CDS 70 - 285
  /gene="1"
  /product="gp1"
  /function="Hypothetical Protein"
  /locus tag="Benllo_1"
    /note=Original Glimmer call @bp 70 has strength 6.27; Genemark calls start at 70
    /note=SSC: 70-285 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp01 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 9.15196E-45 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.745, -4.170102567841746, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp01 [Arthrobacter phage Circum] ],,YP_009603090,100.0,9.15196E-45 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 70
    /note=Region encompasses all coding potential
    /note=Multiple phages with this gene have high alignment, such as Arcadia and BenitoAntonio with e-values of 2e-35. There is no significant overlap with other genes
    /note=
    /note=Start site data:
    /note=Start 12, which has the start site 70, was found in 34 of 34 genes in the pham, with 24 MA`s.
    /note=This is the longest ORF without significant overlap
    /note=The start site 70 has a z-score of 2.745 and a final score of -4.170 which is the best score for this ORF
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this function to be a hypothetical protein with function unknown.

CDS 736 - 1083
  /gene="2"
  /product="gp2"
  /function="Hypothetical Protein"
  /locus tag="Benllo_2"
    /note=Original Glimmer call @bp 736 has strength 5.26; Genemark calls start at 736
    /note=SSC: 736-1083 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp03 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 1.03325E-76 GAP: 450 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.872, -3.4367891292046218, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp03 [Arthrobacter phage Mudcat] ],,YP_009300692,100.0,1.03325E-76 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer and GeneMark both call start at 736
    /note=Region encompasses all coding potential
    /note=Multiple phages with this gene have high alignment, such as Arcadia and BenitoAntonio with e-values of 1e-58. The is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 736 corresponds to the start number 31, which is found in 21 of 211 genes in the pham, with 19 MA`s. This is not the longest ORF. However, the start codon is ATG, whereas the longest ORF is GTG. 
    /note=The start site 736 has a z-score of 2.872 and a final score of -3.437 which is the best score for this ORF
    /note=
    /note=Evidence for a function: 
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with function unknown.

CDS 1076 - 1483
  /gene="3"
  /product="gp3"
  /function="HNH endonuclease"
  /locus tag="Benllo_3"
    /note=Original Glimmer call @bp 1076 has strength 6.93; Genemark calls start at 1076
    /note=SSC: 1076-1483 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Arthrobacter phage Tribby] ],,NCBI, q1:s1 100.0% 1.40679E-96 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.562, -5.78257814227218, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage Tribby] ],,YP_010666089,100.0,1.40679E-96 SIF-HHPRED: HNH endonuclease; Thermophilic bacteriophage, HNH Endonuclease, DNA nicking, HYDROLASE; 1.52A {Geobacillus virus E2},,,5H0M_A,59.2593,96.9 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 1076.
    /note=Region encompasses all coding potential.
    /note=Multiple phages with this gene have high alignment, such as Arcadia and BenitoAntonio with e-values of 2e-77. There is no significant overlap with other genes. 
    /note=
    /note=Start site data:
    /note=Start site at 1076 corresponds to the most commonly called start number. Starterator supports start site 1076. This predicted start is the longest ORF without significant overlap
    /note=In both phagesdb and NCBI blast, the start site matches 1:1 with genes in several phages in the pham.
    /note=
    /note=Evidence for a function
    /note=All similar phages in NCBI BLAST call this gene a “HNH endonuclease." All annotated phages on PhagesDB BLAST call this gene “HNH endonuclease." HHPRED aligns to “HNH endonuclease; Thermophilic bacteriophage, HNH Endonuclease, DNA nicking, HYDROLASE; 1.52A {Geobacillus virus E2}” with a probability of 96.9% and an e-value of 0.000023.

CDS 1506 - 2432
  /gene="4"
  /product="gp4"
  /function="endolysin"
  /locus tag="Benllo_4"
    /note=Original Glimmer call @bp 1506 has strength 7.1; Genemark calls start at 1506
    /note=SSC: 1506-2432 CP: yes SCS: both ST: SS BLAST-Start: [endolysin [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 0.0 GAP: 22 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.446, -2.45827804503836, yes F: endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Circum] ],,YP_009603094,100.0,0.0 SIF-HHPRED: b.84.3.2 (A:) Peptidoglycan hydrolase LytM {Staphylococcus aureus [TaxId: 1280]},,,d1qwya_,51.9481,99.3 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 1506
    /note=Region encompasses all coding potential.
    /note=Aligns with other phages, Arcadia and BenitoAntontio with e-value of 0. This start site is the longest ORF. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 1506 corresponds to the most commonly called start number 1. Starterator supports start site 1506. In both PhagesDB and NCBI BLAST, the start site matches 1:1 with genes in several phages in the pham.
    /note=
    /note=Evidence for a function
    /note=Most similar phages in NCBI BLAST call this gene “endolysin." All annotated phages on PhagesDB BLAST call this gene “endolysin." The Conserved Domain Database calls this gene “endopeptidase”. 
    /note=HHPRED aligns to “b.84.3.2 (A:) Peptidoglycan hydrolase LytM {Staphylococcus aureus [TaxId: 1280]}” with a probability of 99.1% and an e-value of 7.9e-16.

CDS 2458 - 2826
  /gene="5"
  /product="gp5"
  /function="Hypothetical Protein"
  /locus tag="Benllo_5"
    /note=Original Glimmer call @bp 2458 has strength 10.08; Genemark calls start at 2458
    /note=SSC: 2458-2826 CP: yes SCS: both ST: SS BLAST-Start: [virion structural protein [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 2.14095E-84 GAP: 25 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.931, -3.7960205838585104, yes F: Hypothetical Protein SIF-BLAST: ,,[virion structural protein [Arthrobacter phage Circum] ],,YP_009603095,99.1803,2.14095E-84 SIF-HHPRED: Gp6; 13-membered ring, VIRAL PROTEIN; HET: MPD, MSE; 2.1A {Enterobacteria phage HK97},,,3JVO_E,73.7705,95.7 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start site at 2458
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Circum with e-values of 5e-66. This start site is the longest ORF. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site at 2458 corresponds to the most commonly called start number 14, which is called in 45 of the 178 non-draft genes in the pham. The start site at 2458 has a z-score of 2.931 and a final score of -3.796 which is the best score for this ORF
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this function to be a hypothetical protein with function unknown.

CDS 2819 - 3826
  /gene="6"
  /product="gp6"
  /function="Hypothetical Protein"
  /locus tag="Benllo_6"
    /note=Original Glimmer call @bp 2819 has strength 5.93; Genemark calls start at 2819
    /note=SSC: 2819-3826 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB74_gp07 [Arthrobacter phage Arcadia] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.017, -2.8564937087383147, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB74_gp07 [Arthrobacter phage Arcadia] ],,YP_010665995,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call a start site at 2819.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Arcadia and Dynamite with an e-value of zero. This start site is the longest ORF. No significant overlap with other genes.
    /note= 
    /note=Start site data: 
    /note=The start site was found in 20/20 of the genes in pham. Start site 2819 corresponds to start site 1 which is found in 18/18 phages in the pham and has 18 MA’s. 
    /note=The start site has a z score of 3.017 and a final score of -2.856 which is the best score for this ORF. 
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with function unknown.

CDS 3847 - 5601
  /gene="7"
  /product="gp7"
  /function="terminase"
  /locus tag="Benllo_7"
    /note=Original Glimmer call @bp 3940 has strength 6.05; Genemark calls start at 3847
    /note=SSC: 3847-5601 CP: yes SCS: both-gm ST: SS BLAST-Start: [terminase [Arthrobacter phage BenitoAntonio]],,NCBI, q1:s3 100.0% 0.0 GAP: 20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.435, -2.0949393225970705, yes F: terminase SIF-BLAST: ,,[terminase [Arthrobacter phage BenitoAntonio]],,UYL87271,99.6587,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,90.5822,100.0 SIF-Syn: 
    /note=Evidence for a gene
    /note=Glimmer calls a start site of 3940 and GeneMark calls a start site of 3847.
    /note=Both start sites contain coding potential. Multiple phages with this gene have high alignment such as Arcadia and BenitoAntonio with an e-value of 0. There is no significant overlap with other genes. 
    /note=
    /note=Start site data:
    /note=Start site 16 which has a start at 3940 was found in 118/178 of genes in pham with no MA’s of this start.
    /note=Start site 3847 has the longest ORF. 
    /note=In NCBI Blast, the gene shows 100% identity with phages Arcadia and BenitoAntonio with a e value of 0.
    /note=Start site 3847 has a z-score of 3.435 and a final score of -2.095 which is a better score than the start site 3940. This data supports the predicted start site of 3847
    /note=
    /note=Evidence for a function: 
    /note=PhagesDB and NCBI BLAST call this gene to be a terminase with e-values of 0 and 1.6e-42 respectively.
    /note=HHpred aligns Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria; with a probability of 100 and an evalue of 1.3e-42.

CDS 5610 - 6119
  /gene="8"
  /product="gp8"
  /function="Hypothetical Protein"
  /locus tag="Benllo_8"
    /note=Original Glimmer call @bp 5610 has strength 11.63; Genemark calls start at 5610
    /note=SSC: 5610-6119 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp09 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 1.06717E-118 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.409, -4.0962544390943965, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp09 [Arthrobacter phage Mudcat] ],,YP_009300698,100.0,1.06717E-118 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call a start site at 5610.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Arcadia and BenitoAntonio with an e value of  3e-91. This start site is the longest ORF. There is no significant overlap with other genes.
    /note=
    /note=Start site data: 
    /note=The start site 5610 (start site 2) was found in 20/115 of genes in pham. MA’s of this start were 18/96.
    /note=In NCBI Blast, the gene shows 100% identity with phage Mudcat with an evalue of 1e-118 and 99% identity with Arcadia with an e value of 2e-118. The start site has a z-score of 2.409 and a final score of -4.096.
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 6134 - 7444
  /gene="9"
  /product="gp9"
  /function="portal protein"
  /locus tag="Benllo_9"
    /note=Original Glimmer call @bp 6134 has strength 9.95; Genemark calls start at 6134
    /note=SSC: 6134-7444 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 0.0 GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.435, -2.0162541296952132, yes F: portal protein SIF-BLAST: ,,[portal protein [Arthrobacter phage Mudcat] ],,YP_009300699,100.0,0.0 SIF-HHPRED: Portal protein; Prohead I, icosahedral symmetry, HK97, phage, capsid, VIRUS; 3.6A {Escherichia phage HK97},,,8FQL_D,82.1101,100.0 SIF-Syn: 
    /note=Evidence for a gene
    /note=Both Glimmer and GeneMark call start site at 6134.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Arcadia and BenitoAntonio with an e value of 0. Start site is the longest ORF. There is no significant overlap with other genes.
    /note=
    /note=Start site data: 
    /note=Start site 5 was found in 152/178 genes in pham. MA’s of this start were 103/146. 
    /note=In NCBI Blast, the gene shows 100% identity with phage Mudcat with an evalue of 1e-118 and 99% identity with Arcadia with an e value of 2e-118. The start site has a z-score of 3.435 and a final score of -2.016.
    /note=
    /note=Evidence for a function
    /note=All similar phages in NCBI blast call this gene “portal protein” mudcat and Arcadia call this “portal protein” with e values of 0. All similar phages on PhagesDB BLAST call this “portal protein.” 
    /note=HHpred aligns portal protein HK97 with a probability of 100 and an evalue of 8.9e-39.

CDS 7441 - 8052
  /gene="10"
  /product="gp10"
  /function="Hypothetical Protein"
  /locus tag="Benllo_10"
    /note=Original Glimmer call @bp 7441 has strength 10.42; Genemark calls start at 7441
    /note=SSC: 7441-8052 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp11 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 4.13974E-143 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.113, -2.66371296573402, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp11 [Arthrobacter phage Mudcat] ],,YP_009300700,99.5074,4.13974E-143 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and Genemark call start site at 7441.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Arcadia and BenitoAntonio with an e value of 1e-111. This start site is the longest ORF. There is no significant overlap with other genes.
    /note=
    /note=Start site data: 
    /note=Start site 9 found 29/44 genes in pham. MA’s of this start were 22/33.
    /note=In NCBI Blast, the gene shows 99% identity with phage Mudcat with an evalue of 4e-143 and 99% identity with Hankly with an e value of 1e-142. The start site has a z-score of 3.113, and a final score of -2.664. 
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with unknown function.

