261984504012, yes F: phosphatase SIF-BLAST: ,,[phosphatase [Arthrobacter phage Atuin]],,UDL16822,94.7368,9.40658E-106 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and glimmer both agree on the start site. The score is good. The Z score is good and the final score is decent. There is coding potential. does not have the most annotated start site but this start is always annotated when present. Could be a HAD protein with 99.9% probability. Needs checked could be potential phosphatase JL
    /note=
    /note=Checked: As there is no HAD protein option in the official functions list and I believe the protein HHPred found is not related to bacteriophages as it mentions that it was found in eukaryotic cells. I believe that phosphatase is the correct function. -C.A.R
    /note=
    /note=Multiple other hits on HHpred to phosphatases and the HAD domain is a phosphatase as well.

tRNA 107846 - 107918
  /gene="156"
  /product="tRNA-Thr(ggt)"
  /locus tag="DUNNEGANBOMO_156"
    /note=tRNA-Thr(ggt)

tRNA 107923 - 107995
  /gene="157"
  /product="tRNA-Cys(gca)"
  /locus tag="DUNNEGANBOMO_157"
    /note=tRNA-Cys(gca)

CDS 108033 - 108545
  /gene="158"
  /product="gp158"
  /function="nuclease"
  /locus tag="DunneganBoMo_158"
    /note=Original Glimmer call @bp 108033 has strength 12.97; Genemark calls start at 108033
    /note=SSC: 108033-108545 CP: no SCS: both ST: NI BLAST-Start: [HNH endonuclease [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 3.30893E-121 GAP: 194 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.925, -2.723328252647382, yes F: nuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage Atuin]],,UDL16823,98.8235,3.30893E-121 SIF-HHPRED:  SIF-Syn: 
    /note=The genemark and glimmer score agree. The Z and final score are really good. There is coding potential. This gene does not have the most annotated start site but this start site is always chosen when present (2 MAs). There is a large gap that needs to be checked. The gene could be HNH endonuclease. JL
    /note=
    /note=Checked: There is a small amount of coding potential around 107900 which could possibly explain the large gap, however I am not sure if it should be called a gene or not. Everything else regarding this gene I agree with.  -C.A.R
    /note=
    /note=Multiple hits to endonucleases in HHpred. however, there is not a H-N-H over a 30 aa span. 
    /note=
    /note=There are two tRNAs in the gap between this gene and the previous gene.

CDS 108594 - 108791
  /gene="159"
  /product="gp159"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_159"
    /note=Original Glimmer call @bp 108594 has strength 6.04; Genemark calls start at 108594
    /note=SSC: 108594-108791 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_260 [Arthrobacter phage Atuin]],,NCBI, q1:s1 98.4615% 4.80916E-31 GAP: 48 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.219, -2.033982896655645, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_260 [Arthrobacter phage Atuin]],,UDL16824,89.0625,4.80916E-31 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark agree on the start site. The score is decent. The Z and Final score are great. There is coding potential. includes all coding potential. The start site is conserved and annotated 100% of the time in the pham. Function unknown. JL
    /note=
    /note=Checked: C.A.R
    /note=
    /note=There are no hits above 90% on HHpred; Only BLAST hits are to hypothetical proteins.

CDS complement (108825 - 110252)
  /gene="160"
  /product="gp160"
  /function="phosphoesterase"
  /locus tag="DunneganBoMo_160"
    /note=Original Glimmer call @bp 110252 has strength 8.74; Genemark calls start at 110261
    /note=SSC: 110252-108825 CP: no SCS: both-gl ST: NI BLAST-Start: [MRE11 double-strand break endo/exonuclease [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.912, -5.580677818518754, no F: phosphoesterase SIF-BLAST: ,,[MRE11 double-strand break endo/exonuclease [Arthrobacter phage Atuin]],,UDL16825,85.3175,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=There is coding potential and enough of a gap between the start sites to allow for the reverse gene to fit here. The start site is called differently by glimmer and genemark, but the Glimmer call seems the better choice. It includes all of the coding potential, has better Z and final scores. The start site is only present in a small fraction of genes within the pham but is called every time it is present (2 MAs).
    /note=
    /note=Mulitple HHpred hits to MRE11 double-strand break endo/exonuclease however when looking at the comparisons to the crystal structures the domain that is matching is just the phosphoesterase domain, not the MRE11 domain so the best call appears to be a phosphoesterase
    /note=Checked: -C.A.R

CDS 110317 - 110694
  /gene="161"
  /product="gp161"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_161"
    /note=Original Glimmer call @bp 110317 has strength 7.75; Genemark calls start at 110317
    /note=SSC: 110317-110694 CP: no SCS: both ST: NI BLAST-Start: [DUF3310 domain-containing protein [Loktanella sp. 3ANDIMAR09] ],,NCBI, q13:s2 54.4% 5.0687E-30 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.299, -4.830816207622987, yes F: Hypothetical Protein SIF-BLAST: ,,[DUF3310 domain-containing protein [Loktanella sp. 3ANDIMAR09] ],,WP_056039087,80.2817,5.0687E-30 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark both agree on start site. The score is decent. the Z and Final score are good. There is coding potential. This start site is required to allow a large enough gap for the reverse gene before this gene. Unknown function. JL
    /note=Checked: not a membrane protein. -JT
    /note=
    /note=There are multiple HHpred and BLAST hits to a domain of unknown function.

CDS 110687 - 110875
  /gene="162"
  /product="gp162"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_162"
    /note=Original Glimmer call @bp 110684 has strength 12.4; Genemark calls start at 110687
    /note=SSC: 110687-110875 CP: no SCS: both-gm ST: NI BLAST-Start: [Hypothetical Protein OBI_RACECAR_173 [Arthrobacter phage Racecar] ],,NCBI, q1:s2 100.0% 1.17879E-27 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.096, -5.009000456184513, yes F: Hypothetical Protein SIF-BLAST: ,,[Hypothetical Protein OBI_RACECAR_173 [Arthrobacter phage Racecar] ],,QFG12268,93.6508,1.17879E-27 SIF-HHPRED:  SIF-Syn: 
    /note=The glimmer score is high and I will stick with the original start site because of the better Z score. The difference isnt that much. There is coding potential. unknown function. JL
    /note=
    /note=Checked: not a membrane protein JT
    /note=
    /note=The genemark start site is the correct start site. When two start codons are back-to-back always choose the second start site. There are no significant matches on HHpred; only BLAST matches are to hypothetical proteins. No conserved domains, and no transmembrane domains

CDS 110875 - 111933
  /gene="163"
  /product="gp163"
  /function="glycosyltransferase"
  /locus tag="DunneganBoMo_163"
    /note=Original Glimmer call @bp 110875 has strength 11.5; Genemark calls start at 110875
    /note=SSC: 110875-111933 CP: no SCS: both ST: NI BLAST-Start: [glycosyltransferase [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.7159% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.926, -5.2484617369160205, no F: glycosyltransferase SIF-BLAST: ,,[glycosyltransferase [Arthrobacter phage Atuin]],,UDL16828,94.9008,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Both glimmer and genemark agree on start site with high number. The Z score is alright and the final score is okay. There is coding potential. -1 gap. glycosyltransferase. JL
    /note=
    /note=Checked: not a membrane protein JT
    /note=
    /note=Multiple HHpred hits to glycosyltransferase with high likelihood of significance. Many BLAST hits as well.

CDS 111926 - 112165
  /gene="164"
  /product="gp164"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_164"
    /note=Original Glimmer call @bp 111926 has strength 12.03; Genemark calls start at 111926
    /note=SSC: 111926-112165 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_265 [Arthrobacter phage Atuin]],,NCBI, q1:s2 100.0% 3.19028E-32 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.604, -5.761910518318305, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_265 [Arthrobacter phage Atuin]],,UDL16829,85.1852,3.19028E-32 SIF-HHPRED:  SIF-Syn: 
    /note=Both glimmer and genemark agree on start site with high number. The Z score is okay and the Final score is okay, not the greatest. Only other start site would lose a lot of coding potential. There is coding potential. only significant hits on HHpred and BLAST are to hypothetical proteins. JL
    /note=
    /note=Checked: not a membrane protein JT

CDS 112270 - 113247
  /gene="165"
  /product="gp165"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_165"
    /note=Original Glimmer call @bp 112270 has strength 10.78; Genemark calls start at 112270
    /note=SSC: 112270-113247 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_266 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.68154E-179 GAP: 104 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -2.2186743274732437, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_266 [Arthrobacter phage Atuin]],,UDL16830,84.1791,1.68154E-179 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and genemark called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 1112,270; it has good Z-score and final score; includes coding potential; and is called every time it is present in a gene.
    /note=What is the function?: There is no known function. The only hits in HHpred or BLAST are to hypothetical proteins, no transmembrane domain. The only conserved domains are of unknown function
    /note=
    /note=Checked: C.A.R, JT

CDS 113360 - 114262
  /gene="166"
  /product="gp166"
  /function="membrane protein, Band-7 -like"
  /locus tag="DunneganBoMo_166"
    /note=Original Glimmer call @bp 113360 has strength 13.04; Genemark calls start at 113375
    /note=SSC: 113360-114262 CP: no SCS: both-gl ST: NI BLAST-Start: [band-7-like membrane protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 97.6667% 4.03077E-157 GAP: 112 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.925, -3.109529858048176, yes F: membrane protein, Band-7 -like SIF-BLAST: ,,[band-7-like membrane protein [Arthrobacter phage Atuin]],,UDL16831,91.4966,4.03077E-157 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 113,360; it has good Z-score and final score; includes coding potential; and is called every time it is present in a gene.
    /note=What is the function?: band 7-like membrane protein; Almost all phages within the pham called this function, Many phagesDB and NCBI BLAST hits to this function; HHPred predicted this result.
    /note=
    /note=Checked: C.A.R, JT

CDS 114342 - 114947
  /gene="167"
  /product="gp167"
  /function="glycosyltransferase"
  /locus tag="DunneganBoMo_167"
    /note=Original Glimmer call @bp 114342 has strength 9.82; Genemark calls start at 114342
    /note=SSC: 114342-114947 CP: no SCS: both ST: NI BLAST-Start: [glycosyltransferase [Arthrobacter phage Atuin]],,NCBI, q2:s3 99.5025% 1.82631E-133 GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.758, -3.7679082124642584, no F: glycosyltransferase SIF-BLAST: ,,[glycosyltransferase [Arthrobacter phage Atuin]],,UDL16832,94.0594,1.82631E-133 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 114,342; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: glycosyltransferase; Almost all phages within the pham called this function, Many phagesDB and NCBI BLAST hits to this function; HHPred predicted this result.
    /note=
    /note=Checked: C.A.R, JT

CDS 114941 - 115603
  /gene="168"
  /product="gp168"
  /function="glycosyltransferase"
  /locus tag="DunneganBoMo_168"
    /note=Original Glimmer call @bp 114941 has strength 7.6; Genemark calls start at 114941
    /note=SSC: 114941-115603 CP: no SCS: both ST: NI BLAST-Start: [glycosyltransferase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 3.12547E-113 GAP: -7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.061, -2.9440753374441266, yes F: glycosyltransferase SIF-BLAST: ,,[glycosyltransferase [Arthrobacter phage Atuin]],,UDL16833,84.8624,3.12547E-113 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 114,941; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: glycosyltransferase; Almost all phages within the pham called this function, Many phagesDB and NCBI BLAST hits to this function; HHPred predicted this result.
    /note=
    /note=Checked: C.A.R, JT

CDS 115600 - 116034
  /gene="169"
  /product="gp169"
  /function="nucleotidyl transferase"
  /locus tag="DunneganBoMo_169"
    /note=Original Glimmer call @bp 115609 has strength 13.84; Genemark calls start at 115600
    /note=SSC: 115600-116034 CP: no SCS: both-gm ST: NI BLAST-Start: [nucleotidyl transferase [Arthrobacter phage Racecar] ],,NCBI, q1:s1 100.0% 5.71015E-87 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.648, -3.317541576732964, no F: nucleotidyl transferase SIF-BLAST: ,,[nucleotidyl transferase [Arthrobacter phage Racecar] ],,QFG12274,90.9722,5.71015E-87 SIF-HHPRED:  SIF-Syn: 
    /note=is this a gene? it has a start site and an end site but coding potential based on genemark is extremely low.
    /note=what is the start site? 115600 genemark; z-score is not greater than 2 but the gap is small and other researchers found this; -4 overlap
    /note=what is its function? gene to code as a nucleotidyl transferase in the FC cluster and the 2411 pham on phagesdb blast, NCBI blast, and HHpred
    /note=
    /note=Checked: I agree with the function, but I think the start site should be changed to the -4 start site as it has 31 MA`s and is a -4 start site compared to the other start site which has no MA`s. -C.A.R
    /note=
    /note=I agree that the start site should be changed to -4. JT

CDS 116111 - 116392
  /gene="170"
  /product="gp170"
  /function="membrane protein"
  /locus tag="DunneganBoMo_170"
    /note=Original Glimmer call @bp 116111 has strength 7.01; Genemark calls start at 116111
    /note=SSC: 116111-116392 CP: no SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 94.6237% 8.81245E-35 GAP: 76 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.295, -6.1534266455957765, no F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Atuin]],,UDL16835,78.2609,8.81245E-35 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, it has a start and end site and high coding potential based on genemark 
    /note=what is the start site? based on glimmer and genemark the start site is 116111, not the most annotated start site but called 100% of the time when present (1 MA)
    /note=what is the function? membrane protein; one hit on HHpred for a protein with a function above 90% but the protein does not hit in the functional region of that protein
    /note=
    /note=Checked: I agree with the start site, but am not in full agreement with the function. HHPred did give a result above 90% for an unknown function, and I do not feel like there is enough evidence to call the function that it currently has, as there is only two phages in the phagesdb blast that call the function originally listed. It should also be noted that this gene has transmembrane domains, so if it is called as a hypothetical protein it should be called a membrane protein. - C.A.R
    /note=
    /note=I believe that the function should be changed to membrane protein based on the phamerator`s DeepTMHMM reading. JT

CDS 116408 - 117622
  /gene="171"
  /product="gp171"
  /function="RNA ligase"
  /locus tag="DunneganBoMo_171"
    /note=Original Glimmer call @bp 116408 has strength 12.52; Genemark calls start at 116408
    /note=SSC: 116408-117622 CP: no SCS: both ST: NI BLAST-Start: [RNA ligase [Arthrobacter phage Atuin]],,NCBI, q17:s17 96.0396% 0.0 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.748, -4.01261984504012, yes F: RNA ligase SIF-BLAST: ,,[RNA ligase [Arthrobacter phage Atuin]],,UDL16836,76.1421,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, it has a start site, an end site, and high coding potential based on genemark
    /note=what is the start site? based on glimmer and genemark the start site is 116408, includes all coding potential, good Z and final scores, not the most annotated start site but annotated 100% of the time when present (13 MAs)
    /note=what is the function? based on phagesdb blast, HHpred and NCBI blast this gene acts as an rna ligase
    /note=Checked by CM
    /note=Checked: C.A.R

CDS 117623 - 118024
  /gene="172"
  /product="gp172"
  /function="lipoprotein"
  /locus tag="DunneganBoMo_172"
    /note=Original Glimmer call @bp 117623 has strength 12.45; Genemark calls start at 117623
    /note=SSC: 117623-118024 CP: no SCS: both ST: NI BLAST-Start:  GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.896, -2.996490344739583, yes F: lipoprotein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, it has start and end sites but has coding potential based on genemark
    /note=what is the start site? based on glimmer and genemark the start site is 117623, only possible option
    /note=what is the function? the z-score is above 2 at 2.896 and the gap is at 0 which are good factors to consider for the gene function. phagesdb blast claims this gene as a lysm-like binding protein and HHpred claims that this gene functions as a lipoprotein which holds a higher probability rate but has a higher e-value to consider since lower e-values are better
    /note=Checked by CM
    /note=Checked: C.A.R

CDS 118036 - 118965
  /gene="173"
  /product="gp173"
  /function="polynucleotide kinase"
  /locus tag="DunneganBoMo_173"
    /note=Original Glimmer call @bp 118036 has strength 8.43; Genemark calls start at 118036
    /note=SSC: 118036-118965 CP: no SCS: both ST: NI BLAST-Start: [polynucleotide kinase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.701, -4.111740012853293, no F: polynucleotide kinase SIF-BLAST: ,,[polynucleotide kinase [Arthrobacter phage Atuin]],,UDL16838,91.2621,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Has excellent coding potential. Glimmer score is decent. Glimmer and genemark agree on start site. Starterator agrees on the call site. Z score is great and the final score is good. multiple hits on HHpred and Blast to polynucleotide kinase. JL
    /note=Checked by CM
    /note=Checked: C.A.R

CDS 118965 - 119147
  /gene="174"
  /product="gp174"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_174"
    /note=Original Glimmer call @bp 118965 has strength 1.91
    /note=SSC: 118965-119147 CP: no SCS: glimmer ST: NI BLAST-Start:  GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.213, -4.2482196028815515, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene: Coding potential is not large but is present, Glimmer does call it
    /note=Start: 118965, -1 gap, only start site that would include the largest region of coding potential
    /note=Function: hypothetical proteins; no significant hits on HHpred or BLAST, no conserved domains, no transmembrane domains
    /note=Checked by CM
    /note=Checked: ciding potential looks good. -C.A.R

CDS 119214 - 119468
  /gene="175"
  /product="gp175"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_175"
    /note=Original Glimmer call @bp 119214 has strength 8.99; Genemark calls start at 119214
    /note=SSC: 119214-119468 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_266 [Arthrobacter phage Racecar]],,NCBI, q1:s1 100.0% 3.35318E-42 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.970161406017234, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_266 [Arthrobacter phage Racecar]],,QFG12279,85.7143,3.35318E-42 SIF-HHPRED:  SIF-Syn: 
    /note=Has excellent coding potential. Glimmer score is good. Glimmer and genemark agree on start site. Starterator agrees on the call site. Z score is amazing and the final score is good. One HHpred hit to a typre of protease but the coverage is small. Hypothetical protein is the best call via BLAST JL
    /note=Checked by CM, JT

