CDS 25 - 474
  /gene="1"
  /product="gp1"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="NathanVaag_1"
    /note=Original Glimmer call @bp 25 has strength 18.62
    /note=SSC: 25-474 CP: yes SCS: glimmer ST: SS BLAST-Start: [HTH DNA binding domain protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 9.01803E-105 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.722, -3.5864307146499876, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding domain protein [Arthrobacter phage Piccoletto] ],,YP_009612380,100.0,9.01803E-105 SIF-HHPRED:  SIF-Syn: same position as phages Picolletto & King2
    /note=completed together in class

CDS 471 - 1940
  /gene="2"
  /product="gp2"
  /function="terminase, large subunit"
  /locus tag="NathanVaag_2"
    /note=Original Glimmer call @bp 471 has strength 16.88; Genemark calls start at 471
    /note=SSC: 471-1940 CP: yes SCS: both ST: SS BLAST-Start: [terminase large subunit [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.273, -5.942549405124707, no F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Arthrobacter phage Piccoletto] ],,YP_009612381,100.0,0.0 SIF-HHPRED: Large subunit terminase; large terminase, VIRAL PROTEIN; 2.2A {Deep-sea thermophilic phage D6E},,,5OE8_B,92.8425,100.0 SIF-Syn: Other phages in the same subcluster have the same sequence length and e- value (0) with terminase, large subunit listed as its function.

Piccoletto has the same also has the same score as NathanVaag, and gene 2 is listed as a terminase, large subunit function.
    /note=HHpred, NCBI BLAST, PhagesDB Function Frequency, and PhagesDB BLAST all show evidence supporting terminase, large subunit as a function for gene 2.

CDS 1982 - 3427
  /gene="3"
  /product="gp3"
  /function="portal protein"
  /locus tag="NathanVaag_3"
    /note=Original Glimmer call @bp 1982 has strength 14.14; Genemark calls start at 1982
    /note=SSC: 1982-3427 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI26_gp03 [Arthrobacter phage Beans] ],,NCBI, q1:s1 100.0% 0.0 GAP: 41 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.304, -4.926874829490106, no F: portal protein SIF-BLAST: ,,[hypothetical protein FDI26_gp03 [Arthrobacter phage Beans] ],,YP_009609944,99.5842,0.0 SIF-HHPRED: Portal protein; G20C, portal protein, bacteriophage, transport protein; 1.9A {Thermus phage P7426},,,5NGD_B,81.289,100.0 SIF-Syn: Synteny with phage "Beans" and phage "Picoletto"

CDS 3427 - 5187
  /gene="4"
  /product="gp4"
  /function="capsid maturation protease"
  /locus tag="NathanVaag_4"
    /note=Original Glimmer call @bp 3427 has strength 11.57; Genemark calls start at 3427
    /note=SSC: 3427-5187 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp04 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.702, -6.376677624715306, no F: capsid maturation protease SIF-BLAST: ,,[hypothetical protein FDI41_gp04 [Arthrobacter phage Piccoletto] ],,YP_009612383,99.4881,0.0 SIF-HHPRED:  SIF-Syn: Very high synteny with any AO cluster.
    /note=CDD unreliable, as only one entry with lower e-12 evalue and 17% coverage.
    /note="muf-like minor capsid protein" has 33% frequency in PhagesDB Function Frequency, however in my eyes overruled by multiple instances of evidence that its function is "capsid maturation protease"

CDS 5184 - 5465
  /gene="5"
  /product="gp5"
  /function="Hypothetical Protein"
  /locus tag="NathanVaag_5"
    /note=Original Glimmer call @bp 5184 has strength 14.55; Genemark calls start at 5184
    /note=SSC: 5184-5465 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp05 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 8.14583E-61 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.793, -3.3861058366776207, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDI41_gp05 [Arthrobacter phage Piccoletto] ],,YP_009612384,100.0,8.14583E-61 SIF-HHPRED: Imm35 ; Immunity protein 35,,,PF15567.9,79.5699,99.9 SIF-Syn: same position as phages Jawnski and King2
    /note=Adjusted nomenclature from "function unknown" to "Hypothetical Protein" as described in the SEAPHAGES Function list.
    /note=Hypothetical Protein function supported by comparing to Piccoletto and Beans.
    /note=-Edited by: DSG

CDS 5622 - 6770
  /gene="6"
  /product="gp6"
  /function="scaffolding protein"
  /locus tag="NathanVaag_6"
    /note=Original Glimmer call @bp 5622 has strength 11.17; Genemark calls start at 5622
    /note=SSC: 5622-6770 CP: yes SCS: both ST: SS BLAST-Start: [scaffolding protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: 156 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.866, -4.211035238975397, no F: scaffolding protein SIF-BLAST: ,,[scaffolding protein [Arthrobacter phage Piccoletto] ],,YP_009612385,100.0,0.0 SIF-HHPRED: Phage_GPO ; Phage capsid scaffolding protein (GPO) serine peptidase,,,PF05929.14,35.8639,99.8 SIF-Syn: same position as phages Jawnski and Franzy

CDS 6812 - 7198
  /gene="7"
  /product="gp7"
  /function="minor capsid protein"
  /locus tag="NathanVaag_7"
    /note=Original Glimmer call @bp 6812 has strength 19.91; Genemark calls start at 6812
    /note=SSC: 6812-7198 CP: yes SCS: both ST: SS BLAST-Start: [minor capsid protein [Arthrobacter phage EastWest]],,NCBI, q1:s1 100.0% 5.49499E-51 GAP: 41 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.537, -3.8761054743559344, yes F: minor capsid protein SIF-BLAST: ,,[minor capsid protein [Arthrobacter phage EastWest]],,UGL61893,83.4646,5.49499E-51 SIF-HHPRED: Capsid fiber protein; bacteriophage, phi29, prohead, VIRUS; HET: SO4; 1.8A {Bacillus phage phi29},,,6QYY_E,86.7188,99.7 SIF-Syn: Synteny is shared with all phages in the AO1 subcluster, but no designated function for gene 7. However, synteny is shared with gene 7 of phage Abba (AO3) and gene 9 of phage EastWest (AO), each with the minor capsid protein function.
    /note=This gene exists across phage genomes and is present in phages outside of cluster AO1. 
    /note=
    /note=I agree with the information and I added evidence from HHPRED. V.G.N

CDS 7217 - 8110
  /gene="8"
  /product="gp8"
  /function="major capsid protein"
  /locus tag="NathanVaag_8"
    /note=Original Glimmer call @bp 7217 has strength 15.1; Genemark calls start at 7217
    /note=SSC: 7217-8110 CP: yes SCS: both ST: SS BLAST-Start: [major capsid subunit [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 0.0 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.937, -3.0194634687155197, yes F: major capsid protein SIF-BLAST: ,,[major capsid subunit [Arthrobacter phage Jawnski] ],,YP_009601568,100.0,0.0 SIF-HHPRED: Gp27 major capsid protein; phage G, major capsid protein, decoration protein, capsid, icosahedral, gp26, gp27, VIRUS; 6.1A {Bacillus virus G},,,6WKK_F,89.5623,99.9 SIF-Syn: syntenic with other AO1 phages

CDS 8116 - 8673
  /gene="9"
  /product="gp9"
  /function="hypothetical protein"
  /locus tag="NathanVaag_9"
    /note=Original Glimmer call @bp 8116 has strength 15.32; Genemark calls start at 8116
    /note=SSC: 8116-8673 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp09 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 6.95072E-126 GAP: 5 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.63, -4.280611589027404, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp09 [Arthrobacter phage Piccoletto] ],,YP_009612388,100.0,6.95072E-126 SIF-HHPRED:  SIF-Syn: Gene 9 of NathanVaag shared synteny with many phages in the pham such as Beans, Jawnski and Piccoletto.
    /note=PhagesDB Function Frequency: various capsid proteins with no real relationship to the cluster or pham of NathanVaag. Evidence not strong to be used. 
    /note=PhagesDB Blast: Function unknown for all hits, e value of 3e-99
    /note=HHPRED: best hit unknown function, probability 43, 39.45% coverage, e value of 200, very high, not sufficient evidence 
    /note=NCBI Blast: multiple hits of hypothetical protein, with the highest being with Piccoletto with a 99.45% identity, 100% alignment
    /note=CDD: No data available
    /note=Group discussion confirmed unknown function best fit for Gene 9 on 02/22/2022.