CDS 8036 - 10009
  /gene="11"
  /product="gp11"
  /function="major capsid and protease fusion protein"
  /locus tag="Benllo_11"
    /note=Original Glimmer call @bp 8036 has strength 4.94; Genemark calls start at 8036
    /note=SSC: 8036-10009 CP: yes SCS: both ST: SS BLAST-Start: [head maturation protease [Arthrobacter phage JEGGS] ],,NCBI, q1:s1 100.0% 0.0 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.091, -3.5527928455068705, no F: major capsid and protease fusion protein SIF-BLAST: ,,[head maturation protease [Arthrobacter phage JEGGS] ],,YP_010666591,99.8478,0.0 SIF-HHPRED: d.183.1.1 (A:104-383) Major capsid protein gp5 {Bacteriophage HK97 [TaxId: 37554]},,,d2ft1a1,50.2283,99.9 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start site at 8036.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as JEGGS and Correa with an e value of 0. Start site is the longest ORF. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 9 was found in 173/178 of genes in pham. MA’s of this start are 143/146.
    /note=In NCBI Blast, the gene shows 99% identity with multiple phages, two of which being JEGGS and Correa with an evalue of 0. The start site has a z score of 3.091 and a final score of -3.553
    /note=
    /note=Evidence for a function
    /note=All similar phages in NCBI blast call this gene “head maturation protease” Jeggs and Correa call this “head maturation protease” with e values of 0. All similar phages on PhagesDB BLAST call this “major capsid and protease fusion protein." HHpred aligns with L_lactis_ph-MCP ; Lactococcus lactis bacteriophage major capsid protein with a probability of 99.94 and an evalue of 3e-25 .

CDS 10029 - 10364
  /gene="12"
  /product="gp12"
  /function="Hypothetical Protein"
  /locus tag="Benllo_12"
    /note=Original Glimmer call @bp 10029 has strength 5.65; Genemark calls start at 10029
    /note=SSC: 10029-10364 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp13 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 1.22913E-73 GAP: 19 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.901, -5.389187297999249, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp13 [Arthrobacter phage Mudcat] ],,YP_009300702,100.0,1.22913E-73 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark support a start site at 10029.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Arcadia and BenitoAntonio with an e value of 1e-60. Start site is longest ORF. There is no significant overlap with other genes.
    /note=
    /note=Start site data
    /note=Start site 1 was found in 152/176 of genes in pham. MA’s of this start were 120/145. 
    /note=In NCBI Blast, the gene shows 100% identity with Mudcat, with an e-value of 1e-73 and 99% identity with Kardesai with an e-value of 4e-73. The start site has a z score of 1.901 and a final score of -5.389
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with unknown function.

CDS 10339 - 10641
  /gene="13"
  /product="gp13"
  /function="Hypothetical Protein"
  /locus tag="Benllo_13"
    /note=Original Glimmer call @bp 10339 has strength 4.33; Genemark calls start at 10423
    /note=SSC: 10339-10641 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein BI184_gp14 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 1.5459E-67 GAP: -26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.602, -3.628472733356124, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp14 [Arthrobacter phage Mudcat] ],,YP_009300703,100.0,1.5459E-67 SIF-HHPRED: DUF806 ; Protein of unknown function (DUF806),,,PF05657.14,95.0,98.8 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls start site of 10339 and GeneMark calls start site of 10423.
    /note=Both regions encompass all coding potential. Multiple phages with this gene have high alignment such as Arcadia and BenitoAntonio with an e value of 2e-54. There is no significant overlap with other genes.
    /note=
    /note=Start site data
    /note=Start site 17 was found in 179/212 of genes in pham. MA’s of this start are 133/170. In NCBI Blast, the gene shows 99% identity with Mudcat, with an e-value of 2e-67 and 98% identity with KeaneyLin with an e-value of 5e-67. The start site 10339 has the longest ORF, a z score of 2.602 and a final score of -3.628.
    /note=This data supports the predicted start site of 10339
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with unknown function.

CDS 10654 - 11520
  /gene="14"
  /product="gp14"
  /function="major tail protein"
  /locus tag="Benllo_14"
    /note=Original Glimmer call @bp 10654 has strength 6.61; Genemark calls start at 10654
    /note=SSC: 10654-11520 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Arthrobacter phage Cheesy] ],,NCBI, q1:s1 100.0% 0.0 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.031, -2.7653702713535186, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage Cheesy] ],,YP_010666202,99.3056,0.0 SIF-HHPRED: Phage_TTP_1 ; Phage tail tube protein,,,PF04630.15,64.9306,99.8 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start site at 10654. 
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Cheesy with an evalue of 1e-167 and Dynamite with an e value of 1e-166. Start site is the longest ORF. There is no significant overlap with other genes.
    /note=
    /note=Start site data
    /note=Start site 13 was found in  322/357 of genes in pham. MA’s of this start are 265/293
    /note=In NCBI Blast, the gene shows 98.9% identity with Cheesy, with an e-value of 0 and 98.6% identity with Dynamite with an e-value of 0. The start site, 10654 has the longest ORF, a z score of 3.031 and a final score of -2.765.
    /note=
    /note=Evidence for a function
    /note=All similar phages in NCBI blast call this gene “major tail protein." All similar phages on PhagesDB BLAST call this “major tail protein.” HHpred aligns L_lac_phage_MSP ; Phage tail tube protein with a probability of 99.94 and an evalue of 2.1e-24.

CDS 11546 - 12103
  /gene="15"
  /product="gp15"
  /function="Hypothetical Protein"
  /locus tag="Benllo_15"
    /note=Original Glimmer call @bp 11546 has strength 5.56; Genemark calls start at 11546
    /note=SSC: 11546-12103 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB83_gp15 [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 9.22031E-133 GAP: 25 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.435, -2.0949393225970705, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB83_gp15 [Arthrobacter phage KeaneyLin] ],,YP_010666893,99.4595,9.22031E-133 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start site at 11546
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as GoCrazy with an evalue of 1e-103 and KeaneyLin with an e value of 1e-103. There is no significant overlap with other genes.
    /note=
    /note=Start site data
    /note=Start site 32 which has the start site, 11546 was found in 176/176 of genes in pham with MA’s of 146/146. 
    /note=In NCBI Blast, the gene shows 98% identity with KeaneyLin, with an e-value of 9e-133 and 97.8% identity with Cheesy with an e-value of 1e-132. The start site, 11546 has the longest ORF, a z score of 1.806 and a final score of -5.756.
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with unknown function.

CDS 12122 - 12925
  /gene="16"
  /product="gp16"
  /function="major tail protein"
  /locus tag="Benllo_16"
    /note=Original Glimmer call @bp 12122 has strength 8.91; Genemark calls start at 12122
    /note=SSC: 12122-12925 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Arthrobacter phage Correa] ],,NCBI, q1:s1 100.0% 0.0 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.435, -2.033982896655645, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage Correa] ],,YP_010666305,99.2509,0.0 SIF-HHPRED: Phage_TTP_1 ; Phage tail tube protein,,,PF04630.15,55.4307,99.7 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start site at 12122.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Corea with an evalue of 1e-155 and Xenomorph with an e value of 1e-155. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 13 which has the start, 12122, was found in 322/357 genes in pham. MA’s of this start were 265/293. In NCBI Blast, the gene shows 98.8% identity with Corea, with an e-value of 0 and 97% identity with BenitoAntonio with an e-value of 0. The start site, 12122 has the longest ORF, a z score of 3.435 and a final score of -2.034.
    /note=
    /note=Evidence for a function
    /note=All similar phages in NCBI blast call this gene “major tail protein." All similar phages on PhagesDB BLAST call this “major tail protein.” HHpred aligns L_lac_phage_MSP ; Phage tail tube protein with a probability of 99.92 and an evalue of 1e-22.

CDS 12925 - 14991
  /gene="17"
  /product="gp17"
  /function="Hypothetical Protein"
  /locus tag="Benllo_17"
    /note=Original Glimmer call @bp 12925 has strength 7.26; Genemark calls start at 12925
    /note=SSC: 12925-14991 CP: yes SCS: both ST: SS BLAST-Start: [MAG: hypothetical protein A2707_02015 [Candidatus Saccharibacteria bacterium RIFCSPHIGHO2_01_FULL_45_15] ],,NCBI, q48:s107 93.0233% 1.64453E-71 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.534, -4.816561286066204, no F: Hypothetical Protein SIF-BLAST: ,,[MAG: hypothetical protein A2707_02015 [Candidatus Saccharibacteria bacterium RIFCSPHIGHO2_01_FULL_45_15] ],,OGL22105,44.4,1.64453E-71 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start site at 12925. There are phages that show high alignment such as BritBrat with an evalue of 2e-44 and Ecliptus with an e value of 3e-40 however these are not from the the AM cluster. There is no significant overlap with other genes in this phage.
    /note=
    /note=Start site data:
    /note=Glimmer and GeneMark call same start site. Starterator does not support a start site as this is probably an orpham.
    /note=Evidence for a function
    /note=All similar phages in NCBI blast call this gene “hypothetical protein.” Some phages on PhagesDB BLAST call this “tail spike-like protein” such as Brit-Brat with an evalue of 2e-44 while other phages call this “minor tail protein” like Phabuloso with an e value of 4e-40. HHpred aligns with tailspike gp27; Beta-helix, tailspike, Lyase; HET: NA, ACT, EDO; 1.52A {Pseudomonas phage phi297} with a probability of 99.94 and an evalue of 2.4e-22. 
    /note=Coverage however is poor. No genes in this pham have a known function.

CDS 15086 - 17173
  /gene="18"
  /product="gp18"
  /function="minor tail protein"
  /locus tag="Benllo_18"
    /note=Original Glimmer call @bp 15086 has strength 7.23; Genemark calls start at 15086
    /note=SSC: 15086-17173 CP: yes SCS: both ST: SS BLAST-Start: [tail protein [Arthrobacter phage Correa] ],,NCBI, q1:s1 100.0% 0.0 GAP: 94 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.816, -5.290324183593171, no F: minor tail protein SIF-BLAST: ,,[tail protein [Arthrobacter phage Correa] ],,YP_010666307,98.5611,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start site at 15086.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Correa with an evalue of 0 and Xenomorph with an e value of 0. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 5 which has the start, 15086, was found in 8/20 of genes in pham. MA’s of this start were 6/19.  
    /note=In NCBI Blast, the gene shows 95% identity with Correa with an e value of 0, and 94% identity with Xenomorph with an e value of 0. The start site, 12925 has the longest ORF, a z score of 1.816 and a final score of -5.290.
    /note=
    /note=Evidence for a function
    /note=All similar phages in NCBI blast call this gene “tail protein." All similar phages on PhagesDB BLAST call this “function unknown.” HHpred aligns CE4_u6; Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily with a probability of 99.75 and an evalue of 9.2e-17.
    /note=All genes in the pham function as a “minor tail protein”

CDS 17193 - 17573
  /gene="19"
  /product="gp19"
  /function="Hypothetical Protein"
  /locus tag="Benllo_19"
    /note=Original Glimmer call @bp 17193 has strength 3.66; Genemark calls start at 17253
    /note=SSC: 17193-17573 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein BI184_gp20 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 1.91233E-86 GAP: 19 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.499, -3.8366550365551095, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp20 [Arthrobacter phage Mudcat] ],,YP_009300709,100.0,1.91233E-86 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene
    /note=Glimmer calls start at 17193 and GeneMark calls start at 17253.
    /note=Both regions encompass all coding potential. Multiple phages with this gene have high alignment such as BenitoAntonio and Cheesy with e-values of 2e-69. There is no significant overlap with other genes.
    /note=
    /note=Start site data
    /note=Start site 17193, which corresponds to start 42, was found in 161 of 218 genes in the pham and has 116 MA’s. This start site was called 97.5% of the time when present. The start site 17193 has the longest ORF.
    /note=In NCBI BLAST, the gene shows 100% identity with Mudcat and 99% identity with Arcadia. The start site 17193 has a z-score of 2.499 and a final score of -3.837 which is the best score for this ORF.
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with unknown function.

CDS 17570 - 22048
  /gene="20"
  /product="gp20"
  /function="tape measure protein"
  /locus tag="Benllo_20"
    /note=Original Glimmer call @bp 17570 has strength 7.03; Genemark calls start at 17570
    /note=SSC: 17570-22048 CP: yes SCS: both ST: SS BLAST-Start: [tail length tape measure protein [Arthrobacter phage Correa] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.824, -3.3226484487933954, no F: tape measure protein SIF-BLAST: ,,[tail length tape measure protein [Arthrobacter phage Correa] ],,YP_010666309,97.7882,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BF,3.28418,98.5 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 17570.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Kardesai with an evalue of 0 and Hankly with an e value of 0. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 20, which has the start, 17570, was found in 86/130 genes in pham. MA’s of this start are 69/109. The start site 17549 has the longest ORF (4500), a z score of 1.208 and a final score of -6.494. 
    /note=This data supports the predicted start site of 17570
    /note=
    /note=Evidence for a function
    /note=All similar phages in NCBI blast call this gene “tape measure protein." All similar phages on PhagesDB BLAST call this “Tape measure protein.” HHpred aligns Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alph with a probability of 99.86 and an e-value of 9.5e-11.

