CDS 125 - 451
    /note=Phagesdb Function: terminase, small subunit
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97}
    /note=
    /note=
    /note=NCBI BLAST: terminase small subunit
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese to support the start position of this gene

CDS 432 - 1991
    /note=Phagesdb Function: terminase, large subunit
    /note=Phagesdb BLAST:  function unknown
    /note=HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97}
    /note=NCBI BLAST: terminase, large subunit
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese to support the start position of this gene

CDS 2031 - 3443
    /note=Phagesdb Function:
    /note=portal protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Portal protein
    /note=NCBI BLAST: portal protein
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 4;1 ratio with MakCheese to support the start position of this gene

CDS 3443 - 4942
    /note=Phagesdb Function: capsid maturation protease
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Mu-like_Pro ; Mu-like prophage I protein
    /note=NCBI BLAST: head maturation protease
    /note=
    /note=sometimes the CMP hits to ClpP proteases. If so, look for a serine-type endopeptidase activity.  A significant hit to the CMP of D29 and L5 is sufficient evidence.
    /note=
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 4945 - 5391
    /note=Phagesdb Function:  scaffolding protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Capsid fiber protein; bacteriophage, phi29, prohead,
    /note=NCBI BLAST: scaffolding protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 5418 - 6350
    /note=Phagesdb Function: major capsid protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED:  CAPSID PROTEIN
    /note=NCBI BLAST:  major capsid protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 6347 - 6769
    /note=Phagesdb Function: head-to-tail connector protein
    /note=Phagesdb BLAST:  function unknown
    /note=HHPRED: Hypothetical protein yqb
    /note=NCBI BLAST:hypothetical protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 6772 - 7164
    /note=Phagesdb Function: head-to-tail adaptor
    /note=Phagesdb BLAST:  function unknown
    /note=HHPRED: Head-to-tail adaptor; Bacteriophage, portal
    /note=NCBI BLAST: head-to-tail adaptor
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 7164 - 7487
    /note=Phagesdb Function: head-to-tail stopper
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Head-to-tail stopper;
    /note=NCBI BLAST:  head-to-tail stopped
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 7490 - 7870
    /note=Phagesdb Function: tail terminator
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED:  Tail terminator;
    /note=NCBI BLAST: hypothetical protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 7870 - 8145
    /note=Phagesdb Function: head-to-tail connector protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED:  DUF5403 ; Family of unknown function
    /note=NCBI BLAST: hypothetical protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 8235 - 8777
    /note=Phagesdb Function:  major tail protein
    /note=Phagesdb BLAST::  function unknown 
    /note=Phagesdb BLAST:
    /note=HHPRED:  Major tail protein;
    /note=NCBI BLAST: hypothetical protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 8780 - 9097
    /note=Phagesdb Function: major capsid and protease fusion protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: GINS_B_archaea_Gins23; beta-strand (B) domain of archaeal GINS complex protein Gins23. The GIN
    /note=NCBI BLAST:  hypothetical protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 9098 - 9445
    /note=Phagesdb Function: tail assembly chaperone
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Phage_TAC_10 ; Phage tail assembly chaperone
    /note=NCBI BLAST: tail assembly chaperone
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 9481 - 9930
    /note=Phagesdb Function: tail assembly chaperone
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Phage_Gp15 ; Bacteriophage Gp15 protein
    /note=NCBI BLAST: hypothetical protein
    /note=
    /note=slippery sequence; GGGAAAA