CDS 8680 - 9192
  /gene="10"
  /product="gp10"
  /function="hypothetical protein"
  /locus tag="NathanVaag_10"
    /note=Original Glimmer call @bp 8680 has strength 11.46; Genemark calls start at 8680
    /note=SSC: 8680-9192 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp10 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 1.60516E-117 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.843, -5.330723697772664, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp10 [Arthrobacter phage Piccoletto] ],,YP_009612389,99.4118,1.60516E-117 SIF-HHPRED:  SIF-Syn: High degree of synteny among subcluster AO1: Beans, Brent, Jawnski, Franzy, King2, Piccoletto
    /note=All appropriately low e-value hits are listed unknown/hypothetical protein matches. There is no evidence to suggest a known function.
    /note=
    /note=
    /note=Edited by Cade Kane

CDS 9192 - 9656
  /gene="11"
  /product="gp11"
  /function="head-to-tail adaptor"
  /locus tag="NathanVaag_11"
    /note=Original Glimmer call @bp 9192 has strength 8.73; Genemark calls start at 9192
    /note=SSC: 9192-9656 CP: yes SCS: both ST: SS BLAST-Start: [head-tail connector [Arthrobacter phage Brent] ],,NCBI, q1:s1 100.0% 7.94351E-105 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.702, -6.1214051196120005, no F: head-to-tail adaptor SIF-BLAST: ,,[head-tail connector [Arthrobacter phage Brent] ],,YP_009601497,98.7013,7.94351E-105 SIF-HHPRED: Phage_tail_S ; Phage virion morphogenesis family,,,PF05069.16,89.6104,99.7 SIF-Syn: Synteny with phage "Picoletto"

CDS 9659 - 10270
  /gene="12"
  /product="gp12"
  /function="tail terminator"
  /locus tag="NathanVaag_12"
    /note=Original Glimmer call @bp 9659 has strength 20.63; Genemark calls start at 9659
    /note=SSC: 9659-10270 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp12 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 3.2373E-146 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.69, -4.16062280240617, no F: tail terminator SIF-BLAST: ,,[hypothetical protein FDI41_gp12 [Arthrobacter phage Piccoletto] ],,YP_009612391,100.0,3.2373E-146 SIF-HHPRED:  SIF-Syn: High degree of synteny with all phages in the same sub cluster, AO1.
    /note=Function was discussed and approved in class, one hit in phagesDB BLAST with a suitable e-value, calling for a tail terminator protein.

CDS 10324 - 10563
  /gene="13"
  /product="gp13"
  /function="hypothetical protein"
  /locus tag="NathanVaag_13"
    /note=Original Glimmer call @bp 10324 has strength 12.76; Genemark calls start at 10324
    /note=SSC: 10324-10563 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI26_gp13 [Arthrobacter phage Beans] ],,NCBI, q1:s1 100.0% 1.37986E-48 GAP: 53 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.569, -6.261769525437431, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI26_gp13 [Arthrobacter phage Beans] ],,YP_009609954,100.0,1.37986E-48 SIF-HHPRED:  SIF-Syn: Syntenic with other AO1 phages
    /note=Out of the five entries on Function Frequency, the tail assembly chaperone function appears twice and both have frequencies of 29% coming from the DR cluster.
    /note=
    /note=No designated function for any phages within the AO1 cluster on Phamerator, however the gene appears to be close to other genes that code for tail related proteins.

CDS 10566 - 12014
  /gene="14"
  /product="gp14"
  /function="tail sheath protein"
  /locus tag="NathanVaag_14"
    /note=Original Glimmer call @bp 10566 has strength 17.06; Genemark calls start at 10566
    /note=SSC: 10566-12014 CP: yes SCS: both ST: SS BLAST-Start: [tail sheath protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.394, -2.17469248771465, yes F: tail sheath protein SIF-BLAST: ,,[tail sheath protein [Arthrobacter phage Piccoletto] ],,YP_009612393,100.0,0.0 SIF-HHPRED: Tail sheath protein Gp18; bacteriophage T4, phage tail terminator protein, phage sheath protein, VIRAL PROTEIN; 15.0A {Enterobacteria phage T4},,,3J2M_Y,99.5851,100.0 SIF-Syn: Each phage within the AO1 cluster on Phamerator contains gene 14 in the same position with the same determined function.
    /note=This gene exists across phage genomes and is present in phages outside of cluster AO1.

CDS 12028 - 12447
  /gene="15"
  /product="gp15"
  /function="tail tube protein"
  /locus tag="NathanVaag_15"
    /note=Original Glimmer call @bp 12028 has strength 15.64; Genemark calls start at 12028
    /note=SSC: 12028-12447 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH48_gp15 [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 2.01549E-95 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.876, -3.2017655760970833, yes F: tail tube protein SIF-BLAST: ,,[hypothetical protein FDH48_gp15 [Arthrobacter phage Jawnski] ],,YP_009601575,100.0,2.01549E-95 SIF-HHPRED: Phage_T4_gp19 ; T4-like virus tail tube protein gp19,,,PF06841.15,93.5252,100.0 SIF-Syn: Syntenic with AO1 phages
    /note=Protein number 15 within the subcluster AO1 provide supporting evidence for function of "tail tube protein"

CDS 12628 - 13221
  /gene="16"
  /product="gp16"
  /function="tail assembly chaperone"
  /locus tag="NathanVaag_16"
    /note=Original Glimmer call @bp 12628 has strength 22.37; Genemark calls start at 12628
    /note=SSC: 12628-13221 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Arthrobacter phage EastWest]],,NCBI, q43:s46 77.665% 5.27421E-65 GAP: 180 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.372, -2.8084998623841946, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage EastWest]],,UGL61902,62.1212,5.27421E-65 SIF-HHPRED: Phage_TAC_5 ; Phage XkdN-like tail assembly chaperone protein, TAC,,,PF08890.14,70.5584,99.8 SIF-Syn: EastWest, Klevey, Lilmac1015, and Praire are all within the same pham and share synteny.
    /note=NCBI BLAST shows this function with a 5.3e-65 e-value and  PhagesDB BLAST has this function with an e-value of 5e-54.
    /note= HHPRED has an e-value of 7.6e-19

CDS 13446 - 16073
  /gene="17"
  /product="gp17"
  /function="tape measure protein"
  /locus tag="NathanVaag_17"
    /note=Original Glimmer call @bp 13446 has strength 14.68; Genemark calls start at 13446
    /note=SSC: 13446-16073 CP: yes SCS: both ST: SS BLAST-Start: [tapemeasure protein [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 0.0 GAP: 224 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.69, -4.609715333525589, yes F: tape measure protein SIF-BLAST: ,,[tapemeasure protein [Arthrobacter phage Jawnski] ],,YP_009601577,98.8571,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_AF,8.68571,99.9 SIF-Syn: Syntenic with other AO1 phages

CDS 16073 - 16738
  /gene="18"
  /product="gp18"
  /function="LysM-like peptidoglycan binding protein"
  /locus tag="NathanVaag_18"
    /note=Original Glimmer call @bp 16073 has strength 13.82; Genemark calls start at 16073
    /note=SSC: 16073-16738 CP: yes SCS: both ST: SS BLAST-Start: [LysM domain protein [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 6.3953E-160 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.311, -2.2763497933341483, yes F: LysM-like peptidoglycan binding protein SIF-BLAST: ,,[LysM domain protein [Arthrobacter phage Jawnski] ],,YP_009601578,100.0,6.3953E-160 SIF-HHPRED: Pvc7; assembly, Photorhabdus asymbiotica, PVC, contractile injection system, bacteriophage-like, PROTEIN TRANSPORT; 3.5A {Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)},,,6J0N_f,95.9276,99.8 SIF-Syn: This gene shares synteny with the other phages in Subcluster AO1 such as Piccoletto, King2, Jawnski, Franzy, Brent, and Beans.