CDS 119659 - 120315
  /gene="176"
  /product="gp176"
  /function="tRNA nucleotidyltransferase"
  /locus tag="DunneganBoMo_176"
    /note=Original Glimmer call @bp 119659 has strength 8.93; Genemark calls start at 119659
    /note=SSC: 119659-120315 CP: no SCS: both ST: NI BLAST-Start: [tRNA nucleotidyltransferase [Arthrobacter phage Atuin]],,NCBI, q1:s26 100.0% 1.31218E-121 GAP: 190 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.143, -7.304152110582258, no F: tRNA nucleotidyltransferase SIF-BLAST: ,,[tRNA nucleotidyltransferase [Arthrobacter phage Atuin]],,UDL16841,77.7778,1.31218E-121 SIF-HHPRED:  SIF-Syn: 
    /note=Has great coding potential. Glimmer score is good. Glimmer and genemark agree on start site. Starterator agrees on the call site. Z score is not the greatest and the final score is really good. top hits on HHpred are all to tRNA nucleotudyltransferases.  Others have called tRNA nulceotidyltranferase on phagesDB, so that seems to have more evidence.  JL
    /note=Checked by CM, JT

CDS 120386 - 121678
  /gene="177"
  /product="gp177"
  /function="ASCE ATPase"
  /locus tag="DunneganBoMo_177"
    /note=Original Glimmer call @bp 120386 has strength 14.09; Genemark calls start at 120386
    /note=SSC: 120386-121678 CP: no SCS: both ST: NI BLAST-Start: [RecA-like DNA recombinase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 70 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.933, -4.848494831654204, no F: ASCE ATPase SIF-BLAST: ,,[RecA-like DNA recombinase [Arthrobacter phage Atuin]],,UDL16842,93.4884,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Gene: Yes, it has coding potential and Glimmer and GeneMark both call it
    /note=Start: 120386, only start that includes all coding potential, Glimmer and GeneMark both call it, Most annotated start site, called 100% of time when present for manual annotations (starterator)
    /note=Function: The HHpred matches to AAA domains,
    /note=Checked by CM, JT

CDS 121820 - 124354
  /gene="178"
  /product="gp178"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_178"
    /note=Original Glimmer call @bp 121820 has strength 6.66; Genemark calls start at 121820
    /note=SSC: 121820-124354 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_280 [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.8815% 0.0 GAP: 141 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.135, -2.13349812375341, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_280 [Arthrobacter phage Atuin]],,UDL16844,79.7885,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 121820. best Z and final scores. Most annotated start site in the pham (3 MAs) Codes for a hypothetical protein. there are a few matches on HHpred but they are not on the approved function list
    /note=Checked by CM, JT

CDS 124459 - 125241
  /gene="179"
  /product="gp179"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_179"
    /note=Original Glimmer call @bp 124459 has strength 9.66; Genemark calls start at 124459
    /note=SSC: 124459-125241 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_270 [Arthrobacter phage Racecar]],,NCBI, q1:s1 100.0% 6.62055E-150 GAP: 104 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.756, -6.1362443005807785, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_270 [Arthrobacter phage Racecar]],,QFG12283,91.9231,6.62055E-150 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 124459. called by glimmer and genemark, only start site to include all coding potential, Called when present in starterator, although no manual annotations. Codes for a hypothetical protein. no significant hits on HHpred, only BLAST hits to hypothetical proteins, no conserved domains, no transmembrane domains
    /note=Checked by CM, JT

CDS 125234 - 133039
  /gene="180"
  /product="gp180"
  /function="glycoside hydrolase"
  /locus tag="DunneganBoMo_180"
    /note=Original Glimmer call @bp 125234 has strength 3.56; Genemark calls start at 125234
    /note=SSC: 125234-133039 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Mimi]],,NCBI, q1014:s526 42.1761% 3.05289E-62 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.145, -2.4634880269616195, yes F: glycoside hydrolase SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Mimi]],,QFG12910,28.9904,3.05289E-62 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 125234. called by Glimmer and genemark, only start site that includes all coding potential, best Z and final scores, no manual annotations in this pham but this is the most common auto-annotated site. glycoside hydrolase - multiple hits well above 99% to the glycoside hydrolases.
    /note=Checked by CM, JT

CDS 133110 - 133877
  /gene="181"
  /product="gp181"
  /function="membrane protein"
  /locus tag="DunneganBoMo_181"
    /note=Original Glimmer call @bp 133110 has strength 8.66; Genemark calls start at 133110
    /note=SSC: 133110-133877 CP: no SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.6078% 1.12237E-121 GAP: 70 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.135, -4.801936092881806, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Atuin]],,UDL16845,83.2031,1.12237E-121 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 133110. Codes for a membrane protein.
    /note=
    /note=Start: Includes all coding potential; Glimmer and GeneMark both agree; starterator data called this start site almost every time - both auto and manual except once (this gene does not have the other called start site)
    /note=Function: No significant HHpred hits; BLAST hits are to membrane proteins; Has a transmembrane domain and a signal domain (DeepTMHMM)
    /note=
    /note=Checked by: JP, JT

CDS 133952 - 134626
  /gene="182"
  /product="gp182"
  /function="nucleotidyl transferase"
  /locus tag="DunneganBoMo_182"
    /note=Original Glimmer call @bp 133952 has strength 12.75; Genemark calls start at 133952
    /note=SSC: 133952-134626 CP: no SCS: both ST: NI BLAST-Start: [nucleotidyl transferase [Arthrobacter phage Atuin]],,NCBI, q10:s4 95.9821% 1.34917E-129 GAP: 74 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.689, -5.370073534694293, no F: nucleotidyl transferase SIF-BLAST: ,,[nucleotidyl transferase [Arthrobacter phage Atuin]],,UDL16846,89.5928,1.34917E-129 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 133952. Codes for a nucleotidyl transferase protein.
    /note=
    /note=Start: includes all coding potential; Glimmer and GeneMark both agree; best raw and Z scores of the start sites including the coding potential
    /note=Function: Multiple hits on both HHpred and BLAST to nucleotidyl transferase
    /note=
    /note=Checked by: JP, JT

CDS 134648 - 136015
  /gene="183"
  /product="gp183"
  /function="AAA-ATPase"
  /locus tag="DunneganBoMo_183"
    /note=Original Glimmer call @bp 134648 has strength 12.51; Genemark calls start at 134648
    /note=SSC: 134648-136015 CP: no SCS: both ST: NI BLAST-Start: [AAA-ATPase [Arthrobacter phage Atuin]],,NCBI, q2:s1 99.7802% 0.0 GAP: 21 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.017, -4.588508397773405, no F: AAA-ATPase SIF-BLAST: ,,[AAA-ATPase [Arthrobacter phage Atuin]],,UDL16847,78.9247,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 134648, Glimmer and GeneMark both call this start site. It has a good Z-score and final score. 
    /note=Function? : AAA-ATPase. No transmembrane domain on DeepTMHMM. (TH)
    /note=
    /note=Start: Includes all coding potential; 
    /note=Function: Multiple hits on both HHpred and BLAST to AAA-ATPase
    /note=
    /note=Checked by: JP, JT

CDS 136080 - 136349
  /gene="184"
  /product="gp184"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_184"
    /note=Original Glimmer call @bp 136080 has strength 9.89; Genemark calls start at 136080
    /note=SSC: 136080-136349 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_284 [Arthrobacter phage Atuin]],,NCBI, q4:s10 96.6292% 3.1821E-38 GAP: 64 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.402, -5.844258411975837, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_284 [Arthrobacter phage Atuin]],,UDL16848,77.8947,3.1821E-38 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 136080, Glimmer and GeneMark both call this start site. It has a good Z-score and final score and aligns with the coding potential best.
    /note=Function? : Hypothetical protein
    /note=(TH)
    /note=
    /note=Start: Includes all coding potential; all manual annotations call this start site and auto annotation call it when present
    /note=Function: No significant hits on HHpred or BLAST; No transmembrane domains (DeepTMHMM)
    /note=
    /note=Checked by: JP, JT

CDS 136342 - 136770
  /gene="185"
  /product="gp185"
  /function="WhiB family transcription factor"
  /locus tag="DunneganBoMo_185"
    /note=Original Glimmer call @bp 136342 has strength 6.8; Genemark calls start at 136342
    /note=SSC: 136342-136770 CP: no SCS: both ST: NI BLAST-Start: [WhiB family transcription factor [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 6.65723E-85 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.519, -3.8026703187234707, yes F: WhiB family transcription factor SIF-BLAST: ,,[WhiB family transcription factor [Arthrobacter phage Atuin]],,UDL16849,92.9078,6.65723E-85 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 136342, Glimmer and GeneMark both call this start site. It has a good Z-score and final score. 
    /note=Function? : WhiB transcription factor.
    /note=(TH)
    /note=
    /note=Start: -8 overlap; Only option that includes all coding potential; Only start site in our gene with any other annotations in starterator
    /note=Function: Multiple BLAST and HHpred hits to WhiB transcription factors
    /note=
    /note=Checked by: JP
    /note=Checked by CM

CDS 136806 - 137657
  /gene="186"
  /product="gp186"
  /function="G-I-Y Y-I-G endonuclease"
  /locus tag="DunneganBoMo_186"
    /note=Original Glimmer call @bp 136806 has strength 5.55; Genemark calls start at 136806
    /note=SSC: 136806-137657 CP: no SCS: both ST: NI BLAST-Start: [NUMOD3 domain-containing DNA-binding protein [Sanguibacter gelidistatuariae] ],,NCBI, q6:s13 90.4594% 3.80688E-30 GAP: 35 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.299, -4.575543702519681, no F: G-I-Y Y-I-G endonuclease SIF-BLAST: ,,[NUMOD3 domain-containing DNA-binding protein [Sanguibacter gelidistatuariae] ],,WP_093185674,49.0566,3.80688E-30 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 136806, Glimmer and GeneMark both call this start site. It has a good Z-score and final score. 
    /note=Function? : GIY YIG endonuclease
    /note=(TH)
    /note=
    /note=Start: Includes all coding potential, 
    /note=Function: multiple HHpred hits to GIY-YIG endonuclease on HHpred
    /note=
    /note=Checked by: JP, CM

CDS 137638 - 139731
  /gene="187"
  /product="gp187"
  /function="DNA helicase"
  /locus tag="DunneganBoMo_187"
    /note=Original Glimmer call @bp 137674 has strength 7.62; Genemark calls start at 137638
    /note=SSC: 137638-139731 CP: no SCS: both-gm ST: NI BLAST-Start: [DNA helicase [Arthrobacter phage Atuin]],,NCBI, q13:s1 98.1349% 0.0 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.933, -5.234696437054997, no F: DNA helicase SIF-BLAST: ,,[DNA helicase [Arthrobacter phage Atuin]],,UDL16850,89.0029,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 137638 it has a good Z-score and final score. Aligns with coding potential.
    /note=Function? : ATP-dependent DNA helicase
    /note=(TH)
    /note=
    /note=Start:
    /note=Function: Mulitple hits to DNA helicase in both HHpred and BLAST
    /note=
    /note=Checked by: JP, CM

CDS 139739 - 140890
  /gene="188"
  /product="gp188"
  /function="DNA primase"
  /locus tag="DunneganBoMo_188"
    /note=Original Glimmer call @bp 139739 has strength 10.3; Genemark calls start at 139739
    /note=SSC: 139739-140890 CP: no SCS: both ST: NI BLAST-Start: [DNA primase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.135, -2.9617282384803714, yes F: DNA primase SIF-BLAST: ,,[DNA primase [Arthrobacter phage Atuin]],,UDL16851,87.0466,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: yes, it has a start and stop site, coding potential and Glimmer and GeneMark both call the gene
    /note=What is the start site?: 139739, this start site is call by both Glimmer and GeneMark, it has the best Z- and final score, it is called in all genes with the start site in starterator.
    /note=What is the function?: DNA primase, it is called this functional by all annotated genes within our cluster, as well as in similar gene outside the cluster, Several similar matches on HHPred (JP)
    /note=Checked by CM
    /note=
    /note=Checked: C.A.R

CDS 140923 - 141033
  /gene="189"
  /product="gp189"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_189"
    /note=Genemark calls start at 140923
    /note=SSC: 140923-141033 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_288 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.07197E-9 GAP: 32 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.943, -5.989984804479136, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_288 [Arthrobacter phage Atuin]],,UDL16852,83.3333,1.07197E-9 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: yes, It has a start and stop site, coding potential, and is called by GeneMark
    /note=What is the start site?: 140923, this is the start site called by GeneMark, it includes all coding potential, it is called when present (starterator), it has the best Z-score and final score (although these are not good)
    /note=What is the function?: Hypothetical Protein - Only phagesDB and NCBI matches are to hypothetical proteins; No significant matches in HHPred; no conserved domains; There is not a membrane domain (DeepTMHMM via Phamerator) (JP)
    /note=Checked by CM
    /note=
    /note=Checked: C.A.R

CDS 141037 - 141381
  /gene="190"
  /product="gp190"
  /function="nuclease"
  /locus tag="DunneganBoMo_190"
    /note=Original Glimmer call @bp 141037 has strength 2.25
    /note=SSC: 141037-141381 CP: no SCS: glimmer ST: NI BLAST-Start: [HNH endonuclease [Arthrobacter phage Racecar] ],,NCBI, q20:s3 82.4561% 2.41938E-42 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.778, -5.866308552718912, no F: nuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage Racecar] ],,QFG12293,80.2083,2.41938E-42 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: it has minimal coding potential. It is only called by Glimmer.
    /note=What is the start site?: 141037, if it is a gene, that is the only start site that would have all the coding potential, called by Glimmer, This is the only gene to have this start site in the Pham according to starterator
    /note=What is the function?: Appears to be a nuclease. the specific type of nuclease cannot be determined, several hits to HNH endonucleases but there is not an H-N-H over 30 AAs (only one H)
    /note=Checked by CM
    /note=
    /note=Checked: C.A.R

CDS 141455 - 141733
  /gene="191"
  /product="gp191"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_191"
    /note=Original Glimmer call @bp 141455 has strength 13.21; Genemark calls start at 141455
    /note=SSC: 141455-141733 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_290 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.07412E-50 GAP: 73 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.896, -2.6453814847322845, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_290 [Arthrobacter phage Atuin]],,UDL16854,92.3077,2.07412E-50 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a Gene?: Yes, it has a start and stop site, it has coding potential, It is call by both Glimmer and GeneMark
    /note=What is the start site?: 141455, this start site includes all coding potential, it has the best Z- and final scores, it is called by both Glimmer and GeneMark, it is called every time by the genes in this pham and cluster.
    /note=What is the function?: hypothetical protein, there are no significant matches in HHPred, there are only matches to other hypothetical proteins in both phagesdb and NCBI BLASTs, there is not a transmembrane domain.
    /note=Checked by CM, TH

CDS 141786 - 143459
  /gene="192"
  /product="gp192"
  /function="DNA primase/helicase"
  /locus tag="DunneganBoMo_192"
    /note=Original Glimmer call @bp 141786 has strength 9.85; Genemark calls start at 141786
    /note=SSC: 141786-143459 CP: no SCS: both ST: NI BLAST-Start: [DNA helicase [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 0.0 GAP: 52 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.701, -3.588861267572955, no F: DNA primase/helicase SIF-BLAST: ,,[DNA helicase [Arthrobacter phage Atuin]],,UDL16855,89.009,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: Yes, it has a start and stop site, it has good coding potential, and Glimmer and GeneMark both call it
    /note=What is the start site?: 141786, this is the only start site that contains all coding potential, it is called by both Glimmer and GeneMark, this start site is called in all members of the pham and cluster (starterator), it has the best Z- and final score (other than one start site that excludes a large amount of coding potential)
    /note=What is the function?: DNA primase/helicase, there are several HHPred results (with 100% probability) that match the primase/helicase functional call, all other members within the cluster have called a DNA helicase but the conserved domain database also matches to DNA primase domain.
    /note=Checked by CM, TH

CDS 143531 - 143827
  /gene="193"
  /product="gp193"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_193"
    /note=Original Glimmer call @bp 143531 has strength 15.79; Genemark calls start at 143531
    /note=SSC: 143531-143827 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_292 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 5.50772E-22 GAP: 71 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.806, -3.4906862459040946, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_292 [Arthrobacter phage Atuin]],,UDL16856,72.6316,5.50772E-22 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 143531, Glimmer and GeneMark both call this start site. It has a good Z-score and final score.  includes all coding potential, start site called 100% of the time when present (1 MA)
    /note=Function? : hypothetical protein; no significant hits on HHpred; only BLAST hits to hypothetical proteins, no conserved domains, no transmembrane domains,
    /note=(TH)           
    /note=Checked by CM

CDS 143824 - 143991
  /gene="194"
  /product="gp194"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_194"
    /note=Original Glimmer call @bp 143863 has strength 2.9
    /note=SSC: 143824-143991 CP: no SCS: glimmer-cs ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_194 [Arthrobacter phage Atuin]],,NCBI, q14:s1 76.3636% 1.57558E-10 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.427, -4.177176971714429, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_194 [Arthrobacter phage Atuin]],,UDL16857,83.3333,1.57558E-10 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 143863, It has a good Z-score and final score. -4 overlap, includes all coding potential
    /note=Function? : hypothetical protein; only significant hit on HHpred to a function not on the authorized list; all BLAST hits to hypothetical proteins; no conserved domains; no transmembrane domains
    /note=(TH)
    /note=Checked by CM

