CDS 92 - 430
  /gene="1"
  /product="gp1"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_1"
    /note=Original Glimmer call @bp 92 has strength 5.17; Genemark calls start at 92
    /note=SSC: 92-430 CP: yes SCS: both ST: SS BLAST-Start: [terminase large subunit, ATPase domain [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 2.0881E-54 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.088, -4.534720538854348, no F: hypothetical protein SIF-BLAST: ,,[terminase large subunit, ATPase domain [Arthrobacter phage LittleTokyo]],,QGZ16893,86.6071,2.0881E-54 SIF-HHPRED: DNA packaging protein Gp17; large terminase, Alternative initiation, ATP-binding, DNA-binding, Hydrolase, Nuclease, Nucleotide-binding; HET: PO4; 2.8A {Bacteriophage T4},,,3CPE_A,84.8214,99.1 SIF-Syn: Yes

When compared to LittleTokyo and Cygnet, a solid purple background surrounds gene 1 of zhuangyuan, indicating high nucleotide similarity, call terminase large subunit
    /note=HHPred and blast
    /note=
    /note=Top phage hits call terminase large subunit
    /note=
    /note=Multiple hits with greater than 90% probability and 80% coverage, call terminase large subunit

CDS 439 - 780
  /gene="2"
  /product="gp2"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_2"
    /note=Original Glimmer call @bp 439 has strength 3.92; Genemark calls start at 439
    /note=SSC: 439-780 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein VB1_CDS0001, partial [Arthrobacter phage Marchesin]],,NCBI, q1:s6 100.0% 1.65134E-39 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.145, -2.7806870294376242, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein VB1_CDS0001, partial [Arthrobacter phage Marchesin]],,WPM94250,75.6302,1.65134E-39 SIF-HHPRED: Tripartite terminase subunit 3; viral protein; HET: ADP; 4.5A {Human alphaherpesvirus 1 strain 17},,,6M5V_A,96.4602,99.2 SIF-Syn: No

When compared to other phage at this location, no known functions are being assigned to proteins upstream of the genome, a solid purple colored background indicates high nucleotide similarity. Antrice and Coral  has the same pham number as Zhuangyuan, 250578, and there are 55 genes in this sample.

All comparator phages do not call a function for this protein
    /note=Coverage of the query is high (100%); however, the coverage of the target protein is low (17%) since the target is significantly large). There are a few high probability matches; however, the query only matches up with small percentages of the targets.

CDS 794 - 1099
  /gene="3"
  /product="gp3"
  /function="terminase, small subunit"
  /locus tag="Zhuangyuan_3"
    /note=Original Glimmer call @bp 794 has strength 5.39; Genemark calls start at 794
    /note=SSC: 794-1099 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_2 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 3.11283E-63 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.145, -2.604595770381943, yes F: terminase, small subunit SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_2 [Arthrobacter phage LittleTokyo]],,QGZ16894,98.0198,3.11283E-63 SIF-HHPRED: Terminase_6 ; Terminase small subunit,,,PF23931.1,89.1089,99.8 SIF-Syn: Yes

When compared to LittleTokyo and Antrice, a solid purple background surrounds gene 1 of zhuangyuan, indicating high nucleotide similarity, call terminase small subunit
    /note=terminase, small subunit
    /note=
    /note=Top hits call terminase small subunit
    /note=
    /note=Multiple hits with greater than 90% probability and 80% coverage, call terminase small subunit

CDS 1041 - 2672
  /gene="4"
  /product="gp4"
  /function="terminase, large subunit"
  /locus tag="Zhuangyuan_4"
    /note=Original Glimmer call @bp 1206 has strength 9.71; Genemark calls start at 1206
    /note=SSC: 1041-2672 CP: yes SCS: both-cs ST: SS BLAST-Start: [terminase [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 0.0 GAP: -59 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -2.5052746077145835, yes F: terminase, large subunit SIF-BLAST: ,,[terminase [Arthrobacter phage LittleTokyo]],,QGZ16895,97.7901,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,90.0553,100.0 SIF-Syn: 

CDS 2685 - 3011
  /gene="5"
  /product="gp5"
  /function="RNA binding protein"
  /locus tag="Zhuangyuan_5"
    /note=Original Glimmer call @bp 2685 has strength 9.39; Genemark calls start at 2685
    /note=SSC: 2685-3011 CP: yes SCS: both ST: SS BLAST-Start: [RNA binding protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 1.85071E-39 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.145, -2.394485424036831, yes F: RNA binding protein SIF-BLAST: ,,[RNA binding protein [Arthrobacter phage LittleTokyo]],,QGZ16896,89.4231,1.85071E-39 SIF-HHPRED: N-alpha-acetyltransferase 38, NatC auxiliary subunit; NatB, NAA20, NAA25, TRANSFERASE; HET: IHP, CMC; 3.16A {Schizosaccharomyces pombe (strain 972 / ATCC 24843)},,,7L1K_C,68.5185,99.4 SIF-Syn: 

CDS 3024 - 4982
  /gene="6"
  /product="gp6"
  /function="portal protein"
  /locus tag="Zhuangyuan_6"
    /note=Original Glimmer call @bp 3024 has strength 5.63; Genemark calls start at 3024
    /note=SSC: 3024-4982 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 0.0 GAP: 12 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.858, -5.075057988041409, no F: portal protein SIF-BLAST: ,,[portal protein [Arthrobacter phage LittleTokyo]],,QGZ16897,94.5736,0.0 SIF-HHPRED: Portal protein; Archaeal virus, portal, portal capsid interface, Mg ions, VIRUS; HET: HIP, MG; 2.342A {Haloferax tailed virus 1},,,8QQN_PD,94.7853,100.0 SIF-Syn: High synteny with other phage in the AS2 pham with protein function marked as portal protein.

CDS 5002 - 5754
  /gene="7"
  /product="gp7"
  /function="capsid maturation protease"
  /locus tag="Zhuangyuan_7"
    /note=Original Glimmer call @bp 5002 has strength 6.13; Genemark calls start at 5002
    /note=SSC: 5002-5754 CP: yes SCS: both ST: SS BLAST-Start: [capsid maturation protease [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 93.6% 1.69827E-158 GAP: 19 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.145, -2.394485424036831, yes F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease [Arthrobacter phage LittleTokyo]],,QGZ16898,90.8,1.69827E-158 SIF-HHPRED: Peptidase_S78 ; Caudovirus prohead serine protease,,,PF04586.22,61.2,99.9 SIF-Syn: High synteny, aligns with many AS2 phage with marked function of capsid maturation protease.

CDS 5825 - 7132
  /gene="8"
  /product="gp8"
  /function="major capsid protein"
  /locus tag="Zhuangyuan_8"
    /note=Original Glimmer call @bp 5825 has strength 7.51; Genemark calls start at 5801
    /note=SSC: 5825-7132 CP: yes SCS: both-gl ST: SS BLAST-Start: [major capsid protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 0.0 GAP: 70 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.64, -3.95820260462814, no F: major capsid protein SIF-BLAST: ,,[major capsid protein [Arthrobacter phage LittleTokyo]],,QGZ16899,93.8215,0.0 SIF-HHPRED: major capsid protein gp3; Xanthomonas phage, capsid, icosahedron, VIRUS; 3.5A {Xanthomonas phage phiXacJX1},,,9LBM_G,99.5402,100.0 SIF-Syn: High synteny with other AS2 phage with marked function of major capsid protein.

CDS 7207 - 7446
  /gene="9"
  /product="gp9"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_9"
    /note=Original Glimmer call @bp 7207 has strength 8.11; Genemark calls start at 7207
    /note=SSC: 7207-7446 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_8 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 82.2785% 1.18409E-17 GAP: 74 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.72, -3.2804507689989406, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_8 [Arthrobacter phage LittleTokyo]],,QGZ16900,78.125,1.18409E-17 SIF-HHPRED: conserved hypothetical protein; T1445, NYSGXRC, UNKNOWN ORF, COG3027, PSI, Protein Structure Initiative, New York SGX Research Center for Structural; HET: MSE; 2.5A {Pseudomonas aeruginosa PAO1} SCOP: d.244.1.1,,,1T3U_C,29.1139,89.9 SIF-Syn: High synteny with AS2 pham with marked hypothetical protein.