CDS 16738 - 18087
  /gene="19"
  /product="gp19"
  /function="minor tail protein"
  /locus tag="NathanVaag_19"
    /note=Original Glimmer call @bp 16738 has strength 10.23; Genemark calls start at 16738
    /note=SSC: 16738-18087 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.771, -3.4892599424135016, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Piccoletto] ],,YP_009612398,99.5546,0.0 SIF-HHPRED: Pvc8; assembly, Photorhabdus asymbiotica, PVC, contractile injection system, bacteriophage-like, PROTEIN TRANSPORT; 3.9A {Photorhabdus asymbiotica},,,6J0M_C,60.5791,99.9 SIF-Syn: This gene shares synteny with other phages in the same AO1 sub cluster such as Piccoletto, King2, Jawnski, Franzy, Brent, and Beans.

CDS 18091 - 18501
  /gene="20"
  /product="gp20"
  /function="hypothetical protein"
  /locus tag="NathanVaag_20"
    /note=Original Glimmer call @bp 18091 has strength 13.8; Genemark calls start at 18091
    /note=SSC: 18091-18501 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp20 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 3.94424E-87 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.926, -3.103280908771174, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp20 [Arthrobacter phage Piccoletto] ],,YP_009612399,98.5294,3.94424E-87 SIF-HHPRED:  SIF-Syn: High degrees of synteny with all phages within the same sub cluster, AO1
    /note=All hits in BLAST databases with suitably low e-values call an unknown function or hypothetical protein.

CDS 18498 - 20567
  /gene="21"
  /product="gp21"
  /function="minor tail protein"
  /locus tag="NathanVaag_21"
    /note=Original Glimmer call @bp 18513 has strength 11.99; Genemark calls start at 18498
    /note=SSC: 18498-20567 CP: yes SCS: both-gm ST: NA BLAST-Start: [minor tail protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.211, -4.522979412939132, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Piccoletto] ],,YP_009612400,99.7097,0.0 SIF-HHPRED:  SIF-Syn: High synteny with AO1, AO2, and AR clusters
    /note=Overwhelming evidence on function being "minor tail protein".

CDS 20602 - 22467
  /gene="22"
  /product="gp22"
  /function="minor tail protein"
  /locus tag="NathanVaag_22"
    /note=Original Glimmer call @bp 20626 has strength 12.96; Genemark calls start at 20626
    /note=SSC: 20602-22467 CP: yes SCS: both-cs ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.593, -5.007001221682044, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Piccoletto] ],,YP_009612401,99.839,0.0 SIF-HHPRED:  SIF-Syn: Syntenic with phages in the same Pham as NathanVaag, Piccoletto, Brent, Beans, and Jawnski
    /note=The z score and final score for start 20602 better fits the criteria than what Glimmer and GeneMark suggested. The z-score and final score for 20626 don’t quite fit the criteria, as well as 20602 does. Additionally, start 20602 has the longest ORF. Starterator data shows that other phages in this Pham all have that same start.

CDS 22467 - 22754
  /gene="23"
  /product="gp23"
  /function="Hypothetical Protein"
  /locus tag="NathanVaag_23"
    /note=Original Glimmer call @bp 22467 has strength 13.51; Genemark calls start at 22467
    /note=SSC: 22467-22754 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein FDH47_gp23 [Arthrobacter phage Brent] ],,NCBI, q1:s1 100.0% 1.84108E-60 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.16, -4.702334767722353, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH47_gp23 [Arthrobacter phage Brent] ],,YP_009601509,100.0,1.84108E-60 SIF-HHPRED:  SIF-Syn: Syntenic with other AO1 phages

CDS 22751 - 22969
  /gene="24"
  /product="gp24"
  /function="hypothetical protein"
  /locus tag="NathanVaag_24"
    /note=Original Glimmer call @bp 22751 has strength 7.61; Genemark calls start at 22751
    /note=SSC: 22751-22969 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH48_gp24 [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 1.79952E-44 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.644, -5.646677400615975, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH48_gp24 [Arthrobacter phage Jawnski] ],,YP_009601584,100.0,1.79952E-44 SIF-HHPRED:  SIF-Syn: Syntenic with other AO1 phages

CDS 22969 - 23379
  /gene="25"
  /product="gp25"
  /function="holin"
  /locus tag="NathanVaag_25"
    /note=Original Glimmer call @bp 22969 has strength 14.74; Genemark calls start at 22969
    /note=SSC: 22969-23379 CP: yes SCS: both ST: SS BLAST-Start: [holin [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 6.56343E-90 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.474, -2.4811409279978642, yes F: holin SIF-BLAST: ,,[holin [Arthrobacter phage Jawnski] ],,YP_009601585,99.2647,6.56343E-90 SIF-HHPRED:  SIF-Syn: Has synteny with all genes in subcluster AO1.
    /note=Is a transmembrane protein. HHPRED has no supporting evidence.

CDS 23369 - 24958
  /gene="26"
  /product="gp26"
  /function="endolysin"
  /locus tag="NathanVaag_26"
    /note=Original Glimmer call @bp 23369 has strength 16.48; Genemark calls start at 23399
    /note=SSC: 23369-24958 CP: yes SCS: both-gl ST: SS BLAST-Start: [endolysin [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.022, -4.897971560974249, no F: endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Piccoletto] ],,YP_009612405,98.3019,0.0 SIF-HHPRED:  SIF-Syn: shares same position as in phages Jawnski and Piccoletto

CDS 24958 - 25326
  /gene="27"
  /product="gp27"
  /function="holin"
  /locus tag="NathanVaag_27"
    /note=Original Glimmer call @bp 24958 has strength 22.23; Genemark calls start at 24958
    /note=SSC: 24958-25326 CP: yes SCS: both ST: SS BLAST-Start: [holin [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 2.35164E-78 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.372, -2.297359520375101, yes F: holin SIF-BLAST: ,,[holin [Arthrobacter phage Piccoletto] ],,YP_009612406,99.1803,2.35164E-78 SIF-HHPRED:  SIF-Syn: syntenic with phages Piccoletto and King2

CDS 25410 - 25742
  /gene="28"
  /product="gp28"
  /function="baseplate wedge protein"
  /locus tag="NathanVaag_28"
    /note=Original Glimmer call @bp 25410 has strength 9.13; Genemark calls start at 25410
    /note=SSC: 25410-25742 CP: yes SCS: both ST: SS BLAST-Start: [baseplate wedge protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 3.49143E-74 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.462, -4.868630278533925, no F: baseplate wedge protein SIF-BLAST: ,,[baseplate wedge protein [Arthrobacter phage Piccoletto] ],,YP_009612407,100.0,3.49143E-74 SIF-HHPRED: Baseplate wedge protein gp25; contractile sheath, baseplate, wedge, sheath polymerization, viral protein; HET: MSE; 2.47A {Enterobacteria phage T4},,,5IW9_A,93.6364,99.8 SIF-Syn: Phamerator shows synteny between NathanVaag`s gene 28 and a lot of other AO1 phages such as Beans, Brent, Franzy and Jawnski.

CDS 25735 - 26865
  /gene="29"
  /product="gp29"
  /function="baseplate J protein"
  /locus tag="NathanVaag_29"
    /note=Original Glimmer call @bp 25735 has strength 14.86; Genemark calls start at 25735
    /note=SSC: 25735-26865 CP: yes SCS: both ST: SS BLAST-Start: [baseplate J-like protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.525, -4.187763896562409, yes F: baseplate J protein SIF-BLAST: ,,[baseplate J-like protein [Arthrobacter phage Piccoletto] ],,YP_009612408,100.0,0.0 SIF-HHPRED: Baseplate wedge protein gp6; T4, baseplate, complex, VIRAL PROTEIN; 3.8A {Enterobacteria phage T4},,,5HX2_D,91.4894,100.0 SIF-Syn: Phamerator shows synteny between NathanVaag`s gene 29 and a lot of other AO1 phages such as Beans, Brent, Franzy and Jawnski.