CDS 9944 - 15100
    /note=Phagesdb Function: tape measure protein
    /note=Phagesdb BLAST: no function 
    /note=HHPRED: Tape Measure Protein, gp57;
    /note=NCBI BLAST:  tail length tape measure protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 15106 - 16167
    /note=Phagesdb Function: minor tail protein
    /note=Phagesdb BLAST: function unknown 
    /note=HHPRED:  Minor tail protein
    /note=NCBI BLAST: hypothetical protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 16157 - 17863
    /note=Phagesdb Function:  minor tail protein
    /note=Phagesdb BLAST: minor tail protein
    /note=HHPRED: Minor tail protein;
    /note=NCBI BLAST: hypothetical protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 17879 - 18322
    /note=Phagesdb Function: minor tail protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: DUF2744 ; Protein of unknown function
    /note=NCBI BLAST: minor tail protein [Gordonia phage Ruthy] >gb|AXH50483.1| minor tail protein [Gordonia phage
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 18322 - 19425
    /note=Phagesdb Function: minor tail protein
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Pulmonary surfactant-associated protein D; collectin, c-type lectin, alpha-helical coiled coil,
    /note=NCBI BLAST: minor tail protein [Gordonia phage Ruthy] >gb|AXH50484.1| minor tail protein [Gordonia phage
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 19427 - 21907
    /note=Phagesdb Function: minor tail protein
    /note=Phagesdb BLAST: minor tail protein 
    /note=HHPRED: Minor tail protein; Bacteriophage, tail tip
    /note=NCBI BLAST: minor tail protein
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 2:3 ratio with MakCheese a to support the start position of this gene

CDS 21904 - 22950
    /note=Phagesdb Function: minor tail protein
    /note=Phagesdb BLAST: unknown fucntion 
    /note=HHPRED: Minor tail protein;
    /note=NCBI BLAST:  minor tail protein
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 22978 - 23340
    /note=Phagesdb Function: unknown 
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein

CDS 23393 - 23932
    /note=Phagesdb Function: lysin a, l-ala-d-glu peptidase domain
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Peptidase_M15_4 ; D-alanyl-D-alanine carboxypeptidase	
    /note=NCBI BLAST: endolysin [Gordonia phage Kenna] >ref|YP_009819067.1| endolysin [Gordonia phage Asapag] >gb|QCG77179.1| lysin A, L-Ala-D-Glu peptidase domain [Gordonia phage Lutum] >gb|WVX88567.1| lysin A, L-Ala-D-Glu peptidase domain [Gordonia phage CheeseTouch] >gb|AZS12298.1| lysin A, L-Ala-D-Glu peptidase domain [Gordonia phage Kenna] >gb|QAU07173.1| lysin A, L-Ala-D-Glu peptidase domain [Gordonia phage Asapag]
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 23934 - 24923
    /note=Phagesdb Function:: lysin a, glycosyl hydrolase domain
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: ENDOLYSIN; STRUCTURAL PROTEIN, ENDOLYSIN, SECONDARY TRANSLATION PRODUCT, BACTERIOPHAGE; HET: GOL, 1PE; 1.9A {CLOSTRIDIUM PHAGE PHICTP1}
    /note=NCBI BLAST:endolysin [Gordonia phage Kenna] >gb|AZS12299.1| lysin A, glycosyl hydrolase domain [Gordonia phage Kenna]
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 24926 - 25345
    /note=Phagesdb Function:holin
    /note=Phagesdb BLAST: Function Unknown
    /note=HHPRED:  Phage_holin_7_1 ; Mycobacterial 2 TMS Phage Holin (M2 Hol) Family
    /note=NCBI BLAST:  	hypothetical protein [Gordonia sp. KTR9] >gb|AFR48017.1| hypothetical protein KTR9_1377 [Gordonia sp. KTR9]
    /note=
    /note=4 membrane domain hits with DeepTMHMM. Two potential holins are back-to-back, so kept the function as membrane protein as suggested by the official functions list.
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 25345 - 25734
    /note=Phagesdb Function: holin
    /note=Phagesdb BLAST: function Unknown 
    /note=HHPRED: DUF4383 ; Domain of unknown function (DUF4383)
    /note=NCBI BLAST: holin [Gordonia phage Ruthy] >gb|AXH50490.1| holin [Gordonia phage Ruthy]
    /note=
    /note=4 membrane domain hits with DeepTMHMM. Two potential holins are back-to-back, so kept the function as membrane protein as suggested by the official functions list.
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 25731 - 26120
    /note=Phagesdb Function; scaffolding protein, tape measure protein,capsid maturation protease
    /note=Phagesdb BLAST: Function Unknown 
    /note=HHPRED: DUF2730 ; Protein of unknown function (DUF2730)
    /note=NCBI BLAST: hypothetical protein [Gordonia sp. KTR9]
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 26113 - 26916
    /note=Phagesdb Function: lysin b
    /note=Phagesdb BLAST: unknown function
    /note=HHPRED: Gene 12 protein; alpha/beta sandwich, CELL ADHESION; 2.0A {Mycobacterium phage D29}
    /note=NCBI BLAST: cutinase family protein [Gordonia sp. KTR9] >gb|AFR48018.1| hypothetical protein KTR9_1378 [Gordonia sp. KTR9]
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS complement (27066 - 27188)
    /note=Phagesdb Function : function unknown 
    /note=Phagesdb BLAST : unknown 
    /note=HHPRED:DUF3576 : Domain of unknown function (DUF3576)
    /note=NCBI BLAST : unknown