CDS 144050 - 144415
  /gene="195"
  /product="gp195"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_195"
    /note=Original Glimmer call @bp 144050 has strength 18.88; Genemark calls start at 144050
    /note=SSC: 144050-144415 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_294 [Arthrobacter phage Atuin]],,NCBI, q8:s4 93.3884% 7.04664E-22 GAP: 58 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.345, -3.8879567634597363, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_294 [Arthrobacter phage Atuin]],,UDL16858,59.375,7.04664E-22 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 144050, Glimmer and GeneMark both call this start site. It has a good Z-score and final score. longest open reading frame with coding potential extending beyond the start site; only start site called within the pham
    /note=Function? : hypothetical protein; no 90% or greater hits on HHpred; only hypothetical proteins on BLAST; no conserved domains, no transmembrane domain
    /note=(TH)
    /note=
    /note=Start site includes all coding potential possible to capture. Start site is called when present according to starterator (only one manual annotation though).
    /note=Function: no significant hits on BLAST comparisons or HHpred (best on HHpred were to proteins of unknown function)
    /note=
    /note=Checked by: JP

CDS 144463 - 144699
  /gene="196"
  /product="gp196"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_196"
    /note=Original Glimmer call @bp 144463 has strength 12.39; Genemark calls start at 144463
    /note=SSC: 144463-144699 CP: no SCS: both ST: NI BLAST-Start:  GAP: 47 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.748, -2.9625409806968013, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 144463, it has a good Z-score and final score. 
    /note=Function? : hypothetical protein
    /note=(TH)
    /note=
    /note=Start site: Includes the maximum coding potential that can be included; Starterator - no manual annotations but this start site called in all auto annotations when present
    /note=Function: No significant hits on HHpred or BLAST; no conserved domains; no transmembrane domains
    /note=
    /note=Checked by: JP

CDS 144696 - 144959
  /gene="197"
  /product="gp197"
  /function="lipoprotein"
  /locus tag="DunneganBoMo_197"
    /note=Original Glimmer call @bp 144696 has strength 7.99; Genemark calls start at 144696
    /note=SSC: 144696-144959 CP: no SCS: both ST: NI BLAST-Start: [lipoprotein [Arthrobacter phage Atuin]],,NCBI, q3:s4 97.7011% 5.27985E-39 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.974, -3.5288488554554966, yes F: lipoprotein SIF-BLAST: ,,[lipoprotein [Arthrobacter phage Atuin]],,UDL16860,82.0225,5.27985E-39 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 144696, Glimmer and GeneMark both call this start site. It has a good Z-score and final score. 
    /note=Function? :  membrane lipoprotein
    /note=(TH)
    /note=
    /note=Start site: -4 overlap
    /note=Function: Lipoprotein supported by several HHpred matches and one BLAST match
    /note=
    /note=Checked by: JP, TM

CDS 144956 - 145123
  /gene="198"
  /product="gp198"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_198"
    /note=Original Glimmer call @bp 144956 has strength 8.06; Genemark calls start at 144956
    /note=SSC: 144956-145123 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.445, -5.216381181846213, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 144956, Glimmer and GeneMark both call this start site. It has a good Z-score and final score. 
    /note=Function? : Hypothetical protein. No transmembrane domain on DeepTMHMM. 
    /note=(TH)
    /note=
    /note=Start site: -4 overlap, includes all coding potential
    /note=Function: No significant matches on HHpred or BLAST
    /note=Checked by: JL

CDS 145120 - 145371
  /gene="199"
  /product="gp199"
  /function="lipoprotein"
  /locus tag="DunneganBoMo_199"
    /note=Original Glimmer call @bp 145120 has strength 7.03; Genemark calls start at 145120
    /note=SSC: 145120-145371 CP: no SCS: both ST: NI BLAST-Start: [lipoprotein [Arthrobacter phage Atuin]],,NCBI, q1:s1 97.5904% 4.70232E-12 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -2.8084998623841946, yes F: lipoprotein SIF-BLAST: ,,[lipoprotein [Arthrobacter phage Atuin]],,UDL16861,58.3333,4.70232E-12 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 145120, Glimmer and GeneMark both call this start site. It has a good Z-score and final score. 
    /note=Function? : Lipoprotein. No transmembrane domain on DeepTMHMM. (TH)
    /note=
    /note=Start site: -4 overlap; including all coding potential
    /note=Function: Matches on HHpred and BLAST for lipoprotein
    /note=
    /note=Checked by: JP, JL

CDS 145368 - 145490
  /gene="200"
  /product="gp200"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_200"
    /note=Genemark calls start at 145368
    /note=SSC: 145368-145490 CP: no SCS: genemark ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.294, -4.7626827937341325, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 145368, Glimmer and GeneMark both call this start site. It has a good Z-score and final score. 
    /note=Function? : Hypothetical protein. No transmembrane domain on DeepTMHMM. 
    /note=(TH)
    /note=
    /note=Start site: Glimmer does not call the gene only GeneMark. -4 start site and includes all coding potential.
    /note=Function: No significant matches on BLAST or HHpred.
    /note=
    /note=Checked by: JP, JL

CDS 145534 - 146244
  /gene="201"
  /product="gp201"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_201"
    /note=Original Glimmer call @bp 145534 has strength 11.7; Genemark calls start at 145534
    /note=SSC: 145534-146244 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_298 [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.5763% 1.38709E-27 GAP: 43 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -2.9845911214398755, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_298 [Arthrobacter phage Atuin]],,UDL16862,53.8793,1.38709E-27 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 145534, Glimmer and GeneMark both call this start site. It has a good Z-score and final score. 
    /note=Function? : Hypothetical protein. No transmembrane domain on DeepTMHMM. (TH)
    /note=
    /note=Start site: Starterator data has this start site as being called all the time in this pham (only one manual annotation though; 7 automated), includes all coding potential.
    /note=Function: No significant matches on BLAST or HHpred.
    /note=
    /note=Checked by: JP, JL

CDS 146262 - 146486
  /gene="202"
  /product="gp202"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_202"
    /note=Original Glimmer call @bp 146262 has strength 13.94; Genemark calls start at 146262
    /note=SSC: 146262-146486 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_299 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.10137E-30 GAP: 17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -2.6835611257758942, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_299 [Arthrobacter phage Atuin]],,UDL16863,88.7324,1.10137E-30 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 146,262; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: There is no known function.
    /note=
    /note=Function: No significant hits on HHpred; only hypothetical proteins in BLAST significant hit.
    /note=
    /note=Checked by: JP, JL

CDS 146492 - 147016
  /gene="203"
  /product="gp203"
  /function="protease"
  /locus tag="DunneganBoMo_203"
    /note=Original Glimmer call @bp 146492 has strength 12.14; Genemark calls start at 146492
    /note=SSC: 146492-147016 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein [Arthrobacter koreensis] ],,NCBI, q1:s1 91.954% 1.1886E-34 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.951, -4.749088834314575, no F: protease SIF-BLAST: ,,[hypothetical protein [Arthrobacter koreensis] ],,WP_263127499,59.2814,1.1886E-34 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 146,492; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: Protease; Almost all phages within the pham called this function, Many phagesDB and NCBI BLAST hits to this function; HHPred predicted this result.
    /note=
    /note=Checked by: JP, JL

CDS 147018 - 147209
  /gene="204"
  /product="gp204"
  /function="membrane protein"
  /locus tag="DunneganBoMo_204"
    /note=Original Glimmer call @bp 147018 has strength 12.83; Genemark calls start at 147018
    /note=SSC: 147018-147209 CP: no SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.86491E-19 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.494, -3.506699786770751, no F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Atuin]],,UDL16864,93.6508,1.86491E-19 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene? Yes, it has a start and stop site, it has good coding potential, and Glimmer and GeneMark both call it
    /note=
    /note=What is the start site? 147018, this is the only start site that contains all coding potential, it is called by both Glimmer and GeneMark, this start site is called in all members of the pham and cluster (starterator), it has the best Z- and final score (other than one start site that excludes a large amount of coding potential)
    /note=
    /note=What is the function? There is no known function.
    /note=
    /note=Function: There is a transmembrane domain; Changed function to membrane protein
    /note=
    /note=Checked by: JP, JL, TM

CDS complement (147243 - 148697)
  /gene="205"
  /product="gp205"
  /function="terminase, large subunit"
  /locus tag="DunneganBoMo_205"
    /note=Original Glimmer call @bp 148697 has strength 10.68; Genemark calls start at 148697
    /note=SSC: 148697-147243 CP: no SCS: both ST: NI BLAST-Start: [terminase [Arthrobacter phage Atuin]],,NCBI, q1:s1 97.5207% 0.0 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.007, -4.629100047693341, no F: terminase, large subunit SIF-BLAST: ,,[terminase [Arthrobacter phage Atuin]],,UDL16596,94.3089,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene? Yes, it has a start and stop site, it has good coding potential, and Glimmer and GeneMark both call it
    /note=
    /note=What is the start site? 148697, this is the only start site that contains all coding potential, it is called by both Glimmer and GeneMark, this start site is called in all members of the pham and cluster (starterator), it has the best Z- and final score (other than one start site that excludes a large amount of coding potential)
    /note=What is the function? terminase, large subunit, there are several HHPred results (with 100% probability) that match the same function. and a small subunit of a terminase is found later in the genome
    /note=
    /note=Reviewed: TM, JL

CDS complement (148678 - 148956)
  /gene="206"
  /product="gp206"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_206"
    /note=Original Glimmer call @bp 148956 has strength 6.2; Genemark calls start at 148956
    /note=SSC: 148956-148678 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_2 [Arthrobacter phage Atuin]],,NCBI, q11:s1 88.0435% 2.46317E-25 GAP: 57 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.579, -6.371458531038818, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_2 [Arthrobacter phage Atuin]],,UDL16597,78.75,2.46317E-25 SIF-HHPRED:  SIF-Syn: 
    /note=coding potential? it does have coding potential based on genemark 
    /note=start site? 146596 is the start site matched by glimmer and genemark 
    /note=function? no significant hits on HHpred; only BLAST hits to hypothetical proteins; no conserved domain, no transmembrane domain
    /note=
    /note=SB
    /note=
    /note=Reviewed: Tm, Reviewed by Class, JL

CDS 149014 - 149466
  /gene="207"
  /product="gp207"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_207"
    /note=Original Glimmer call @bp 149014 has strength 14.2; Genemark calls start at 149014
    /note=SSC: 149014-149466 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_3 [Arthrobacter phage Atuin]],,NCBI, q23:s21 80.6667% 6.36563E-15 GAP: 57 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.138, -5.176088074981756, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_3 [Arthrobacter phage Atuin]],,UDL16598,46.0123,6.36563E-15 SIF-HHPRED:  SIF-Syn: 
    /note=coding potential? it does have high coding potential based on genemark 
    /note=start site? 149014 based on glimmer and genemark, only start site to allow a big enough gap for the reverse genes that come before it
    /note=function? based on unknown findings, the function might be a hypothetical protein; no significant HHpred hits; only hypothetical proteins on BLAST; no conserved domains, on transmembrane domains
    /note=
    /note=Reviewed; TM, JL

CDS 149511 - 149723
  /gene="208"
  /product="gp208"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_208"
    /note=Original Glimmer call @bp 149511 has strength 5.58; Genemark calls start at 149511
    /note=SSC: 149511-149723 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_4 [Arthrobacter phage Atuin]],,NCBI, q1:s1 98.5714% 3.43035E-36 GAP: 44 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.339, -4.664885151282071, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_4 [Arthrobacter phage Atuin]],,UDL16599,91.4286,3.43035E-36 SIF-HHPRED:  SIF-Syn: 
    /note=coding potential? yes this gene has coding potential 
    /note=start site? 149511 is the start site matched by glimmer and genemark; best Z and final scores, includes all coding potential, most annotated start site (100 % when present with 4 MAs)
    /note=function? no 90% or greater matches on HHpred; BLAST hits all hypothetical proteins; no conserved domains, no transmembrane domains
    /note=
    /note=Reviewed: TM

CDS 149713 - 149943
  /gene="209"
  /product="gp209"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_209"
    /note=Original Glimmer call @bp 149713 has strength 6.82; Genemark calls start at 149713
    /note=SSC: 149713-149943 CP: no SCS: both ST: NI BLAST-Start: [flippase-like domain-containing protein [Candidatus Saccharibacteria bacterium]],,NCBI, q10:s8 86.8421% 0.0135785 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.701, -3.713800004181255, yes F: Hypothetical Protein SIF-BLAST: ,,[flippase-like domain-containing protein [Candidatus Saccharibacteria bacterium]],,MCA9348447,28.3582,0.0135785 SIF-HHPRED:  SIF-Syn: 
    /note=coding potential? yes, this gene does have coding potential based on genemark. However, there is a slight deter from higher potential readings around 149875
    /note=start site? 149713 is the matched start site from glimmer and genemark 
    /note=function? PnuC-like Nicotinamide riboside transporter is the given function due to findings from Phagesdb function frequency and blast. However, there are high probabilities indicated in HHpred that it may be a part of the SLATT clan as a pore-forming effector overlaid in domains 1-4. 
    /note=SB
    /note=
    /note=Reviewed: TM, Reviewed by Class

CDS 149943 - 150044
  /gene="210"
  /product="gp210"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_210"
    /note=Genemark calls start at 149943
    /note=SSC: 149943-150044 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_6 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.09392E-5 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.068, -3.1837611541087343, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_6 [Arthrobacter phage Atuin]],,UDL16601,84.375,2.09392E-5 SIF-HHPRED:  SIF-Syn: 
    /note=Genemarks start site seems to be correct after checking the coding potential it falls in that range. The Z score is great and the final score isn`t bad. The only start site without a huge amount of overlap with the previous gene (-1 overlap as well)
    /note=hypothetical protein. NCBI/PhagesDB BLAST didn`t have nay answers worth noting along with HHpred.
    /note=
    /note=JL
    /note=Reviewed by: TM

CDS 150028 - 150339
  /gene="211"
  /product="gp211"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_211"
    /note=Original Glimmer call @bp 150028 has strength 5.65; Genemark calls start at 150028
    /note=SSC: 150028-150339 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_7 [Arthrobacter phage Atuin]],,NCBI, q8:s6 91.2621% 1.19936E-6 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.369, -3.8362837638757656, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_7 [Arthrobacter phage Atuin]],,UDL16602,50.0,1.19936E-6 SIF-HHPRED:  SIF-Syn: 
    /note=Both Glimmer and Genemark agree on the start site. The score is okay. The Z score is good and the final score is okay. there is coding potential. Has a small overlap. Only start site with a manual annotation
    /note=Hypothetical protein. No applicable results were provided by PhagesDB/NCBI BLAST or HHpred.
    /note=JL
    /note=Reviewed: TM

CDS 150382 - 150546
  /gene="212"
  /product="gp212"
  /function="membrane protein"
  /locus tag="DunneganBoMo_212"
    /note=Original Glimmer call @bp 150382 has strength 5.25; Genemark calls start at 150382
    /note=SSC: 150382-150546 CP: no SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.82191E-12 GAP: 42 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.322, -3.9531326986493704, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Atuin]],,UDL16603,83.3333,2.82191E-12 SIF-HHPRED:  SIF-Syn: 
    /note=Both Glimmer and Genemark agree on the start site. The score is okay. The Z score is good and the final score is okay. there is coding potential.  
    /note=Membrane protein due to the presence of transmembrane domains, found on Phamerator. PhagesDB/NCBI BLAST + HHpred din`t provide any applicable data.
    /note=JL
    /note=Reviewed By: TM

CDS 150703 - 150984
  /gene="213"
  /product="gp213"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_213"
    /note=Original Glimmer call @bp 150703 has strength 18.61; Genemark calls start at 150703
    /note=SSC: 150703-150984 CP: no SCS: both ST: NI BLAST-Start:  GAP: 156 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -2.2186743274732437, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Both Glimmer and Genemark agree on the start site. The score is amazing. The Z score is great and the final score is great. there is coding potential. only annotated start site in the pham
    /note=Hypothetical protein. No applical results were provided by HHpred or PhagesDb/NCBI BLAST. no conserved domains; no transmembrane domains
    /note=JL
    /note=Reviewed by: TM
    /note=No coding potential in the gap before this gene.