CDS 26865 - 28142
  /gene="30"
  /product="gp30"
  /function="minor tail protein"
  /locus tag="NathanVaag_30"
    /note=Original Glimmer call @bp 26865 has strength 12.05; Genemark calls start at 26865
    /note=SSC: 26865-28142 CP: yes SCS: both ST: SS BLAST-Start: [tail protein [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.189, -4.582905859694018, no F: minor tail protein SIF-BLAST: ,,[tail protein [Arthrobacter phage Jawnski] ],,YP_009601590,88.2353,0.0 SIF-HHPRED: Tail_P2_I ; Phage tail protein (Tail_P2_I),,,PF09684.13,25.8824,98.9 SIF-Syn: synteny with other AO1 phages

CDS 28285 - 28467
  /gene="31"
  /product="gp31"
  /function="hypothetical protein"
  /locus tag="NathanVaag_31"
    /note=Original Glimmer call @bp 28336 has strength 9.02
    /note=SSC: 28285-28467 CP: yes SCS: glimmer-cs ST: NI BLAST-Start: [hypothetical protein FDI41_gp31 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 3.97759E-34 GAP: 142 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.288, -4.387217987046989, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp31 [Arthrobacter phage Piccoletto] ],,YP_009612410,100.0,3.97759E-34 SIF-HHPRED:  SIF-Syn: synteny with phages King2, Picoletto

CDS 28464 - 29492
  /gene="32"
  /product="gp32"
  /function="exonuclease"
  /locus tag="NathanVaag_32"
    /note=Original Glimmer call @bp 28464 has strength 19.78; Genemark calls start at 28464
    /note=SSC: 28464-29492 CP: yes SCS: both ST: SS BLAST-Start: [exonuclease [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.71, -5.515975007183163, no F: exonuclease SIF-BLAST: ,,[exonuclease [Arthrobacter phage Jawnski] ],,YP_009601592,99.7076,0.0 SIF-HHPRED: Uncharacterized protein R354; MIMIVIRE, Cas4-like, nuclease, R354, NUCLEAR PROTEIN; 2.806A {Acanthamoeba polyphaga mimivirus},,,5YET_B,86.5497,100.0 SIF-Syn: synteny with AO1 phages (e.g. Beans, Jawnski)

CDS 29495 - 30340
  /gene="33"
  /product="gp33"
  /function="RecT-like ssDNA binding protein"
  /locus tag="NathanVaag_33"
    /note=Original Glimmer call @bp 29495 has strength 18.71; Genemark calls start at 29495
    /note=SSC: 29495-30340 CP: yes SCS: both ST: SS BLAST-Start: [RecT-like protein [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.004, -4.871466944371845, no F: RecT-like ssDNA binding protein SIF-BLAST: ,,[RecT-like protein [Arthrobacter phage Jawnski] ],,YP_009601593,100.0,0.0 SIF-HHPRED: RecT ; RecT family,,,PF03837.17,69.395,100.0 SIF-Syn: High degree of synteny of gene 33 among subcluster AO1.

CDS 30357 - 30566
  /gene="34"
  /product="gp34"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="NathanVaag_34"
    /note=Original Glimmer call @bp 30357 has strength 7.57; Genemark calls start at 30333
    /note=SSC: 30357-30566 CP: yes SCS: both-gl ST: NI BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage King2]],,NCBI, q1:s1 100.0% 4.74606E-40 GAP: 16 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.774, -3.9940113087860643, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage King2]],,QNJ59604,98.5507,4.74606E-40 SIF-HHPRED:  SIF-Syn: High degree of synteny with all phages within subcluster AO1

CDS 30573 - 31163
  /gene="35"
  /product="gp35"
  /function="ssDNA binding protein"
  /locus tag="NathanVaag_35"
    /note=Original Glimmer call @bp 30573 has strength 12.27; Genemark calls start at 30573
    /note=SSC: 30573-31163 CP: yes SCS: both ST: SS BLAST-Start: [ssDNA-binding protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 2.14782E-127 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.268, -4.697746622201849, yes F: ssDNA binding protein SIF-BLAST: ,,[ssDNA-binding protein [Arthrobacter phage Piccoletto] ],,YP_009612414,96.9231,2.14782E-127 SIF-HHPRED: Single-stranded DNA-binding protein; Single strand DNA-binding domain, SSB, RecO, ExoI, RecQ, DnaG, HolC, DNA BINDING PROTEIN; 2.2A {Escherichia coli} SCOP: b.40.4.3,,,4MZ9_A,53.5714,100.0 SIF-Syn: This gene shares synteny with other phages in the AO1 sub cluster such as Piccoletto, King2, Jawnsky, Franzy, Brent, and Beans.

CDS 31408 - 31620
  /gene="36"
  /product="gp36"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="NathanVaag_36"
    /note=Original Glimmer call @bp 31441 has strength 14.84; Genemark calls start at 31408
    /note=SSC: 31408-31620 CP: yes SCS: both-gm ST: SS BLAST-Start: [DNA binding domain protein [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 1.38012E-42 GAP: 244 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.897, -3.449225315764033, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[DNA binding domain protein [Arthrobacter phage Jawnski] ],,YP_009601596,100.0,1.38012E-42 SIF-HHPRED:  SIF-Syn: synteny with other AO1 phages

CDS 31617 - 32165
  /gene="37"
  /product="gp37"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="NathanVaag_37"
    /note=Original Glimmer call @bp 31617 has strength 15.29; Genemark calls start at 31617
    /note=SSC: 31617-32165 CP: yes SCS: both ST: SS BLAST-Start: [HTH DNA binding protein [Arthrobacter phage Beans] ],,NCBI, q1:s1 100.0% 1.97763E-130 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.09, -4.700704706091107, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding protein [Arthrobacter phage Beans] ],,YP_009609978,100.0,1.97763E-130 SIF-HHPRED:  SIF-Syn: closely related to Beans and Piccoletto

I agree VO

CDS 32456 - 33238
  /gene="38"
  /product="gp38"
  /function="hypothetical protein"
  /locus tag="NathanVaag_38"
    /note=Original Glimmer call @bp 32456 has strength 11.52; Genemark calls start at 32456
    /note=SSC: 32456-33238 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDI26_gp38 [Arthrobacter phage Beans] ],,NCBI, q1:s1 100.0% 0.0 GAP: 290 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.028, -3.4906862459040946, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI26_gp38 [Arthrobacter phage Beans] ],,YP_009609979,100.0,0.0 SIF-HHPRED:  SIF-Syn: High synteny with AO1 cluster.
    /note=This is debatable, as most evidence in PhagesDB Blast and NCBI Blast point toward a hypothetical protein, with its function being unknown and information from other sources is debatable. 
    /note=However, function frequency points toward a tape measure protein with high frequency values, so if there was a protein to choose from, it would be that.
    /note=
    /note=Reviewed by TJ.

CDS 33235 - 33768
  /gene="39"
  /product="gp39"
  /function="hypothetical protein"
  /locus tag="NathanVaag_39"
    /note=Original Glimmer call @bp 33235 has strength 1.43
    /note=SSC: 33235-33768 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein FDH48_gp39 [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 6.43967E-106 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.394, -2.253377680616507, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH48_gp39 [Arthrobacter phage Jawnski] ],,YP_009601599,97.1751,6.43967E-106 SIF-HHPRED:  SIF-Syn: Phamerator shows similar gene placement between NathanVaag`s gene 39 and a lot of other AO1 phages such as Beans, Brent, Franzy and Jawnski but none of them have a function assigned.
    /note=Start Determination: The gene mark LORF elected start was not a viable option because the overlap was over 300 bp which goes against the guidelines of annotation majorly. I am choosing the second option because it only overlaps by 4 bp which is in accordance with guidelines. It also has an acceptable Z score and Final Score. There was a gene listed a bit lower with a start codon of TTG, but because that is so rare, I decided against it.
    /note=
    /note=Function: Hypothetical protein, do not have sufficient evidence to classify a function. 
    /note=
    /note=Function Determination: HHPred showed interesting results, the closest relation is actually to us, as Homo sapiens. It shows a 54.8 probability with approx. 30% coverage which is not good support. It is listed in humans as an alpha-helical cell cycle. NCBI Blast showed high similarities to a gene found in Jawnski, another phage from cluster AO1, but there was no function assigned to that one as well.. Phages DB showed the top hit as a tail assembly chaperone but only had a 28% frequency, which I don’t think is conclusive evidence. Conserved Domain Database, Topcons and TmHmm were referenced but showed no supporting evidence. HHPred did not have conclusive results either when checked.
    /note=
    /note=I agree JR

CDS 33677 - 34231
  /gene="40"
  /product="gp40"
  /function="RusA-like resolvase (endonuclease)"
  /locus tag="NathanVaag_40"
    /note=Original Glimmer call @bp 34040 has strength 14.02; Genemark calls start at 33677
    /note=SSC: 33677-34231 CP: yes SCS: both-gm ST: NA BLAST-Start: [resolvase [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 1.68487E-124 GAP: -92 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.106, -4.669046746593814, no F: RusA-like resolvase (endonuclease) SIF-BLAST: ,,[resolvase [Arthrobacter phage Piccoletto] ],,YP_009612419,98.913,1.68487E-124 SIF-HHPRED: Crossover junction endodeoxyribonuclease rusA; Homologous recombination, DNA repair, resolvase, HYDROLASE; 1.2A {Escherichia coli} SCOP: d.79.6.1,,,2H8E_A,66.3043,99.7 SIF-Syn: Has no synteny within its subcluster.