CDS 7471 - 8058
  /gene="10"
  /product="gp10"
  /function="head-to-tail adaptor"
  /locus tag="Zhuangyuan_10"
    /note=Original Glimmer call @bp 7471 has strength 6.87; Genemark calls start at 7471
    /note=SSC: 7471-8058 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail adaptor [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 5.70549E-114 GAP: 24 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.485, -3.769471247018311, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Arthrobacter phage LittleTokyo]],,QGZ16901,93.8462,5.70549E-114 SIF-HHPRED: Adaptor protein gp8; Mycobacterium, bacteriophage, prolate head, head-to-tail connector, portal protein, adaptor protein, VIRUS, VIRAL PROTEIN; 3.46A {Mycolicibacterium phage Mycofy1},,,9LW9_D,91.7949,100.0 SIF-Syn: High synteny with other AS2 phage with marked function of head-to-tail adaptor.

CDS 8069 - 8407
  /gene="11"
  /product="gp11"
  /function="head-to-tail stopper"
  /locus tag="Zhuangyuan_11"
    /note=Genemark calls start at 8177
    /note=SSC: 8069-8407 CP: yes SCS: genemark-cs ST: SS BLAST-Start: [head-to-tail stopper [Arthrobacter phage Cygnet]],,NCBI, q1:s1 100.0% 1.19802E-73 GAP: 10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.982, -4.73920793635854, no F: head-to-tail stopper SIF-BLAST: ,,[head-to-tail stopper [Arthrobacter phage Cygnet]],,YAS75296,100.0,1.19802E-73 SIF-HHPRED: Head-to-tail stopper; Mycobacterium, bacteriophage, prolate head, head-to-tail interface, connector protein, terminator protein, tail tube protein, VIRUS, VIRAL PROTEIN;{Mycolicibacterium phage Mycofy1},,,9LWA_A,99.1071,99.8 SIF-Syn: Aligns with gene 10 of Little Tokyo. High synteny surrounding gene. When compared to Little Tokyo, gene 12 has a light purple background, indicating a 86% similarity with the bacteriophage. Gene 12 matches best with gene 10 in Little Tokyo which is a Head-to-tail stopper.
    /note=HHPred, Synteny, BLAST all indicate a head-to-tail stopper function. Low to no coding potential throughout the gene. The small pockets that show high coding potential is only because gene 12 overlaps completely with gene 11. Best hit is a head-to-tail stopper with a 99.79% probability. There are 21 other notable hits greater than 90%.

CDS 8412 - 8666
  /gene="12"
  /product="gp12"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_12"
    /note=Genemark calls start at 8412
    /note=SSC: 8412-8666 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_11 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 1.04868E-38 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.863, -5.064680329293257, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_11 [Arthrobacter phage LittleTokyo]],,QGZ16903,91.6667,1.04868E-38 SIF-HHPRED: DUF5403 ; Family of unknown function (DUF5403),,,PF17395.7,77.381,93.4 SIF-Syn: Aligns best with their protein of unknown function. When compared to Little Tokyo, gene 13 has a light purple background indicating a 86% high similarity with the bacteriophage. Gene 13 matches best with gene 11 in Little Tokyo which has an unknown function.
    /note=Phamerator, HHPred, BLAST data all support a protein of unknown function. Best hit is a family of unknown function with a 93.09% probability. There are no other hits greater than 90%.

CDS 8659 - 9102
  /gene="13"
  /product="gp13"
  /function="tail terminator"
  /locus tag="Zhuangyuan_13"
    /note=Original Glimmer call @bp 8650 has strength 5.07; Genemark calls start at 8650
    /note=SSC: 8659-9102 CP: yes SCS: both-cs ST: SS BLAST-Start: [tail terminator [Arthrobacter phage Cygnet]],,NCBI, q1:s1 100.0% 1.38374E-88 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.526, -5.626561759650101, no F: tail terminator SIF-BLAST: ,,[tail terminator [Arthrobacter phage Cygnet]],,YAS75298,92.517,1.38374E-88 SIF-HHPRED: Tail terminator; Bacteriophage, portal, VIRAL PROTEIN;{Mycobacterium phage Bxb1},,,9D94_Ic,95.9184,99.8 SIF-Syn: High synteny found when comparing with Little Tokyo bacteriophage. 86% similarity with a light purple background. Matches best with gene 12 of Little Tokyo which is a Tail terminator protein.
    /note=HHPred, Phamerator, and BLAST all support the function of this gene to be a tail terminator function. Best hit is a tail terminator protein with a 99.79% probability. There are 31 other probable hits greater than 90%, however, it is worth noting that most of the hits has some variation of a tail terminator protein.

CDS 9137 - 9718
  /gene="14"
  /product="gp14"
  /function="major tail protein"
  /locus tag="Zhuangyuan_14"
    /note=Original Glimmer call @bp 9137 has strength 11.69; Genemark calls start at 9137
    /note=SSC: 9137-9718 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 2.68978E-115 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.64, -3.4470622626190464, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage LittleTokyo]],,QGZ16905,90.2062,2.68978E-115 SIF-HHPRED: Major tail protein; Bacteriophage, portal, VIRAL PROTEIN;{Mycobacterium phage Bxb1},,,9D94_Jj,97.4093,99.9 SIF-Syn: Light purple background indicating an 86% similarity when comparing it to Little Tokyo. Matches best with Little Tokyo gene 13 which is a major tail protein.
    /note=Phamerator and BLAST both support a major tail protein to be the function, however, it is worth mentioning that HHPred found major tail protein to have a 99.93% probability for this gene. Best hit is a Phage tail tube protein with a 99.94% proability. It is worth noting that the next best hit is a major tail protein with a 99.93% probability. There are 3 hits greater than 90% probability.

CDS 9822 - 10175
  /gene="15"
  /product="gp15"
  /function="tail assembly chaperone"
  /locus tag="Zhuangyuan_15"
    /note=Original Glimmer call @bp 9822 has strength 7.84; Genemark calls start at 9822
    /note=SSC: 9822-10175 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 4.69895E-69 GAP: 103 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.735, -5.252038504870807, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage LittleTokyo]],,QGZ16906,97.4359,4.69895E-69 SIF-HHPRED: GP24_25 ; Mycobacteriophage tail assembly protein,,,PF17388.7,84.6154,96.2 SIF-Syn: When compared with LittleTokyo, there is a solid purple background behind the gene, indicating high nucleotide synteny. LittleTokyo calls "tail chaperone protein" for its genes 14/15 (which are linked to Zhuangyuan`s genes 16/17).
    /note=Phamerator, HHPred, and NCBI Blast all support this function. Genes 16 and 17 are part of a frameshift. Best hit is Mycobacteriophage tail assembly protein with a 96.41% probability. There are no other hits greater than 90% probability.

CDS join(9822..10148,10148..10546)
  /gene="16"
  /product="gp16"
  /function="tail assembly chaperone"
  /locus tag="Zhuangyuan_16"
    /note=
    /note=SSC: 9822-10546 CP: yes SCS: neither ST: NA BLAST-Start: [tail assembly chaperone [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 3.77841E-156 GAP: -354 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.735, -5.252038504870807, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage LittleTokyo]],,QGZ16907,97.5104,3.77841E-156 SIF-HHPRED: GP24_25 ; Mycobacteriophage tail assembly protein,,,PF17388.7,41.9087,98.8 SIF-Syn: When compared with LittleTokyo, there is a solid purple background behind the gene, indicating high nucleotide synteny. LittleTokyo calls "tail chaperone protein" for its genes 14/15 (which are linked to Zhuangyuan`s genes 16/17).
    /note=Phamerator, HHPred, and NCBI Blast all support this function. Genes 16 and 17 are part of a frameshift.