CDS 22048 - 22899
  /gene="21"
  /product="gp21"
  /function="minor tail protein"
  /locus tag="Benllo_21"
    /note=Original Glimmer call @bp 22048 has strength 7.68; Genemark calls start at 22048
    /note=SSC: 22048-22899 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Cheesy] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -4.122394640384114, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Cheesy] ],,YP_010666210,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 22048. 
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Cheesy with an evalue of 1e-161 and Correa with an e value of 1e-161. There is no significant overlap with other genes. 
    /note=
    /note=Start site data:
    /note=Start site 3, which has the start, 22048, was found in 129/178 genes in pham. MA’s of this start were 108/146. In NCBI Blast, the gene shows 100% identity with Cheesy with an e value of 0, and 99% identity with Xenomorph with an e value of 0. The start site, 22048 has the longest ORF, a z score of 3.006 and a final score of -4.122. 
    /note=
    /note=Evidence for a function
    /note=All similar phages in NCBI blast call this gene “minor tail protein." All similar phages on PhagesDB BLAST call this “minor tail protein.”

CDS 22900 - 23961
  /gene="22"
  /product="gp22"
  /function="minor tail protein"
  /locus tag="Benllo_22"
    /note=Original Glimmer call @bp 22900 has strength 7.13; Genemark calls start at 22900
    /note=SSC: 22900-23961 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Correa] ],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.641, -5.561501196896141, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Correa] ],,YP_010666311,99.7167,0.0 SIF-HHPRED: Sipho_Gp37 ; Siphovirus ReqiPepy6 Gp37-like protein,,,PF14594.9,94.051,99.9 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 22900. 
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Kardesai with an evalue of 0 and Cheesy with an e value of 0. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 9, which has the start 22900 was only found in 11% of genes in pham. MA’s of this start were only 18/146. In NCBI Blast, the gene shows 100% identity with multiple other phages with an e value of 0. Two of which are Cheesy and Kardesai. The start site, 22900 has the longest ORF, a z score of 1.641 and a final score of -5.562. 
    /note=
    /note=Evidence for a function
    /note=All similar phages in NCBI blast call this gene “minor tail protein." All similar phages on PhagesDB BLAST call this “minor tail protein.” HHpred aligns ; Sipho_Gp37 ; Siphovirus ReqiPepy6 Gp37-like protein with a probability of 99.97 and an evalue of 1.9e-26.

CDS 24013 - 24441
  /gene="23"
  /product="gp23"
  /function="Hypothetical Protein"
  /locus tag="Benllo_23"
    /note=Original Glimmer call @bp 24013 has strength 5.93; Genemark calls start at 24013
    /note=SSC: 24013-24441 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB79_gp024 [Arthrobacter phage Heisenberger] ],,NCBI, q1:s14 100.0% 2.29735E-95 GAP: 51 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.69, -3.978761577779152, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB79_gp024 [Arthrobacter phage Heisenberger] ],,YP_010666503,91.6129,2.29735E-95 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 24013. 
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Arcadia with an evalue of 2e-76 and Circum with an e value of 2e-76. There is no significant overlap with other genes.
    /note=
    /note=Start site data: 
    /note=Start 17, which has the start 24013, was found in 36/99 of genes in pham. MA’s of this start were 2/71. In NCBI Blast, the gene shows 100% identity with Heisenberger with an evalue of 2e-95 and 100% identity with Arcadia with an evalue of 4e-95. Start site 23974 has the longest ORF, a z score of 2.577 and a final score of -4.729.  
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with unknown function

CDS 24445 - 24726
  /gene="24"
  /product="gp24"
  /function="Hypothetical Protein"
  /locus tag="Benllo_24"
    /note=Original Glimmer call @bp 24445 has strength 4.79; Genemark calls start at 24445
    /note=SSC: 24445-24726 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp25 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 3.17197E-57 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.845, -3.139452255336754, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp25 [Arthrobacter phage Mudcat] ],,YP_009300714,100.0,3.17197E-57 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 24445.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Arcadia with an evalue of 4e-46 and BenitoAntonio with an e value of 4e-46. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start 33, which has the start site 24445, was found in 54/164 of genes in pham. MA’s of this start were 44/133 and was called 92.6% of the time when present. In NCBI Blast, the gene shows 100% identity with Mudcat with an e value of 3e-57. Start site 24445 has the longest ORF, a z score of 2.845 and a final score of -3.139. 
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 24736 - 25152
  /gene="25"
  /product="gp25"
  /function="Hypothetical Protein"
  /locus tag="Benllo_25"
    /note=Original Glimmer call @bp 24736 has strength 10.06; Genemark calls start at 24736
    /note=SSC: 24736-25152 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp27 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 8.18821E-92 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.499, -3.8366550365551095, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp27 [Arthrobacter phage Circum] ],,YP_009603116,100.0,8.18821E-92 SIF-HHPRED: Phage_holin_Dp1 ; Putative phage holin Dp-1,,,PF16938.8,44.2029,99.8 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 24736.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as Circum with an evalue of 9e-73 and Heisenberger with an e value of 9e-73. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start 8, which has the start site 24736, was found in 21/81 of genes in pham. MA’s of this start were 19/64 and was called 100% of the time when present. In NCBI Blast, the gene shows 100% identity with Circum with an e value of 8e-92 and 99% identity with Hankly with an e value of 3e-91.  
    /note=The start site, 24736 has the longest ORF, a z score of 2.499 and a final score of -3.837. 
    /note=
    /note=Evidence for a function
    /note=PhagesDB and NCBI BLAST call this gene to be a hypothetical protein with unknown function.
    /note=HHpred aligns ; Phage_holin_Dp1 ; Putative phage holin Dp-1 with a probability of 99.93 and an evalue of 1.7e-25 but only 44% coverage therefore not assigning it a function of a Holin

CDS 25179 - 25484
  /gene="26"
  /product="gp26"
  /function="Hypothetical Protein"
  /locus tag="Benllo_26"
    /note=Original Glimmer call @bp 25194 has strength 5.16; Genemark calls start at 25194
    /note=SSC: 25179-25484 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein PQB76_gp028 [Arthrobacter phage Cheesy] ],,NCBI, q1:s1 100.0% 4.53389E-66 GAP: 26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.256, -4.323774879235046, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB76_gp028 [Arthrobacter phage Cheesy] ],,YP_010666215,100.0,4.53389E-66 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 25194. 
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment such as BenitoAntonio with an e-value of 5e-48 and Cheesy with an e value of 5e-48. There is no significant overlap with other genes.
    /note=
    /note=Start site data: 
    /note=Start 20, which has the start site, 25194, was found in 78/178 of genes in pham. MA’s of this start are 58/146 and this start was called 93.6% of the time when present. In NCBI Blast, the gene shows 100% identity with KaeneyLin with an e value of 4e-62 and 99% identity with Heisenberger with an e value of 6e-62. The start site, 25179 has the longest ORF, a z score of 2.256 and a final score of -4.324. The start site that Glimmer and GeneMark recognized, 25194, has the second longest ORF, a z score of 3.435, and a final score of -2.034 but starts with an ATG. This data supports the predicted start site of 25179.
    /note=
    /note=Evidence for a function
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 25646 - 25879
  /gene="27"
  /product="gp27"
  /function="Hypothetical Protein"
  /locus tag="Benllo_27"
    /note=Original Glimmer call @bp 25646 has strength 9.21; Genemark calls start at 25646
    /note=SSC: 25646-25879 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB74_gp29 [Arthrobacter phage Arcadia] ],,NCBI, q1:s1 100.0% 2.92121E-44 GAP: 161 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.334, -2.156361006712914, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB74_gp29 [Arthrobacter phage Arcadia] ],,YP_010666017,98.7013,2.92121E-44 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 25646. 
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Circum and Hankly with e-values of 1e-36. There is no significant overlap with other genes
    /note=
    /note=Start site data:
    /note=Start site at 25646 corresponds to the most commonly called start number 3, which is called in 16 of the 16 non-draft genes in the pham. The start number has 16 MA’s. This is the longest ORF without significant overlap. In NCBI Blast, the gene shows 100% identity with the phage Circum and 98% identify with the phage Kardesai. The start site at 25646 has a z-score of 3.334 and a final score of -2.256 which is the best score for this ORF
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 25952 - 26221
  /gene="28"
  /product="gp28"
  /function="Hypothetical Protein"
  /locus tag="Benllo_28"
    /note=Original Glimmer call @bp 25952 has strength 4.55; Genemark calls start at 25952
    /note=SSC: 25952-26221 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HANKLY_28 [Arthrobacter phage Hankly]],,NCBI, q1:s1 100.0% 3.31124E-56 GAP: 72 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.156, -4.526195077013075, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_HANKLY_28 [Arthrobacter phage Hankly]],,WBF79074,100.0,3.31124E-56 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 25952. 
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Hankly and Circum with e-values of 4e-45 and 1e-44. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site at 25952 corresponds to the most commonly called start number 1, which is called in 5 of the 5 genes in the pham. That start number has 3 MA’s. This is the longest ORF without significant overlap
    /note=In NCBI Blast, the gene shows 100% identity with Hankley and 98% identity with Circum
    /note=The start site 25952 has a z-score of 2.156 and a final score of -4.526
    /note=
    /note=Evidence for a gene:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 26322 - 26522
  /gene="29"
  /product="gp29"
  /function="Hypothetical Protein"
  /locus tag="Benllo_29"
    /note=Original Glimmer call @bp 26322 has strength 9.23; Genemark calls start at 26322
    /note=SSC: 26322-26522 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB81_gp031 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 2.11304E-36 GAP: 100 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.446, -1.9310779259753799, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp031 [Arthrobacter phage Kardesai] ],,YP_010666710,100.0,2.11304E-36 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 26322. 
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Dynamite and Kardesai with e-values of 4e-30. There is no significant overlap with other genes
    /note=
    /note=Start site data:
    /note=Start site 26322 corresponds to the most commonly called start number 4, which is called in 19 of the 19 non-draft genes in the pham. That start number has 19 MA’s. This is the longest ORF without significant overlap. In NCBI Blast, the gene shows 100% identity with Kardesai and 98% identity with Circum
    /note=The start site 26322 has a z-score of 3.446 and a final score of -1.931 which is the best score for this ORF.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED call this gene a hypothetical protein with unknown function.

CDS 26598 - 26876
  /gene="30"
  /product="gp30"
  /function="Hypothetical Protein"
  /locus tag="Benllo_30"
    /note=Original Glimmer call @bp 26598 has strength 5.51; Genemark calls start at 26598
    /note=SSC: 26598-26876 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB83_gp29 [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 1.81366E-58 GAP: 75 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.465, -3.9663833707737797, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB83_gp29 [Arthrobacter phage KeaneyLin] ],,YP_010666907,100.0,1.81366E-58 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 26598
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as GoCrazy and KeaneyLin with e-values of 3e-47. There is no significant overlap with other genes
    /note=
    /note=Start site data:
    /note=Start site 26598 corresponds to the most commonly called start number 2, which is called in 7 of the 7 genes in the pham. The start number has 7 MA’s. This is the longest ORF without significant overlap
    /note=In NCBI Blast, the gene shows 98% identity with the phages KeaneyLin and Circum
    /note=The start site 26598 has a z-score of 2.465 and a final score of -3.966 which is the best score for this ORF
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 26873 - 27070
  /gene="31"
  /product="gp31"
  /function="Hypothetical Protein"
  /locus tag="Benllo_31"
    /note=Original Glimmer call @bp 26873 has strength 5.23; Genemark calls start at 26873
    /note=SSC: 26873-27070 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB76_gp032 [Arthrobacter phage Cheesy] ],,NCBI, q1:s1 100.0% 4.5334E-39 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.144, -5.20119681564386, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB76_gp032 [Arthrobacter phage Cheesy] ],,YP_010666219,100.0,4.5334E-39 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 26873.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Cheesy and Heisenberger with e-values of 1e-31. There is no significant overlap with other genes
    /note=
    /note=Start site data:
    /note=Start site 26873 corresponds to the most commonly called start number 1, which is called in 19 of 19 non-draft genes in the pham. That start number has 19 MA’s. This is the longest ORF without significant overlap
    /note=In NCBI Blast, the gene shows 100% identity with Cheesy and 98% identity with JEGGS
    /note=The start site 26872 has a z-score of 2.144 and a final score of -5.201 which is the best score for this ORF
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 27060 - 27278
  /gene="32"
  /product="gp32"
  /function="Hypothetical Protein"
  /locus tag="Benllo_32"
    /note=Original Glimmer call @bp 27060 has strength 5.72; Genemark calls start at 27060
    /note=SSC: 27060-27278 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 2.80012E-43 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.435, -1.953940808934884, yes F: Hypothetical Protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Kardesai] ],,YP_010666713,98.6111,2.80012E-43 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 27060.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Kardesai and Arcadia with e-values such as 6e-34 and 8e-34. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 27060 corresponds to the most commonly called start number 4, which is called in 19 of the 21 genes in the pham. That start number has 19 MA’s. This is the longest ORF without significant overlap
    /note=In NCBI Blast, the gene shows a 98% identity with Kardesai and a 97% identity with Arcadia
    /note=The start site 27060 has a z-score of 3.435 and a final score of -1.954 which is the best score for this ORF.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 27318 - 27506
  /gene="33"
  /product="gp33"
  /function="Hypothetical Protein"
  /locus tag="Benllo_33"
    /note=Original Glimmer call @bp 27318 has strength 6.96; Genemark calls start at 27318
    /note=SSC: 27318-27506 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp32 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 1.92629E-34 GAP: 39 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.334, -2.2364030944336752, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp32 [Arthrobacter phage Mudcat] ],,YP_009300721,100.0,1.92629E-34 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 27318
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Circum and Dynamite with e-values such as 1e-27. There is no significant overlap with other genes
    /note=
    /note=Start site data:
    /note=Start site 27318 corresponds to the most commonly called start number 1, which is called in 19 of the 19 genes in the pham. That start number has 19 MA’s. This is the longest ORF without significant overlap
    /note=In NCBI Blast, the gene shows 100% identity with Mudcat and 98% identity with Arcadia
    /note=The start site 27318 has a z-score of 3.334 and a final score of -2.236 which is the best score for this ORF.
    /note=
    /note=Evidence for a gene:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function,