I agree WR
    /note=Very large overlap of 92 bp. No information from starterator. GeneMark start was chosen and does not agree with Glimmer start.
    /note=
    /note=I agree WR
    /note=HHPRED has a e-value of 1e-11 for this function but only 50% coverage. 
    /note=NCBI BLAST an e-value of 1.68e-124 for this function.
    /note=WR

CDS 34276 - 34602
  /gene="41"
  /product="gp41"
  /function="hypothetical protein"
  /locus tag="NathanVaag_41"
    /note=Original Glimmer call @bp 34276 has strength 21.13; Genemark calls start at 34276
    /note=SSC: 34276-34602 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp41 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 1.39844E-66 GAP: 44 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.086, -5.058605177999316, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp41 [Arthrobacter phage Piccoletto] ],,YP_009612420,99.0741,1.39844E-66 SIF-HHPRED:  SIF-Syn: Has synteny with all others within the subcluster except for King2.

I agree WR
    /note=Only good information was from NCBI Blast and phagesdb because of the e-value.
    /note=
    /note=I agree WR
    /note=The NCBI BLAST also has an e-value of 1.4e-66.
    /note=Phages DB BLAST has an e-value of 4e-54.
    /note=WR

CDS 34655 - 34888
  /gene="42"
  /product="gp42"
  /function="hypothetical protein"
  /locus tag="NathanVaag_42"
    /note=Original Glimmer call @bp 34655 has strength 7.14; Genemark calls start at 34655
    /note=SSC: 34655-34888 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp42 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 1.64515E-48 GAP: 52 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.08, -4.719774612079602, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp42 [Arthrobacter phage Piccoletto] ],,YP_009612421,100.0,1.64515E-48 SIF-HHPRED:  SIF-Syn: Piccoletto
    /note=Not sure about coding potential as this start doesn`t capture all of it.
    /note=3/6/22 WS- I agree with the annotation.

CDS 34885 - 35499
  /gene="43"
  /product="gp43"
  /function="hypothetical protein"
  /locus tag="NathanVaag_43"
    /note=Original Glimmer call @bp 34885 has strength 16.89; Genemark calls start at 34885
    /note=SSC: 34885-35499 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH48_gp42 [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 1.56957E-109 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.125, -2.996490344739583, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH48_gp42 [Arthrobacter phage Jawnski] ],,YP_009601602,95.5801,1.56957E-109 SIF-HHPRED:  SIF-Syn: Jawnski
Updated 3/5/2022:
Do not agree with Jawnski. Rather, synteny seems to be shared with phages Beans, Brent, Franzy, and Piccoletto. Not entirely sure. - TS
    /note=Updated 3/5/2022:
    /note=Phagesdb BLAST does not offer the most conclusive line of evidence due to the majority of entries having an unknown function.
    /note=HHPRED does not offer the most conclusive line of evidence due to a high variability in function and extremely high e-values ranging from 20 to 440 for the first ten entries
    /note=NCBI BLAST does not offer the most conclusive line of evidence due to all of the entries being hypothetical proteins
    /note=No supporting evidence from Topcons, the Conserved Domain Database, or TmHmm
    /note=TS

CDS 35496 - 35939
  /gene="44"
  /product="gp44"
  /function="hypothetical protein"
  /locus tag="NathanVaag_44"
    /note=Original Glimmer call @bp 35496 has strength 9.99; Genemark calls start at 35496
    /note=SSC: 35496-35939 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH47_gp44 [Arthrobacter phage Brent] ],,NCBI, q1:s1 100.0% 6.50578E-78 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.224, -4.513216419559024, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH47_gp44 [Arthrobacter phage Brent] ],,YP_009601530,84.0,6.50578E-78 SIF-HHPRED:  SIF-Syn: Shares synteny with phage Beans - TS
    /note=Not sure about possible syntenies between Brent and Franzy
    /note=Updated 3/5/2022:
    /note=Phagesdb BLAST indicates that minor tail protein shows up a number of times with the lowest e-value being 0.008. Worth noting that the associated phages are found within different clusters.
    /note=HHPRED does not offer the most conclusive line of evidence due to a high variability in function and extremely high e-values ranging from 7.4 to 250 for the first ten entries
    /note=NCBI BLAST does not offer the most conclusive line of evidence due to all of the entries being hypothetical proteins
    /note=No supporting evidence from Topcons, the Conserved Domain Database, or TmHmm 
    /note=TS

CDS 35939 - 36430
  /gene="45"
  /product="gp45"
  /function="hypothetical protein"
  /locus tag="NathanVaag_45"
    /note=Original Glimmer call @bp 35939 has strength 13.81; Genemark calls start at 35936
    /note=SSC: 35939-36430 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein FDH47_gp45 [Arthrobacter phage Brent] ],,NCBI, q1:s1 100.0% 2.03717E-89 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.394, -2.7645180226256008, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH47_gp45 [Arthrobacter phage Brent] ],,YP_009601531,86.3905,2.03717E-89 SIF-HHPRED:  SIF-Syn: Other phages in this pham with this gene have no known function, as shown in PECAAN.
    /note=doesn`t have strong enough evidence or consistent shared data to know the function

CDS 36427 - 36678
  /gene="46"
  /product="gp46"
  /function="hypothetical protein"
  /locus tag="NathanVaag_46"
    /note=Original Glimmer call @bp 36427 has strength 8.27; Genemark calls start at 36427
    /note=SSC: 36427-36678 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp46 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 6.2847E-51 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.184, -5.420490675428641, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp46 [Arthrobacter phage Piccoletto] ],,YP_009612425,98.7952,6.2847E-51 SIF-HHPRED:  SIF-Syn: The other genes in this pham have no known function, along with the rest of the genes that are compared on PECAAN
    /note=Phagesdb Function Frequency: no data available
    /note=Phagesdb BLAST: function unknown for all genes
    /note=HHPRED: most genes have low coverage
    /note=NCBI BLAST: All genes are labeled `hypothetical protein`
    /note=Conserved Domain Database: no data available
    /note=Transmembrane Prediction: 1 predicted TMH
    /note=Additional: This gene doesn`t have enough data or shared functions in the pham to know the function

CDS 36675 - 37091
  /gene="47"
  /product="gp47"
  /function="hypothetical protein"
  /locus tag="NathanVaag_47"
    /note=Original Glimmer call @bp 36675 has strength 8.84; Genemark calls start at 36675
    /note=SSC: 36675-37091 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH47_gp47 [Arthrobacter phage Brent] ],,NCBI, q1:s1 92.029% 4.41679E-81 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.423, -4.039645525073382, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH47_gp47 [Arthrobacter phage Brent] ],,YP_009601533,90.2256,4.41679E-81 SIF-HHPRED:  SIF-Syn: Almost all genes in PECAAN have no known function
All genes in pham have no known function
    /note=Phagesdb Function Frequency: only 2 functions shown, and they`re in different phams
    /note=Phagesdb BLAST: Function is unknown for almost all genes
    /note=HHPRED: low coverage and not enough genes share the same function
    /note=NCBI BLAST: all genes are labeled as `hypothetical protein` for their description
    /note=Conserved Domain Database: no data available
    /note=Transmembrane Prediction: 0 predicted TMHs

CDS 37088 - 37384
  /gene="48"
  /product="gp48"
  /function="hypothetical protein"
  /locus tag="NathanVaag_48"
    /note=Original Glimmer call @bp 37088 has strength 8.36; Genemark calls start at 37088
    /note=SSC: 37088-37384 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp48 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 92.8571% 7.97E-58 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.384, -4.468252183926043, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp48 [Arthrobacter phage Piccoletto] ],,YP_009612427,96.7391,7.97E-58 SIF-HHPRED:  SIF-Syn: High degree of synteny of gene 48 with genomes from Beans and Piccoletto of subcluster AO1.
    /note=All appropriately low e-value hits are listed unknown/hypothetical protein matches. There is no evidence to suggest a known function.
    /note=
    /note=
    /note=Edited by Cade Kane
    /note=3/6/22 WS I agree with the annotation.