CDS 10550 - 12916
  /gene="17"
  /product="gp17"
  /function="tape measure protein"
  /locus tag="Zhuangyuan_17"
    /note=Original Glimmer call @bp 10550 has strength 4.18; Genemark calls start at 10565
    /note=SSC: 10550-12916 CP: yes SCS: both-gl ST: SS BLAST-Start: [tape measure protein [Arthrobacter phage LittleTokyo]],,NCBI, q12:s12 98.4772% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.62, -3.4892599424135016, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Arthrobacter phage LittleTokyo]],,QGZ16908,91.3596,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_AF,12.4365,99.9 SIF-Syn: When compared with LittleTokyo, there is a solid purple background behind the gene, indicating high nucleotide synteny. LittleTokyo calls "tape measure protein" for its gene 16 (which is linked to Zhuangyuan`s gene 18).
    /note=Phamerator, HHPred, and NCBI Blast all support this function.

CDS 12919 - 13767
  /gene="18"
  /product="gp18"
  /function="minor tail protein"
  /locus tag="Zhuangyuan_18"
    /note=Original Glimmer call @bp 12919 has strength 9.09; Genemark calls start at 12919
    /note=SSC: 12919-13767 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 2.50804E-163 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.982, -4.6768946155982105, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage LittleTokyo]],,QGZ16909,87.9433,2.50804E-163 SIF-HHPRED: Baseplate Centerpiece, gp25; Myophage, redox trigger, disulfides, VIRUS; 3.2A {Agrobacterium phage Milano},,,8FQC_U1,59.2199,90.0 SIF-Syn: When compared with LittleTokyo, there is a solid purple background behind the gene, indicating high nucleotide synteny. LittleTokyo calls "minor tail protein" for its gene 17 (which is linked to Zhuangyuan`s gene 19).
    /note=Phamerator and NCBI Blast support this function. HHPred does not support this function. The top HHPred function hit is a baseplate centerpiece protein.

CDS 13779 - 15026
  /gene="19"
  /product="gp19"
  /function="minor tail protein"
  /locus tag="Zhuangyuan_19"
    /note=Original Glimmer call @bp 13779 has strength 6.33; Genemark calls start at 13779
    /note=SSC: 13779-15026 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 99.2771% 0.0 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.886, -2.8564937087383147, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage LittleTokyo]],,QGZ16910,93.2692,0.0 SIF-HHPRED: Prophage MuSo2, 43 kDa tail protein; MuSo2, Shewanella oneidensis MR-1, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG; HET: MSE; 2.1A {Shewanella oneidensis} SCOP: b.106.1.1,,,3CDD_A,90.8434,99.9 SIF-Syn: When compared with LittleTokyo, there is a solid purple background behind the gene, indicating high nucleotide synteny. LittleTokyo calls "minor tail protein" for its gene 18 (which is linked to Zhuangyuan`s gene 20).
    /note=Phamerator, HHPred, and NCBI Blast all support this function.

CDS 15026 - 15979
  /gene="20"
  /product="gp20"
  /function="minor tail protein"
  /locus tag="Zhuangyuan_20"
    /note=Original Glimmer call @bp 15026 has strength 3.46; Genemark calls start at 15026
    /note=SSC: 15026-15979 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 99.6845% 2.67297E-150 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.04, -5.08247711351149, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage LittleTokyo]],,QGZ16911,87.9747,2.67297E-150 SIF-HHPRED: DUF3540 ; Protein of unknown function (DUF3540),,,PF12059.13,31.8612,91.6 SIF-Syn: No comparator phage call their gene in the same pham tail assembly chaperone so phamerator does data support this function
    /note=Genemark, BLAST, Glimmer, Staterator, and Gap/Overlap all support this call.

CDS 15984 - 16586
  /gene="21"
  /product="gp21"
  /function="minor tail protein"
  /locus tag="Zhuangyuan_21"
    /note=Original Glimmer call @bp 15984 has strength 6.67; Genemark calls start at 15984
    /note=SSC: 15984-16586 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Andrew] ],,NCBI, q1:s1 100.0% 1.02182E-62 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.543, -3.5707972674952195, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Andrew] ],,YP_009815706,67.0,1.02182E-62 SIF-HHPRED: putative baseplate protein; Phage, Lactococcus lactis, receptor binding protein, head domain, VIRAL PROTEIN; 2.3A {unidentified phage},,,2FSD_A,58.5,96.8 SIF-Syn: When compared to Cote, LittleTokyo, and other genes there is a purple background around gene 22 indicating large similarity. Additionally, most gene 22 are labelled minor tail protein directly downstream of the endolysin gene. The pham number does match for these genes, and there are 51 genes in this sample.
    /note=Start-site call: 15,026 (FS = −5.082). 1 bp overlap with the upstream gene; acceptable. Strong RBS (ATG) and the start best captures the CP.
    /note=
    /note=GeneMark/CP: Strong coding potential (>0.5) across >90% of the ORF in the forward frame; CP fully contained between 15,026–15,979.
    /note=
    /note=Homology: NCBI/PhagesDB hits to minor tail protein; HHpred top hits (≥85–90% prob.) also recover minor tail proteins; strong agreement across tools.
    /note=
    /note=Synteny: 1:1 neighborhood with LittleTokyo/Vulpecula; gene order conserved.
    /note=
    /note=TM domains: DeepTMHMM predicts 2 TMs; consistent with a tail fiber/tail tip–associated protein.
    /note=
    /note=Final function: Minor Tail Protein.

CDS 16586 - 17002
  /gene="22"
  /product="gp22"
  /function="membrane protein"
  /locus tag="Zhuangyuan_22"
    /note=Original Glimmer call @bp 16586 has strength 5.37; Genemark calls start at 16586
    /note=SSC: 16586-17002 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage Orcanus]],,NCBI, q3:s4 98.5507% 8.33446E-64 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.261, -4.2352789546214265, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Orcanus]],,QOI67666,86.4286,8.33446E-64 SIF-HHPRED:  SIF-Syn: When compared to Cote, LittleTokyo, and other genes there is a purple background around gene 23 indicating large similarity. Additionally, most gene 23 are not labelled a function directly downstream of the endolysin gene. The pham number does match for these genes, and there are 61 genes in this sample.
    /note=Start-site call: 15,984 (FS = −3.571). Creates a small +4 bp gap downstream; acceptable tradeoff to keep CP and RBS support aligned with the ORF.
    /note=
    /note=GeneMark/CP: Strong CP (>0.5) across >90% of the ORF; CP contained within 15,984–16,586.
    /note=
    /note=Homology: PhagesDB/NCBI hits and HHpred (≥95% prob.) both support minor tail protein; broad 1:1 conservation across close relatives.
    /note=
    /note=Synteny: Perfect 1:1 with neighbors in AS2 phages (“everything” in your sheet).
    /note=
    /note=TM domains: No TM helices predicted; still compatible with soluble tail component.
    /note=
    /note=Final function: Minor Tail Protein.