CDS 150996 - 151289
  /gene="214"
  /product="gp214"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_214"
    /note=Original Glimmer call @bp 150996 has strength 8.01; Genemark calls start at 150996
    /note=SSC: 150996-151289 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_11 [Arthrobacter phage Atuin]],,NCBI, q1:s1 92.7835% 5.30549E-5 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.796, -3.3864410697949245, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_11 [Arthrobacter phage Atuin]],,UDL16606,51.0417,5.30549E-5 SIF-HHPRED:  SIF-Syn: 
    /note=Both Glimmer and Genemark agree on the start site. The score is good. The Z score is good and the final score is okay. there is coding potential. start site always called in the pham
    /note=Hypothetical protein. No applicable results from HHpred, NCBI/PhagesDB BLAST. no transmembrane domain, no conserved domains
    /note=JL
    /note=Reviewed By: TM

CDS 151282 - 151662
  /gene="215"
  /product="gp215"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_215"
    /note=Original Glimmer call @bp 151282 has strength 10.02; Genemark calls start at 151282
    /note=SSC: 151282-151662 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_13 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.8341E-68 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.174, -4.331668843916977, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_13 [Arthrobacter phage Atuin]],,UDL16608,93.5484,1.8341E-68 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 151282. best z and final score, includes all coding potential, most commonly called start site in the pham with 5 MAs. Codes for a hypothetical protein. no significant matches in HHpred to the regions that matched according to the crystal structures, BLAST only matches to hypothetical proteins; no conserved domains; only a signal domain - no transmembrane
    /note=
    /note=Checked: RR

CDS 151729 - 152100
  /gene="216"
  /product="gp216"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_216"
    /note=Original Glimmer call @bp 151729 has strength 11.94; Genemark calls start at 151729
    /note=SSC: 151729-152100 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_15 [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.187% 7.02457E-30 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.135, -4.354778061539587, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_15 [Arthrobacter phage Atuin]],,UDL16610,66.3934,7.02457E-30 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 151729, called by glimmer and genemark, has the best Z and final scores (of the reasonable start sites), includes all coding potential, only start site called in the pham. Codes for a hypothetical protein, no significant matches on HHpred, only hypothetical proteins in BLAST, no conserved domains, no transmembrane domains.
    /note=
    /note=Checked: RR

CDS 152097 - 152336
  /gene="217"
  /product="gp217"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_217"
    /note=Original Glimmer call @bp 152097 has strength 9.08; Genemark calls start at 152097
    /note=SSC: 152097-152336 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.796, -2.9392830384527056, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 152097. Gap of -4. best Z and final scores, glimmer and genemark both call it, most called start site in the pham (always when present)
    /note=Codes for a hypothetical protein. No sufficient evidence to call it otherwise. no significant hits on HHpred, BLAST, conserved domains, or transmembrane domain
    /note=
    /note=Checked:  RR, TM

CDS 152336 - 152773
  /gene="218"
  /product="gp218"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_218"
    /note=Original Glimmer call @bp 152336 has strength 5.86; Genemark calls start at 152336
    /note=SSC: 152336-152773 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_17 [Arthrobacter phage Atuin]],,NCBI, q18:s24 82.069% 8.99343E-16 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.99, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_17 [Arthrobacter phage Atuin]],,UDL16612,46.1538,8.99343E-16 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 152336. -1 overlap, best Z and final score, conserved and always annotated start site in the pham, includes all coding potential
    /note=Codes for a hypothetical protein. No significant hits on HHpred, only hypothetical proteins on BLAST, no transmembrane or conserved domains
    /note=
    /note=Checked,
    /note=Reviewed by TM

CDS 152775 - 153074
  /gene="219"
  /product="gp219"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_219"
    /note=Original Glimmer call @bp 152775 has strength 11.14; Genemark calls start at 152775
    /note=SSC: 152775-153074 CP: no SCS: both ST: NI BLAST-Start:  GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.157, -4.306521122133476, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 152775. best Z and final scores, includes all coding potential, does not have the most annotated start site but this one is always called when present
    /note=Codes for a hypothetical protein. no significant hits on HHpred and BLAST, no conserved domains or trnamembrane domains
    /note=
    /note=Checked: RR, TM

CDS 153071 - 153355
  /gene="220"
  /product="gp220"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_220"
    /note=Original Glimmer call @bp 153059 has strength 11.93; Genemark calls start at 153071
    /note=SSC: 153071-153355 CP: no SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_219 [Arthrobacter phage Atuin]],,NCBI, q1:s1 97.8723% 2.66199E-18 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.512, -3.466936320283126, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_219 [Arthrobacter phage Atuin]],,UDL16613,61.0,2.66199E-18 SIF-HHPRED:  SIF-Syn: 
    /note=I moved the start site to 153071 because the coding potential seemed to align with this better. The Z score and Final scores are a lot better. The gap is -4, includes all coding potential, only start site with a MA in the pham. Hypothetical protein. no significant hits on HHpred, only hypothetical proteins on BLAST, no conserved or transmembrane domains. JL
    /note=
    /note=Checked: RR, TM

CDS 153348 - 153524
  /gene="221"
  /product="gp221"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_221"
    /note=Original Glimmer call @bp 153348 has strength 7.5; Genemark calls start at 153348
    /note=SSC: 153348-153524 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_20 [Arthrobacter phage Atuin]],,NCBI, q4:s2 94.8276% 5.40912E-14 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.799, -5.074138685954117, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_20 [Arthrobacter phage Atuin]],,UDL16615,74.1379,5.40912E-14 SIF-HHPRED:  SIF-Syn: 
    /note=Both Glimmer and Genemark agree on the start site. The score is okay. The Z score is good and the final score is okay. there is coding potential. The overlap looks fine. only start site with a manual annotation. Hypothetical protein. no hits over 90% on HHpred, only hypothetical proteins on BLAST, no conserved or transmembrane domains JL
    /note=Checked:  RR, TM

CDS 153518 - 153745
  /gene="222"
  /product="gp222"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_222"
    /note=Original Glimmer call @bp 153518 has strength 7.4; Genemark calls start at 153518
    /note=SSC: 153518-153745 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_21 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.89956E-31 GAP: -7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.016, -5.18023456802379, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_21 [Arthrobacter phage Atuin]],,UDL16616,86.8421,2.89956E-31 SIF-HHPRED:  SIF-Syn: 
    /note=Both Glimmer and Genemark agree on the start site. The score is okay. The Z score is good and the final score is okay. there is coding potential. The overlap is good. includes all coding potential, start site called when present (1 MA). Hypothetical protein, No significant hits on HHpred, only hypothetical proteins on BLAST, no conserved or transmembrane domains. JL
    /note=Checked: RR, TM

CDS 153759 - 154439
  /gene="223"
  /product="gp223"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_223"
    /note=Original Glimmer call @bp 153759 has strength 13.95; Genemark calls start at 153759
    /note=SSC: 153759-154439 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_23 [Arthrobacter phage Atuin]],,NCBI, q9:s65 95.5752% 5.54794E-30 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.778, -5.03807843799195, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_23 [Arthrobacter phage Atuin]],,UDL16618,43.4028,5.54794E-30 SIF-HHPRED:  SIF-Syn: 
    /note=Both Glimmer and Genemark agree on the start site. The score is high. The Z score is good and the final score is okay. there is coding potential. The gap is good. Start site is annotated when present. only hits on HHpred are to YorP protein which has an unknown function, only BLAST hits are to hypothetical proteins, no conserved or transmembrane domains. JL
    /note=Checked:  RR, TM

CDS 154522 - 154926
  /gene="224"
  /product="gp224"
  /function="membrane protein"
  /locus tag="DunneganBoMo_224"
    /note=Original Glimmer call @bp 154522 has strength 14.48; Genemark calls start at 154522
    /note=SSC: 154522-154926 CP: no SCS: both ST: NI BLAST-Start:  GAP: 82 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.493, -3.5707972674952195, no F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Both Glimmer and Genemark agree on the start site. The score is high. The Z score is good and the final score is good. there is coding potential. includes all coding potential, only 3 members in the pham but all call this start site. only HHpred hit is to a protein with a function not on the approved list, only BLAST hits to hypothetical proteins, there are 3 transmembrane domains. JL
    /note=
    /note=Not a Cytadesin: 
    /note=
    /note=Checked: RR
    /note=TM: Changed function to membrane protein, evidence on Phamerator.

CDS 154919 - 155188
  /gene="225"
  /product="gp225"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_225"
    /note=Original Glimmer call @bp 154919 has strength 7.35; Genemark calls start at 154919
    /note=SSC: 154919-155188 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_25 [Arthrobacter phage Atuin]],,NCBI, q1:s1 98.8764% 1.20142E-34 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.748, -3.4897410997597818, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_25 [Arthrobacter phage Atuin]],,UDL16620,85.3933,1.20142E-34 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: yes, it has coding potential, Glimmer and GeneMark both call it
    /note=What is the start site?: 154919, This start site captures all coding potential, Glimmer and GeneMark both call the start site, the Z- and final scores are the best of any potential start site, the starterator data show that this start site is called in the similar gene (no manual annotations though)
    /note=What is the function?: hypothetical protein, There are no signicant matches on HHPred, there are no matches in the conserved domain database, there is not a membrane domain, the only BLAST matches are for hypothetical proteins
    /note=Checked by Josh Leazer and KJ

CDS 155185 - 155394
  /gene="226"
  /product="gp226"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_226"
    /note=Original Glimmer call @bp 155185 has strength 11.18; Genemark calls start at 155185
    /note=SSC: 155185-155394 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.775, -3.812150084159046, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene?: yes, it has coding potential and is called by both Glimmer and GeneMark
    /note=Start site?: 155185, there is a -4 overlap with the previous gene, it is called by both Glimmer and GeneMark, it has the best Z- and Final scores of the potential start sites, no starterator data - orpham
    /note=Function?: hypothetical protein, no significant HHPred matches, no matches in the conserved domain database, there is not a membrane domain, only BLAST matches are in phagesdb and are for hypothetical proteins and the matches are not significant.
    /note=Checked by Josh Leazer and KJ, TM

CDS 155428 - 155781
  /gene="227"
  /product="gp227"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_227"
    /note=Original Glimmer call @bp 155428 has strength 10.46; Genemark calls start at 155428
    /note=SSC: 155428-155781 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein [Brevibacillus halotolerans] ],,NCBI, q5:s4 94.8718% 3.13803E-23 GAP: 33 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.274, -4.5038504778646065, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Brevibacillus halotolerans] ],,WP_181749070,59.8425,3.13803E-23 SIF-HHPRED:  SIF-Syn: 
    /note=Gene?: yes, coding potential and Glimmer and GeneMark both call it
    /note=Start site?: 155428, Glimmer and GeneMark both call the same start site, it has the best Z- and final score without losing coding potential, it includes all coding potential, no starterator data
    /note=Function?: hypothetical protein, there are no significant matches with HHPred or the conserved domain database, the only significant BLAST matches are for hypothetical proteins, there is not a membrane domain
    /note=Checked by Josh Leazer and KJ; RR

CDS 155778 - 156266
  /gene="228"
  /product="gp228"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_228"
    /note=Original Glimmer call @bp 155778 has strength 8.05; Genemark calls start at 155778
    /note=SSC: 155778-156266 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_29 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 7.73736E-36 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.829, -5.008614874058139, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_29 [Arthrobacter phage Atuin]],,UDL16624,62.7219,7.73736E-36 SIF-HHPRED:  SIF-Syn: 
    /note=Gene?: yes, it has coding potential, Glimmer and GeneMark both call it
    /note=Start site?: 155778, -4 overlap with the previous gene, it includes all coding potential, No other gene with this start site in the pham
    /note=Function?: Hypothetical Protein, there are no significant matches in HHPred or the conserved domain DB, The only NCBI BLAST match is to a hypothetical protein, as is the only significant phages DB BLAST result, there is not a membrane domain
    /note=Checked by Josh Leazer and KJ; RR

CDS 156263 - 156475
  /gene="229"
  /product="gp229"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_229"
    /note=Original Glimmer call @bp 156263 has strength 7.47; Genemark calls start at 156263
    /note=SSC: 156263-156475 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.512, -4.374347681057712, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene?: yes, it has coding potential and is called by both Glimmer and GeneMark
    /note=Start site?: 156263, -4 overlap with the previous gene, good Z- and Final score, includes all coding potential, Glimmer and GeneMark both call this start site, no starterator data available
    /note=Function?: Hypothetical protein, there are no significant matches in HHPred or the conserved domain DB, there is not a membrane domain, the only significant match in the BLAST data is to a hypothetical protein. 
    /note=Checked by Josh Leazer and KJ; RR

CDS 156447 - 156761
  /gene="230"
  /product="gp230"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_230"
    /note=Original Glimmer call @bp 156447 has strength 5.59; Genemark calls start at 156447
    /note=SSC: 156447-156761 CP: no SCS: both ST: NI BLAST-Start:  GAP: -29 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.145, -3.2136105537450197, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark call, has coding potential, includes all coding potential, best Z and final score of reasonable start sites, always present and annotated in the pham (1 MA), does not match other proteins in phagesdb blast, does not have good coverage in HHpred. no transmembrane of conserved domains (AP) (JL)
    /note=Checked: RR

CDS 156825 - 157217
  /gene="231"
  /product="gp231"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_231"
    /note=Original Glimmer call @bp 156825 has strength 15.22; Genemark calls start at 156825
    /note=SSC: 156825-157217 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_32 [Arthrobacter phage Atuin]],,NCBI, q1:s23 100.0% 1.20602E-8 GAP: 63 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.345, -3.905685530420168, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_32 [Arthrobacter phage Atuin]],,UDL16627,38.9189,1.20602E-8 SIF-HHPRED:  SIF-Syn: 
    /note=Gimmer and Genemark both have the same starting point. Has a high glimmer score. The Z and final score values are good. GenemarkS shows great coding potential. Starterator has indicates that this start site is called when present.  No known function. no significant hits on HHpred, only a hypothetical protein on BLAST, no conserved or transmembrane domains (JL) (KJ)
    /note=Checked:RR

CDS 157217 - 157381
  /gene="232"
  /product="gp232"
  /function="membrane protein"
  /locus tag="DunneganBoMo_232"
    /note=Original Glimmer call @bp 157217 has strength 6.09; Genemark calls start at 157259
    /note=SSC: 157217-157381 CP: no SCS: both-gl ST: NI BLAST-Start:  GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.658, -6.202329390951275, no F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Coding potential extends beyond the genemark start site so glimmer start site was chosen, -1 overlap, includes all coding potential, this start site is class most commonly when present, 
    /note=no significant hits on HHpred or BLAST, No conserved domains, Two transmembrane domains (JL) (KJ)
    /note=Checked: RR

CDS 157378 - 157581
  /gene="233"
  /product="gp233"
  /function="membrane protein"
  /locus tag="DunneganBoMo_233"
    /note=Original Glimmer call @bp 157378 has strength 6.95; Genemark calls start at 157378
    /note=SSC: 157378-157581 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.245, -4.039645525073382, no F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=This does have coding potential for this start and end site. The Z score was optimal but the final score is decent. Glimmer and Genemark agree on start site but the score isnt to high. start site called when present in the pham. -4 overlap
    /note=Function is unknown. no significant hits on HHpred, none on BLAST, no conserved domains, It does have transmembrane domains. (JL) (KJ)
    /note=Checked: RR
    /note=Reviewed by TM: Changed function to membrane protein, evidence on Phamerator

CDS 157572 - 157994
  /gene="234"
  /product="gp234"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_234"
    /note=Original Glimmer call @bp 157572 has strength 8.27; Genemark calls start at 157572
    /note=SSC: 157572-157994 CP: no SCS: both ST: NI BLAST-Start:  GAP: -10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.925, -2.644643059745525, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree on the start site. The glimmer score is decent. There is coding potential for this start and end site. this start includes the maximum possible coding potential. The Z and Final score are great. start site called when present in the pham.
    /note=No significant hits on HHpred or BLAST, No conserved or transmembrane domains (JL) (KJ)
    /note=Checked: RR

CDS 157958 - 158149
  /gene="235"
  /product="gp235"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_235"
    /note=Original Glimmer call @bp 157958 has strength 1.75
    /note=SSC: 157958-158149 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_27 [Arthrobacter phage Racecar] ],,NCBI, q11:s9 84.127% 2.58508E-17 GAP: -37 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.597, -4.59030133454269, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_27 [Arthrobacter phage Racecar] ],,QFG12080,67.1875,2.58508E-17 SIF-HHPRED:  SIF-Syn: 
    /note=Only has a glimmer start site. The Z score is good but the Final score is okay. There is coding potential. The glimmer score is extremely low. start site called when present in the pham. includes all coding potential
    /note=No significant hits on HHpred, only hypothetical proteins on BLAST, no conserved or transmembrane domains (JL)
    /note=Checked:  RR

CDS 158165 - 158599
  /gene="236"
  /product="gp236"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_236"
    /note=Original Glimmer call @bp 158165 has strength 7.27; Genemark calls start at 158210
    /note=SSC: 158165-158599 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_41 [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.3056% 3.57826E-47 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -3.206439871056232, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_41 [Arthrobacter phage Atuin]],,UDL16635,74.4681,3.57826E-47 SIF-HHPRED:  SIF-Syn: 
    /note=The glimmer start site seems to be correct. There is coding potential the extend close to this start site. The Z and final score are great. The glimmer score is decent.  start site is conserved and called within the pham. 
    /note=Only matches in HHpred were to proteins of unknown functions, only hypothetical proteins on BLAST, no conserved or transmembrane domains(JL) 
    /note=Reviewed: KJ; RR

CDS 158652 - 159065
  /gene="237"
  /product="gp237"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_237"
    /note=Original Glimmer call @bp 158652 has strength 9.53; Genemark calls start at 158652
    /note=SSC: 158652-159065 CP: no SCS: both ST: NI BLAST-Start:  GAP: 52 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.721, -3.099505556436281, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. The Z score and Final score are good. does not have the most common start site. 
    /note=only hits over 90% on HHpred are to YorP protein which has an unknown function, no BLAST matches, no conserved or transmembrane domains. (JL)
    /note=Reviewed: KJ

CDS 159065 - 159331
  /gene="238"
  /product="gp238"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_238"
    /note=Original Glimmer call @bp 159065 has strength 12.84; Genemark calls start at 159065
    /note=SSC: 159065-159331 CP: no SCS: both ST: NI BLAST-Start:  GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.124, -2.297359520375101, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. -1 overlap. The Z score and Final score are good. start site is conserved and called in the pham.  No significant hits on HHpred, no BLAST hits, no conserved domains, no transmembrane domains. (JL)
    /note=Reviewed: KJ

CDS 159407 - 159712
  /gene="239"
  /product="gp239"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_239"
    /note=Original Glimmer call @bp 159407 has strength 11.18; Genemark calls start at 159407
    /note=SSC: 159407-159712 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_53 [Arthrobacter phage Atuin]],,NCBI, q1:s17 100.0% 2.40028E-58 GAP: 75 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.625, -6.41689868289573, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_53 [Arthrobacter phage Atuin]],,UDL16647,85.4701,2.40028E-58 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. The Z score and Final score are good. start site is called 75% of the time when present with 3 MAs. several HHpred hits to unknown proteins and membrane proteins but the match is to the signal region in this gene. No BLAST hits other than hypothetical proteins. no conserved domains So I marked it as hypothetical. (JL).
    /note=Reviewed: KJ