CDS 37569 - 37871
  /gene="49"
  /product="gp49"
  /function="hypothetical protein"
  /locus tag="NathanVaag_49"
    /note=Original Glimmer call @bp 37569 has strength 22.2; Genemark calls start at 37569
    /note=SSC: 37569-37871 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH47_gp50 [Arthrobacter phage Brent] ],,NCBI, q1:s1 99.0% 1.11364E-30 GAP: 184 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.106, -4.810045260256, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH47_gp50 [Arthrobacter phage Brent] ],,YP_009601536,72.2772,1.11364E-30 SIF-HHPRED:  SIF-Syn: Similar gene placement is found in the phage Jawnski.
    /note=Reviewed by Cade: all evidence listed looks agreeable.

CDS 37875 - 38168
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="NathanVaag_50"
    /note=Original Glimmer call @bp 37875 has strength 15.38; Genemark calls start at 37875
    /note=SSC: 37875-38168 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FRANZY_51 [Arthrobacter phage Franzy]],,NCBI, q1:s1 100.0% 1.42578E-50 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.1, -4.679270584912496, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FRANZY_51 [Arthrobacter phage Franzy]],,ASR78153,87.6289,1.42578E-50 SIF-HHPRED:  SIF-Syn: Phages Jawnski, Franzy, and Brent all display this gene to be of a similar length and location.
    /note=Reviewed by Cade: all listed evidence looks agreeable.

CDS 38223 - 38597
  /gene="51"
  /product="gp51"
  /function="hypothetical protein"
  /locus tag="NathanVaag_51"
    /note=Original Glimmer call @bp 38223 has strength 20.4; Genemark calls start at 38223
    /note=SSC: 38223-38597 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp52 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 8.02824E-81 GAP: 54 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.525, -3.8995386480556817, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp52 [Arthrobacter phage Piccoletto] ],,YP_009612431,100.0,8.02824E-81 SIF-HHPRED:  SIF-Syn: Phages King 2, and Jawnski share a gene with a similar length and location within the genome.
    /note=Reviewed by Cade: all evidence listed looks agreeable.

CDS 38687 - 39637
  /gene="52"
  /product="gp52"
  /function="DNA binding protein"
  /locus tag="NathanVaag_52"
    /note=Original Glimmer call @bp 38687 has strength 18.89; Genemark calls start at 38687
    /note=SSC: 38687-39637 CP: yes SCS: both ST: SS BLAST-Start: [RNA polymerase sigma factor [Arthrobacter phage JKerns]],,NCBI, q1:s1 81.962% 7.5463E-102 GAP: 89 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.022, -4.835658240213919, no F: DNA binding protein SIF-BLAST: ,,[RNA polymerase sigma factor [Arthrobacter phage JKerns]],,QIQ62868,66.3158,7.5463E-102 SIF-HHPRED: DUF4314 ; Domain of unknown function (DUF4314),,,PF14192.9,18.9873,99.6 SIF-Syn: Phamerator: phages Jawnski, King2 both have Synteny with NathanVaag gene 52. 
Reviewed By: CMC
    /note=Compared to genes "JKerns" and "StevieBay"
    /note=SEAPHAGES Functional Assignments sheet states that function "RNA Polmerase Sigma Factor" should be labeled as "DNA binding protein"
    /note=Edited by: DSG
    /note=
    /note=JKerns and StevieBay are not in the same Pham cluster or subcluster as NathanVaag, so it`s not sufficient enough evidence to determine DNA binding protein as evidence. Jawnski and King2 are from the same subcluster and on Phamerator, the Gene 52 looks identical to NathanVaag. There is more supporting evidence to determine NKF as the correct function. 
    /note=Phagesdb BLAST: unknown function for all hits, Piccoletto, Beans, Brent, Franzy from same cluster and subcluster, low e value 1e-180
    /note=PhagesDB Function Frequency: integrase, high frequency of 64% in A1, limited hits
    /note=NCBI Blast: 98% identity 99% alignment 100% coverage, evalue of 0 with 0 gaps for unknown function
    /note=HHPRED: unknown function, high probability (99.6%) and 18% coverage with the smallest e-value of all the hits
    /note=CDD: No data available
    /note=TmHmm: 0 predicted TMHs, .03100 probability
    /note=Reviewed By: CMC
    /note=
    /note=Changed to function of "DNA binding protein"
    /note=Reviewed By: class

CDS 39634 - 39903
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="NathanVaag_53"
    /note=Original Glimmer call @bp 39634 has strength 19.77; Genemark calls start at 39634
    /note=SSC: 39634-39903 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp54 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 6.62153E-56 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.437, -5.996567512266903, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp54 [Arthrobacter phage Piccoletto] ],,YP_009612433,98.8764,6.62153E-56 SIF-HHPRED:  SIF-Syn: Phmerator: Synteny with King, Jawnski
Reviewed By: CMC
    /note=Compared with Piccoletto and Beans
    /note=Edited by: DSG
    /note=
    /note=PhagesDB Function Frequency: one hit, helix-turn-helix dna binding domain from subcluster J, 100% frequency, very high
    /note=PhagesDB Blast: unknown function for cluster AO1
    /note=HHPRED: top hit description “human homo sapiens,” req further examination; possible immunity or binding domain, all with low scores in 50% range
    /note=NCBI Blast: Hypothetical protein, high evidence values of 90-100% for multiple phages in the cluster
    /note=CDD: no data available
    /note=TmHmm: 0 TMHs, 0.44740% probability
    /note=Reviewed By: CMC

CDS 39900 - 40184
  /gene="54"
  /product="gp54"
  /function="hypothetical protein"
  /locus tag="NathanVaag_54"
    /note=Original Glimmer call @bp 39900 has strength 13.33; Genemark calls start at 39900
    /note=SSC: 39900-40184 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp55 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 1.31524E-60 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.166, -4.611371280732909, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp55 [Arthrobacter phage Piccoletto] ],,YP_009612434,98.9362,1.31524E-60 SIF-HHPRED:  SIF-Syn: Phamerator: Synteny with King, Jawnski
Reviewed by: CMC
    /note=Compared with Piccoletto and Beans
    /note=Edited by: DSG
    /note=
    /note=PhagesDB Function Frequency: helix-turn-helix dna binding domain from subcluster DN1, 100% frequency, very high, req further examination
    /note=PhagesDB Blast: multiple hits, all unknown function
    /note=HHPRED: top hit Ribulose 1,5-bisphosphate carboxylase-oxygenase, evidence not high at all, req further examination
    /note=NCBI Blast: hypothetical protein, high evidence 98% identity and alignment, 100% coverage
    /note=CDD: No data available
    /note=TmHmm: 0 TMHs,   0.57608% probability
    /note=Reviewed By: CMC

CDS 40184 - 40396
  /gene="55"
  /product="gp55"
  /function="hypothetical protein"
  /locus tag="NathanVaag_55"
    /note=Original Glimmer call @bp 40184 has strength 0.78
    /note=SSC: 40184-40396 CP: no SCS: glimmer ST: NA BLAST-Start: [hypothetical protein FDI26_gp56 [Arthrobacter phage Beans] ],,NCBI, q1:s1 100.0% 4.97305E-43 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.731, -5.473777327388708, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI26_gp56 [Arthrobacter phage Beans] ],,YP_009609997,100.0,4.97305E-43 SIF-HHPRED:  SIF-Syn: There is no function for this protein throughout the whole pham.
    /note=This gene should not be included. There is no potential coding between any of the start locations to the stop on GeneMark. Even with only a small spike of coding potential this gene would have to be in the reverse direction which phamerator doesn`t show for this genes in any of the other phages in cluster AO1.  Staterator shows this is the only gene with start 4 with only 1 MA.
    /note=
    /note=I disagree. I believe this a gene after the class discussion. Although there is very little coding potential in GeneMark, all the other evidence heavily supports this as a gene. In Starterator, those with start 5 are in the same cluster as NathanVaag and has its sites approved, despite it not having the most annotated start. Removing this gene would also make a big gap since the length is in the right range. Z-score and final score may not be the best. But it`s still in a good standing unlike start 40268. I`m calling synteny with Piccoletto and Beans with a NKF function. Under NCBI, it has really nice and the highest values in all categories. Values also match under phagesdb BLAST. (SS)