CDS 17013 - 17321
  /gene="23"
  /product="gp23"
  /function="membrane protein"
  /locus tag="Zhuangyuan_23"
    /note=Original Glimmer call @bp 17013 has strength 4.59; Genemark calls start at 17013
    /note=SSC: 17013-17321 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ03_gp22 [Arthrobacter phage Kuleana] ],,NCBI, q1:s1 100.0% 4.77231E-62 GAP: 10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.858, -4.934059474379222, no F: membrane protein SIF-BLAST: ,,[hypothetical protein HYQ03_gp22 [Arthrobacter phage Kuleana] ],,YP_009884830,99.0196,4.77231E-62 SIF-HHPRED: PspB ; Phage shock protein B,,,PF06667.17,60.7843,97.4 SIF-Syn: When compared to Cote, LittleTokyo, and other genes there is a purple background around gene 24 indicating large similarity. Additionally, most gene 24 are not labelled a function directly downstream of the endolysin gene. The pham number does match for these genes, and there are 228 genes in this sample.
    /note=Start-site call: 16,586 (FS = −4.235). −1 bp gap/overlap boundary; start fits CP and keeps clean boundaries.
    /note=
    /note=GeneMark/CP: CP present across >70% of ORF in the forward frame; CP lies within 16,586–17,002.
    /note=
    /note=Homology: BLAST to Orcanus (∼70% id.; 65% aligned) but annotations are vague/inconclusive; HHpred does not give a confident single function.
    /note=
    /note=Synteny: Locally conserved with AS2 neighbors (matches Orcanus/LittleTokyo neighborhood), but no clear functional consensus.
    /note=
    /note=TM domains: No compelling TM signal; treat as globular.
    /note=
    /note=Final function: Hypothetical protein (insufficient evidence to assign a specific function).

CDS 17386 - 18453
  /gene="24"
  /product="gp24"
  /function="endolysin"
  /locus tag="Zhuangyuan_24"
    /note=Original Glimmer call @bp 17386 has strength 4.67; Genemark calls start at 17386
    /note=SSC: 17386-18453 CP: yes SCS: both ST: SS BLAST-Start: [endolysin [Arthrobacter phage Andrew] ],,NCBI, q1:s1 99.7183% 0.0 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.64, -3.3060637489568596, no F: endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Andrew] ],,YP_009815709,90.5172,0.0 SIF-HHPRED: N-acetylmuramoyl-L-alanine amidase amiD; ZINC AMIDASE, PGRP, Peptidoglycan Recognizing Protein, AmpD, N-ACETYLMURAMYL-L-ALANINE AMIDASE, Cell wall biogenesis/degradation, Hydrolase, Lipoprotein, Membrane, Metal-binding; HET: GOL, AH0; 1.75A {Escherichia coli},,,3D2Y_A,49.2958,99.5 SIF-Syn: When compared to Cote, LittleTokyo, and other genes there is a purple background around gene 25 indicating large similarity. Additionally, most gene 25 are labelled Lysin A, N-acetylmuramoyl-L-alanine amidase domain. The pham number does match for these genes, and there are 50 genes in this sample.
    /note=Start-site call: 17,013 (FS = −4.934). Leaves a +10 bp gap—acceptable and best-supported by RBS/CP.
    /note=
    /note=GeneMark/CP: CP >0.5 across ~80% of ORF; fully contained within 17,013–17,321.
    /note=
    /note=Homology: BLAST to LittleTokyo (~83% id.; 75% aligned) but top hits are mixed/“random” for function; HHpred probabilities are high for disparate families → not convincing.
    /note=
    /note=Synteny: 1:1 with flanking genes across close AS2 relatives; still no specific functional consensus.
    /note=
    /note=TM domains: No confident TM prediction here.
    /note=
    /note=Final function: Hypothetical protein.

CDS 18457 - 18819
  /gene="25"
  /product="gp25"
  /function="membrane protein"
  /locus tag="Zhuangyuan_25"
    /note=Original Glimmer call @bp 18457 has strength 6.59; Genemark calls start at 18541
    /note=SSC: 18457-18819 CP: yes SCS: both-gl ST: SS BLAST-Start: [membrane protein [Arthrobacter phage Leona]],,NCBI, q1:s1 84.1667% 1.72312E-50 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -2.794070146961553, no F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Leona]],,QRI45432,89.5238,1.72312E-50 SIF-HHPRED:  SIF-Syn: Highly conserved with Little Tokyo
    /note=Start-site call: 17,386 (FS = −3.306). Large +64 bp gap upstream noted, but this start best matches CP/RBS and aligns with conserved homologs.
    /note=
    /note=GeneMark/CP: CP present across >60% of ORF; contained within 17,386–18,453.
    /note=
    /note=Homology: Strong BLAST (AS2/Andrew-like; ~85% id., ~88% aligned). HHpred high-probability hits to cell wall hydrolases/lysozyme-like amidases.
    /note=
    /note=Synteny: 1:1 with neighbors across AS2; sits in the expected lysin module.
    /note=
    /note=TM domains: None predicted; consistent with a soluble enzymatic domain.
    /note=
    /note=Final function: Endolysin (lysin A), N-acetylmuramoyl-L-alanine amidase.

CDS complement (18951 - 19118)
  /gene="26"
  /product="gp26"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_26"
    /note=Original Glimmer call @bp 19118 has strength 5.88; Genemark calls start at 19139
    /note=SSC: 19118-18951 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein FDI29_gp26 [Arthrobacter phage Abidatro] ],,NCBI, q9:s19 85.4545% 1.37955E-14 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.234, -4.213516249738288, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI29_gp26 [Arthrobacter phage Abidatro] ],,YP_009610246,58.4615,1.37955E-14 SIF-HHPRED:  SIF-Syn: Not conserved well with other phages, no similar genes on others

CDS complement (19115 - 19450)
  /gene="27"
  /product="gp27"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_27"
    /note=Original Glimmer call @bp 19450 has strength 4.61; Genemark calls start at 19450
    /note=SSC: 19450-19115 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_25 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 92.7928% 1.38599E-58 GAP: 26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.192, -2.5074698667202133, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_25 [Arthrobacter phage LittleTokyo]],,QGZ16917,90.3846,1.38599E-58 SIF-HHPRED: DUF4429 ; Domain of unknown function (DUF4429),,,PF14472.11,74.7748,99.5 SIF-Syn: Domain of unknown function (DUF4429). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and viruses, and is approximately 90 amino acids in length. This domain is often found in two tandem copies.

CDS complement (19477 - 19827)
  /gene="28"
  /product="gp28"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Zhuangyuan_28"
    /note=Original Glimmer call @bp 19827 has strength 7.25; Genemark calls start at 19827
    /note=SSC: 19827-19477 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA-binding domain protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 97.4138% 1.69612E-74 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.054, -3.3503726477288405, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA-binding domain protein [Arthrobacter phage LittleTokyo]],,QGZ16918,94.8718,1.69612E-74 SIF-HHPRED: Recombination Directionality Factor RdfS; Excisionase, Recombination Directionality Factor, winged helix-turn-helix, superhelix, DNA BINDING PROTEIN; HET: GOL; 2.45A {Mesorhizobium japonicum R7A},,,8DGL_B,45.6897,98.7 SIF-Syn: Conserved in bothHHPred and Blast

CDS complement (19824 - 20057)
  /gene="29"
  /product="gp29"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_29"
    /note=Original Glimmer call @bp 20003 has strength 6.08; Genemark calls start at 20057
    /note=SSC: 20057-19824 CP: yes SCS: both-gm ST: NI BLAST-Start:  GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.424, -3.8183153089559627, no F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: no synteny, HHPred calls lipoprotein

CDS complement (20054 - 20320)
  /gene="30"
  /product="gp30"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_30"
    /note=Original Glimmer call @bp 20224 has strength 2.17; Genemark calls start at 20287
    /note=SSC: 20320-20054 CP: yes SCS: both-cs ST: NA BLAST-Start:  GAP: 19 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.875, -2.8793565916978188, yes F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: Orpham, however, placement of the gene is not uncommon compared to other phages and the following gene confirms normal placement as well.
    /note=Not enough data to fully support the gene, but the RBS data sounds promising. GM and Glimmer are both non supportive of start site.