CDS 159767 - 160147
  /gene="240"
  /product="gp240"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_240"
    /note=Original Glimmer call @bp 159767 has strength 11.82; Genemark calls start at 159767
    /note=SSC: 159767-160147 CP: no SCS: both ST: NI BLAST-Start: [MULTISPECIES: DUF3846 domain-containing protein [Kocuria] ],,NCBI, q10:s13 86.5079% 2.70936E-13 GAP: 54 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.068, -2.2763497933341483, yes F: Hypothetical Protein SIF-BLAST: ,,[MULTISPECIES: DUF3846 domain-containing protein [Kocuria] ],,WP_068466727,55.6452,2.70936E-13 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. The Z score and Final score are good. Annotated when present with 6 MAs. unknown function. only significant HHpred hits are to domains of unknown functions, sme with BLAST hits, no conserved domains, no transmembrane domains. (JL)
    /note=Reviewed: KJ

CDS 160182 - 160400
  /gene="241"
  /product="gp241"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_241"
    /note=Original Glimmer call @bp 160182 has strength 6.07; Genemark calls start at 160182
    /note=SSC: 160182-160400 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_114 [Arthrobacter phage Racecar] ],,NCBI, q1:s1 100.0% 8.37393E-24 GAP: 34 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.721, -3.0194634687155197, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_114 [Arthrobacter phage Racecar] ],,QFG12161,77.4648,8.37393E-24 SIF-HHPRED:  SIF-Syn: 
    /note=I changed the start site to 160122-160400 because the Z score is better and the Final score isn`t that much different from the original called site. Also the glimmer score for the original site was low. There is coding potential for the start site and it seems to start at 160122. Starterator said that site 7 (160182) was called the most but may need to be rechecked to see. I will still start it at 160122 but could be 160182. Unknown function. no significant hits on HHpred, only hypothetical proteins on BLAST, No conserved domains or transmembrane domains(JL)
    /note=Reviewed: (KJ)- I changed the start cite to 160182, more coding potential. start site called in 100% of genes when present with 6 MAs

CDS 160397 - 160591
  /gene="242"
  /product="gp242"
  /function="membrane protein"
  /locus tag="DunneganBoMo_242"
    /note=Original Glimmer call @bp 160397 has strength 6.61; Genemark calls start at 160397
    /note=SSC: 160397-160591 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.493, -4.16062280240617, yes F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is okay. There is coding potential for the start site. The Z score is good and Final score is okay. -4 overlap. start site is called when present.  (JL)
    /note=Reviewed: TM- Function is a membrane protein, evidence on Phamerator. no significant hits on HHpred or BLAST
    /note=Revewied: KJ

CDS 160658 - 160906
  /gene="243"
  /product="gp243"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_243"
    /note=Original Glimmer call @bp 160658 has strength 10.7; Genemark calls start at 160658
    /note=SSC: 160658-160906 CP: no SCS: both ST: NI BLAST-Start:  GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.23, -1.9310779259753799, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. The Z score and Final score are excellent. start site called when present in the pham. Function Unknown. no significant hits on HHpred or BLAST, no conserved or transmembrane domains(JL)
    /note=Revewied: KJ, TM

CDS 160903 - 161172
  /gene="244"
  /product="gp244"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_244"
    /note=Original Glimmer call @bp 160903 has strength 11.25; Genemark calls start at 160903
    /note=SSC: 160903-161172 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein ASD29_07285 [Streptomyces sp. Root1295] ],,NCBI, q1:s1 75.2809% 5.76008E-5 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.538, -5.631526093152131, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein ASD29_07285 [Streptomyces sp. Root1295] ],,KQX37016,38.2353,5.76008E-5 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. The Z score and Final score are decent. -4 overlap, Starterator calls this site when present and the earlier start site is not present. only significant hits on HHpred and Blast are to hypothetical proteins, no conserved domains or transmembrane domains. (JL)
    /note=Reviewed: KJ, TM

CDS 161249 - 161899
  /gene="245"
  /product="gp245"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_245"
    /note=Original Glimmer call @bp 161249 has strength 10.03; Genemark calls start at 161249
    /note=SSC: 161249-161899 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_39 [Arthrobacter phage Racecar] ],,NCBI, q5:s8 87.963% 4.48843E-11 GAP: 76 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.23, -5.121035876719934, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_39 [Arthrobacter phage Racecar] ],,QFG12092,41.048,4.48843E-11 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. The Z score and Final score are decent. includes al coding potential. this start site is called 80% of the time when present. only hits on HHpred over 90% are to YorP which has an unknown function, only hypothetical proteins on BLAST, no conserved or transmembrane domains (JL)
    /note=Reviewed: KJ,TM

CDS 161908 - 162771
  /gene="246"
  /product="gp246"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_246"
    /note=Original Glimmer call @bp 161908 has strength 13.97; Genemark calls start at 161908
    /note=SSC: 161908-162771 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_39 [Arthrobacter phage Racecar] ],,NCBI, q82:s7 68.6411% 4.77058E-16 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.124, -2.9845911214398755, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_39 [Arthrobacter phage Racecar] ],,QFG12092,44.5415,4.77058E-16 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. The Z score and Final score are excellent.   (JL)
    /note=Reviewed: (KJ) Function?
    /note=TM - Hypothetical preotein due to lack of evidence to call it anything else., best matches are to YorP proteins which have no known function, other hits all match to the SH3 domains of various proteins, only hypothetical proteins are hit in BLAST, no conserved or transmembrane domains

CDS 162842 - 163462
  /gene="247"
  /product="gp247"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_247"
    /note=Original Glimmer call @bp 162842 has strength 11.19; Genemark calls start at 162842
    /note=SSC: 162842-163462 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_39 [Arthrobacter phage Racecar] ],,NCBI, q1:s5 82.5243% 1.30039E-11 GAP: 70 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.124, -2.9845911214398755, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_39 [Arthrobacter phage Racecar] ],,QFG12092,37.5546,1.30039E-11 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. The Z score and Final score are good. Starterator calls it when present 83% of the time but no MAs. Best hits in HHpred are to YorP, which has an unknown function, only hypothetical proteins in BLAST, no conserved or transmembrane domains. (JL)

CDS 163462 - 163692
  /gene="248"
  /product="gp248"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_248"
    /note=Original Glimmer call @bp 163462 has strength 6.35; Genemark calls start at 163462
    /note=SSC: 163462-163692 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_58 [Arthrobacter phage Atuin]],,NCBI, q3:s6 92.1053% 1.73111E-23 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.503, -4.3934175870462076, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_58 [Arthrobacter phage Atuin]],,UDL16652,68.4211,1.73111E-23 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene? Yes, it has a start and stop site, it has good coding potential, and Glimmer and GeneMark both call it
    /note=What is the start site? 163462, this is the only start site that contains all coding potential, it is called by both Glimmer and GeneMark, this start site is called in all members of the pham and cluster (starterator), it has the best Z- and final score (other than one start site that excludes a large amount of coding potential)
    /note=What is the function? There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains

CDS 163685 - 163900
  /gene="249"
  /product="gp249"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_249"
    /note=Original Glimmer call @bp 163685 has strength 7.34; Genemark calls start at 163685
    /note=SSC: 163685-163900 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_20 [Arthrobacter phage Racecar] ],,NCBI, q3:s5 97.1831% 2.95632E-6 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.695, -5.278804743622975, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_20 [Arthrobacter phage Racecar] ],,QFG12073,55.7143,2.95632E-6 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene? Yes, it has a start and stop site, it has good coding potential, and Glimmer and GeneMark both call it
    /note=
    /note=What is the start site? 163685, this is the only start site that contains all coding potential, it is called by both Glimmer and GeneMark, this start site is called in all members of the pham and cluster (starterator), it has the best Z- and final score (other than one start site that excludes a large amount of coding potential)
    /note=What is the function? There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains

CDS 163918 - 164130
  /gene="250"
  /product="gp250"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_250"
    /note=Original Glimmer call @bp 163933 has strength 11.7; Genemark calls start at 163918
    /note=SSC: 163918-164130 CP: no SCS: both-gm ST: NI BLAST-Start: [Hypothetical Protein OBI_RACECAR_251 [Arthrobacter phage Racecar] ],,NCBI, q1:s42 100.0% 3.65079E-20 GAP: 17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.748, -4.267892350143425, no F: Hypothetical Protein SIF-BLAST: ,,[Hypothetical Protein OBI_RACECAR_251 [Arthrobacter phage Racecar] ],,QFG12096,49.1379,3.65079E-20 SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene? Yes, it has a start and stop site, it has good coding potential, and Glimmer and GeneMark both call it
    /note=
    /note=What is the start site? 163918, this is the only start site that contains all coding potential, it is called by GeneMark but not Glimmer, there are no manual annotations in this pham and this start site is only in in gene, it has the best Z- and final score (other than one start site that excludes a large amount of coding potential)
    /note=What is the function? There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains

CDS 164123 - 164338
  /gene="251"
  /product="gp251"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_251"
    /note=Original Glimmer call @bp 164123 has strength 10.31; Genemark calls start at 164123
    /note=SSC: 164123-164338 CP: no SCS: both ST: NI BLAST-Start:  GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.513, -3.8156109669835954, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene? Yes, it has a start and stop site, it has good coding potential, and Glimmer and GeneMark both call it
    /note=
    /note=What is the start site? 164123, this is the only start site that contains the maximum amount of coding potential without a very large overlap, it is called by both Glimmer and GeneMark, this start site is called in all members of the pham (starterator), it has the best Z- and final score (other than one start site that excludes a large amount of coding potential)
    /note=What is the function? There is no known function; no significant hits on HHpred or on BLAST, no conserved domains, no transmembrane domains

CDS 164335 - 164466
  /gene="252"
  /product="gp252"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_252"
    /note=Original Glimmer call @bp 164335 has strength 12.26; Genemark calls start at 164335
    /note=SSC: 164335-164466 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.419, -4.319061160425607, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Is it a gene? Yes, it has a start and stop site, it has good coding potential, and Glimmer and GeneMark both call it
    /note=
    /note=What is the start site? 164335, this is the only start site that contains all coding potential, has a -4 overlap, it is called by both Glimmer and GeneMark, this start site is called in all members of the pham (starterator), it has the best Z- and final score 
    /note=What is the function? There is no known function; no significant hits on HHpred, or on BLAST, no conserved domains, no transmembrane domains

CDS 164459 - 164722
  /gene="253"
  /product="gp253"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_253"
    /note=Original Glimmer call @bp 164459 has strength 6.32; Genemark calls start at 164459
    /note=SSC: 164459-164722 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_55 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 6.33011E-17 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.925, -3.2344685946564757, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_55 [Arthrobacter phage Atuin]],,UDL16649,59.0,6.33011E-17 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 164495, it has good Z-score and final score; includes coding potential; and is called every time it is present in a gene.
    /note=What is the function?: There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains

CDS 164781 - 165308
  /gene="254"
  /product="gp254"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_254"
    /note=Original Glimmer call @bp 164781 has strength 10.03; Genemark calls start at 164781
    /note=SSC: 164781-165308 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_50 [Arthrobacter phage Atuin]],,NCBI, q3:s4 94.2857% 4.11605E-10 GAP: 58 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.23, -2.0111200136961407, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_50 [Arthrobacter phage Atuin]],,UDL16644,47.5936,4.11605E-10 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 164781; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains

CDS 165301 - 165573
  /gene="255"
  /product="gp255"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_255"
    /note=Original Glimmer call @bp 165301 has strength 14.57; Genemark calls start at 165301
    /note=SSC: 165301-165573 CP: no SCS: both ST: NI BLAST-Start:  GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.503, -3.54831954703195, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 165,301; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: There is no known function; no significant hits on HHpred, or on BLAST, no conserved domains, no transmembrane domains
    /note=
    /note=Checked: C.A.R, TM

CDS 165631 - 165885
  /gene="256"
  /product="gp256"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_256"
    /note=Genemark calls start at 165631
    /note=SSC: 165631-165885 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_46 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.25189E-41 GAP: 57 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_46 [Arthrobacter phage Atuin]],,UDL16640,86.9048,1.25189E-41 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, GeneMark called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 165,631; the start cite is called by GeneMark, only start that would include all coding potential, always called within the pham on starterator, best Z and final scores
    /note=What is the function?: There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=
    /note=Checked: C.A.R, TM

CDS 165964 - 166257
  /gene="257"
  /product="gp257"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_257"
    /note=Original Glimmer call @bp 165964 has strength 10.51; Genemark calls start at 165964
    /note=SSC: 165964-166257 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_53 [Arthrobacter phage Racecar] ],,NCBI, q1:s1 100.0% 1.52058E-49 GAP: 78 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.523003374675015, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_53 [Arthrobacter phage Racecar] ],,QFG12106,88.6598,1.52058E-49 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 165,964; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene (4 MAs).
    /note=What is the function?: There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=
    /note=Checked: C.A.R, TM

CDS 166257 - 166433
  /gene="258"
  /product="gp258"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_258"
    /note=Original Glimmer call @bp 166257 has strength 5.2; Genemark calls start at 166257
    /note=SSC: 166257-166433 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_55 [Arthrobacter phage Racecar] ],,NCBI, q1:s1 100.0% 4.20341E-31 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.655, -3.160956374632079, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_55 [Arthrobacter phage Racecar] ],,QFG12108,96.5517,4.20341E-31 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 166,257; Glimmer and GeneMark b-1 overlap; oth called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene (2 MAs).
    /note=What is the function?: There is no known function; the only significant hit on HHpred is to a region of the EcoRI endonuclease that is necessary for nuclease and ATPase activity but there are no crystal structures to ensure the appropriate coverage;  Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=
    /note=Checked: C.A.R, TM

CDS 166476 - 166673
  /gene="259"
  /product="gp259"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_259"
    /note=Original Glimmer call @bp 166476 has strength 3.97
    /note=SSC: 166476-166673 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_56 [Arthrobacter phage Racecar] ],,NCBI, q1:s1 96.9231% 2.76209E-26 GAP: 42 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.328, -6.14369528365746, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_56 [Arthrobacter phage Racecar] ],,QFG12109,93.9394,2.76209E-26 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 166482, includes all coding potential, other genes in the pham with both of these start sites call the second one, 
    /note=What is the function?: There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=
    /note=Checked: C.A.R, TM

CDS 166704 - 166955
  /gene="260"
  /product="gp260"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_260"
    /note=Original Glimmer call @bp 166704 has strength 13.27; Genemark calls start at 166704
    /note=SSC: 166704-166955 CP: no SCS: both ST: NI BLAST-Start:  GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.816, -2.895726594994071, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, based on gene mark there is coding potential
    /note=start site? glimmer and gene mark both agree with 166704 as the start site, only possible start site
    /note=function? There is no known function; no significant hits on HHpred or on BLAST, no conserved domains, no transmembrane domains
    /note=SB
    /note=
    /note=Checked: C.A.R, TM

CDS 166957 - 167322
  /gene="261"
  /product="gp261"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_261"
    /note=Original Glimmer call @bp 166957 has strength 8.73; Genemark calls start at 166957
    /note=SSC: 166957-167322 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_57 [Arthrobacter phage Racecar] ],,NCBI, q1:s3 97.5207% 2.34605E-19 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.896, -2.6453814847322845, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_57 [Arthrobacter phage Racecar] ],,QFG12110,58.1967,2.34605E-19 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree on start site. The glimmer score is good. There is coding potential for the start site. The Z score and Final score are good. Starterator - no manually annotated start site in this gene but this start is usually called when present. There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains. (JL)
    /note=
    /note=Checked: C.A.R, TM

CDS 167322 - 167684
  /gene="262"
  /product="gp262"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_262"
    /note=Original Glimmer call @bp 167322 has strength 10.4; Genemark calls start at 167322
    /note=SSC: 167322-167684 CP: no SCS: both ST: NI BLAST-Start:  GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.816, -3.1681521309447884, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes based on gene mark it does have coding potential 
    /note=start site? glimmer and gene mark both agree that the start site is at 167322 for this gene, -1 overlap, best Z and final scores, always called within the pham (1 MA), includes all coding potential
    /note=function? There is no known function; no significant hits on HHpred or on BLAST, no conserved domains, no transmembrane domains
    /note=SB
    /note=
    /note=Checked: I am not sure I agree on the function as all HHPred results I am seeing for it are under 84%. I agree on the start site. -C.A.R
    /note=I agree with C.A.R., start site is correct but function should be Hypothetical Protein - TM

CDS 167821 - 168075
  /gene="263"
  /product="gp263"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_263"
    /note=Original Glimmer call @bp 167821 has strength 11.54; Genemark calls start at 167821
    /note=SSC: 167821-168075 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_60 [Arthrobacter phage Atuin]],,NCBI, q3:s4 97.619% 2.44771E-21 GAP: 136 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.925, -2.6623718267059564, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_60 [Arthrobacter phage Atuin]],,UDL16654,65.1685,2.44771E-21 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, based on gene mark there is coding potential
    /note=start site? glimmer and gene mark both agree that the start site of this gene is set at 167821, includes all coding potential, best Z and Final scores, Not the most annotated start site in the pham but is call 100% of the time when present (1 MA)
    /note=function? There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=SB
    /note=
    /note=Checked: C.A.R, TM

CDS 168125 - 168460
  /gene="264"
  /product="gp264"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_264"
    /note=Original Glimmer call @bp 168125 has strength 12.56; Genemark calls start at 168125
    /note=SSC: 168125-168460 CP: no SCS: both ST: NI BLAST-Start:  GAP: 49 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.748, -2.9625409806968013, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes based on gene mark there is coding potential 
    /note=start site? glimmer and genemark agree that the start site is 168125
    /note=function? There is no known function; there are many hits on HHpred that seem to be to related to an SH3 domain possibly from a transcription factor or ribosomal protein but nothing with an approved function, no matches on BLAST, no conserved domains, no transmembrane domains
    /note=SB
    /note=Checked: not a transmembrane protein JT, TM