CDS 40427 - 40744
  /gene="56"
  /product="gp56"
  /function="hypothetical protein"
  /locus tag="NathanVaag_56"
    /note=Original Glimmer call @bp 40427 has strength 22.61; Genemark calls start at 40442
    /note=SSC: 40427-40744 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein FDI41_gp57 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 2.59914E-64 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.304, -4.354778061539587, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp57 [Arthrobacter phage Piccoletto] ],,YP_009612436,95.2381,2.59914E-64 SIF-HHPRED:  SIF-Syn: All phages in this pham have the same function for this gene.
    /note=PhagesDB BLAST shows  an e-value of 2e-53. 
    /note=NCBI BLAST has  an e-value of 2.6e-64 for a hypothetical protein.
    /note=HHPRED has no good e-values.
    /note=
    /note=I agree with function, but not with the evidence to prove it. Synteny should be only with Piccoletto and not all phages. Under NCBI BLAST, it has the best values in all categories even if the rest of the phages have high values in all categories. Plus, the other phages are not in the same cluster as NathanVaag. Piccoletto is. (SS)

CDS 40737 - 40940
  /gene="57"
  /product="gp57"
  /function="hypothetical protein"
  /locus tag="NathanVaag_57"
    /note=Original Glimmer call @bp 40737 has strength 17.63; Genemark calls start at 40737
    /note=SSC: 40737-40940 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp58 [Arthrobacter phage Piccoletto] ],,NCBI, q6:s3 92.5373% 2.36969E-35 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.204, -4.473102278738214, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp58 [Arthrobacter phage Piccoletto] ],,YP_009612437,96.875,2.36969E-35 SIF-HHPRED:  SIF-Syn: Possible synteny with Piccoletto

CDS 40937 - 41287
  /gene="58"
  /product="gp58"
  /function="hypothetical protein"
  /locus tag="NathanVaag_58"
    /note=Original Glimmer call @bp 40937 has strength 22.26; Genemark calls start at 40937
    /note=SSC: 40937-41287 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI26_gp59 [Arthrobacter phage Beans] ],,NCBI, q1:s1 100.0% 4.71453E-57 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.69, -3.5707972674952195, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI26_gp59 [Arthrobacter phage Beans] ],,YP_009610000,84.3478,4.71453E-57 SIF-HHPRED:  SIF-Syn: The entire cluster AO1 and pham 55196 shows synteny for this function and start site.
    /note=PhagesDB BLAST shows an e-value of 2e-44.
    /note=NCBI BLAST shows that for a hypothetical protein theres an e-value of 4.7e-57. 
    /note=HHPRED doesn`t show any solid e-values.

CDS 41287 - 41445
  /gene="59"
  /product="gp59"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="NathanVaag_59"
    /note=Original Glimmer call @bp 41287 has strength 15.24; Genemark calls start at 41287
    /note=SSC: 41287-41445 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI26_gp60 [Arthrobacter phage Beans] ],,NCBI, q1:s1 100.0% 3.00041E-29 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.411, -4.413617268040186, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein FDI26_gp60 [Arthrobacter phage Beans] ],,YP_009610001,100.0,3.00041E-29 SIF-HHPRED:  SIF-Syn: This gene shows synteny with Picolletto and other phages in the AO1 subcluster.
    /note=This start position was chosen because the gene mark ORF elected start. It has an overlap of 1 bp which is reasonable as a little overlap is allowable under guidelines. The other two gene options are both extremely short overall, in total length, sitting at 72 bp and 12 bp respectively. Because of the length alone, I believe the first option is the only viable option as the majority protein coding genes are minimum 120 bp.
    /note=
    /note=Phagesdb Function Frequency shows the highest frequency at 55% for helix-turn-helix dna binding domain. Phagesdb Blast also has a top hit of helix-turn-helix dna binding domain protein, with Beans, another phage from AO1. NCBI BLAST had the most conclusive results, it showed that Beans has the identical gene with 100%  alignment and identity. This gene is characterized as a helix-turn-helix dna binding domain protein. 
    /note=
    /note=Conserved Domain Database, Topcons and TmHmm were referenced but showed no supporting evidence. HHPred did not have conclusive results either when checked.
    /note=
    /note=Gene is quite short but it was discussed in class and aligns with all other guidelines, so it is acceptable. at 2022-03-08T03:49:29

CDS 41450 - 41578
  /gene="60"
  /product="gp60"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="NathanVaag_60"
    /note=Original Glimmer call @bp 41450 has strength 16.25; Genemark calls start at 41450
    /note=SSC: 41450-41578 CP: yes SCS: both ST: SS BLAST-Start: [HTH DNA binding protein [Arthrobacter phage Beans] ],,NCBI, q1:s1 100.0% 1.90299E-20 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.649, -6.879698257837498, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding protein [Arthrobacter phage Beans] ],,YP_009610002,100.0,1.90299E-20 SIF-HHPRED:  SIF-Syn: Piccoletto_61
    /note=Phages "Beans" and "Picoletto" have same e-value, cluster, score, and sequence length as NathanVaag.

CDS 41571 - 42545
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="NathanVaag_61"
    /note=Original Glimmer call @bp 41571 has strength 12.03; Genemark calls start at 41571
    /note=SSC: 41571-42545 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH48_gp60 [Arthrobacter phage Jawnski] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.597, -5.739960239116061, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH48_gp60 [Arthrobacter phage Jawnski] ],,YP_009601620,94.2675,0.0 SIF-HHPRED:  SIF-Syn: This gene shows synteny with picolletto and other phages in the AO1 sub cluster
    /note=This start position was chosen and is the LORF  the gene mark ORF elected start. It has an overlap of 8 bp which is reasonable, under annotation guidelines.  The second option listed is also a potential start site, but I chose the first because it is the LORF and it has a slightly lower Z-Score. 
    /note=
    /note=Function: hypothetical protein, not enough evidence to determine. 
    /note=
    /note=Function Determination: Phagesdb Function Frequency top hit was for a minor tail protein, with a 22% frequency which is not conclusive. Phagesdb BLAST showed many other phages within AO1 that had very similar genes but not exact. HHPred did not show conclusive results, because of very low coverage percentages. NCBI BLAST showed high similarities with other phages within AO1 but did not have an assigned function. I don’t think I have enough evidence to determine and assign a function for gene 61 currently.
    /note=
    /note=This gene has not gone through the class review yet. MFP 20220307 5:50PM HST

CDS 42538 - 42939
  /gene="62"
  /product="gp62"
  /function="hypothetical protein"
  /locus tag="NathanVaag_62"
    /note=Original Glimmer call @bp 42538 has strength 13.42; Genemark calls start at 42538
    /note=SSC: 42538-42939 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp63 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 3.80476E-95 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.148, -3.2535385006449706, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp63 [Arthrobacter phage Piccoletto] ],,YP_009612442,100.0,3.80476E-95 SIF-HHPRED:  SIF-Syn: PICCOLETTO_63

CDS 42936 - 43565
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="NathanVaag_63"
    /note=Original Glimmer call @bp 42936 has strength 18.41; Genemark calls start at 42936
    /note=SSC: 42936-43565 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp64 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 2.54685E-145 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.268, -4.408951082954879, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp64 [Arthrobacter phage Piccoletto] ],,YP_009612443,97.6077,2.54685E-145 SIF-HHPRED:  SIF-Syn: PICCOLETTO_64