CDS 27573 - 27794
  /gene="34"
  /product="gp34"
  /function="Hypothetical Protein"
  /locus tag="Benllo_34"
    /note=Original Glimmer call @bp 27573 has strength 7.73; Genemark calls start at 27573
    /note=SSC: 27573-27794 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp36 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 5.31964E-43 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.446, -2.0111200136961407, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp36 [Arthrobacter phage Circum] ],,YP_009603125,100.0,5.31964E-43 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 27573
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Circum and Hankly with e-values of 1e-34. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 27573 corresponds to the most commonly called start number 3, which is called in 9 of the 9 genes in the pham. This start number has 9 MA’s. This is the longest ORF without significant overlap
    /note=In NCBI Blast, the gene shows 100% identity with Circum and 97% identity with Dynamite. The start site 27573 has a z-score of 3.446 and a final score of -2.011 which is the best score for this ORF.
    /note=
    /note=Evidence for a gene:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 27807 - 28133
  /gene="35"
  /product="gp35"
  /function="Hypothetical Protein"
  /locus tag="Benllo_35"
    /note=Original Glimmer call @bp 27807 has strength 9.11; Genemark calls start at 27819
    /note=SSC: 27807-28133 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein PQB82_gp36 [Arthrobacter phage Dynamite] ],,NCBI, q1:s1 100.0% 1.99593E-68 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.446, -2.0720764396375664, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB82_gp36 [Arthrobacter phage Dynamite] ],,YP_010666815,97.2222,1.99593E-68 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls start at 27807, GeneMark calls start at 27819.
    /note=Both regions encompass all coding potential. Multiple phages with this gene have high alignment, such as Dynamite and GoCrazy with e-values of 2e-53. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 27807 corresponds to the most commonly called start number 1, which is called in 12 of the 19 genes in the pham. This start site has 12 MA’s. This is the longest ORF without significant overlap
    /note=In NCBI Blast, the gene shows 96% identity with Dynamite and 93% identity with Circum
    /note=The start site 27807 has a z-score of 3.446 and a final score of -2.072 which is the best score for this ORF
    /note=This data supports the predicted start site of 27807.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 28135 - 28344
  /gene="36"
  /product="gp36"
  /function="Hypothetical Protein"
  /locus tag="Benllo_36"
    /note=Original Glimmer call @bp 28135 has strength 6.73; Genemark calls start at 28135
    /note=SSC: 28135-28344 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB82_gp37 [Arthrobacter phage Dynamite] ],,NCBI, q1:s1 100.0% 7.40517E-41 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.693, -3.5077455217481304, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB82_gp37 [Arthrobacter phage Dynamite] ],,YP_010666816,100.0,7.40517E-41 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 28135.
    /note=Region encompasses all coding potential.Multiple phages with this gene have high alignment, such as BenitoAntonio and Dynamite with e-values of 3e-32. There is no significant overlap with other genes
    /note=
    /note=Start site data:
    /note=Start site 28135 corresponds to the most commonly called start number 11, which is found in 18 of 28 genes in the pham. This start site has 16 MA’s. This is the longest ORF without significant overlap.
    /note=The start site 28135 has a z-score of 2.693 and a final score of -3.508 which is the best score for the ORF
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with unknown function.

CDS 28439 - 28660
  /gene="37"
  /product="gp37"
  /function="Hypothetical Protein"
  /locus tag="Benllo_37"
    /note=Original Glimmer call @bp 28439 has strength 5.69; Genemark calls start at 28439
    /note=SSC: 28439-28660 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB76_gp037 [Arthrobacter phage Cheesy] ],,NCBI, q1:s1 100.0% 2.26742E-42 GAP: 94 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.367, -2.0895162839948163, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB76_gp037 [Arthrobacter phage Cheesy] ],,YP_010666224,100.0,2.26742E-42 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 28439.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as BenitoAntonio and Cheesy with e-values of 3e-33. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 28439 does not correspond to the most commonly called start number. Instead, it calls for start number 15, which is found in 20 of the 112 genes in the pham. This start site has 19 MA’s. This is the longest ORF without significant overlap. In NCBI Blast, the gene shows 100% identity with Cheesy and 98% identity with Mudcat. The start site 28439 has a z-score of 3.367 and a final score of -2.090 which is the best score for this ORF
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with unknown function.

CDS 28724 - 29095
  /gene="38"
  /product="gp38"
  /function="Hypothetical Protein"
  /locus tag="Benllo_38"
    /note=Original Glimmer call @bp 28724 has strength 4.92; Genemark calls start at 28724
    /note=SSC: 28724-29095 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BENITOANTONIO_39 [Arthrobacter phage BenitoAntonio]],,NCBI, q1:s1 100.0% 2.23817E-74 GAP: 63 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.286, -2.3335289980954053, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BENITOANTONIO_39 [Arthrobacter phage BenitoAntonio]],,UYL87302,95.935,2.23817E-74 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer and Genemark both call start at 28724.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio (3e-60) and Tribby (6e-61). There is no significant overlap with other genes.
    /note=
    /note=Start site data: 
    /note=Starterator support start site at 28,724 (16 MA’s). Doesn`t contain all coding potential.  The length is 372. It has a lot of 1:1. Z-score (3,286) and Final Score (-2.334).
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 29085 - 29399
  /gene="39"
  /product="gp39"
  /function="acetyltransferase"
  /locus tag="Benllo_39"
    /note=Original Glimmer call @bp 29085 has strength 3.78; Genemark calls start at 29085
    /note=SSC: 29085-29399 CP: no SCS: both ST: SS BLAST-Start: [acetyltransferase [Arthrobacter phage BenitoAntonio]],,NCBI, q1:s1 100.0% 1.11438E-69 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.611, -3.751507965036804, no F: acetyltransferase SIF-BLAST: ,,[acetyltransferase [Arthrobacter phage BenitoAntonio]],,UYL87303,100.0,1.11438E-69 SIF-HHPRED: d.108.1.1 (A:) Putative acetyltransferase EF0945 {Enterococcus faecalis [TaxId: 1351]},,,d1u6ma_,75.9615,99.0 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 29085.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio (4e-55) and Circum (3e-54). There is no significant overlap with other genes. 
    /note=
    /note=Start site data:
    /note=Starterator supports site 29,085 (22 MA’s). It doesn`t contain all coding potential. Both Glimmer and Genemark agree with the start. The length is 315. There are a lot of 1:1. Z-score (2.611) and Final Score (-3.752). 
    /note=
    /note=Evidence for a function:
    /note=The function is acetyltransferase. HHPred Data does Support Function. Almost 100% of annotated genes are with same pham.

CDS 29550 - 29864
  /gene="40"
  /product="gp40"
  /function="Hypothetical Protein"
  /locus tag="Benllo_40"
    /note=Original Glimmer call @bp 29550 has strength 8.73; Genemark calls start at 29550
    /note=SSC: 29550-29864 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB78_gp37 [Arthrobacter phage Xenomorph] ],,NCBI, q1:s1 100.0% 2.07755E-18 GAP: 150 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.435, -1.953940808934884, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB78_gp37 [Arthrobacter phage Xenomorph] ],,YP_010666421,68.3168,2.07755E-18 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 29550
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Xenomorph and Correa with e-values of 1e-15 and 8e-16. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 29550 corresponds to the most commonly called start number 1, which is found in 20 of the 20 genes in the pham. This start number has 19 MA’s. This is the longest ORF without significant overlap
    /note=In NCBI Blast, the gene shows 49% identity with Xenomorph and 48% identity with Tribby. The start site 29550 has a z-score of 3.435 and a final score of -1.954 which is the best score for this ORF.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 29865 - 29981
  /gene="41"
  /product="gp41"
  /function="Hypothetical Protein"
  /locus tag="Benllo_41"
    /note=Original Glimmer call @bp 29865 has strength 9.48; Genemark calls start at 29865
    /note=SSC: 29865-29981 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp39 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 9.55772E-18 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.091, -2.7254235724530456, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp39 [Arthrobacter phage Mudcat] ],,YP_009300728,100.0,9.55772E-18 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 29865.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Arcadia and BenitoAntonio with e-values of 2e-14. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start site 29865 corresponds to the most commonly called start number 1, which is found in 20 of the 20 genes in the pham. This start site has 19 MA’s. This is the longest ORF without significant overlap. In NCBI Blast, the gene shows 100% identity with Mudcat and 97% identity with Hankly. The start site 29865 has a z-score of 3.091 and a final score of -2.725 which is the best score for this ORF.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 29978 - 30736
  /gene="42"
  /product="gp42"
  /function="Hypothetical Protein"
  /locus tag="Benllo_42"
    /note=Original Glimmer call @bp 29978 has strength 7.89; Genemark calls start at 29978
    /note=SSC: 29978-30736 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp40 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.884, -3.969072509284561, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp40 [Arthrobacter phage Mudcat] ],,YP_009300729,100.0,0.0 SIF-HHPRED: DUF6353 ; Family of unknown function (DUF6353),,,PF19880.2,93.254,100.0 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 29978.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Arcadia and Cheesy with e-values of 1e-142. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=The start site 28878 corresponds to the most commonly called start number 25, which is found in 35 of 356 genes in the pham. This start site has 30 MA’s. This is the longest ORF without significant overlap. In NCBI Blast, the gene shows 100% identity with Mudcat and 99% identity with Arcadia. The start site 29978 has a z-score of 2.884 and a final score of -3.969 which is the best score for this ORF
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 30751 - 31116
  /gene="43"
  /product="gp43"
  /function="Hypothetical Protein"
  /locus tag="Benllo_43"
    /note=Original Glimmer call @bp 30751 has strength 10.87; Genemark calls start at 30751
    /note=SSC: 30751-31116 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB81_gp045 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 1.69014E-83 GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.245, -4.34663776219455, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp045 [Arthrobacter phage Kardesai] ],,YP_010666724,100.0,1.69014E-83 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 30751.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Kardesai and Arcadia with e-values of 6e-64 and 8e-64. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=No site found- starterator does not have a page for this gene. This is the longest ORF without significant overlap. In NCBI Blast, the gene shows 100% identity with Kardesai and 99% identity with Arcadia
    /note=The start site 30752 has a z-score of 2.245 and a final score of -4.347 which is the best score for this ORF
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to by a hypothetical protein with unknown function.

CDS 31100 - 31420
  /gene="44"
  /product="gp44"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Benllo_44"
    /note=Genemark calls start at 31100
    /note=SSC: 31100-31420 CP: yes SCS: genemark ST: SS BLAST-Start: [helix-turn-helix DNA-binding domain protein [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 2.82889E-71 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.726, -5.451996022272246, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA-binding domain protein [Arthrobacter phage Kardesai] ],,YP_010666725,100.0,2.82889E-71 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls no start site and GeneMark calls start at 31100.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Kardesal with an e-value of 7e-57 and BenitoAnito with an e-value of 3e-55. There is a significant overlap with gene 45.
    /note=
    /note=Start site data:
    /note=Start site 31100 does not correspond to the most commonly called start number. Instead, it corresponds to start number 6, which is found in 20 of 40 genes in the pham. This start site has 14 MA’s. This predicted start site is not the longest ORF without significant overlap. 
    /note=
    /note=Evidence for a function:
    /note=Similar phages in NCBI BLAST call this gene “helix-turn-helix DNA binding domain protein”. All annotated phages on PhagesDB BLAST call this gene “helix-turn-helix DNA binding domain protein." All genes in the pham function as a helix-turn-helix DNA binding domain protein.