CDS 168460 - 168609
  /gene="265"
  /product="gp265"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_265"
    /note=Original Glimmer call @bp 168460 has strength 20.02; Genemark calls start at 168460
    /note=SSC: 168460-168609 CP: no SCS: both ST: NI BLAST-Start:  GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.417, -3.75071250087134, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes genemark shows high coding potential
    /note=start site? glimmer and genemark agree on 168460 as the start site; only possible start site
    /note=function? There is no known function; no significant hits on HHpred or on BLAST, no conserved domains, no transmembrane domains
    /note=Checked: Not a transmembrane protein and couldn`t find enough evidence of it being a DNA primase/ polymerase JT

CDS 168602 - 168904
  /gene="266"
  /product="gp266"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_266"
    /note=Original Glimmer call @bp 168602 has strength 9.41; Genemark calls start at 168602
    /note=SSC: 168602-168904 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_68 [Arthrobacter phage Atuin]],,NCBI, q1:s1 95.0% 5.9666E-54 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.156, -2.0895162839948163, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_68 [Arthrobacter phage Atuin]],,UDL16662,94.7368,5.9666E-54 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, genemark shows high coding potential
    /note=start site? glimmer and genemark agree on 168602; the start site is annotated most of the time when present in the pham (1 MA), has the best Z and final scores, includes all coding potential
    /note=function? There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=SB
    /note=
    /note=Checked: C.A.R, JT

CDS 168897 - 169274
  /gene="267"
  /product="gp267"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_267"
    /note=Original Glimmer call @bp 169002 has strength 4.76; Genemark calls start at 168897
    /note=SSC: 168897-169274 CP: no SCS: both-gm ST: NI BLAST-Start: [Hypothetical Protein OBI_RACECAR_255 [Arthrobacter phage Racecar] ],,NCBI, q5:s1 96.8% 5.68691E-49 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.608, -3.324400402896891, no F: Hypothetical Protein SIF-BLAST: ,,[Hypothetical Protein OBI_RACECAR_255 [Arthrobacter phage Racecar] ],,QFG12100,79.6748,5.68691E-49 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes based on genemark`s relay of high coding potential
    /note=start site? glimmer is 169002
    /note=function? the largest probability findings point towards hydrolase as the main function but other researches previously concluded on its properties as a capsid protein; while there are matches to a hydrolase in HHpred - the region that is matching is small and only includes part of the DNA binding motif - hypothetical protein would be a better choice
    /note=SB
    /note=
    /note=Checked: I disagree with the start site of 169002. I believe the start site is more likely to be the one genemark chose, which is 168897 as it has 4 MA`s and also has better z-scores and final scores than the start site that glimmer chose. I agree with the function. -C.A.R
    /note=
    /note=I also disagree with the start site chosen and it should be 168897. JT

CDS 169332 - 169622
  /gene="268"
  /product="gp268"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_268"
    /note=Original Glimmer call @bp 169332 has strength 7.33; Genemark calls start at 169332
    /note=SSC: 169332-169622 CP: no SCS: both ST: NI BLAST-Start:  GAP: 57 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.745, -3.3188993291388478, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, based on genemark`s relay of high coding potential
    /note=start site? glimmer and genemark both agree on 169332 as the start site; best Z and final scores; includes all coding potential; starterator - data is mixed but this start site is only found in 3 genes and is the only real option that includes all coding potential for this gene
    /note=function? 
    /note=SB
    /note=
    /note=Checked: I agree with the start site, but however do not know where the function came from as I was unable to find any HHPred or NCBI results above a 90%. I believe a hypothetical protein may be a more fitting function for this gene. -C.A.R
    /note=
    /note=I also believe the function should be hypothetical. JT

CDS 169638 - 169820
  /gene="269"
  /product="gp269"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_269"
    /note=Original Glimmer call @bp 169638 has strength 4.14; Genemark calls start at 169638
    /note=SSC: 169638-169820 CP: no SCS: both ST: NI BLAST-Start:  GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.068, -2.356391881054909, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, genemark does show coding potential for this gene 
    /note=start site? glimmer and genemark agree on 169638 as the start site; includes maximum possible coding potential; best Z and final scores; conserved and called throughout the pham
    /note=function? There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=SB
    /note=
    /note=Checked: C.A.R, JT

CDS 169817 - 170197
  /gene="270"
  /product="gp270"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_270"
    /note=Original Glimmer call @bp 169817 has strength 10.62; Genemark calls start at 169817
    /note=SSC: 169817-170197 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_27 [Arthrobacter phage Atuin]],,NCBI, q3:s5 83.3333% 0.0236882 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.721, -3.8476935834424815, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_27 [Arthrobacter phage Atuin]],,UDL16622,37.3134,0.0236882 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, based on genemark, high coding potential is seen
    /note=start site? glimmer and genemark both agree on 169817 as the start site; -4 overlap, best Z and final scores, includes all coding potential, not the most annotated start site but this one is usually called when present
    /note=function? There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=SB
    /note=
    /note=Checked: I agree with the start site, but once again cannot find any evidence for the current function in HHPred or NCBI. I believe a hypothetical protein may be most appropriate for this gene. -C.A.R
    /note=
    /note=I also believe that the function should be hypothetical. JT

CDS 170194 - 170616
  /gene="271"
  /product="gp271"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_271"
    /note=Original Glimmer call @bp 170194 has strength 10.02; Genemark calls start at 170194
    /note=SSC: 170194-170616 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.568, -3.4283035164720754, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, genemark shows coding potential
    /note=start site? glimmer and genemark both agree on 170194 for the start site, -4 overlap, no starterator data, best Z and final score
    /note=function? There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=SB
    /note=
    /note=Checked: I agree with the start site, however due to the lack of HHPred or NCBI results above an 85% probability I believe a hypothetical protein would be most appropriate. It is also worth noting that the HHPred result with the highest probability is that on an unknown function. -C.A.R
    /note=
    /note=I also agree that the function should be a hypothetical protein JT

CDS 170613 - 170909
  /gene="272"
  /product="gp272"
  /function="membrane protein"
  /locus tag="DunneganBoMo_272"
    /note=Original Glimmer call @bp 170613 has strength 4.75; Genemark calls start at 170613
    /note=SSC: 170613-170909 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.896, -2.7254235724530456, yes F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene? yes, but genemark shows a low frequency at the start site of this gene
    /note=start site? glimmer and genemark both agree on 170613 as the start site, -4 overlap, best Z and final scores, includes all coding potential
    /note=function? There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, it does have two transmembrane domains
    /note=SB
    /note=
    /note=Checked: C.A.R, JT

CDS 170897 - 171169
  /gene="273"
  /product="gp273"
  /function="membrane protein"
  /locus tag="DunneganBoMo_273"
    /note=Original Glimmer call @bp 170897 has strength 11.21; Genemark calls start at 170897
    /note=SSC: 170897-171169 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_71 [Arthrobacter phage Atuin]],,NCBI, q1:s2 92.2222% 3.41794E-10 GAP: -13 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.99, -2.523003374675015, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_71 [Arthrobacter phage Atuin]],,UDL16665,58.0645,3.41794E-10 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 170897 has the best Z score and final score gap and Glimmer and Genemark agree--also aligns with coding potential, start site is called when present in the pham. several hits on HHpred align with ABC transporters but the region that partially aligns in each case is the membrane domain, there are two transmembrane domains so best function would be membrane protein
    /note=
    /note=Checked: C.A.R, JT

CDS 171245 - 171673
  /gene="274"
  /product="gp274"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_274"
    /note=Original Glimmer call @bp 171245 has strength 13.7; Genemark calls start at 171245
    /note=SSC: 171245-171673 CP: no SCS: both ST: NI BLAST-Start:  GAP: 75 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -2.6835611257758942, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 171245 has the best Z score and final score and gap and Glimmer and Genemark agree--also aligns with coding potential, start site is conserved and called in the pham. There is no known function; no significant hits on HHpred or on BLAST, no conserved domains, no transmembrane domains.
    /note=Checked by CM
    /note=
    /note=Checked: C.A.R

CDS 171704 - 171964
  /gene="275"
  /product="gp275"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_275"
    /note=Original Glimmer call @bp 171704 has strength 3.1; Genemark calls start at 171704
    /note=SSC: 171704-171964 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_87 [Arthrobacter phage Atuin]],,NCBI, q1:s8 100.0% 7.14868E-16 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.523003374675015, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_87 [Arthrobacter phage Atuin]],,UDL16681,57.4468,7.14868E-16 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 171704 has the best Z and final score and gap and Glimmer and Genemark agree--also aligns with coding potential, start site called when present. There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=Checked by CM
    /note=
    /note=Checked: C.A.R

CDS 171977 - 172381
  /gene="276"
  /product="gp276"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_276"
    /note=Original Glimmer call @bp 171977 has strength 8.7; Genemark calls start at 171977
    /note=SSC: 171977-172381 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_84 [Arthrobacter phage Atuin]],,NCBI, q66:s1 51.4925% 1.17468E-20 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.748, -3.4897410997597818, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_84 [Arthrobacter phage Atuin]],,UDL16678,75.0,1.17468E-20 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 171977 has the best Z and final score and gap and Glimmer and Genemark agree--also aligns with coding potential, start site is conserved and called within the pham. Gene aligns with a YorP protein with adequate probability percentage--although the protein has no known function. Does not code for transmembrane protein.
    /note=Checked by CM, JT

CDS 172390 - 172620
  /gene="277"
  /product="gp277"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_277"
    /note=Original Glimmer call @bp 172390 has strength 6.54; Genemark calls start at 172390
    /note=SSC: 172390-172620 CP: no SCS: both ST: NI BLAST-Start: [HNH endonuclease [Arthrobacter phage Darby] ],,NCBI, q3:s4 93.4211% 2.07771E-31 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.84, -3.8154491356968365, yes F: Hypothetical Protein SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage Darby] ],,YP_010750521,32.1429,2.07771E-31 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 172390 has the best Z and final score and gap and Glimmer and Genemark agree--also aligns with coding potential. No functions with adequate probability percentage--hypothetical protein. Does not code for transmembrane protein.
    /note=Checked by CM, JT

CDS 172626 - 172829
  /gene="278"
  /product="gp278"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_278"
    /note=Original Glimmer call @bp 172626 has strength 11.5; Genemark calls start at 172626
    /note=SSC: 172626-172829 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_85 [Arthrobacter phage Atuin]],,NCBI, q2:s3 98.5075% 1.78198E-25 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.124, -3.0637723674875006, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_85 [Arthrobacter phage Atuin]],,UDL16679,77.4648,1.78198E-25 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 172626 has the best Z and final score and gap and Glimmer and Genemark agree--also aligns with coding potential. No functions with adequate probability percentage--hypothetical protein. Does not code for transmembrane protein.
    /note=Checked by CM, JT

CDS 172826 - 173032
  /gene="279"
  /product="gp279"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_279"
    /note=Original Glimmer call @bp 172826 has strength 6.3; Genemark calls start at 172826
    /note=SSC: 172826-173032 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.99, -2.523003374675015, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 172826 has the best Z and final score and gap and Glimmer and Genemark agree--also aligns with coding potential, -4 overlap, always called in the pham. No functions with adequate probability percentage--hypothetical protein. Does not code for transmembrane protein.
    /note=Checked by CM, JT

CDS 173025 - 173408
  /gene="280"
  /product="gp280"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_280"
    /note=Original Glimmer call @bp 173025 has strength 4.57; Genemark calls start at 173025
    /note=SSC: 173025-173408 CP: no SCS: both ST: NI BLAST-Start:  GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.124, -2.5074698667202133, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 173025 has the best Z and final score and gap and Glimmer and Genemark agree--also aligns with coding potential, always called within the pham. No functions with adequate probability percentage--hypothetical protein. Does not code for transmembrane protein.
    /note=Checked by CM, JT

CDS 173464 - 173739
  /gene="281"
  /product="gp281"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_281"
    /note=Original Glimmer call @bp 173464 has strength 6.86; Genemark calls start at 173464
    /note=SSC: 173464-173739 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_87 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 8.34587E-44 GAP: 55 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.84, -2.9063687850157054, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_87 [Arthrobacter phage Atuin]],,UDL16681,86.1702,8.34587E-44 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 173464 has the best Z score and Glimmer and Genemark agree--also aligns with coding potential, start site called when present in the pham. No functions with adequate probability percentage--hypothetical protein. Does not code for transmembrane protein.
    /note=Checked by CM, JT

CDS 173822 - 174013
  /gene="282"
  /product="gp282"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_282"
    /note=Genemark calls start at 173822
    /note=SSC: 173822-174013 CP: no SCS: genemark ST: NI BLAST-Start:  GAP: 82 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.437, -4.729704120146823, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 173822 has the best Z and final score and gap--also aligns with coding potential, start site called in the pham when present. No functions with adequate probability percentage--hypothetical protein. Does not code for transmembrane protein.
    /note=Checked by CM
    /note=It looks like it codes for a membrane protein on phamerator. JT
    /note=Signal domain - not a transmembrane domain

CDS 174194 - 174592
  /gene="283"
  /product="gp283"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_283"
    /note=Original Glimmer call @bp 174194 has strength 15.44; Genemark calls start at 174194
    /note=SSC: 174194-174592 CP: no SCS: both ST: NI BLAST-Start:  GAP: 180 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.148, -4.897952686918946, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 174194 has the best Z and final score without cutting off coding potential and gap and Glimmer and Genemark agree--also aligns with coding potential. No functions with adequate probability percentage--hypothetical protein. Does not code for transmembrane protein.
    /note=Checked by CM, JT

CDS 174595 - 175206
  /gene="284"
  /product="gp284"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_284"
    /note=Original Glimmer call @bp 174595 has strength 8.41; Genemark calls start at 174595
    /note=SSC: 174595-175206 CP: no SCS: both ST: NI BLAST-Start:  GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.155, -4.230754134060232, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 174595 has the best gap and Glimmer and Genemark agree. No functions with adequate probability percentage--hypothetical protein. Does not code for transmembrane protein.
    /note=
    /note=Start: Includes all coding potential; called by starterator when present but only autoannotations (this gene does not contain the most commonly manually annotated start site)
    /note=Function: No significant hits on BLAST or HHpred.
    /note=
    /note=Checked by: JP, JT

CDS 175206 - 175622
  /gene="285"
  /product="gp285"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_285"
    /note=Original Glimmer call @bp 175206 has strength 6.4; Genemark calls start at 175206
    /note=SSC: 175206-175622 CP: no SCS: both ST: NI BLAST-Start:  GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.745, -3.108788982793736, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark S has adequate coding potential for this to be a gene. Start site of 1755622 has the best Z score and gap. No functions with adequate probability percentage--hypothetical protein. Does not code for transmembrane protein.
    /note=
    /note=Start: -1 overlap; includes all coding potential
    /note=Function: No significant hits on HHpred or BLAST
    /note=
    /note=Checked by: JP, JT

CDS 175622 - 175945
  /gene="286"
  /product="gp286"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_286"
    /note=Original Glimmer call @bp 175619 has strength 14.75; Genemark calls start at 175619
    /note=SSC: 175622-175945 CP: no SCS: both-cs ST: NI BLAST-Start:  GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.873, -5.743069600988506, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 175619. Codes for a hypothetical protein.
    /note=
    /note=Start: -4 or -1 overlap but always choose the second start site. (175622) This includes all coding potential
    /note=Function: No hits on HHpred or BLAST, No transmembrane domains according to DeepTMHMM
    /note=
    /note=Checked by: JP, CM

CDS 175945 - 176463
  /gene="287"
  /product="gp287"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_287"
    /note=Original Glimmer call @bp 175945 has strength 13.67; Genemark calls start at 175978
    /note=SSC: 175945-176463 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_93 [Arthrobacter phage Atuin]],,NCBI, q1:s1 98.2558% 3.8047E-34 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.05, -2.66590822473965, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_93 [Arthrobacter phage Atuin]],,UDL16687,62.1469,3.8047E-34 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 175945. Codes for a hypothetical protein.
    /note=
    /note=Start site: -1 overlap, includes all coding potential
    /note=Function: No significant hits on HHpred or BLAST, No transmembrane domains (DeepTMHMM)
    /note=
    /note=Checked by: JP and CM

CDS 176516 - 176629
  /gene="288"
  /product="gp288"
  /function="membrane protein"
  /locus tag="DunneganBoMo_288"
    /note=Original Glimmer call @bp 176516 has strength 8.88; Genemark calls start at 176525
    /note=SSC: 176516-176629 CP: no SCS: both-gl ST: NI BLAST-Start:  GAP: 52 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.942, -6.827985161086941, no F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 176516. Codes for a hypothetical protein.
    /note=
    /note=Start: The earlier start site would create too large of an overlap; only one other draft phage in starterator.
    /note=Function: no significant hits on HHpred or BLAST; It does have a transmembrane domain: change to Membrane protein
    /note=
    /note=Checked by: JP and CM

CDS 176622 - 176870
  /gene="289"
  /product="gp289"
  /function="membrane protein"
  /locus tag="DunneganBoMo_289"
    /note=Original Glimmer call @bp 176622 has strength 7.35; Genemark calls start at 176622
    /note=SSC: 176622-176870 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_94 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.08543E-28 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.695, -5.357489936524832, no F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_94 [Arthrobacter phage Atuin]],,UDL16688,80.4878,2.08543E-28 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 176622. Codes for a hypothetical protein.
    /note=
    /note=Start: Includes all coding potetial; Glimmer and GeneMarkS agree; called when present (although only one manual annotation)
    /note=Function: Only one significant hit on HHpred - not an approved function; has a transmembrane domain; change to membrane protein
    /note=
    /note=Checked by: JP and CM