CDS 43684 - 44301
  /gene="64"
  /product="gp64"
  /function="hypothetical protein"
  /locus tag="NathanVaag_64"
    /note=Original Glimmer call @bp 43684 has strength 13.93; Genemark calls start at 43675
    /note=SSC: 43684-44301 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein FDI41_gp65 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s9 100.0% 2.50899E-142 GAP: 118 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.711, -4.2951664350100875, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp65 [Arthrobacter phage Piccoletto] ],,YP_009612444,96.2441,2.50899E-142 SIF-HHPRED:  SIF-Syn: High degrees of synteny within the same sub cluster, AO1.
    /note=All hits in BLAST databases call with suitably low e-values call for an unknown function or hypothetical protein.
    /note=
    /note=Edited by Kirsten Kasal

CDS 44298 - 44876
  /gene="65"
  /product="gp65"
  /function="DNA Binding Protein"
  /locus tag="NathanVaag_65"
    /note=Original Glimmer call @bp 44298 has strength 20.56; Genemark calls start at 44298
    /note=SSC: 44298-44876 CP: yes SCS: both ST: SS BLAST-Start: [DNA binding protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 1.79194E-134 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.166, -4.629100047693341, no F: DNA Binding Protein SIF-BLAST: ,,[DNA binding protein [Arthrobacter phage Piccoletto] ],,YP_009612445,98.9583,1.79194E-134 SIF-HHPRED:  SIF-Syn: High degrees of synteny with all phages within the same subcluster, AO1.
    /note=BLAST database hits with the best e-values call for a DNA binding protein. 
    /note=
    /note=Edited by Kirsten Kasal

CDS 44877 - 45104
  /gene="66"
  /product="gp66"
  /function="hypothetical protein"
  /locus tag="NathanVaag_66"
    /note=Original Glimmer call @bp 44877 has strength 8.99; Genemark calls start at 44877
    /note=SSC: 44877-45104 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp67 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 2.05005E-48 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.68, -3.529988066030215, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp67 [Arthrobacter phage Piccoletto] ],,YP_009612446,100.0,2.05005E-48 SIF-HHPRED:  SIF-Syn: Piccoletto has the same sequence length, score, and e- value as NathanVaag and also has NKF listed as its function for the same gene.
    /note=other similar phages in this Pham (Piccoletto, Beans, Brent, Jawnsky) all have NKF listed as their function for this gene.

CDS 45107 - 45346
  /gene="67"
  /product="gp67"
  /function="hypothetical protein"
  /locus tag="NathanVaag_67"
    /note=Original Glimmer call @bp 45107 has strength 21.24; Genemark calls start at 45107
    /note=SSC: 45107-45346 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein FDH47_gp68 [Arthrobacter phage Brent] ],,NCBI, q1:s1 98.7342% 3.05346E-44 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.774, -3.6929813131220834, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH47_gp68 [Arthrobacter phage Brent] ],,YP_009601554,93.6709,3.05346E-44 SIF-HHPRED:  SIF-Syn: Has synteny within its subcluster.
    /note=The start is not the best numbers but the best has a TTG start.

CDS complement (45487 - 45795)
  /gene="68"
  /product="gp68"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="NathanVaag_68"
    /note=Original Glimmer call @bp 45795 has strength 8.57; Genemark calls start at 45795
    /note=SSC: 45795-45487 CP: yes SCS: both ST: SS BLAST-Start: [HTH DNA binding protein [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 1.24366E-68 GAP: 41 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.823, -5.309117108752867, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding protein [Arthrobacter phage Piccoletto] ],,YP_009612448,100.0,1.24366E-68 SIF-HHPRED:  SIF-Syn: It does have good synteny within the subcluster.
    /note=Does not have the best scores.

CDS complement (45837 - 47108)
  /gene="69"
  /product="gp69"
  /function="DNA polymerase III sliding clamp (Beta)"
  /locus tag="NathanVaag_69"
    /note=Original Glimmer call @bp 47108 has strength 19.67; Genemark calls start at 47108
    /note=SSC: 47108-45837 CP: no SCS: both ST: SS BLAST-Start: [DNA polymerase III subunit beta [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 0.0 GAP: 81 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.304, -4.4157344874810125, yes F: DNA polymerase III sliding clamp (Beta) SIF-BLAST: ,,[DNA polymerase III subunit beta [Arthrobacter phage Piccoletto] ],,YP_009612449,99.2908,0.0 SIF-HHPRED: DNA polymerase III, beta subunit; DNA clamp, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, TRANSFERASE; HET: ACT, MSE, EDO, PGR; 2.26A {Eubacterium rectale},,,3T0P_A,96.2175,100.0 SIF-Syn: Shares location with phages Jawnski and Beans

CDS complement (47190 - 47834)
  /gene="70"
  /product="gp70"
  /function="hypothetical protein"
  /locus tag="NathanVaag_70"
    /note=Original Glimmer call @bp 47834 has strength 17.12; Genemark calls start at 47834
    /note=SSC: 47834-47190 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI41_gp71 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 5.01984E-153 GAP: 70 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.268, -4.34663776219455, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp71 [Arthrobacter phage Piccoletto] ],,YP_009612450,100.0,5.01984E-153 SIF-HHPRED:  SIF-Syn: Shares synteny with phages Jawnski and Beans
    /note=Phagesdb BLAST does not offer the most conclusive line of evidence due to the majority of entries having an unknown function. Although the tape measure protein appears most frequently, the associated e-values are relatively large, ranging from 0.19 to 2.1
    /note=HHPRED does not offer the most conclusive line of evidence due to the presence of relatively high e-values, variety of possible functions, and low probabilities and coverages
    /note=NCBI BLAST does not offer the most conclusive line of evidence due to the majority of entries being hypothetical proteins
    /note=No supporting evidence from Topcons, the Conserved Domain Database, or TmHmm

CDS complement (47905 - 48120)
  /gene="71"
  /product="gp71"
  /function="hypothetical protein"
  /locus tag="NathanVaag_71"
    /note=Original Glimmer call @bp 48120 has strength 17.24; Genemark calls start at 48150
    /note=SSC: 48120-47905 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein FDI41_gp72 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s11 100.0% 3.73461E-45 GAP: 137 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.268, -4.34663776219455, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp72 [Arthrobacter phage Piccoletto] ],,YP_009612451,87.6543,3.73461E-45 SIF-HHPRED:  SIF-Syn: Shares synteny with phage Jawnski
    /note=No information for function frequency displayed
    /note=Phagesdb BLAST does not offer the most conclusive line of evidence due to all entries having an unknown function
    /note=HHPRED does not offer the most conclusive line of evidence due to the presence of high e-values and variety of possible functions with overall low coverage
    /note=NCBI BLAST does not offer the most conclusive line of evidence due to all entries being hypothetical proteins
    /note=No supporting evidence from Topcons, the Conserved Domain Database, or TmHmm (TMH number of 0 and probability of 0.47376)

CDS complement (48258 - 49262)
  /gene="72"
  /product="gp72"
  /function="hypothetical protein"
  /locus tag="NathanVaag_72"
    /note=Original Glimmer call @bp 49325 has strength 18.12; Genemark calls start at 49262
    /note=SSC: 49262-48258 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein FDI41_gp73 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s22 100.0% 0.0 GAP: 84 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.731, -5.553158935637373, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp73 [Arthrobacter phage Piccoletto] ],,YP_009612452,94.0845,0.0 SIF-HHPRED: DUF932 ; Domain of unknown function (DUF932),,,PF06067.14,63.7725,99.9 SIF-Syn: Closely related to Piccoletto and Beans in Starterator

CDS complement (49347 - 49568)
  /gene="73"
  /product="gp73"
  /function="hypothetical protein"
  /locus tag="NathanVaag_73"
    /note=Original Glimmer call @bp 49568 has strength 7.94
    /note=SSC: 49568-49347 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein FDI41_gp74 [Arthrobacter phage Piccoletto] ],,NCBI, q1:s1 100.0% 4.54917E-44 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.394, -6.733262232980597, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI41_gp74 [Arthrobacter phage Piccoletto] ],,YP_009612453,98.6301,4.54917E-44 SIF-HHPRED:  SIF-Syn: This gene shares synteny with Piccoletto, King2, Jawnsky, Franzy, Brent and Beans.
    /note=The only databases that showed a low e-values were Phagesdb BLAST and NCBI BLAST for a unknown function or hypothetical protein. ZK