CDS 31468 - 31662
  /gene="45"
  /product="gp45"
  /function="Hypothetical Protein"
  /locus tag="Benllo_45"
    /note=Genemark calls start at 31468
    /note=SSC: 31468-31662 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_BENITOANTONIO_46 [Arthrobacter phage BenitoAntonio]],,NCBI, q1:s6 100.0% 3.27031E-36 GAP: 47 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.334, -2.2364030944336752, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BENITOANTONIO_46 [Arthrobacter phage BenitoAntonio]],,UYL87309,92.7536,3.27031E-36 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=GeneMark calls start at 31468.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as BenitoAntonio and Cheesy with e-values of 1e-29. There is no significant overlap with other genes
    /note=
    /note=Start site data:
    /note=Start site 31468 corresponds to the most commonly called start number 2, which is called in 20 of 20 genes in the pham. The start number has 17 MA’s. This is not the longest ORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 31735 - 32091
  /gene="46"
  /product="gp46"
  /function="Hypothetical Protein"
  /locus tag="Benllo_46"
    /note=Genemark calls start at 31735
    /note=SSC: 31735-32091 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein PQB81_gp048 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 8.6406E-83 GAP: 72 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.435, -1.953940808934884, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp048 [Arthrobacter phage Kardesai] ],,YP_010666727,100.0,8.6406E-83 SIF-HHPRED: DUF6275 ; Family of unknown function (DUF6275),,,PF19791.2,66.1017,100.0 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls no start site and GeneMark calls start at 31735.
    /note=Region encompasses all coding potential. Multiple phages with this gene have high alignment, such as Hankly and Kardesal with e-values of 1e-66. There is a significant overlap with gene 45
    /note=
    /note=Start site data:
    /note=Start site 31735 corresponds to the most commonly called start number 4, which is found in 19 of the 20 phages in the pham. This start site has 18 MA’s. This is the longest ORF but there is significant overlap with gene 45. The start site 31735 has a z-score of 3.435 and a final score of -1.954 which is the best score for this ORF.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 32107 - 32676
  /gene="47"
  /product="gp47"
  /function="Hypothetical Protein"
  /locus tag="Benllo_47"
    /note=Original Glimmer call @bp 32107 has strength 7.0; Genemark calls start at 32107
    /note=SSC: 32107-32676 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB75_gp048 [Arthrobacter phage Tribby] ],,NCBI, q1:s1 100.0% 1.5738E-133 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.245, -4.34663776219455, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB75_gp048 [Arthrobacter phage Tribby] ],,YP_010666133,99.4709,1.5738E-133 SIF-HHPRED:  SIF-Syn: 
    /note=Both Glimmer and Genemark have a start site at 32107. 
    /note=Region encompasses all coding potential.
    /note=Tribby and cheesy both have high alignment with e values of 1e-101. No overlap with other genes. This data does not support this ORF as a gene
    /note=
    /note=Start site data:
    /note=Starterator supports the start site, 32107 with 122 MA’s. This start site has the longest ORF without significant overlap. Phagesdb blast: Tribby and Cheesy both show a 1:1 query to subject ratio with evalues of 1e-101 and 1e-100. NCBI blast: This start site has a z score of 2.245 and final score of -4.347
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 32800 - 33102
  /gene="48"
  /product="gp48"
  /function="Hypothetical Protein"
  /locus tag="Benllo_48"
    /note=Original Glimmer call @bp 32800 has strength 9.92; Genemark calls start at 32800
    /note=SSC: 32800-33102 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB83_gp48 [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 1.40741E-62 GAP: 123 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.334, -2.2364030944336752, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB83_gp48 [Arthrobacter phage KeaneyLin] ],,YP_010666926,100.0,1.40741E-62 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 32800.
    /note=Region includes almost all coding potential. Phages with high alignment such as Circum and KeaneyLin with e-value of 1e-50. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Staterator supports start site at 32800 as the most annotated start with 16 MA`s, however it is not the LORF. 
    /note=
    /note=Evidence for a function: 
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 33103 - 33294
  /gene="49"
  /product="gp49"
  /function="Hypothetical Protein"
  /locus tag="Benllo_49"
    /note=Original Glimmer call @bp 33103 has strength 4.74; Genemark calls start at 33103
    /note=SSC: 33103-33294 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp47 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 1.01728E-35 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.031, -3.59360038608048, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp47 [Arthrobacter phage Mudcat] ],,YP_009300736,96.8254,1.01728E-35 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start 33103.
    /note=Region encompasses all coding potential.
    /note=
    /note=Start site data:
    /note=Start was confirmed on Starterator at 33103 with 19 MA`s
    /note=Phagesdb Identified AM phages BenitoAntonio and Circum as conserving the gene
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein.

CDS 33319 - 33453
  /gene="50"
  /product="gp50"
  /function="Hypothetical Protein"
  /locus tag="Benllo_50"
    /note=Original Glimmer call @bp 33319 has strength 11.03; Genemark calls start at 33319
    /note=SSC: 33319-33453 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB83_gp50 [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 7.36176E-23 GAP: 24 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.435, -2.033982896655645, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB83_gp50 [Arthrobacter phage KeaneyLin] ],,YP_010666928,100.0,7.36176E-23 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 53319. 
    /note=Region encompasses all coding potential.
    /note=
    /note=Start site data:
    /note=Start was confirmed on Starterator at 53319 with 15 MA`s. Phagesdb Identified AM phages GoCrazy, Hankly, and KeaneyLin as conserving the gene.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 33450 - 33548
  /gene="51"
  /product="gp51"
  /function="Hypothetical Protein"
  /locus tag="Benllo_51"
    /note=Genemark calls start at 33450
    /note=SSC: 33450-33548 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein BI184_gp49 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 4.46398E-12 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.435, -2.606079664606164, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp49 [Arthrobacter phage Mudcat] ],,YP_009300738,100.0,4.46398E-12 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Only GeneMark called start at 33450 .
    /note=Region encompasses all coding potential.
    /note=
    /note=Start site data:
    /note=Start was confirmed on Starterator at 33450 with 19 MA`s. Phagesdb Identified AM phages Elsa and GoCrazy as conserving the gene.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein.

CDS 33558 - 34247
  /gene="52"
  /product="gp52"
  /function="Hypothetical Protein"
  /locus tag="Benllo_52"
    /note=Original Glimmer call @bp 33558 has strength 10.43; Genemark calls start at 33558
    /note=SSC: 33558-34247 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp55 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 1.57485E-166 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.884, -3.588861267572955, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp55 [Arthrobacter phage Circum] ],,YP_009603144,100.0,1.57485E-166 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 33558.
    /note=Region encompasses all coding potential.
    /note=
    /note=Start site data:
    /note=Start was confirmed on Starterator at 33558 with 91 MA`s. Phagesdb Identified AM phages KeaneyLin and NapoleanB as conserving the gene.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 34240 - 34458
  /gene="53"
  /product="gp53"
  /function="Hypothetical Protein"
  /locus tag="Benllo_53"
    /note=Original Glimmer call @bp 34240 has strength 1.84
    /note=SSC: 34240-34458 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein PQB82_gp54 [Arthrobacter phage Dynamite] ],,NCBI, q1:s1 100.0% 2.09586E-44 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.422, -6.353805630002573, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB82_gp54 [Arthrobacter phage Dynamite] ],,YP_010666833,100.0,2.09586E-44 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls start at 34240.
    /note=Region does not include all coding potential. Phages with high alignment such as BenitoAntonio (1e-35) and KeaneyLin (3e-35). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 34240 as the most annotated start, with 13 MA`s. Found in 100% of genes within the Pham.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 34476 - 34601
  /gene="54"
  /product="gp54"
  /function="Hypothetical Protein"
  /locus tag="Benllo_54"
    /note=Original Glimmer call @bp 34476 has strength 1.98; Genemark calls start at 34476
    /note=SSC: 34476-34601 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB83_gp54 [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 2.39827E-20 GAP: 17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.281, -4.926874829490106, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB83_gp54 [Arthrobacter phage KeaneyLin] ],,YP_010666932,100.0,2.39827E-20 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 34476.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio (2e-16) and GoCrazy (2e-16). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 34476 as the most annotated start, with 65 MA`s. Called 100% of the time when present. This start site also corresponds to the LORF.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 34601 - 34894
  /gene="55"
  /product="gp55"
  /function="Hypothetical Protein"
  /locus tag="Benllo_55"
    /note=Original Glimmer call @bp 34601 has strength 4.52; Genemark calls start at 34601
    /note=SSC: 34601-34894 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB83_gp55 [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 4.83759E-64 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.245, -4.426679849915311, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB83_gp55 [Arthrobacter phage KeaneyLin] ],,YP_010666933,100.0,4.83759E-64 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 34601.
    /note=Region encompasses all coding potential. Phages with high alignment such as GoCrazy (2e-49) and KeaneyLin (2e-49). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 34601 with 9 MA`s. Called 100% of the time when present. This start site is not the most annotated site, but is the LORF with no significant overlap.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 34894 - 35805
  /gene="56"
  /product="gp56"
  /function="Hypothetical Protein"
  /locus tag="Benllo_56"
    /note=Original Glimmer call @bp 34894 has strength 8.53; Genemark calls start at 34894
    /note=SSC: 34894-35805 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB83_gp56 [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.192, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB83_gp56 [Arthrobacter phage KeaneyLin] ],,YP_010666934,100.0,0.0 SIF-HHPRED: DUF6353 ; Family of unknown function (DUF6353),,,PF19880.2,91.4191,100.0 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 34894.
    /note=Region encompasses all coding potential. Phages with high alignment such as GoCrazy and KeaneyLin with e-value of 1e-170. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 34894 with 34 MA`s. It does not correspond to the most annotated start, but is the LORF without significant overlap. 
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 35835 - 36191
  /gene="57"
  /product="gp57"
  /function="Hypothetical Protein"
  /locus tag="Benllo_57"
    /note=Original Glimmer call @bp 35835 has strength 6.16; Genemark calls start at 35835
    /note=SSC: 35835-36191 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp60 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 6.86597E-79 GAP: 29 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.398, -4.101958845833712, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp60 [Arthrobacter phage Circum] ],,YP_009603149,100.0,6.86597E-79 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 35835.
    /note=Region encompasses all coding potential. Phages with high alignment such as GoCrazy and KeaneyLin with an e-value of 3e-63. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 35835 as the most annotated start with 19 MA`s. It also corresponds to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 36188 - 36988
  /gene="58"
  /product="gp58"
  /function="Hypothetical Protein"
  /locus tag="Benllo_58"
    /note=Original Glimmer call @bp 36188 has strength 11.03; Genemark calls start at 36188
    /note=SSC: 36188-36988 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp61 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.741, -3.410574749511644, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp61 [Arthrobacter phage Circum] ],,YP_009603150,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 36188.
    /note=Region encompasses all coding potential. Phages with high alignment such as Circum and BenitoAntonio with e-value of 1e-154. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 36188 with 22 MA`s. This is not the most annotated start but does correspond to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 36978 - 37538
  /gene="59"
  /product="gp59"
  /function="Hypothetical Protein"
  /locus tag="Benllo_59"
    /note=Original Glimmer call @bp 36975 has strength 6.79; Genemark calls start at 36978
    /note=SSC: 36978-37538 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein PQB81_gp061 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 1.41455E-134 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.267, -3.1993478425474327, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp061 [Arthrobacter phage Kardesai] ],,YP_010666740,100.0,1.41455E-134 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls start at 36975, while GeneMark calls start at 36978.
    /note=Both regions encompass all coding potential. Phages with high alignment such as Kardesai and BenitoAntonio with e-value of 1e-108. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Start 36978 has more mannual annotations, gets 1:1 match with several members of the Pham with low e values and is a smaller overlap of - 11bp with the previous gene. Therefore selected that and not the Glimmer prediction of 3675 which gave a slightly longer ORF with similar scores.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene a hypothetical protein with unknown function.