CDS complement (20340 - 21065)
  /gene="31"
  /product="gp31"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_31"
    /note=Original Glimmer call @bp 21065 has strength 10.13; Genemark calls start at 21065
    /note=SSC: 21065-20340 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_REDFOX_27 [Arthrobacter phage RedFox]],,NCBI, q1:s1 99.5851% 7.28645E-137 GAP: 551 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.978, -2.7423981586358774, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_REDFOX_27 [Arthrobacter phage RedFox]],,WNM72814,91.6318,7.28645E-137 SIF-HHPRED:  SIF-Syn: A very commonly conserved gene, none have a direct function noted, however.
    /note=All data lines up for a gene; however, the function is very unclear.

tRNA 21317 - 21384
  /gene="32"
  /product="tRNA-Asn(gtt)"
  /locus tag="ZHUANGYUAN_32"
    /note=tRNA-Asn(gtt)

CDS complement (21617 - 21877)
  /gene="33"
  /product="gp33"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_33"
    /note=Original Glimmer call @bp 21877 has strength 6.71; Genemark calls start at 21877
    /note=SSC: 21877-21617 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_30 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 2.26604E-52 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.145, -2.3158002311349737, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_30 [Arthrobacter phage LittleTokyo]],,QGZ16922,96.5116,2.26604E-52 SIF-HHPRED:  SIF-Syn: found within multiple other phages
    /note=All data support gene, but the function is unknown, and there is no concrete data for anything other than hypothetical proteins

CDS complement (21889 - 22227)
  /gene="34"
  /product="gp34"
  /function="DNA binding protein"
  /locus tag="Zhuangyuan_34"
    /note=Original Glimmer call @bp 22227 has strength 4.66; Genemark calls start at 22227
    /note=SSC: 22227-21889 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_COTE_31 [Arthrobacter phage Cote]],,NCBI, q1:s1 100.0% 1.69296E-71 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.62, -3.4283035164720754, yes F: DNA binding protein SIF-BLAST: ,,[hypothetical protein PBI_COTE_31 [Arthrobacter phage Cote]],,AYN57604,95.5357,1.69296E-71 SIF-HHPRED: Zn_ribbon_13 ; Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082),,,PF09855.14,41.0714,95.3 SIF-Syn: Aligned in a similar composition with others in pham, leads to believe it is a working protein
    /note=All RBS and Blast data support hypothetical proteins, and HHPred data are hypothetical proteins as well.

CDS complement (22224 - 22580)
  /gene="35"
  /product="gp35"
  /function="HNH endonuclease"
  /locus tag="Zhuangyuan_35"
    /note=Original Glimmer call @bp 22580 has strength 3.81; Genemark calls start at 22580
    /note=SSC: 22580-22224 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Arthrobacter phage LittleTokyo]],,NCBI, q4:s3 97.4576% 5.07998E-67 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.715, -5.372242857154667, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage LittleTokyo]],,QGZ16924,89.7436,5.07998E-67 SIF-HHPRED: 5-methylcytosine-specific restriction enzyme A; HNH ENDONUCLEASE, MODIFICATION DEPENDENT RESTRICTION, 5-METHYLCYTOSINE, 5MC, 5-HYDROXYMETHYLCYTOSINE, 5HMC, BBA-ME NUCLEASE, ScoMcrA, HYDROLASE; 2.85A {Escherichia coli (strain K12)},,,6GHC_B,61.0169,94.0 SIF-Syn: Other genes in the pham are labeled as HNH nucleases.
    /note=All BLAST data supports, HHPred gives decent support, and only the conserved domain is a Nuclease

CDS complement (22577 - 22960)
  /gene="36"
  /product="gp36"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Zhuangyuan_36"
    /note=Original Glimmer call @bp 22960 has strength 11.75; Genemark calls start at 22960
    /note=SSC: 22960-22577 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA-binding domain protein [Arthrobacter phage Ruchi]],,NCBI, q22:s13 77.1654% 4.04573E-21 GAP: 103 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.899, -2.9063687850157054, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA-binding domain protein [Arthrobacter phage Ruchi]],,WNM69478,58.7719,4.04573E-21 SIF-HHPRED: Putative uncharacterized protein; DNA BINDING PROTEIN; NMR {Hyperthermus butylicus},,,2LVS_A,72.4409,99.1 SIF-Syn: 
    /note=Though BLAST is weak, synteny and HHPRED , along with the official phage naming list support

CDS complement (23064 - 23204)
  /gene="37"
  /product="gp37"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_37"
    /note=Genemark calls start at 23204
    /note=SSC: 23204-23064 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein HYQ00_gp68 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 95.6522% 6.045E-18 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.14, -4.697746622201849, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp68 [Arthrobacter phage TripleJ] ],,YP_009884471,81.25,6.045E-18 SIF-HHPRED:  SIF-Syn: Phamerator shows a white background with Antrice and LittleTokyo, which means that Zhuangyuan`s gene has low synteny with genes of known function among closely related phages (Antrice and LittleTokyo). No function could be determined from this data.
    /note=Despite its relatively small length (141 bp), GeneMark evidence and coding potential, RBS data, 1:1 BLAST alignment, and high conservation (Starterator data) all support this being a gene. However, BLAST hits are all with hypothetical proteins and HHPred hit probability and coverage is not enough to support a specific function.

CDS complement (23214 - 23402)
  /gene="38"
  /product="gp38"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_38"
    /note=Original Glimmer call @bp 23402 has strength 11.89; Genemark calls start at 23402
    /note=SSC: 23402-23214 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOU53_gp35 [Arthrobacter phage Andrew] ],,NCBI, q1:s1 100.0% 2.85874E-23 GAP: 123 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -2.7653702713535186, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOU53_gp35 [Arthrobacter phage Andrew] ],,YP_009815721,85.4839,2.85874E-23 SIF-HHPRED: DNA-binding protein HU; protein HU, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, DNA BINDING PROTEIN; 2.48A {Bacillus anthracis} SCOP: a.55.1.1,,,3RHI_A,98.3871,94.8 SIF-Syn: Phamerator: Orange background with Antrice, green background with Andrew. Weak homology. However, close to a helix-turn-helix DNA binding gene in Antrice, which could serve as supporting evidence. Synteny is relatively conserved in this region.
    /note=HHPred crosses the confidence bar for this gene, with the top hit with a probability of 94.8 and 08.3871% coverage, which supports a functional call. Additionally, although with a low 20% identity, the Conserved Domain Database matches this to pfam18175, consistent with HU/IHF superfamily DNA-binding folds.

CDS complement (23526 - 24716)
  /gene="39"
  /product="gp39"
  /function="tyrosine integrase"
  /locus tag="Zhuangyuan_39"
    /note=Original Glimmer call @bp 24716 has strength 9.63; Genemark calls start at 24716
    /note=SSC: 24716-23526 CP: yes SCS: both ST: SS BLAST-Start: [tyrosine integrase [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.431, -5.903691177536518, yes F: tyrosine integrase SIF-BLAST: ,,[tyrosine integrase [Arthrobacter phage LittleTokyo]],,QGZ16928,96.7172,0.0 SIF-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,,,1Z1B_A,94.9495,100.0 SIF-Syn: High synteny with LittleTokyo, Cygnet, and Antrice, which all call a tyrosine integrase.
    /note=Very strong HHPred data, BLAST data, and synteny all support this gene`s function as a tyrosine integrase.