CDS 177027 - 177347
  /gene="290"
  /product="gp290"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_290"
    /note=Original Glimmer call @bp 177027 has strength 7.93; Genemark calls start at 177027
    /note=SSC: 177027-177347 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein [Arthrobacter liuii] ],,NCBI, q12:s7 89.6226% 2.49984E-7 GAP: 156 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.856, -4.933780265132174, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Arthrobacter liuii] ],,WP_188571095,46.8085,2.49984E-7 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 177027. Codes for a hypothetical protein.
    /note=
    /note=Start: Includes all coding potential; Glimmer and GeneMark both agree; Called when present on Starterator but no manual annotation
    /note=Function: No significant hits on HHpred; only hits on BLAST are to hypothetical proteins; No transmembrane domain (DeepTMHMM)
    /note=
    /note=checked by: JP and CM

CDS 177344 - 177499
  /gene="291"
  /product="gp291"
  /function="membrane protein"
  /locus tag="DunneganBoMo_291"
    /note=Original Glimmer call @bp 177344 has strength 0.4; Genemark calls start at 177344
    /note=SSC: 177344-177499 CP: no SCS: both ST: NI BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.193, -4.229460856734581, no F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S--albeit very little. Start site is most likely at 177344. Codes for a hypothetical protein.
    /note=
    /note=Start: -4 overlap, Includes all coding potential
    /note=Function: No significant hits on HHpred or BLAST; Has a transmembrane domain (DeepTMHMM); change to membrane protein
    /note=
    /note=Checked by: JP and CM

CDS 177553 - 178044
  /gene="292"
  /product="gp292"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_292"
    /note=Original Glimmer call @bp 177553 has strength 12.79; Genemark calls start at 177553
    /note=SSC: 177553-178044 CP: no SCS: both ST: NI BLAST-Start:  GAP: 53 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.721, -3.5466635877785, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 177553. Codes for a hypothetical protein.
    /note=
    /note=Start: includes all coding potential; Glimmer and GeneMark both agree, best Z and raw score; all other genes in pham called this start site on starterator (no manual annotations though)
    /note=Function: No significant hits on HHpred or BLAST; No transmembrane domain (DeepTMHMM)
    /note=
    /note=Checked by: JP and CM

CDS 178044 - 178265
  /gene="293"
  /product="gp293"
  /function="membrane protein"
  /locus tag="DunneganBoMo_293"
    /note=Original Glimmer call @bp 178044 has strength 7.63; Genemark calls start at 178044
    /note=SSC: 178044-178265 CP: no SCS: both ST: NI BLAST-Start:  GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.84, -2.9063687850157054, yes F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 178044. Codes for a transmembrane protein.
    /note=
    /note=Start: has 3 consecutive start codons - choose the last with a -1 overlap; Glimmer and GeneMark both agree. Called in starterator on other draft genes in the pham
    /note=Function: No significant hits on BLAST or HHpred (although less significant hits include transmembrane proteins); Has transmembrane domains (DeepTMHMM)
    /note=
    /note=Checked by: JP and CM

CDS 178301 - 178540
  /gene="294"
  /product="gp294"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_294"
    /note=Original Glimmer call @bp 178301 has strength 6.78; Genemark calls start at 178301
    /note=SSC: 178301-178540 CP: no SCS: both ST: NI BLAST-Start:  GAP: 35 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -5.932056879685085, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 178301, includes all coding potential, best Z and final scores without cutting off a lot of coding potential, start site is conserved and called within the pham. Codes for a hypothetical protein--There is no known function; no significant hits on HHpred or on BLAST, no conserved domains, no transmembrane domains
    /note=I don`t think we can call this Protease due to the lack of sufficient evidence. -TM
    /note=Checked by CM, TM

CDS 178540 - 178746
  /gene="295"
  /product="gp295"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_295"
    /note=Original Glimmer call @bp 178537 has strength 2.76; Genemark calls start at 178537
    /note=SSC: 178540-178746 CP: no SCS: both-cs ST: NI BLAST-Start:  GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.158, -5.832333925337114, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 178537. Codes for a hypothetical protein. 
    /note=changed start site to 178540 because of the -1 gap and back-to-back start site (choose the second). No good hits on HHPred or NCBI
    /note=Checked by CM, TM

CDS 178841 - 179455
  /gene="296"
  /product="gp296"
  /function="terminase, small subunit"
  /locus tag="DunneganBoMo_296"
    /note=Original Glimmer call @bp 178841 has strength 8.88; Genemark calls start at 178841
    /note=SSC: 178841-179455 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_100 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.68194E-100 GAP: 94 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.603, -5.763811153657739, no F: terminase, small subunit SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_100 [Arthrobacter phage Atuin]],,UDL16694,84.058,1.68194E-100 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is most likely at 178841. 
    /note=HHpred yields results saying that this gene could be a terminase small subunit, the crystal stractures match to a small subunit of the terminase. The large subunit is in a different place in this genome as well.
    /note=
    /note=Reviewed: TM, Checked in Class

CDS 179478 - 179864
  /gene="297"
  /product="gp297"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_297"
    /note=Original Glimmer call @bp 179478 has strength 14.04; Genemark calls start at 179478
    /note=SSC: 179478-179864 CP: no SCS: both ST: NI BLAST-Start:  GAP: 22 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.936, -2.5594668560256912, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 
    /note=
    /note=Glimmer and Genemark both call the gene and the same start site.
    /note=RBS: Best Z-score and final score. 
    /note=Coding potential: Start site includes all coding potential. 
    /note=Starterator: called when present
    /note=
    /note=Function: 
    /note=
    /note=No matches in NCBI, PhagesDB, Conserved domain database, or HHPred (JP)
    /note=Appears for be a gene duplication of DunneganBoMo gene ending at 452
    /note=
    /note=No transmembrane domains based on DeepTMHMM (TH)

CDS complement (180289 - 181785)
  /gene="298"
  /product="gp298"
  /function="ParB-N-terminal-like domain"
  /locus tag="DunneganBoMo_298"
    /note=Original Glimmer call @bp 181785 has strength 11.06; Genemark calls start at 181785
    /note=SSC: 181785-180289 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_103 [Arthrobacter phage Atuin]],,NCBI, q2:s3 99.7992% 0.0 GAP: 236 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.748, -3.6146798363680817, yes F: ParB-N-terminal-like domain SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_103 [Arthrobacter phage Atuin]],,UDL16697,92.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start Site:
    /note=
    /note=Good Coding potential.
    /note=Glimmer and Genemark both call the gene and the same start site that includes all coding potential.
    /note=Starterator: Only this gene and one other from DunneganBoMo (2) have this start site. All other commonly called start sites are missing from this gene.
    /note=RBS: Best Raw score and Z-Score
    /note=
    /note=Function:
    /note=The protein sequence alignment with two other phages in the pham both of which called this function.  (TH) Due to a change in the SEA PHAGES approved function list the function of the gene has been changed (JP)
    /note=
    /note=Reviewed: TM

CDS 182022 - 182234
  /gene="299"
  /product="gp299"
  /function="RNA binding protein"
  /locus tag="DunneganBoMo_299"
    /note=Original Glimmer call @bp 182022 has strength 3.96; Genemark calls start at 182022
    /note=SSC: 182022-182234 CP: no SCS: both ST: NI BLAST-Start:  GAP: 236 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.909, -5.40983604789782, yes F: RNA binding protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start Site:
    /note=RBS: Best Z-score and final score
    /note=Covers all coding potential
    /note=Glimmer and GeneMark both call the start site 
    /note=Most commonly called start site on starterator
    /note=
    /note=Function:
    /note=
    /note=Multiple HHpred hits to transcription antitermination proteins, when examining the crystal structure data the matches are to KOW motifs which are RNA binding motifs
    /note=
    /note=Reviewed: TM

CDS 182381 - 182728
  /gene="300"
  /product="gp300"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_300"
    /note=Genemark calls start at 182381
    /note=SSC: 182381-182728 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_104 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.68286E-56 GAP: 146 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.473, -5.15706299163995, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_104 [Arthrobacter phage Atuin]],,UDL16698,84.3478,1.68286E-56 SIF-HHPRED:  SIF-Syn: 
    /note=Start site:
    /note=Called only by GeneMark
    /note=Best Z-score and final score
    /note=Starterator - most likely start site, not many genes had this start site
    /note=includes all coding potential
    /note=
    /note=Function: 
    /note=There is no known function; no significant hits on HHpred, Only hypothetical proteins on BLAST, no conserved domains, no transmembrane domains
    /note=
    /note=Reviewed: TM

CDS 182848 - 183246
  /gene="301"
  /product="gp301"
  /function="membrane protein"
  /locus tag="DunneganBoMo_301"
    /note=Original Glimmer call @bp 182848 has strength 6.75; Genemark calls start at 182848
    /note=SSC: 182848-183246 CP: no SCS: both ST: NI BLAST-Start:  GAP: 119 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.748, -3.0425830684175623, yes F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start Site:
    /note=RBS: Best Z-score and final score
    /note=Covers all coding potential
    /note=Glimmer and GeneMark both call the start site 
    /note=Starterator calls this start site when present
    /note=
    /note=Function:
    /note=hypothetical protein - No BLAST matches, no significant hits on HHpred, no conserved domains, one transmembrane domain
    /note=
    /note=Reviewed: TM

CDS 183328 - 183651
  /gene="302"
  /product="gp302"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_302"
    /note=Original Glimmer call @bp 183328 has strength 8.52; Genemark calls start at 183328
    /note=SSC: 183328-183651 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_107 [Arthrobacter phage Atuin]],,NCBI, q1:s1 61.6822% 6.28927E-11 GAP: 81 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_107 [Arthrobacter phage Atuin]],,UDL16701,36.7521,6.28927E-11 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 183328
    /note=RBS: Final Score and Z-Score
    /note=Starterator: start site is conserved and called in all genes
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=no transmembrane domains
    /note=no conserved domains
    /note=
    /note=Reviewed: TM

CDS 183739 - 183972
  /gene="303"
  /product="gp303"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_303"
    /note=Original Glimmer call @bp 183739 has strength 10.59; Genemark calls start at 183739
    /note=SSC: 183739-183972 CP: no SCS: both ST: NI BLAST-Start:  GAP: 87 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.145, -2.1123791669543204, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 183739
    /note=RBS: Final Score and Z-Score
    /note=Starterator: conserved and called in this pham
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=No significant HHPred matches
    /note=no transmembrane domains, no conserved domains
    /note=
    /note=Checked: RR

CDS 183982 - 184383
  /gene="304"
  /product="gp304"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_304"
    /note=Original Glimmer call @bp 183982 has strength 11.64; Genemark calls start at 183982
    /note=SSC: 183982-184383 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_100 [Arthrobacter phage Racecar]],,NCBI, q1:s1 92.4812% 7.46775E-31 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.35, -3.8137921535956054, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_100 [Arthrobacter phage Racecar]],,QFG12148,60.7407,7.46775E-31 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 183982
    /note=RBS: Final Score and Z-Score
    /note=Starterator: called when present in the pham (6 MAs)
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=No significant HHPred matches
    /note=no conserved domains, no transmembrane domains
    /note= 
    /note=Checked: RR

CDS 184367 - 184864
  /gene="305"
  /product="gp305"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_305"
    /note=Original Glimmer call @bp 184463 has strength 7.31; Genemark calls start at 184463
    /note=SSC: 184367-184864 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein [Butyricimonas sp. GBGM4] ],,NCBI, q84:s3 45.4545% 8.22742E-15 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.157, -5.8328603995233195, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Butyricimonas sp. GBGM4] ],,WP_306449729,60.2273,8.22742E-15 SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 184,463 Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: There is no known function. (TH)
    /note=
    /note=Checked: RR, JL
    /note=
    /note=Has coding potential as shown by Genemark S. Start site is 184367. Hypothetical protein. there is coding potential that extends beyond the called start site. All others in the pham have two conserved start sites earlier with no manual annotations. I would err on the side of including the coding potential so I moved the start site earlier.
    /note=
    /note=No significant matches on HHpred, no matches on NCBI BLAST, no transmembrane domain.
    /note=
    /note=Checked: C.A.R
    /note=Checked: RR

CDS 184895 - 185179
  /gene="306"
  /product="gp306"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_306"
    /note=Genemark calls start at 184946
    /note=SSC: 184895-185179 CP: no SCS: genemark-cs ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_312 [Arthrobacter phage Atuin]],,NCBI, q4:s6 96.8085% 4.41904E-46 GAP: 30 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.106, -4.988391134024432, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_312 [Arthrobacter phage Atuin]],,WWQ87564,83.3333,4.41904E-46 SIF-HHPRED:  SIF-Syn: 
    /note=Has coding potential according to GeneMark S. Start site is 184895. the coding potential extends beyond the Genemark called start sites. This earlier start site is conserved in all members of the pham. Codes for a hypothetical protein. No significant hits on HHpred, No matches on NCBI BLAST, no transmembrane domains.
    /note=
    /note=Checked: C.A.R
    /note=Checked: R.R.

CDS 185250 - 185384
  /gene="307"
  /product="gp307"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_307"
    /note=Original Glimmer call @bp 185250 has strength 11.1; Genemark calls start at 185250
    /note=SSC: 185250-185384 CP: no SCS: both ST: NI BLAST-Start:  GAP: 70 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.451, -3.597563630176197, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=is it a gene?: Yes, Glimmer and GeneMark both called it, it has a start and stop site, and coding potential.
    /note=What is the start site?: 185250; Glimmer and GeneMark both called the same start site; it has good Z-score and final score; includes all coding potential; and is called every time it is present in a gene.
    /note=What is the function?: There is no known function. (TH)
    /note=Checked:RR, JL

CDS 185395 - 185877
  /gene="308"
  /product="gp308"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_308"
    /note=Original Glimmer call @bp 185395 has strength 15.4; Genemark calls start at 185395
    /note=SSC: 185395-185877 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_112 [Arthrobacter phage Atuin]],,NCBI, q3:s17 62.5% 3.42678E-22 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.245, -4.101388555093469, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_112 [Arthrobacter phage Atuin]],,UDL16706,37.9888,3.42678E-22 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : has coding potential based on GeneMark; Glimmer and GeneMark both call it. it has a start site
    /note=Start site? : 185395; this start includes all coding potential, It has the best Z-and final score that includes all coding potential; It is called by both Glimmer and GeneMark; Starterator is not much help because the only other gene is a duplicate from this genome (start site: 5983) Several more draft phages have been added since but all called the same start site (No manual annotations)
    /note=Function? : There are no significant matches on HHPred, the only BLAST match on NCBI is to a hypothetical protein, there are no transmembrane domains (DeepTMHMM) (TH)
    /note=Checked: RR

CDS 185970 - 186137
  /gene="309"
  /product="gp309"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_309"
    /note=Original Glimmer call @bp 185970 has strength 10.53; Genemark calls start at 185970
    /note=SSC: 185970-186137 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein [Prauserella muralis] ],,NCBI, q2:s59 94.5455% 8.02989E-8 GAP: 92 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prauserella muralis] ],,WP_112282550,35.7143,8.02989E-8 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 185970, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator is not very helpful because the only other gene in the pham is a duplicate of this gene in this genome. (start site 6558)
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM. (TH) 
    /note=Checked: RR

CDS 186225 - 186434
  /gene="310"
  /product="gp310"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_310"
    /note=Original Glimmer call @bp 186225 has strength 9.69; Genemark calls start at 186225
    /note=SSC: 186225-186434 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_115 [Arthrobacter phage Atuin]],,NCBI, q1:s1 98.5507% 7.6206E-40 GAP: 87 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_115 [Arthrobacter phage Atuin]],,UDL16709,100.0,7.6206E-40 SIF-HHPRED:  SIF-Syn: 
    /note=Same as gene ending at 7022. Gene 17 on PECAAN
    /note=Is it a gene?: Yes, Glimmer and GeneMark both call the gene. GeneMark does show coding potential for the gene. It has a start and stop site.
    /note=What is the start site?: 186225 - it is the only option. Glimmer and GeneMark both call the start site. It includes all coding potential for the gene. The Z-score and final score for the start site are good. The only other gene in the Pham has the same start site.
    /note=What is the function?: The protein is a hypothetical protein. The only match in phagesdb or NCBI are hypothetical proteins from phages in this cluster. There are no significant structural alignments on HHPred. No membrane domains. (JP) (TH) (RR)

CDS 186492 - 186773
  /gene="311"
  /product="gp311"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_311"
    /note=Original Glimmer call @bp 186492 has strength 8.51; Genemark calls start at 186492
    /note=SSC: 186492-186773 CP: no SCS: both ST: NI BLAST-Start:  GAP: 57 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.219, -2.033982896655645, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 186492, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator calls this site for all gene but they are all drafts. Now a couple of manual annotations that call this start site too. (Gene 18)
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM. (TH) (KJ)
    /note=Reviewed by: TM

CDS 186770 - 187189
  /gene="312"
  /product="gp312"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_312"
    /note=Original Glimmer call @bp 186770 has strength 7.41; Genemark calls start at 186770
    /note=SSC: 186770-187189 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_112 [Arthrobacter phage Atuin]],,NCBI, q85:s123 37.4101% 3.3186E-15 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.54, -3.5490877672587735, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_112 [Arthrobacter phage Atuin]],,UDL16706,22.905,3.3186E-15 SIF-HHPRED:  SIF-Syn: 
    /note=This is a duplication of gene ending 7777, gene 19 on PECAAN
    /note=Is it a gene?: Yes. It has coding potential. Glimmer and GeneMark both call the gene. It has a start and stop site.
    /note=What is the start site?: 186770. It is the only gene (along with a duplicate gene in this phage) in the Pham. The start site includes all coding potential, has good Z- and final scores. Also has a -4 overlap with the previous gene.
    /note=What is the function?: Hypothetical protein. The matches on phagesdb and NCBI are not strong enough to consider calling a function other than hypothetical protein. The are no significant matches on HHPred. There is no membrane domain identified.(JP) (TH)
    /note=Reviewed by: TM