CDS 37562 - 41509
  /gene="60"
  /product="gp60"
  /function="DNA primase/polymerase"
  /locus tag="Benllo_60"
    /note=Original Glimmer call @bp 37562 has strength 5.37; Genemark calls start at 37607
    /note=SSC: 37562-41509 CP: yes SCS: both-gl ST: SS BLAST-Start: [DNA primase/polymerase [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 0.0 GAP: 23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.501, -3.8308929311341546, no F: DNA primase/polymerase SIF-BLAST: ,,[DNA primase/polymerase [Arthrobacter phage Kardesai] ],,YP_010666741,99.924,0.0 SIF-HHPRED: DNA polymerase; DNA polymerase, primase, DNA replication, DNA BINDING PROTEIN; 3.56A {Saccharomyces cerevisiae},,,8FOK_1,47.1483,100.0 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls start at 37562, while GeneMark calls start at 37607.
    /note=Both regions encompass all coding potential. Phages with high alignment such as Kardesai and BenitoAntonio with an e-value of 0. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports Glimmer start site at 37562 as the most annotated start with 107 MA`s. This start site also corresponds to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=All similar phages in NCBI BLAST call this gene a “DNA primase/polymerase.". All annotated phages on PhagesDB BLAST call this gene “DNA primase/polymerase." The Conserved Domain Database call this gene “DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];”. HHpred aligns to “DNA polymerase; Difluorotoluene Nucleoside, dGTP/dT, Triple mutant, Transferase-DNA complex; HET: DOC, DGT; 1.73A {Enterobacteria phage RB69}” with a probability of 100% and an e-value of 8.68805e-44

CDS 41506 - 41715
  /gene="61"
  /product="gp61"
  /function="Hypothetical Protein"
  /locus tag="Benllo_61"
    /note=Original Glimmer call @bp 41536 has strength 5.07; Genemark calls start at 41506
    /note=SSC: 41506-41715 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein PQB81_gp063 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 2.29104E-44 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.982, -7.028301864955391, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp063 [Arthrobacter phage Kardesai] ],,YP_010666742,100.0,2.29104E-44 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls start at 41536, while GeneMark calls start at 41506.
    /note=Both regions encompass all coding potential, however there is not much. Phages with high alignment such as BenitoAntonio and Kardesai with an e-value of 4e-38. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports GeneMark start site 41506 with 10 MA`s. This is the most annotated start and corresponds to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 41775 - 41996
  /gene="62"
  /product="gp62"
  /function="Hypothetical Protein"
  /locus tag="Benllo_62"
    /note=Original Glimmer call @bp 41775 has strength 2.66
    /note=SSC: 41775-41996 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein PQB79_gp062 [Arthrobacter phage Heisenberger] ],,NCBI, q1:s1 100.0% 2.70015E-45 GAP: 59 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.192, -2.523003374675015, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB79_gp062 [Arthrobacter phage Heisenberger] ],,YP_010666541,98.6301,2.70015E-45 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls start at 41775.
    /note=Region encompasses all coding potential. Phages with high alignment such as Circum and KeaneyLin with e-value of 5e-40. There is no significant overlap with other genes. 
    /note=
    /note=Start site data:
    /note=Starterator supports start at 41775 which is a shorter ORF, with an ATG start and good scores, but it also
    /note= equally supports start at 41730 which is a longer ORF, but a TTG start and poorer score. Both give equal number of 1:1 alignment with 5 similar phages in the cluster each. Will stay with the ATG at 41775.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 42135 - 42263
  /gene="63"
  /product="gp63"
  /function="Hypothetical Protein"
  /locus tag="Benllo_63"
    /note=Original Glimmer call @bp 42135 has strength 7.96; Genemark calls start at 42135
    /note=SSC: 42135-42263 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp62 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 1.16491E-19 GAP: 138 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.446, -2.0111200136961407, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp62 [Arthrobacter phage Mudcat] ],,YP_009300751,100.0,1.16491E-19 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 42135.
    /note=Region encompasses all coding potential.
    /note=
    /note=Start site data:
    /note=Start was confirmed on Starterator at 42135 with 19 MA`s. Phagesdb Identified AM phages NapoleonB and Mudcat as conserving the gene.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 42265 - 42636
  /gene="64"
  /product="gp64"
  /function="Hypothetical Protein"
  /locus tag="Benllo_64"
    /note=Original Glimmer call @bp 42265 has strength 7.58; Genemark calls start at 42265
    /note=SSC: 42265-42636 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB81_gp067 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 6.31497E-81 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.245, -4.87383788125753, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp067 [Arthrobacter phage Kardesai] ],,YP_010666746,100.0,6.31497E-81 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 42265. 
    /note=Region encompasses all coding potential.
    /note=
    /note=Start site data:
    /note=Start was confirmed on Starterator at 42265 with 19 MA`s. Phagesdb Identified AM phages BenitoAntonio and Hankly as conserving the gene.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 42690 - 43184
  /gene="65"
  /product="gp65"
  /function="SSB protein"
  /locus tag="Benllo_65"
    /note=Original Glimmer call @bp 42690 has strength 6.45; Genemark calls start at 42690
    /note=SSC: 42690-43184 CP: yes SCS: both ST: SS BLAST-Start: [single strand annealing protein [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 2.1195E-117 GAP: 53 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.995, -4.84860406141234, no F: SSB protein SIF-BLAST: ,,[single strand annealing protein [Arthrobacter phage Mudcat] ],,YP_009300753,100.0,2.1195E-117 SIF-HHPRED: Single-stranded DNA-binding protein; DNA replication, DUF2815, SSB, OB fold, DNA BINDING PROTEIN; HET: MSE; 1.5A {Enterobacter phage Enc34},,,PF10991.11,92.0732,99.3 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark called 42690 start.
    /note=Region encompasses all coding potential. No significant overlap with other genes.
    /note=
    /note=Stare site data:
    /note=Start was confirmed on Starterator at 42690 with 19 MA`s. Phagesdb Identified AM phages BenitoAntonio, Mudcat and Kardesai as conserving the gene
    /note=
    /note=Evidence for a function:
    /note=NCBI indicates gene is a phage related protein. Some phages on NCBI BLAST call this gene “single strand annealing protein” like Mudcat with an e-value of 3e-117. Some annotated phages on PhagesDB BLAST call this gene “ssDNA binding protein” like Kardesai with an e-value of 9e-92. HHpred aligns to “Single-stranded DNA-binding protein; DNA replication, DUF2815, SSB, OB fold, DNA BINDING PROTEIN; HET: MSE; 1.5A {Enterobacter phage Enc34}” with a probability of 99.3% and an e-value of 1.23-15.

CDS 43185 - 43463
  /gene="66"
  /product="gp66"
  /function="Hypothetical Protein"
  /locus tag="Benllo_66"
    /note=Original Glimmer call @bp 43185 has strength 2.57; Genemark calls start at 43185
    /note=SSC: 43185-43463 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp65 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 8.85289E-60 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.883, -5.1371700089513865, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp65 [Arthrobacter phage Mudcat] ],,YP_009300754,100.0,8.85289E-60 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 43185. 
    /note=Region encompasses all coding potential. Phages with high alignment such as Circum and BenitoAntonio with e-value of 2e-46. There is no significant overlap with other genes.
    /note=
    /note=Evidence for a start site:
    /note=Starterator supports start site 43185 with 19 MA`s. While this is not the most annotated start, it corresponds to the LORF without significant overlap. 
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 43477 - 44046
  /gene="67"
  /product="gp67"
  /function="Hypothetical Protein"
  /locus tag="Benllo_67"
    /note=Original Glimmer call @bp 43477 has strength 7.87; Genemark calls start at 43477
    /note=SSC: 43477-44046 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp71 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 1.01562E-138 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.498, -3.9172674150161133, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp71 [Arthrobacter phage Circum] ],,YP_009603160,100.0,1.01562E-138 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start 43477.
    /note=Region encompasses all coding potential. Phages with high alignment such as Circum and BenitoAntonio with e-value of 1e-111. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 43477 as most annotated start, found in 100% of genes in the Pham, with 7 MA`s. It also corresponds to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 44047 - 44415
  /gene="68"
  /product="gp68"
  /function="Hypothetical Protein"
  /locus tag="Benllo_68"
    /note=Original Glimmer call @bp 44047 has strength 10.8; Genemark calls start at 44047
    /note=SSC: 44047-44415 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB82_gp70 [Arthrobacter phage Dynamite] ],,NCBI, q1:s1 100.0% 3.90533E-81 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.724, -3.384070132909239, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB82_gp70 [Arthrobacter phage Dynamite] ],,YP_010666849,100.0,3.90533E-81 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 44047.
    /note=Region encompasses all coding potential. Phages with high alignment such as Circum (1e-65) and BenitoAntonio (1e-66). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site at 44047 with 19 MA`s. While this is not the most annotated start, it corresponds to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 44505 - 44783
  /gene="69"
  /product="gp69"
  /function="Hypothetical Protein"
  /locus tag="Benllo_69"
    /note=Original Glimmer call @bp 44505 has strength 5.17; Genemark calls start at 44505
    /note=SSC: 44505-44783 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB82_gp71 [Arthrobacter phage Dynamite] ],,NCBI, q1:s1 100.0% 2.04767E-61 GAP: 89 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.945, -3.019720185458058, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB82_gp71 [Arthrobacter phage Dynamite] ],,YP_010666850,100.0,2.04767E-61 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 44505.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio and KeaneyLin with e-value of 1e-47. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 44505 as the most annotated start with 19 MA`s. This also corresponds to the LORF without significant overlap and is called in 100% of genes in the Pham.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 44792 - 45103
  /gene="70"
  /product="gp70"
  /function="Hypothetical Protein"
  /locus tag="Benllo_70"
    /note=Original Glimmer call @bp 44792 has strength 6.42; Genemark calls start at 44792
    /note=SSC: 44792-45103 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp68 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 3.58024E-69 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.705, -5.513437941870332, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp68 [Arthrobacter phage Mudcat] ],,YP_009300757,100.0,3.58024E-69 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 44792.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio and Circum with e-value of 3e-54. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 44792 as the most annotated start with 19 MA`s. This also corresponds to the LORF without significant overlap. 
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 45103 - 45417
  /gene="71"
  /product="gp71"
  /function="Hypothetical Protein"
  /locus tag="Benllo_71"
    /note=Original Glimmer call @bp 45103 has strength 6.39; Genemark calls start at 45103
    /note=SSC: 45103-45417 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp75 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 4.59372E-69 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.523, -3.867218069942777, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp75 [Arthrobacter phage Circum] ],,YP_009603164,99.0385,4.59372E-69 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 45103. 
    /note=Region encompasses all coding potential. Phages with high alignment such as Kardesai and KeaneyLin with e-value of 2e-54. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site at 45103 as the most annotated start with 12 MA`s. This also corresponds to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 45427 - 45624
  /gene="72"
  /product="gp72"
  /function="Hypothetical Protein"
  /locus tag="Benllo_72"
    /note=Original Glimmer call @bp 45427 has strength 5.62; Genemark calls start at 45427
    /note=SSC: 45427-45624 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp76 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 5.84144E-40 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.409, -4.016212351373635, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp76 [Arthrobacter phage Circum] ],,YP_009603165,98.4848,5.84144E-40 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 45427.
    /note=Region encompasses all coding potential. Phages with high alignment such as Circum and BenitoAntonio with e-value of 8e-32. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 45427 as the most annotated start with 19 MA`s. This also corresponds to the LORF without significant overlap and is found in 100% of genes in the Pham.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 45652 - 45924
  /gene="73"
  /product="gp73"
  /function="Hypothetical Protein"
  /locus tag="Benllo_73"
    /note=Original Glimmer call @bp 45652 has strength 3.66; Genemark calls start at 45652
    /note=SSC: 45652-45924 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp77 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 1.19648E-60 GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.45, -4.586591534678451, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp77 [Arthrobacter phage Circum] ],,YP_009603166,98.8889,1.19648E-60 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 45652.
    /note=Region encompasses all coding potential. Phages with high alignment such as Circum (9e-49) and BenitoAntonio (5e-47). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Staterator supports start site 45652 as the most annotated start with 19 MA`s. This also corresponds to the LORF without significant overlap and is called in 100% of genes in the Pham. 
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 46018 - 46530
  /gene="74"
  /product="gp74"
  /function="HNH endonuclease"
  /locus tag="Benllo_74"
    /note=Original Glimmer call @bp 46018 has strength 8.33; Genemark calls start at 46018
    /note=SSC: 46018-46530 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 5.10138E-120 GAP: 93 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.498, -3.8995386480556817, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage Mudcat] ],,YP_009300761,100.0,5.10138E-120 SIF-HHPRED: d.4.1.3 (M:1-105) Intron-encoded homing endonuclease I-HmuI {Bacteriophage SP01 [TaxId: 10685]},,,d1u3em1,58.8235,99.9 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 46018.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio and KeaneyLin with e-value of 1e-96. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 46018 with 33 MA`s. While this is not the most annotated start, it does correspond to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=All similar phages on NCBI BLAST call this gene a “HNH endonuclease." All annotated phages on PhagesDB BLAST call this gene “HNH endonuclease." The Conserved Domain Database calls this gene a “HNH endonuclease;." HHPRED aligns to “d.4.1.3 (M:1-105) Intron-encoded homing endonuclease I-HmuI {Bacteriophage SP01 [TaxId: 10685]}” with a probability of 99.9% and an e-value of 2.9e-32.