CDS complement (24709 - 25083)
  /gene="40"
  /product="gp40"
  /function="immunity repressor"
  /locus tag="Zhuangyuan_40"
    /note=Original Glimmer call @bp 25083 has strength 6.21; Genemark calls start at 25083
    /note=SSC: 25083-24709 CP: yes SCS: both ST: SS BLAST-Start: [immunity repressor [Arthrobacter phage LittleTokyo]],,NCBI, q6:s5 95.9677% 3.34253E-68 GAP: 194 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.905, -4.897971560974249, yes F: immunity repressor SIF-BLAST: ,,[immunity repressor [Arthrobacter phage LittleTokyo]],,QGZ16929,92.126,3.34253E-68 SIF-HHPRED: Nucleoid-associated protein EspR; ALL HELICAL, HELIX-TURN-HELIX MOTIF, TRANSACTIONAL REGULATOR, DNA BINDING, TRANSCRIPTION; 3.3A {Mycobacterium tuberculosis},,,4NDW_B,92.7419,98.8 SIF-Syn: Synteny (in Phamerator) with related AS-cluser phages (Cygnet and Antrice) strongly supports this being an immunity repressor.  Located immediately downstream of the integrase within the conserved lysogeny control module (Integrase, then Repressor , then Cro-like protein). Gene order strongly supports this functional assignment.
    /note=Start site is somewhat uncertain: 25,083 is the auto-annotated start site and what I kept, but it is not conserved at all in Phamerator, and 24939 is more strongly conserved (and shows valid HHPred hits too) However, GeneMark, Glimmer, and Blast data support 25,083.
    /note=With regards to the functional assignment, BLAST data shows strong conservation with known immunity repressors in related AS-cluster phages (e.g, Cygnet, Antrice, LittleTokyo), all sharing the same pham. HHpred data indicates a clear helix-turn-helix DNA-binding fold, which is typical of phage repressors.

CDS 25278 - 25538
  /gene="41"
  /product="gp41"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Zhuangyuan_41"
    /note=Genemark calls start at 25278
    /note=SSC: 25278-25538 CP: yes SCS: genemark ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 1.70406E-45 GAP: 194 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.64, -3.368377069717189, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage LittleTokyo]],,QGZ16930,91.8605,1.70406E-45 SIF-HHPRED: ComR; Streptococcus, Competence, Quorum sensing, ComR, TRANSCRIPTION REGULATOR; 2.9A {Streptococcus suis (strain 05ZYH33)},,,5FD4_A,73.2558,98.3 SIF-Syn: Purple background with Antrice and Andrew in Phamerator, indicating synteny, in a region with highly conserved gene order and function. In all cases, located immediately downstream of the immunity repressors.
    /note=BLAST, HHpred data, and synteny support this being a small Cro-like DNA-binding protein associated with transcriptional regulation of the lysogeny-lysis switch. BLAST data show similarity to short Cro-like or small transcriptional regulator HTH DNA-binding proteins found immediately downstream of immunity repressors (gene 39 in Zhuangyuan) in related phages. Additionally, HHpred data align this gene with multiple HTH DNA-binding regulators, including those of the Cro family, and CDD data confirm a small HTH motif.

CDS 25541 - 25783
  /gene="42"
  /product="gp42"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Zhuangyuan_42"
    /note=Genemark calls start at 25541
    /note=SSC: 25541-25783 CP: yes SCS: genemark ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage Renna12]],,NCBI, q1:s1 97.5% 7.35719E-25 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.475, -3.790975366313636, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage Renna12]],,UXE05389,70.7317,7.35719E-25 SIF-HHPRED: a.6.1.5 (B:1-69) automated matches {Escherichia phage [TaxId: 10710]} | CLASS: All alpha proteins, FOLD: Putative DNA-binding domain, SUPFAM: Putative DNA-binding domain, FAM: Terminase gpNU1 subunit domain,,,SCOP_d6hn7b1,67.5,99.0 SIF-Syn: 

CDS 25780 - 26808
  /gene="43"
  /product="gp43"
  /function="RecE-like exonuclease"
  /locus tag="Zhuangyuan_43"
    /note=Original Glimmer call @bp 25780 has strength 5.04; Genemark calls start at 25795
    /note=SSC: 25780-26808 CP: yes SCS: both-gl ST: SS BLAST-Start: [RecE-like exonuclease [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -2.8454123590742793, no F: RecE-like exonuclease SIF-BLAST: ,,[RecE-like exonuclease [Arthrobacter phage LittleTokyo]],,QGZ16932,94.7368,0.0 SIF-HHPRED: Uncharacterized protein R354; MIMIVIRE, Cas4-like, nuclease, R354, NUCLEAR PROTEIN; 2.806A {Acanthamoeba polyphaga mimivirus},,,5YET_A,92.1053,99.9 SIF-Syn: 

CDS 26808 - 27620
  /gene="44"
  /product="gp44"
  /function="RecT-like DNA pairing protein"
  /locus tag="Zhuangyuan_44"
    /note=Original Glimmer call @bp 26808 has strength 6.06; Genemark calls start at 26808
    /note=SSC: 26808-27620 CP: yes SCS: both ST: SS BLAST-Start: [RecT-like DNA pairing protein [Arthrobacter phage Leona]],,NCBI, q4:s1 98.8889% 7.97001E-171 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -2.827683592113848, no F: RecT-like DNA pairing protein SIF-BLAST: ,,[RecT-like DNA pairing protein [Arthrobacter phage Leona]],,QRI45448,94.3609,7.97001E-171 SIF-HHPRED: RecT; DNA Recombination, DNA Annealing, DNA BINDING PROTEIN; 4.5A {Listeria innocua Clip11262},,,7UBB_C,91.8519,100.0 SIF-Syn: 

CDS 27617 - 28213
  /gene="45"
  /product="gp45"
  /function="DNA methyltransferase"
  /locus tag="Zhuangyuan_45"
    /note=Genemark calls start at 27617
    /note=SSC: 27617-28213 CP: yes SCS: genemark ST: SS BLAST-Start: [DNA methyltransferase [Arthrobacter phage KHumphrey]],,NCBI, q1:s1 97.9798% 5.22997E-124 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.836, -5.887657146695936, no F: DNA methyltransferase SIF-BLAST: ,,[DNA methyltransferase [Arthrobacter phage KHumphrey]],,XIJ70207,92.5743,5.22997E-124 SIF-HHPRED: DNA CYTOSINE METHYLTRANSFERASE DNMT2; Human DNA Methyltransferase homologue, TRANSFERASE; HET: SAH, CSO; 1.8A {Homo sapiens} SCOP: c.66.1.26,,,1G55_A,95.9596,99.9 SIF-Syn: 

CDS 28263 - 28547
  /gene="46"
  /product="gp46"
  /function="DNA methyltransferase"
  /locus tag="Zhuangyuan_46"
    /note=Original Glimmer call @bp 27978 has strength 2.96; Genemark calls start at 28269
    /note=SSC: 28263-28547 CP: yes SCS: both-cs ST: SS BLAST-Start: [DNA methyltransferase [Arthrobacter phage Cygnet]],,NCBI, q1:s129 100.0% 8.04935E-53 GAP: 49 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.989, -7.095644780058815, no F: DNA methyltransferase SIF-BLAST: ,,[DNA methyltransferase [Arthrobacter phage Cygnet]],,YAS75329,40.5405,8.04935E-53 SIF-HHPRED: Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology.,,,cd00315,59.5745,96.6 SIF-Syn: 

CDS 28550 - 28903
  /gene="47"
  /product="gp47"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Zhuangyuan_47"
    /note=Original Glimmer call @bp 28550 has strength 4.76; Genemark calls start at 28550
    /note=SSC: 28550-28903 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA-binding domain protein [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 7.39929E-67 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.899, -2.9063687850157054, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA-binding domain protein [Arthrobacter phage LittleTokyo]],,QGZ16934,91.453,7.39929E-67 SIF-HHPRED: a.4.5.28 (A:) automated matches {Yersinia pseudotuberculosis [TaxId: 502800]} | CLASS: All alpha proteins, FOLD: DNA/RNA-binding 3-helical bundle, SUPFAM: `Winged helix` DNA-binding domain, FAM: MarR-like transcriptional regulators,,,SCOP_d4aiha_,75.2137,98.6 SIF-Syn: 