CDS complement (27231 - 29279)
    /note=Phagesdb Function: riia-like protein, dna helicase, tape measure protein, dna polymerase, dna binding protein
    /note=Phagesdb BLAST:  unknown
    /note=HHPRED: TNF receptor-associated protein 1; Chaperone, ATPase, ATP binding, Mitochondria; HET: ANP; 2.289A {Danio rerio}
    /note=NCBI BLAST: ATP-binding protein [Rhodococcus sp. 06-235-1A] >gb|OZD03396.1| hypothetical protein CH275_16615 [Rhodococcus sp. 06-235-1A]
    /note=
    /note=
    /note=
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese a to support the start position of this gene

CDS 29723 - 29851
    /note=Phagesdb Function:
    /note=Phagesdb BLAST:
    /note=HHPRED:
    /note=NCBI BLAST:

CDS 30618 - 30962
    /note=Phagesdb Function: immunity repressor
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: SITE-SPECIFIC RECOMBINASE XERD; XERD, RECOMBINASE, DNA BINDING, DNA RECOMBINATION; 2.5A {Escherichia coli} SCOP: d.163.1.1, a.60.9.1
    /note=NCBI BLAST: tyrosine integrase [Gordonia phage Pipp]

CDS 30983 - 31150
    /note=Phagesdb Function:integrase, (y-int)
    /note=Phagesdb BLAST:unkown
    /note=HHPRED: d.73.1.1 (M:3-110) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Halothiobacillus neapolitanus [TaxId: 927]} | CLASS: Alpha and beta proteins (a+b), FOLD: RuBisCO, small subunit, SUPFAM: RuBisCO, small subunit, FAM: RuBisCO, small subunit
    /note=NCBI BLAST:

CDS 31217 - 31435
    /note=Phagesdb Function:integrase
    /note=Phagesdb BLAST: tyrosine integrase
    /note=HHPRED:
    /note=NCBI BLAST: tyrosine integrase
    /note=
    /note=Phagesdb Function:esterase
    /note=Phagesdb BLAST: unknown
    /note=HHPRED:
    /note=NCBI BLAST:tyrosine integrase
    /note=
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese to support the start position of this gene

CDS complement (31159 - 31284)
    /note=Phagesdb Function: function unknown
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED:
    /note=NCBI BLAST: no data
    /note=
    /note=Start codon: GTG
    /note=Start codon: not edited because unknown

CDS complement (31624 - 32793)
    /note=Phagesdb Function: integrase
    /note=Phagesdb BLAST: integrase, (y-int)
    /note=HHPRED: Integrase; PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX; HET: PTR; 3.8A {Enterobacteria phage lambda} SCOP: d.163.1.1, d.10.1.4
    /note=NCBI BLAST:
    /note=Start codon: original & unedited; with a target from to: query from, 1:1 ratio with MakCheese to support the start position of this gene

CDS complement (32807 - 33034)
    /note=Phagesdb Function:helix-turn-helix dna binding protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED:
    /note=NCBI BLAST:

CDS complement (33031 - 33225)
    /note=Phagesdb Function:helix-turn-helix dna binding protein,metalloprotease,peptidase
    /note=Phagesdb BLAST:
    /note=HHPRED:
    /note=NCBI BLAST:

CDS 33283 - 33492
    /note=Phagesdb Function:helix-turn-helix DNA binding domain
    /note=Phagesdb BLAST:
    /note=HHPRED:
    /note=NCBI BLAST:

CDS complement (33524 - 34372)
    /note=Phagesdb Function:
    /note=Phagesdb BLAST:
    /note=HHPRED:
    /note=NCBI BLAST:

CDS complement (34372 - 34488)
    /note=Phagesdb BLAST: immunity repressor
    /note=HHPRED: SITE-SPECIFIC RECOMBINASE XERD; XERD, RECOMBINASE, DNA BINDING, DNA RECOMBINATION; 2.5A {Escherichia coli} SCOP: d.163.1.1, a.60.9.1
    /note=NCBI BLAST: tyrosine integrase [Gordonia phage Pipp]
    /note=
    /note=Start codon: ATG
    /note=Start codon: not edited

CDS complement (34485 - 35441)
    /note=Phagesdb Function:
    /note=Phagesdb BLAST:
    /note=HHPRED:
    /note=NCBI BLAST:

CDS complement (35443 - 36174)
    /note=Phagesdb Function:
    /note=Phagesdb BLAST:
    /note=HHPRED:
    /note=NCBI BLAST:

CDS 36395 - 36658
    /note=Phagesdb Function: cro protein
    /note=Phagesdb BLAST:  cro protein
    /note=HHPRED: repressor, DNA-binding domain
    /note=NCBI BLAST: helix-turn-helix DNA binding protein

CDS 36655 - 36921
    /note=Phagesdb Function: unknown functio
    /note=Phagesdb BLAST:unknown functio
    /note=HHPRED: Family of unknown functio
    /note=NCBI BLAST: hypothetical protein

CDS 36918 - 37457
    /note=Phagesdb Function:unknown
    /note=Phagesdb BLAST: unkown
    /note=HHPRED: Acetone carboxylase gamma subunit; carboxylation, ligase; HET: AMP, AE4, MG, ACT; 1.87A {Xanthobacter autotrophicus Py2}
    /note=NCBI BLAST: hypothetical protein

CDS 37518 - 38399
    /note=Phagesdb Function: antirepressor
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: ANT ; Phage antirepressor protein KilAC domain
    /note=NCBI BLAST: antirepressor
    /note=
    /note=changed start to 37518

CDS 38396 - 38686
    /note=Phagesdb Function: hypothetical protein
    /note=Phagesdb BLAST: portal protein
    /note=HHPRED:  Family of unknown function
    /note=NCBI BLAST: hypothetical protein

CDS 38683 - 38997
    /note=Phagesdb Function: excise,immunity repressor
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97}
    /note=NCBI BLAST: small subunit

CDS 38994 - 39212
    /note=Phagesdb Function: unknown
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: 
    /note=NCBI BLAST:
    /note=
    /note=One membrane hit with DeepTMHMM; confirmed by SOSUI
    /note=
    /note=Start codon: GTG

CDS 39209 - 39469
    /note=Phagesdb Function: unknown 
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein
    /note=
    /note=Start codon: GTG
    /note=Start codon: not edited because unknown

CDS 39555 - 39896
    /note=Phagesdb Function: unknown 
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein

CDS 39902 - 40801
    /note=Phagesdb Function: unknown 
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein

CDS 40798 - 41160
    /note=Phagesdb Function: unknown 
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein

CDS 41160 - 41480
    /note=Phagesdb Function: unknown 
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein

CDS 41477 - 42310
    /note=Phagesdb Function: unknown 
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein

CDS 42307 - 43419
    /note=Phagesdb Function: unknown, rect-like ssdna binding protein
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein

CDS 43412 - 43981
    /note=Phagesdb Function: unknown 
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein

CDS 44080 - 45615
    /note=Phagesdb Function: dna methyltranferase 
    /note=Phagesdb BLAST: 
    /note=HHPRED: 
    /note=NCBI BLAST:

CDS 45612 - 46262
    /note=Phagesdb Function: minor tail protein
    /note=Phagesdb BLAST: 
    /note=HHPRED: 
    /note=NCBI BLAST:

CDS complement (45621 - 46214)
    /note=Phagesdb Function: major tail protein, terminase, tape measure protein
    /note=Phagesdb BLAST: 
    /note=HHPRED: 
    /note=NCBI BLAST:
    /note=
    /note=one membrane domain hit with DeepTMHMM; confirmed by SOSUI

CDS 46352 - 46504
    /note=Phagesdb Function:helix-turn-helix dna binding protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED:
    /note=NCBI BLAST:

CDS 46504 - 46875
    /note=Phagesdb Function:unknown
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED:
    /note=NCBI BLAST:
    /note=
    /note=changed start to 46504

CDS 46872 - 47246
    /note=Phagesdb Function:
    /note=portal protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Portal protein
    /note=NCBI BLAST: portal protein

CDS 47246 - 47425
    /note=Phagesdb Function: unknown 
    /note=Phagesdb BLAST: unknown 
    /note=HHPRED: Virion-associated phage protein;
    /note=NCBI BLAST:  hypothetical protein

CDS 47543 - 48511
    /note=Phagesdb Function:RepA-like replication initiator
    /note=Phagesdb BLAST: Function Unknown
    /note=HHPRED:  
    /note=NCBI BLAST:
    /note=
    /note=changed start to 47543

CDS 48840 - 49217
    /note=Phagesdb Function: riia-like protein, dna helicase, tape measure protein, dna polymerase, dna binding protein
    /note=Phagesdb BLAST:  unknown
    /note=HHPRED: TNF receptor-associated protein 1; Chaperone, ATPase, ATP binding, Mitochondria; HET: ANP; 2.289A {Danio rerio}
    /note=NCBI BLAST: ATP-binding protein [Rhodococcus sp. 06-235-1A] >gb|OZD03396.1| hypothetical protein CH275_16615 [Rhodococcus sp. 06-235-1A]

CDS 49214 - 49885
    /note=Phagesdb Function:helix-turn-helix dna binding protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED:
    /note=NCBI BLAST

CDS 50344 - 50766
    /note=Phagesdb Function:terminase
    /note=portal protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: terminase
    /note=NCBI BLAST: terminase
    /note=
    /note=Leaving as hypothetical protein; however, gets significant HHPRED hits to terminase, large subunit

CDS 50763 - 51017
    /note=Phagesdb Function:
    /note=portal protein
    /note=Phagesdb BLAST: function unknown
    /note=HHPRED: Portal protein
    /note=NCBI BLAST: portal protein

Closest annotated phage with Ruthy (53.4% Gene Content Similarity)

•	SEA_ZODIARIAH_33-37: orphams that are directly upstream of a tyrosine integrase. SEA_ZODIARIAH_37 also gets a hit to a tyrosine integrase, while the others are hypothetical. SEA_ZODIARIAH_38 appears to be intact. I am not sure if 33-37 is fragmented. I tried to find a larger ORF to combine them but did not find one.
•	SEA_ZODIARIAH_26&27 are directly downstream of two lysin A genes and are potentially holins. The official function list was followed: “The literature suggests that some phages have more than one holin, for now when we seem multiple possibilities for a holin gene, let's call them membrane proteins.”
•	SEA_ZODIARIAH_63 is a reverse gene in a group of forward genes that gets a hit with pham 86633. There is an orpham in a similar position that is a forward gene (61 in PECAAN). The forward orpham was removed.
•	SEA_ZODIARIAH_73: receives a significant HHPRED hit to terminase large subunit, ATPase domain. Gene was left as hypothetical, given the location and other calls for NCBI BLAST hits.

Genes added in gaps (Only added in the DNA Master Minimal file):
•	SEA_ZODIARIAH_32 (29276-30136; reverse): BLASTs as DNA methyltransferase

Deleted phams in the DNA MASTER minimal file (Genes not deleted in PECAAN):
•	Gene40: Start site for SEA_ZODIARIAH_40 (gene39 in PECAAN) was extended. Gene40 was also a forward gene in a group of reverse genes
•	Gene61: see comment about SEA_ZODIARIAH_63 above.