CDS 46621 - 46908
  /gene="75"
  /product="gp75"
  /function="Hypothetical Protein"
  /locus tag="Benllo_75"
    /note=Original Glimmer call @bp 46621 has strength 4.39; Genemark calls start at 46621
    /note=SSC: 46621-46908 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB82_gp78 [Arthrobacter phage Dynamite] ],,NCBI, q1:s1 100.0% 6.7758E-64 GAP: 90 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.334, -3.206439871056232, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB82_gp78 [Arthrobacter phage Dynamite] ],,YP_010666857,100.0,6.7758E-64 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 46621.
    /note=Region encompasses all coding potential. Phages with high alignment such as Kardesai (3e-50) and KeaneyLin (1e-50). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 46621 as the most annotated start with 19 MA`s. It also corresponds to the LORF without significant overlap and is called in 100% of genes in the Pham.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 46909 - 47043
  /gene="76"
  /product="gp76"
  /function="Hypothetical Protein"
  /locus tag="Benllo_76"
    /note=Original Glimmer call @bp 46909 has strength 1.83
    /note=SSC: 46909-47043 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein PQB81_gp079 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 1.8741E-24 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.481, -4.701320725655571, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp079 [Arthrobacter phage Kardesai] ],,YP_010666758,100.0,1.8741E-24 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer calls start at 46909.
    /note=Poor coding potential in the region, but is encompassed entirely. Phages with high alignment such as BenitoAntonio (2e-20) and KeaneyLin (1e-22). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start 46909 as the most annotated start with 7 MA`s. It also corresponds to the LORF without significant overlap. 
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 47047 - 48357
  /gene="77"
  /product="gp77"
  /function="DNA helicase"
  /locus tag="Benllo_77"
    /note=Original Glimmer call @bp 47047 has strength 3.7; Genemark calls start at 47047
    /note=SSC: 47047-48357 CP: yes SCS: both ST: SS BLAST-Start: [DNA helicase [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.741, -5.3604874223912145, no F: DNA helicase SIF-BLAST: ,,[DNA helicase [Arthrobacter phage KeaneyLin] ],,YP_010666954,100.0,0.0 SIF-HHPRED: Transcription regulatory protein SNF2; SWI/SNF remodeling, Swi-Snf complex, nucleosome, DNA BINDING PROTEIN; 2.89A {Saccharomyces cerevisiae S288C},,,7C4J_H,92.4312,100.0 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 47047.
    /note=Region encompasses all coding potential. Phages with high alignment such as KeaneyLin with an e-value of 0. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 47047 as the most annotated start with 119 MA`s. This also corresponds to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=All similar phages on NCBI BLAST call this gene a “DNA Helicase." All annotated phages on PhagesDB BLAST call this gene “DNA Helicase." The Conserved Domain Database calls this gene “DEAD-like helicases superfamily." HHpred aligns to “Transcription regulatory protein SNF2; SWI/SNF remodeling, Swi-Snf complex, nucleosome, DNA BINDING PROTEIN; 2.89A {Saccharomyces cerevisiae S288C}” with a probability of 100% and an e-value of 6e-35.

CDS 48387 - 49271
  /gene="78"
  /product="gp78"
  /function="Hypothetical Protein"
  /locus tag="Benllo_78"
    /note=Original Glimmer call @bp 48387 has strength 7.15; Genemark calls start at 48387
    /note=SSC: 48387-49271 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp81 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 0.0 GAP: 29 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.435, -2.305049668942183, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp81 [Arthrobacter phage Circum] ],,YP_009603170,99.6599,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 48387.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio (1e-143) and Circum (1e-171). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 48387 as the most annotated start with 12 MA`s. It also corresponds to the LORF without significant overlap.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 49268 - 49474
  /gene="79"
  /product="gp79"
  /function="Hypothetical Protein"
  /locus tag="Benllo_79"
    /note=Original Glimmer call @bp 49268 has strength 6.06; Genemark calls start at 49268
    /note=SSC: 49268-49474 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp82 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 4.598E-41 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.252, -4.332504169956899, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp82 [Arthrobacter phage Circum] ],,YP_009603171,100.0,4.598E-41 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 49268.
    /note=Region encompasses all coding potential. Phages with high alignment such as Kardesai (3e-35) and KeaneyLin (7e-34). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 49268 as the most annotated start with 19 MA`s. It also corresponds to the LORF without significant overlap and is called in 100% of genes in the Pham.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 49541 - 49762
  /gene="80"
  /product="gp80"
  /function="Hypothetical Protein"
  /locus tag="Benllo_80"
    /note=Original Glimmer call @bp 49541 has strength 4.72; Genemark calls start at 49541
    /note=SSC: 49541-49762 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB81_gp083 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 1.20599E-46 GAP: 66 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.672, -3.5676719685030167, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp083 [Arthrobacter phage Kardesai] ],,YP_010666762,100.0,1.20599E-46 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 49541.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio (8e-37) and Kardesai (1e-37). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 49541 as the most annotated start with 17 MA`s. It also corresponds to the LORF without significant overlap and is called in 100% of the genes in the Pham. 
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 49798 - 50472
  /gene="81"
  /product="gp81"
  /function="HNH endonuclease"
  /locus tag="Benllo_81"
    /note=Original Glimmer call @bp 49798 has strength 9.1; Genemark calls start at 49798
    /note=SSC: 49798-50472 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Arthrobacter phage BenitoAntonio]],,NCBI, q1:s1 100.0% 6.10123E-162 GAP: 35 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.498, -4.744636688069939, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage BenitoAntonio]],,UYL87347,99.5536,6.10123E-162 SIF-HHPRED: HNH homing endonuclease; HNH catalytic motif, Helix-turn-helix DNA binding domain, protein-DNA complex, DNA binding protein-DNA COMPLEX; HET: EDO; 2.92A {Bacillus phage SPO1} SCOP: d.285.1.1, d.4.1.3,,,1U3E_M,42.4107,99.5 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 49798.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio and Kardesai with an e-value of 1e-129. There is no significant overlap with other phages.
    /note=
    /note=Start site data:
    /note=Starterator support start site 49798 as the most annotated start with 19 MA`s. It also corresponds to the LORF without significant overlap and is called in 100% of genes in the Pham.
    /note=
    /note=Evidence for a function:
    /note=All similar phages on NCBI BLAST call this gene a “HNH endonuclease." All annotated phages on PhagesDB BLAST call this gene “HNH endonuclease." HHpred aligns to “d.4.1.3 (M:1-105) Intron-encoded homing endonuclease I-HmuI {Bacteriophage SP01 [TaxId: 10685]}” with a probability of 99.9% and an e-value of 2.4e-26

CDS 50469 - 50873
  /gene="82"
  /product="gp82"
  /function="HNH endonuclease"
  /locus tag="Benllo_82"
    /note=Original Glimmer call @bp 50469 has strength 7.93; Genemark calls start at 50469
    /note=SSC: 50469-50873 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 2.39952E-94 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.323, -4.270292194613887, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage KeaneyLin] ],,YP_010666960,99.2537,2.39952E-94 SIF-HHPRED: d.4.1.3 (M:1-105) Intron-encoded homing endonuclease I-HmuI {Bacteriophage SP01 [TaxId: 10685]},,,d1u3em1,58.209,99.7 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 50469.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio and KeaneyLin with an e-value of 5e-77. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator support start site 50469 as the most annotated start with 53 MA`s. This also corresponds to the LORF without significant overlap. Found in 63 of 64 genes in the Pham. 
    /note=
    /note=Evidence for a function:
    /note=All similar phages on NCBI BLAST call this gene a “HNH endonuclease." Most annotated phages on PhagesDB BLAST call this gene “function unknown." HHpred aligns to “d.4.1.3 (M:1-105) Intron-encoded homing endonuclease I-HmuI {Bacteriophage SP01 [TaxId: 10685]}” with a probability of 99.7% and an e-value of 3.6e-21.

CDS 50870 - 51676
  /gene="83"
  /product="gp83"
  /function="thymidylate synthase"
  /locus tag="Benllo_83"
    /note=Original Glimmer call @bp 50870 has strength 7.69; Genemark calls start at 50870
    /note=SSC: 50870-51676 CP: yes SCS: both ST: SS BLAST-Start: [thymidylate synthase [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.286, -2.3335289980954053, yes F: thymidylate synthase SIF-BLAST: ,,[thymidylate synthase [Arthrobacter phage Kardesai] ],,YP_010666765,100.0,0.0 SIF-HHPRED: d.117.1.1 (A:) Thymidylate synthase {Bacteriophage T4 [TaxId: 10665]},,,d1tisa_,98.1343,100.0 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 50870.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio (1e-154) and Kardesai (1e-160). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 50870 with 19 MA`s. While not the most annotated start site, it does correspond to the LORF without significant overlap. 
    /note=
    /note=Evidence for a function:
    /note=All similar phages on NCBI BLAST call this gene a “thymidylate synthase." All annotated phages on PhagesDB BLAST call this gene “thymidylate synthase." The Conserved Domain Database calls this gene “thymidylate synthase”. HHpred aligns to “d.117.1.1 (A:1-264) Thymidylate synthase {Escherichia coli [TaxId: 562]}” with a probability of 100% and an e-value of 0.

CDS 51676 - 52035
  /gene="84"
  /product="gp84"
  /function="Hypothetical Protein"
  /locus tag="Benllo_84"
    /note=Original Glimmer call @bp 51676 has strength 8.84; Genemark calls start at 51676
    /note=SSC: 51676-52035 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage Hankly]],,NCBI, q1:s1 100.0% 3.60283E-81 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.824, -3.3226484487933954, yes F: Hypothetical Protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Hankly]],,WBF79131,100.0,3.60283E-81 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 51676.
    /note=Region encompasses all coding potential. Phages with high alignment such as Kardesai (3e-64) and KeaneyLin (6e-43). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 51676 as the most annotated start with 12 MA`s. While it does not correspond to the LORF without significant overlap, it is called in 100% of genes in the Pham.
    /note=
    /note=Evidence for a function:
    /note=Similar phages on NCBI BLAST call this gene “membrane protein." All annotated phages on PhagesDB BLAST call this gene “function unknown." HHpred aligns to “Sec-independent protein translocase protein TatB; transport protein; NMR {Escherichia coli}” with a probability of 68.4% and an e-value of 5.5.

CDS 52032 - 52391
  /gene="85"
  /product="gp85"
  /function="Hypothetical Protein"
  /locus tag="Benllo_85"
    /note=Original Glimmer call @bp 52032 has strength 8.9; Genemark calls start at 52032
    /note=SSC: 52032-52391 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB79_gp088 [Arthrobacter phage Heisenberger] ],,NCBI, q1:s1 100.0% 4.91326E-80 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.185, -3.284137222879636, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB79_gp088 [Arthrobacter phage Heisenberger] ],,YP_010666567,99.1597,4.91326E-80 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 52032.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio (1e-66) and Kardesai (5e-66). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 52032 as the most annotated start with 18 MA`s. It also corresponds to the LORF without significant overlap and is called in 100% of genes in the Pham.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 52391 - 52699
  /gene="86"
  /product="gp86"
  /function="Hypothetical Protein"
  /locus tag="Benllo_86"
    /note=Genemark calls start at 52391
    /note=SSC: 52391-52699 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein PQB81_gp089 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 2.01383E-68 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.446, -2.0111200136961407, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp089 [Arthrobacter phage Kardesai] ],,YP_010666768,100.0,2.01383E-68 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=GeneMark calls start at 52391.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio and Kardesai with an e-value of 6e-56. There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 52391 as the most annotated start with 9 MA`s. While it does not correspond to the LORF without significant overlap, it is called in 100% of genes in the Pham.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 52696 - 52941
  /gene="87"
  /product="gp87"
  /function="Hypothetical Protein"
  /locus tag="Benllo_87"
    /note=Original Glimmer call @bp 52696 has strength 6.24; Genemark calls start at 52696
    /note=SSC: 52696-52941 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB81_gp090 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 6.87157E-53 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.393, -4.129494980802052, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp090 [Arthrobacter phage Kardesai] ],,YP_010666769,100.0,6.87157E-53 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Glimmer and GeneMark both call start at 52696.
    /note=Region encompasses all coding potential. Phages with high alignment such as BenitoAntonio (2e-41) and Kardesai (9e-44). There is no significant overlap with other genes.
    /note=
    /note=Start site data:
    /note=Starterator supports start site 52696 as the most annotated start with 19 MA`s. It also corresponds to the LORF without significant overlap and is called in 100% of genes in the pham.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 53121 - 53378
  /gene="88"
  /product="gp88"
  /function="PnuC-like Nicotinamide riboside transporter"
  /locus tag="Benllo_88"
    /note=Original Glimmer call @bp 53121 has strength 3.02; Genemark calls start at 53121
    /note=SSC: 53121-53378 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 1.04145E-53 GAP: 179 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.795, -5.603046763998909, yes F: PnuC-like Nicotinamide riboside transporter SIF-BLAST: ,,[membrane protein [Arthrobacter phage Kardesai] ],,YP_010666770,100.0,1.04145E-53 SIF-HHPRED: NMN_transporter ; Nicotinamide mononucleotide transporter,,,PF04973.15,82.3529,99.1 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 53121
    /note=Region encompasses all coding potential. There is no significant overlap with other genes in the area
    /note=
    /note=Start site data:
    /note=Start was confirmed on Starterator at 53121 with 19 MA`s. Phagesdb Identified AM phages Arcadia and Kardesai as conserving the gene.
    /note=
    /note=Evidence for a function:
    /note=Some phages on NCBI BLAST call this gene “PnuC-like nicotinamide riboside transporter”. All annotated phages on PhagesDB BLAST call this gene “PnuC-like nicotinamide riboside transporter." HHpred aligns to “NMN_transporter ; Nicotinamide mononucleotide transporter” with a probability of 99.1% and an e-value of 1.7e-13.