CDS 28900 - 29361
  /gene="48"
  /product="gp48"
  /function="RusA-like resolvase"
  /locus tag="Zhuangyuan_48"
    /note=Original Glimmer call @bp 28900 has strength 5.35; Genemark calls start at 28993
    /note=SSC: 28900-29361 CP: yes SCS: both-gl ST: SS BLAST-Start: [RusA family crossover junction endodeoxyribonuclease [Paenarthrobacter sp. YAF11_1] ],,NCBI, q1:s1 88.2353% 1.0022E-59 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.345, -4.000014702296222, no F: RusA-like resolvase SIF-BLAST: ,,[RusA family crossover junction endodeoxyribonuclease [Paenarthrobacter sp. YAF11_1] ],,WP_442012829,72.3684,1.0022E-59 SIF-HHPRED: d.79.6.1 (A:) automated matches {Escherichia coli [TaxId: 562]} | CLASS: Alpha and beta proteins (a+b), FOLD: Bacillus chorismate mutase-like, SUPFAM: Holliday junction resolvase RusA, FAM: Holliday junction resolvase RusA,,,SCOP_d2h8ea_,98.0392,99.9 SIF-Syn: 

CDS 29358 - 30155
  /gene="49"
  /product="gp49"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Zhuangyuan_49"
    /note=Original Glimmer call @bp 29358 has strength 2.89; Genemark calls start at 29358
    /note=SSC: 29358-30155 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage Juno112] ],,NCBI, q1:s1 100.0% 4.46007E-169 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.91, -4.905314844093283, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage Juno112] ],,XIJ70441,95.3668,4.46007E-169 SIF-HHPRED: Hypothetical Protein; Structural Genomics, NIAID, National Institute of Allergy and Infectious Diseases, Center for Structural Genomics of Infectious; HET: SO4, MSE; 1.8A {Vibrio cholerae O1 biovar El Tor},,,4RO3_A,21.8868,98.2 SIF-Syn: 

CDS 30152 - 31570
  /gene="50"
  /product="gp50"
  /function="DNA methyltransferase"
  /locus tag="Zhuangyuan_50"
    /note=Original Glimmer call @bp 30152 has strength 5.72; Genemark calls start at 30152
    /note=SSC: 30152-31570 CP: yes SCS: both ST: SS BLAST-Start: [DNA methylase [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.06, -4.864188174661353, no F: DNA methyltransferase SIF-BLAST: ,,[DNA methylase [Arthrobacter phage LittleTokyo]],,QGZ16937,96.1187,0.0 SIF-HHPRED: c.66.1.11 (A:) m.PvuII N4 cytosine-specific DNA methyltransferase {Proteus vulgaris [TaxId: 585]} | CLASS: Alpha and beta proteins (a/b), FOLD: S-adenosyl-L-methionine-dependent methyltransferases, SUPFAM: S-adenosyl-L-methionine-dependent methyltransferases, FAM: Type II DNA methylase,,,SCOP_d1booa_,97.0339,99.9 SIF-Syn: Littletokyo
    /note=All data supports, phages db official function list states to name methyltransferase instead of methylase.

CDS 31567 - 32046
  /gene="51"
  /product="gp51"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_51"
    /note=Genemark calls start at 31582
    /note=SSC: 31567-32046 CP: yes SCS: genemark-cs ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_46 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 6.02043E-85 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.782, -5.092497832398658, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_46 [Arthrobacter phage LittleTokyo]],,QGZ16938,97.4684,6.02043E-85 SIF-HHPRED: replisome organizer; helical  bipartite  natively unfolded domain, replication; HET: MSE; 2.4A {Bacillus phage SPP1} SCOP: l.1.1.1, a.179.1.1,,,1NO1_C,44.0252,99.3 SIF-Syn: 
    /note=All signs are pointing towards a gene, but function unnkown without much supporting evidence

CDS 32039 - 32629
  /gene="52"
  /product="gp52"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_52"
    /note=Original Glimmer call @bp 32039 has strength 4.88; Genemark calls start at 32105
    /note=SSC: 32039-32629 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_47 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 99.4898% 2.93756E-119 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.64, -3.3060637489568596, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_47 [Arthrobacter phage LittleTokyo]],,QGZ16939,95.8974,2.93756E-119 SIF-HHPRED: DUF7341 ; Domain of unknown function (DUF7341),,,PF24030.1,58.6735,98.4 SIF-Syn: 
    /note=All data points to 32039 as start site (BLAST, HHPRED, RBS), but not enough supporting data for function.

CDS 32761 - 32988
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_53"
    /note=Original Glimmer call @bp 32761 has strength 5.01; Genemark calls start at 32761
    /note=SSC: 32761-32988 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_48 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 1.54387E-37 GAP: 131 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.042, -4.551528886052257, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_48 [Arthrobacter phage LittleTokyo]],,QGZ16940,89.3333,1.54387E-37 SIF-HHPRED:  SIF-Syn: 
    /note=All data supports gene, but no known function

CDS 33056 - 33211
  /gene="54"
  /product="gp54"
  /function="membrane protein"
  /locus tag="Zhuangyuan_54"
    /note=Original Glimmer call @bp 33056 has strength 7.13; Genemark calls start at 33056
    /note=SSC: 33056-33211 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage RedFox] ],,NCBI, q1:s1 98.0392% 6.09073E-6 GAP: 67 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.054, -3.095100142625534, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage RedFox] ],,WNM72838,82.3529,6.09073E-6 SIF-HHPRED:  SIF-Syn: Very used in the pham, however, none are labeled with an official function.
    /note=All data support the gene; however, it has murky data for function. High likelihood of being a membrane protein,;however, not enough backing evidence

CDS 33208 - 33450
  /gene="55"
  /product="gp55"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_55"
    /note=Original Glimmer call @bp 33208 has strength 7.74; Genemark calls start at 33208
    /note=SSC: 33208-33450 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_50 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 5.49116E-31 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.91, -4.905314844093283, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_50 [Arthrobacter phage LittleTokyo]],,QGZ16942,85.0,5.49116E-31 SIF-HHPRED:  SIF-Syn: No comparator phage call their gene in the same pham tail assembly chaperone so phamerator does data support this function.
    /note=Genemark, BLAST, Glimmer, Staterator, and Gap/Overlap all support this call.

CDS 33443 - 33811
  /gene="56"
  /product="gp56"
  /function="nucleoside deoxyribosyltransferase"
  /locus tag="Zhuangyuan_56"
    /note=Original Glimmer call @bp 33443 has strength 6.14; Genemark calls start at 33443
    /note=SSC: 33443-33811 CP: yes SCS: both ST: SS BLAST-Start: [deoxycytidylate deaminase [Arthrobacter phage LittleTokyo]],,NCBI, q5:s6 95.9016% 8.53005E-60 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.139, -4.700217548281525, no F: nucleoside deoxyribosyltransferase SIF-BLAST: ,,[deoxycytidylate deaminase [Arthrobacter phage LittleTokyo]],,QGZ16943,83.0645,8.53005E-60 SIF-HHPRED: Nucleoside 2-deoxyribosyltransferase; deoxyribosyltransferase, Rossmann-fold, structural genomics, PSI-Biology, Midwest Center for Structural Genomics, MCSG, TRANSFERASE; HET: GOL, MSE, EDO; 2.15A {Enterococcus faecalis},,,7M5H_B,81.9672,99.6 SIF-Syn: No comparator phage calls their gene in the same pham tail assembly chaperone, so Phamerator does data support this function. No known function with no transmembrane domain
    /note=Genemark, BLAST, Glimmer, Staterator, and Gap/Overlap all support this call

CDS 33812 - 34033
  /gene="57"
  /product="gp57"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_57"
    /note=Original Glimmer call @bp 33812 has strength 8.36; Genemark calls start at 33812
    /note=SSC: 33812-34033 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Nocardia cerradoensis] ],,NCBI, q5:s7 90.411% 8.05228E-21 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.037, -4.561336254060166, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Nocardia cerradoensis] ],,WP_039781937,64.1026,8.05228E-21 SIF-HHPRED:  SIF-Syn: No comparator phage call their gene in the same pham tail assembly chaperone so phamerator does data support this function.
    /note=Genemark, BLAST, Glimmer, Staterator, and Gap/Overlap all support this call.