CDS 187276 - 187605
  /gene="313"
  /product="gp313"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_313"
    /note=Original Glimmer call @bp 187276 has strength 17.66; Genemark calls start at 187276
    /note=SSC: 187276-187605 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_RACECAR_116 [Arthrobacter phage Racecar] ],,NCBI, q3:s10 95.4128% 3.52162E-21 GAP: 86 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_RACECAR_116 [Arthrobacter phage Racecar] ],,QFG12163,61.6071,3.52162E-21 SIF-HHPRED:  SIF-Syn: 
    /note=This is a duplicate gene to the one ending 8193, gene 20 on PECAAN.
    /note=Is it a gene?: Yes, It has coding potential. Glimmer and Genemark both call the start site. It has a start and stop site.
    /note=What is the start site?: 187276, Glimmer and GeneMark both call this start site. It includes all coding potential from GeneMark. It has the best Z- and final score, and other with good scores cut off a lot of coding potential. It is the only gene in this Pham with this start site. others have been added since but this gene does not have the manually annotated start sites (and this start is not conserved in the manual annotations)
    /note=What is the function?: hypothetical protein. PhagesDB and NCBI produced only significant matches hypothetical proteins. There were no significant matches in HHPred. There were no identified membrane domains. (JP) (TH)
    /note=Reviewed by: TM

CDS 187774 - 188271
  /gene="314"
  /product="gp314"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_314"
    /note=Original Glimmer call @bp 187774 has strength 8.17; Genemark calls start at 187774
    /note=SSC: 187774-188271 CP: no SCS: both ST: NI BLAST-Start: [MAG: hypothetical protein DCC58_16935 [Chloroflexota bacterium]],,NCBI, q32:s16 76.9697% 1.00935E-4 GAP: 168 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.35, -3.8761054743559344, yes F: Hypothetical Protein SIF-BLAST: ,,[MAG: hypothetical protein DCC58_16935 [Chloroflexota bacterium]],,RIK38244,42.3358,1.00935E-4 SIF-HHPRED:  SIF-Syn: 
    /note=This is a duplicate gene to the one ending 8859, Gene 21 on PECAAN
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 187774, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and Final score for the start site candidates. The only other option that would include all coding potential has a much worse final score. This gene is the only one in the Pham with this start site and is missing the most frequently annotated start site. Others have been added with this start site now and autoannotate this start.
    /note=What is the function?: hypothetical protein, PhagesDB and NCBI only have significant matches to hypothetical proteins. There are no significant matches on HHPred. There is no predicted membrane domain. (JP) (TH)
    /note=Reviewed by: TM

CDS 188364 - 188591
  /gene="315"
  /product="gp315"
  /function="membrane protein"
  /locus tag="DunneganBoMo_315"
    /note=Original Glimmer call @bp 188364 has strength 7.49; Genemark calls start at 188364
    /note=SSC: 188364-188591 CP: no SCS: both ST: NI BLAST-Start:  GAP: 92 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.466674028236667, yes F: membrane protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=This is a duplicate of the gene ending 9179, PECAAN gene 22.
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 188364, Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best Z- and Final score for the start site candidates. This gene is the only one in the Pham. Others have now been added and autoannotate the same start site
    /note=What is the function?: hypothetical protein, PhagesDB and NCBI only have significant matches to hypothetical proteins. There are no significant matches on HHPred. There is a predicted membrane domain. (JP) (TH)
    /note=Reviewed by: TM

CDS 188639 - 189052
  /gene="316"
  /product="gp316"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_316"
    /note=Original Glimmer call @bp 188639 has strength 17.04; Genemark calls start at 188639
    /note=SSC: 188639-189052 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_132 [Arthrobacter phage Atuin]],,NCBI, q2:s3 48.9051% 4.32405E-4 GAP: 47 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_132 [Arthrobacter phage Atuin]],,UDL16726,60.0,4.32405E-4 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 188639, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator is not very helpful because the only other gene in the pham is a duplicate of this gene in this genome. Other genes have now been added to starterator data. All autoannotate this start site as it is conserved in all members of the pham thus far. (Gene 23). It includes all coding potential.
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM.
    /note=(TH) (KJ) (TM)

CDS 189108 - 189314
  /gene="317"
  /product="gp317"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_317"
    /note=Original Glimmer call @bp 189108 has strength 8.67; Genemark calls start at 189108
    /note=SSC: 189108-189314 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_117 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.82247E-27 GAP: 55 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.745, -4.0178693334748665, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_117 [Arthrobacter phage Atuin]],,UDL16711,82.3529,2.82247E-27 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 189108, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator calls this start in all genes with this start site including two manually annotated genes. (duplicate Gene 24) It includes all coding potential; updated starterator data includes 10 manual annotations of this start site which is conserved in 36 members of the pham
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM. 
    /note=(TH) (KJ)
    /note=Reviewed by: TM

CDS 189356 - 189658
  /gene="318"
  /product="gp318"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_318"
    /note=Original Glimmer call @bp 189356 has strength 7.37; Genemark calls start at 189356
    /note=SSC: 189356-189658 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_118 [Arthrobacter phage Atuin]],,NCBI, q1:s1 96.0% 2.58335E-27 GAP: 41 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.156, -2.230514797657003, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_118 [Arthrobacter phage Atuin]],,UDL16712,67.3267,2.58335E-27 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 189356, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator calls this start site every time including two manually annotated genes. (duplicate Gene 25). Includes all coding potential; now ten manual annotations of this start site
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on phagesdb, the only significant match on NCBI is to a hypothetical protein. No transmembrane domain on DeepTMHMM. (TH) (KJ) TM

CDS 189755 - 190069
  /gene="319"
  /product="gp319"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_319"
    /note=Original Glimmer call @bp 189755 has strength 8.85; Genemark calls start at 189755
    /note=SSC: 189755-190069 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_120 [Arthrobacter phage Atuin]],,NCBI, q1:s1 99.0385% 1.22698E-57 GAP: 96 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_120 [Arthrobacter phage Atuin]],,UDL16714,89.4231,1.22698E-57 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 189755, Glimmer and GeneMark both call this start site. It has the second (or third) best Z-score and final score but includes all coding potential which the best start site scores does not. Starterator calls this start site when present but all proteins are drafts (duplicate Gene 26); now 2 manual annotations
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on phagesdb, the significant matches on NBCI are to hypothetical proteins. No transmembrane domain on DeepTMHMM.
    /note=Checked by Tyler Hildebrand and KJ, TM

CDS 190219 - 190530
  /gene="320"
  /product="gp320"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_320"
    /note=Original Glimmer call @bp 190219 has strength 21.4; Genemark calls start at 190219
    /note=SSC: 190219-190530 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein RALTA_B0985 [Cupriavidus taiwanensis LMG 19424]],,NCBI, q52:s22 50.4854% 1.4088E-10 GAP: 149 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.325675514574479, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein RALTA_B0985 [Cupriavidus taiwanensis LMG 19424]],,CAQ71596,51.3889,1.4088E-10 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 190219, Glimmer and GeneMark both call this start site. It has the best Z-score and final score. Starterator is not very helpful because the only other gene in the pham is a duplicate of this gene in this genome. (Gene 27). It is the only possible start site
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM. 
    /note=Checked by Tyler Hildebrand and KJ
    /note=Reviewed by: TM

CDS 190805 - 191215
  /gene="321"
  /product="gp321"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_321"
    /note=Original Glimmer call @bp 190805 has strength 7.62; Genemark calls start at 190805
    /note=SSC: 190805-191215 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_124 [Arthrobacter phage Atuin]],,NCBI, q4:s3 83.0882% 7.03902E-33 GAP: 274 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.951, -4.669046746593814, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_124 [Arthrobacter phage Atuin]],,UDL16718,61.4173,7.03902E-33 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 190805, Glimmer and GeneMark both call this start site. Starterator indicates that this start site is called when present although there are no manual annotations. The Z and final scores are not as good as a couple of other sites but this includes all coding potential. (duplicated Gene 28), only start site in this gene with any manual annotations
    /note=Function? : hypothetical protein, No significant matches on HHPred, No significant matches on phagesdb, the only significant matches on NCBI are to hypothetical proteins. No transmembrane domain on DeepTMHMM.
    /note=Checked: RR

CDS 191313 - 191576
  /gene="322"
  /product="gp322"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_322"
    /note=Original Glimmer call @bp 191358 has strength 12.23; Genemark calls start at 191358
    /note=SSC: 191313-191576 CP: no SCS: both-cs ST: NI BLAST-Start:  GAP: 97 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.089, -4.512860391142743, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : Yes, it has coding potential and a start and stop site. 
    /note=Start site? : 191313, Glimmer and GeneMark do not call this start site. It has the best Z-score and final score and includes all coding potential. Starterator is not very helpful because the only other gene in the pham is a duplicate of this gene in this genome. (Gene 29)
    /note=Function? : hypothetical protein, No significant matches on HHPred, No matches on NCBI or phagesdb, No transmembrane domain on DeepTMHMM.
    /note=Checked: RR

CDS 191634 - 191870
  /gene="323"
  /product="gp323"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_323"
    /note=Original Glimmer call @bp 191634 has strength 2.45; Genemark calls start at 191634
    /note=SSC: 191634-191870 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_126 [Arthrobacter phage Atuin]],,NCBI, q4:s3 96.1538% 8.21215E-39 GAP: 57 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.111, -4.466674028236667, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_126 [Arthrobacter phage Atuin]],,UDL16720,88.3117,8.21215E-39 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 191,634
    /note=RBS: Final Score and Z-Score
    /note=Starterator: all other genes called this conserved start site (in the pham) with 2 manual annotations
    /note=coding potential is good
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=a couple of significant HHPred matches but they are to functions that are not accepted phage functions
    /note=No called proteins in our cluster
    /note=
    /note=Reviewed: KJ; RR

CDS complement (192203 - 192361)
  /gene="324"
  /product="gp324"
  /function="RNA binding protein"
  /locus tag="DunneganBoMo_324"
    /note=Original Glimmer call @bp 192361 has strength 9.17; Genemark calls start at 192361
    /note=SSC: 192361-192203 CP: no SCS: both ST: NI BLAST-Start:  GAP: 17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.156, -2.0895162839948163, yes F: RNA binding protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 192361
    /note=RBS: Final Score and Z-Score
    /note=Starterator: No additional Genes (other than a duplicated gene in this genome) same as gene 31; other genes have been added and all autoannotate the same start site (no manual annotations yet)
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=No NCBI blast results
    /note=HHPred matches to a KOW motif of transcriptions factors which is a conserved RNA binding motif
    /note=No called proteins in our cluster
    /note=Checked: RR

CDS complement (192379 - 192594)
  /gene="325"
  /product="gp325"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_325"
    /note=Original Glimmer call @bp 192594 has strength 2.59; Genemark calls start at 192594
    /note=SSC: 192594-192379 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_128 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.3861E-9 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.156, -2.741655139666096, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_128 [Arthrobacter phage Atuin]],,UDL16722,68.0556,2.3861E-9 SIF-HHPRED:  SIF-Syn: 
    /note=Start site: 13182
    /note=RBS: Final Score and Z-Score
    /note=Starterator: 30 genes in this pham and all have the same predicted start with 8 manual annotations
    /note=Glimmer and GeneMark both call the same start site
    /note=coding potential is good
    /note=
    /note=Function:
    /note=NCBI blast results yield only a hypothetical protein
    /note=No significant HHPred matches
    /note=No called proteins in our cluster
    /note=Checked: RR

CDS complement (192678 - 192896)
  /gene="326"
  /product="gp326"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_326"
    /note=Genemark calls start at 192896
    /note=SSC: 192896-192678 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_129 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 1.86998E-27 GAP: 105 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.068, -2.2763497933341483, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_129 [Arthrobacter phage Atuin]],,UDL16723,84.0,1.86998E-27 SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : yes. It has coding potential, a start and stop codon, called only by GeneMark
    /note=Start site:192896 - This includes all coding potential, is called by GeneMark, Has the best Z-score and final score. Starterator data indicates this start site is annotated when present 100% including 2 manual annotations
    /note=Function: Hypothetical protein: there are no significant matches on HHPred, The only BLAST match is for a hypothetical protein. There are no transmembrane domains and no conserved domains.
    /note=
    /note=Checked: RR

CDS complement (193002 - 193220)
  /gene="327"
  /product="gp327"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_327"
    /note=Original Glimmer call @bp 193220 has strength 6.65; Genemark calls start at 193220
    /note=SSC: 193220-193002 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein KBG_88 [Mycobacterium phage KBG] ],,NCBI, q8:s10 88.8889% 0.00109681 GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.84, -2.8454123590742793, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein KBG_88 [Mycobacterium phage KBG] ],,YP_001994546,55.8442,0.00109681 SIF-HHPRED:  SIF-Syn: 
    /note=Gene: Yes, there is coding potential, Glimmer and GeneMark both called it, it has a start and stop codon
    /note=Start: 193220, this start includes all coding potential, it is called by both Glimmer and GeneMark, it has the best Z-score and final score,Starterator indicates that it does not contain the most commonly annotated start sites.
    /note=Function:  hypothetical protein, there are no significant BLAST hit. The only HHPred matches have small regions of coverage and are for proteins not on the approved list. there are no conserved domains or transmembrane domains
    /note=
    /note=Checked: RR

CDS complement (193300 - 193491)
  /gene="328"
  /product="gp328"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_328"
    /note=Original Glimmer call @bp 193491 has strength 12.19; Genemark calls start at 193491
    /note=SSC: 193491-193300 CP: no SCS: both ST: NI BLAST-Start:  GAP: 91 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.101, -4.34663776219455, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene: yes, there is coding potential, it has a start and stop codon, glimmer and genemark both call it
    /note=Start: 193,491, this start includes all coding potential possible, it is called by both glimmer and genemark, it has the best final score, this start site is indicated on starterator when present (no manual annotations though)
    /note=Function: Hypothetical protein, there are no significant matches on HHPred, Phages DB BLAST or NCBI Blast, There are no conserved domains or transmembrane domains

CDS complement (193583 - 193837)
  /gene="329"
  /product="gp329"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_329"
    /note=Original Glimmer call @bp 193837 has strength 6.82; Genemark calls start at 193837
    /note=SSC: 193837-193583 CP: no SCS: both ST: NI BLAST-Start:  GAP: 282 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.156, -2.1518296047551457, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene? : It has coding potential, a start site and a stop site, and is called by both glimmer and genemark
    /note=Start site?: 193837, called by both glimmer and genemark, it has the best Z- and final score, it includes all coding potential, while there are only 2 manual annotations in starterator all genes in the pham were auto-annotated to this start site (duplicate gene: start site 14425)
    /note=Function? : Hypothetical protein, there are no significant HHPred matches, there are no BLAST matches with a function assigned, there are no conserved domains or membrane domains.
    /note=Checked: RR
    /note=
    /note=No significant ORFs in the gap before this gene

CDS complement (194120 - 194302)
  /gene="330"
  /product="gp330"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_330"
    /note=Genemark calls start at 194302
    /note=SSC: 194302-194120 CP: no SCS: genemark ST: NI BLAST-Start:  GAP: 135 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Gene is same as the gene ending at 14708
    /note=Gene? : It has coding potential, a start and stop site. Called by GeneMark
    /note=Start Site? : 194302 - Called by GeneMark; only start site that includes all coding potential; best Z- and final score; tarterator has several genes within this pham, this start site is called whenever it is present but no manual annotations
    /note=Function? : hypothetical protein; No matches in phages or NCBI BLAST; HHPred has no significant matches; No conserved domains; No transmembrane domains.
    /note=Reviewed: KJ

CDS complement (194438 - 194704)
  /gene="331"
  /product="gp331"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_331"
    /note=Genemark calls start at 194704
    /note=SSC: 194704-194438 CP: no SCS: genemark ST: NI BLAST-Start:  GAP: 213 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.684, -4.199347842547433, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Same as gene ending 15026
    /note=Gene? : It has coding potential; It has a start and stop site; call by GeneMark
    /note=Start Site? : 194704 - It has the best Z- and Final score that includes all coding potential; called by GeneMark; Starterator has a few other genes but most call another start site (no manual annotations). 
    /note=Function? : Hypothetical Protein - No phages or NCBI BLAST matches; no significant matches on HHPred; no conserved domains; no transmembrane domain
    /note=Reviewed: KJ

CDS complement (194918 - 195502)
  /gene="332"
  /product="gp332"
  /function="Hypothetical Protein"
  /locus tag="DunneganBoMo_332"
    /note=Original Glimmer call @bp 195502 has strength 13.62; Genemark calls start at 195502
    /note=SSC: 195502-194918 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ATUIN_135 [Arthrobacter phage Atuin]],,NCBI, q1:s1 100.0% 2.00783E-86 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.698, -5.21028209587241, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ATUIN_135 [Arthrobacter phage Atuin]],,UDL16729,80.1047,2.00783E-86 SIF-HHPRED:  SIF-Syn: 
    /note=This is a duplicate gene to the one ending 15506, gene 41 on PECAAN.
    /note=Is it a gene?: Yes, it has a start and stop site. It has coding potential in GeneMark. Glimmer and GeneMark both call it.
    /note=What is the start site?: 195502, (reverse gene) Glimmer and GeneMark both call the same start site. It includes all coding potential. It has the best final score that includes all the coding potential. This gene is the only one in the Pham with this start site. This gene does not have the most commonly called start site from other proteins in the pham.
    /note=What is the function?: membrane protein, PhagesDB and NCBI only have significant matches to hypothetical proteins. There are no significant matches on HHPred. There is a predicted membrane domain by DeepTMHMM via Phamerator. (JP)
    /note=Reviewed: KJ - not membrane protein, signal protein