CDS 53362 - 53586
  /gene="89"
  /product="gp89"
  /function="Hypothetical Protein"
  /locus tag="Benllo_89"
    /note=Original Glimmer call @bp 53362 has strength 8.17; Genemark calls start at 53362
    /note=SSC: 53362-53586 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI184_gp88 [Arthrobacter phage Mudcat] ],,NCBI, q1:s1 100.0% 5.26583E-44 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.256, -4.975913734906325, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein BI184_gp88 [Arthrobacter phage Mudcat] ],,YP_009300777,98.6487,5.26583E-44 SIF-HHPRED: DUF2663 ; Protein of unknown function (DUF2663),,,PF10864.11,97.2973,50.9 SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 53362.
    /note=Region encompasses all coding potential. There is no significant overlap with other genes
    /note=
    /note=Start site data:
    /note=Start was confirmed on Starterator at 53362 with 11 MA`s. Phagesdb Identified AM phages Hankly and Kardesai as conserving the gene.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 53583 - 54062
  /gene="90"
  /product="gp90"
  /function="Hypothetical Protein"
  /locus tag="Benllo_90"
    /note=Original Glimmer call @bp 53583 has strength 3.87; Genemark calls start at 53583
    /note=SSC: 53583-54062 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB76_gp095 [Arthrobacter phage Cheesy] ],,NCBI, q1:s1 100.0% 2.97055E-98 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.715, -5.492744381371201, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB76_gp095 [Arthrobacter phage Cheesy] ],,YP_010666282,92.4528,2.97055E-98 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 53583.
    /note=Region encompasses all coding potential.
    /note=
    /note=Start site data:
    /note=Start was confirmed on Starterator at 53583 with 17 MA`s. Phagesdb Identified AM phages Hankly and Kardesai as conserving the gene.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 54059 - 54313
  /gene="91"
  /product="gp91"
  /function="Hypothetical Protein"
  /locus tag="Benllo_91"
    /note=Original Glimmer call @bp 54059 has strength 1.99; Genemark calls start at 54059
    /note=SSC: 54059-54313 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB81_gp094 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 3.63263E-55 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.188, -4.601664605840989, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp094 [Arthrobacter phage Kardesai] ],,YP_010666773,100.0,3.63263E-55 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 54059. The host trained Genemark over this region is weak. Phagesdb blast reveals that this gene is present in several pahges being classified in Pham 235823 which has 14 members. Phagesdb blast show similarity to several AM phages such as Mooshroom, Hankly and Kardesai with an e value of e -46
    /note=
    /note=Start site data: The start site corresponds to the longest possible ORF with the second best posiible z and final scores of 2.6 and - 4.3 respectively, however does have an overlap of 4 bp with the gene 93. The chosen start gives a 1:1 alignment with several phages of the AM cluster including Kardesai with an e value of e - 46. Starterator supports this start @54059 with 13 MA`s 
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 54306 - 54569
  /gene="92"
  /product="gp92"
  /function="Hypothetical Protein"
  /locus tag="Benllo_92"
    /note=Original Glimmer call @bp 54306 has strength 6.2; Genemark calls start at 54306
    /note=SSC: 54306-54569 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQB81_gp095 [Arthrobacter phage Kardesai] ],,NCBI, q1:s1 100.0% 2.52988E-57 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.269, -4.379101430921652, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQB81_gp095 [Arthrobacter phage Kardesai] ],,YP_010666774,100.0,2.52988E-57 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call start at 54306.Region encompassing all coding potential is not very clear. There are severa similar phages with this gene that is classified under the pham 106708 which has 15 members. Phagesdb blast show similarity to several AM phages such as Mooshroom, Hankly and Kardesai with an e value of e -46. 
    /note=
    /note=Start site data: The start site corresponds to the longest possible ORF with the second best z and final scores of 2.6 and - 4.3 respectively, however does have an overlap of 8 bp with the gene 94. The chosen start gives a 1:1 alignment with several phages of the AM cluster including Kardesai with an e value of e - 44. Starterator supports this start @ 54306 with 14 MA`s. 
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.

CDS 54652 - 54789
  /gene="93"
  /product="gp93"
  /function="Hypothetical Protein"
  /locus tag="Benllo_93"
    /note=Genemark calls start at 54652
    /note=SSC: 54652-54789 CP: no SCS: genemark ST: SS BLAST-Start: [hypothetical protein FDH65_gp95 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 3.80321E-23 GAP: 82 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.795, -5.331979991712371, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp95 [Arthrobacter phage Circum] ],,YP_009603184,100.0,3.80321E-23 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene: Both GLimmer and Genemark call this a gene. There is coding potential that encompasses the entire region. This gene is classified under phan 714 which has 291 members. NCBI and Phagesdb blast show similarity to several AM phages such as BenitoAntonio, JEGGS and Hankly with an e value of e -108.  
    /note=
    /note=Start site data: The start site corresponds to the longest ORF with the best z and final scores of 2.256 and - 4.59 respectively, however does have an overlap of 35 bp with the gene 97. The chosen start gives a 1:1 alignment with several phages of the AM cluster including BenitoAntonio, Mudcat, Kardesai with an e value of e - 141. Starterator data needs to be added 
    /note=
    /note=Evidence for a function:
    /note=All similar phages on NCBI BLAST call this gene a “exonuclease." All annotated phages on PhagesDB BLAST call this gene “exonuclease." The Conserved Domain Database calls this gene “PD-(D/E)XK nuclease family protein." HHpred aligns to “DNA2_N-like; Nuclease domain of the nuclease/helicase DNA2 and related nucleases.

CDS 54986 - 55288
  /gene="94"
  /product="gp94"
  /function="VRR-Nuc domain protein"
  /locus tag="Benllo_94"
    /note=Original Glimmer call @bp 54986 has strength 2.71; Genemark calls start at 54959
    /note=SSC: 54986-55288 CP: yes SCS: both-gl ST: SS BLAST-Start: [endonuclease [Arthrobacter phage Heisenberger] ],,NCBI, q1:s1 100.0% 2.70639E-67 GAP: 196 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.435, -2.0949393225970705, yes F: VRR-Nuc domain protein SIF-BLAST: ,,[endonuclease [Arthrobacter phage Heisenberger] ],,YP_010666576,100.0,2.70639E-67 SIF-HHPRED: VRR-NUC-like; Virus-type replication repair nuclease. This model characterizes a set of nucleases that resemble Holliday-junction resolving enzymes.,,,cd22365,93.0,99.6 SIF-Syn: N/A
    /note=Evidence for a gene:
    /note=Both Glimmer and GeneMark call this gene. There is coding potential encompassed within the region. Similar phages show high alignment such as BenitoAntonio and GoCrazy with an e-value of 6e-54.
    /note=
    /note=Start site data:
    /note=Glimmer and GeneMark disagree on the start site. Glimmer calls start 54986 while GeneMark calls start 54959. The start site called by Glimmer is associated to start 33 which is found in 41/218 genes within the Pham. Start site 54986 also has 34 MA`s and is shared by other similar phages. 
    /note=
    /note=Evidence for a function:
    /note=All similar phages on NCBI BLAST call this gene a “endonuclease." All annotated phages on PhagesDB BLAST call this gene “VRR-Nuc domain protein." HHpred aligns to “Nuclease; Nuclease, HYDROLASE; HET: SO4; 1.85A {Salmonella phage SETP3} SCOP: c.52.1.35” with a probability of 99.7% and an e-value of 4.5e-20

CDS 55254 - 55832
  /gene="95"
  /product="gp95"
  /function="Cas4 family exonuclease"
  /locus tag="Benllo_95"
    /note=Original Glimmer call @bp 55254 has strength 8.45; Genemark calls start at 55254
    /note=SSC: 55254-55832 CP: yes SCS: both ST: SS BLAST-Start: [exonuclease [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 9.9812E-142 GAP: -35 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.256, -4.975913734906325, no F: Cas4 family exonuclease SIF-BLAST: ,,[exonuclease [Arthrobacter phage Circum] ],,YP_009603186,100.0,9.9812E-142 SIF-HHPRED: DNA2_N-like; Nuclease domain of the nuclease/helicase DNA2 and related nucleases. The eukaryotic nuclease/helicase DNA2 processes double-strand breaks in DNA that have single-stranded ends/overhangs, as well as Okazaki fragments and stalled replication forks.,,,cd22318,86.4583,99.2 SIF-Syn: 
    /note=Evidence for a gene: Both GLimmer and Genemark call this a gene. There is coding potential that encompasses the entire region. This gene is classified under phan 714 which has 291 members. NCBI and Phagesdb blast show similarity to several AM phages such as BenitoAntonio, JEGGS and Hankly with an e value of e -108.  
    /note=
    /note=Start site data: The start site corresponds to the longest ORF with the best z and final scores of 2.256 and - 4.59 respectively, however does have an overlap of 35 bp with the gene 97. The chosen start gives a 1:1 alignment with several phages of the AM cluster including BenitoAntonio, Mudcat, Kardesai with an e value of e - 141. Starterator supports this start with the Start @55254 being confirmed with 121 MA`s.
    /note=Evidence for a function:
    /note=All similar phages on NCBI BLAST call this gene a “exonuclease." On phagesdb members of this Pham are designated as Exonuclease or CAS 4 exonuclease.   On NCBI and The Conserved Domain Database there is the presence of  “PD-(D/E)XK nuclease family protein." HHpred aligns to “DNA2_N-like; Nuclease domain of the nuclease/helicase DNA2 and related nucleases and to the PD-(D/E)XK nuclease superfamily (PF12705.7) with an e value of 1.6 e -14 and 4.1 e-12 making this a member of the CAS 4 exonuclease

CDS 55829 - 58504
  /gene="96"
  /product="gp96"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Benllo_96"
    /note=Original Glimmer call @bp 55829 has strength 7.06; Genemark calls start at 55829
    /note=SSC: 55829-58504 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA-binding domain protein [Arthrobacter phage KeaneyLin] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.085, -4.810045260256, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA-binding domain protein [Arthrobacter phage KeaneyLin] ],,YP_010666972,99.6633,0.0 SIF-HHPRED: a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic},,,d1ijwc_,4.3771,97.6 SIF-Syn: 
    /note=Evidence for a gene: Both GLimmer and Genemark call this a gene. The host trained genemark coding potential that encompasses the entire region is not the greatest. This gene is classified under phan 712 which has 219 members. NCBI and Phagesdb blast show similarity to several AM phages such as Napolean, Keanylin with an e value of 0.
    /note=Start site data: The start site corresponds to the longest ORF with the best z and final scores of 2.0 and - 4.8 respectively, with an overlap of 4 bases with gene 98. The chosen start gives a 1:1 alignment with several phages of the AM cluster including Napolean and KeaneyLin with an e value 0.
    /note=Starterator data needs to be added 
    /note=
    /note=Evidence for a function:
    /note=Similar phages on NCBI BLAST call this gene “helix-turn-helix DNA-binding domain protein." All annotated phages on PhagesDB BLAST call this gene “helix-turn-helix DNA-binding domain protein." The Conserved Domain Database calls this gene “Helix-turn-helix domain of Hin and related proteins." HHpred aligns to “a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}” with a probability of 97.6% and an e-value of 4.6e-7

CDS 58516 - 58773
  /gene="97"
  /product="gp97"
  /function="Hypothetical Protein"
  /locus tag="Benllo_97"
    /note=Original Glimmer call @bp 58516 has strength 4.24; Genemark calls start at 58516
    /note=SSC: 58516-58773 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH65_gp99 [Arthrobacter phage Circum] ],,NCBI, q1:s1 100.0% 3.40949E-56 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.091, -3.1725816037952645, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH65_gp99 [Arthrobacter phage Circum] ],,YP_009603188,100.0,3.40949E-56 SIF-HHPRED:  SIF-Syn: 
    /note=Evidence for a gene: Both GLimmer and Genemark call this a gene. The host trained genemark coding potential that encompasses the entire region is not the greatest. This gene is classified under phan 707 which has 219 members. NCBI and Phagesdb blast show similarity to several AM phages such as Napolean, Hankly and Keanylin with an e value of e-44.
    /note=Start site data: The start site corresponds to the longest ORF with the best z and final scores of 3.0 and - 3.17 respectively, with an gap of 11bp gene 99. The chosen start gives a 1:1 alignment with several phages of the AM cluster including Napolean and KeaneyLin with an e value e-44.
    /note=
    /note=Evidence for a function:
    /note=PhagesDB, NCBI BLAST and HHPRED all call this gene to be a hypothetical protein with unknown function.