CDS 34030 - 34542
  /gene="58"
  /product="gp58"
  /function="SSB protein"
  /locus tag="Zhuangyuan_58"
    /note=Original Glimmer call @bp 34030 has strength 5.28; Genemark calls start at 34030
    /note=SSC: 34030-34542 CP: yes SCS: both ST: SS BLAST-Start: [single strand DNA binding protein [Arthrobacter phage Cupello]],,NCBI, q1:s1 100.0% 2.55369E-89 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -2.8454123590742793, yes F: SSB protein SIF-BLAST: ,,[single strand DNA binding protein [Arthrobacter phage Cupello]],,WPM94380,89.4118,2.55369E-89 SIF-HHPRED: Single-stranded DNA-binding protein; DNA binding, quaternary structure, plasticity, inhibitor development, DNA BINDING PROTEIN; HET: FMT; 1.92A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)},,,7F5Y_A,70.5882,100.0 SIF-Syn: Because the top BLAST hit is marked as ‘unknown’ and none of the other similar genes have a known role, this gene is most likely a hypothetical protein with no identified function.
    /note=Genemark, BLAST, Glimmer, Staterator, and Gap/Overlap all support this call

CDS 34701 - 35435
  /gene="59"
  /product="gp59"
  /function="NucT-like nuclease"
  /locus tag="Zhuangyuan_59"
    /note=Original Glimmer call @bp 34701 has strength 10.9; Genemark calls start at 34701
    /note=SSC: 34701-35435 CP: yes SCS: both ST: SS BLAST-Start: [NucT-like nuclease [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 7.16196E-177 GAP: 158 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.886, -2.935178901640172, yes F: NucT-like nuclease SIF-BLAST: ,,[NucT-like nuclease [Arthrobacter phage LittleTokyo]],,QGZ16945,100.0,7.16196E-177 SIF-HHPRED: Nuclease NucT; Endonuclease, DNA BINDING PROTEIN; HET: ACT, GOL; 1.58A {Helicobacter pylori},,,6EHI_J,61.4754,99.4 SIF-Syn: When compared to LittleTokyo and Kuleana, a solid purple colored background was shown around gene 61 indicating high nucleotide similarity. Both Kuleana gene 57 and LittleTokyo gene 53 have the same pham number as Zhuangyuan gene 61, 263063 and both call for NucT-like nuclease protein.

CDS 35435 - 35701
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_60"
    /note=Genemark calls start at 35435
    /note=SSC: 35435-35701 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_54 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 3.09111E-39 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.971, -4.762070819318045, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_54 [Arthrobacter phage LittleTokyo]],,QGZ16946,86.3636,3.09111E-39 SIF-HHPRED:  SIF-Syn: When compared to LittleTokyo, a solid purple colored background was shown around gene 62 indicating high nucleotide similarity. Both Zhuangyuan gene 62 and LittleTokyo gene 54 have the same pham number, 110637 but it does not call for any protein.
    /note=Longest ORF as well as no major violations; less than ideal RBS scores and alignment, but no glaring issues. While this is most likely a gene, the top hits on HHPred are not unanimous in what the function is. Furthermore, the matches on Phamerator do not have any known function

CDS 35698 - 36057
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_61"
    /note=Genemark calls start at 35680
    /note=SSC: 35698-36057 CP: yes SCS: genemark-cs ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_55 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 9.7443E-56 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.247, -4.125189544139167, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_55 [Arthrobacter phage LittleTokyo]],,QGZ16947,90.678,9.7443E-56 SIF-HHPRED: Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97},,,6Z6E_B,81.5126,99.8 SIF-Syn: When compared to LittleTokyo and Kuleana, a solid purple colored background was shown around gene 63 indicating high nucleotide similarity. Both Kuleana gene 58 and LittleTokyo gene 55 have the same pham number as Zhuangyuan gene 63, 198206 but they do not call for a protein.
    /note=As the auto annotated start site had an excessive overlap, the start site with the second longest ORF had no such violations, higher RBS scores, and is more strongly supported by the coding potential graph. Even though Phamerator has no function assigned, the top hits on BLAST and HHPred generally say terminase small subunit.

CDS 36054 - 36179
  /gene="62"
  /product="gp62"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_62"
    /note=
    /note=SSC: 36054-36179 CP: yes SCS: neither ST: NA BLAST-Start: [hypothetical protein QEO76_gp49 [Arthrobacter phage Cole] ],,NCBI, q1:s1 90.2439% 8.73546E-6 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.58, -3.430952136556091, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QEO76_gp49 [Arthrobacter phage Cole] ],,YP_010761016,18.3099,8.73546E-6 SIF-HHPRED:  SIF-Syn: 

CDS 36179 - 36406
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_63"
    /note=Genemark calls start at 36179
    /note=SSC: 36179-36406 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_56 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 4.70225E-18 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.661, -3.4030855957987485, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_56 [Arthrobacter phage LittleTokyo]],,QGZ16948,68.2927,4.70225E-18 SIF-HHPRED:  SIF-Syn: Multiple hits on Phamerator, but no known gene function.
Good synteny with LittleTokyo and Cote, shares phan number, 198206, with gene 55 on LittleTokyo and gene 59 on Cote but neither call for any function.
    /note=There is another start site with a longer ORF and similar RBS scores, but the fact that it had no MA, while the auto annotated start position did, suggests that 36179 is the most likely start site. Additionally, there are multiple hits, but all are inconclusive; cannot determine a specific gene function. 
    /note=
    /note=Also potentially "Tudor Domain" --> multiple hits, but data remains ambiguous

CDS 36406 - 36573
  /gene="64"
  /product="gp64"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_64"
    /note=
    /note=SSC: 36406-36573 CP: yes SCS: neither ST: NA BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_57 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 4.79914E-29 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.634, -3.460008083817467, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_57 [Arthrobacter phage LittleTokyo]],,QGZ16949,98.1818,4.79914E-29 SIF-HHPRED: DUF7837 ; Domain of unknown function (DUF7837),,,PF25207.1,58.1818,95.6 SIF-Syn: 

CDS 36560 - 36691
  /gene="65"
  /product="gp65"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_65"
    /note=Original Glimmer call @bp 36560 has strength 3.76; Genemark calls start at 36560
    /note=SSC: 36560-36691 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_58 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 5.27555E-13 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.858, -5.014101562099983, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_58 [Arthrobacter phage LittleTokyo]],,QGZ16950,88.6364,5.27555E-13 SIF-HHPRED:  SIF-Syn: synteny with other phages did not show any functions.
    /note=Strong RBS scores, longest ORF, and many manual annotations all support auto annotated start site; only issue is the excessive gap. Could not conclude a final function because did not have enough data in HHPred and BLAST matched it with a hypothetical protein.

CDS 36691 - 36900
  /gene="66"
  /product="gp66"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_66"
    /note=Genemark calls start at 36691
    /note=SSC: 36691-36900 CP: no SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_59 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 76.8116% 9.80799E-20 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.931, -4.924073590240254, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_59 [Arthrobacter phage LittleTokyo]],,QGZ16951,60.274,9.80799E-20 SIF-HHPRED:  SIF-Syn: synteny with other phages did not show any functions
    /note=Could not conclude a final function because did not have enough data in HHPred and BLAST matched it with a hypothetical protein.

CDS 36884 - 37036
  /gene="67"
  /product="gp67"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_67"
    /note=
    /note=SSC: 36884-37036 CP: yes SCS: neither ST: NA BLAST-Start: [hypothetical protein SEA_CYGNET_62 [Arthrobacter phage Cygnet]],,NCBI, q1:s1 98.0% 6.86144E-20 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.236, -4.49916128710597, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CYGNET_62 [Arthrobacter phage Cygnet]],,YAS75348,92.0,6.86144E-20 SIF-HHPRED:  SIF-Syn: 

CDS 37033 - 37320
  /gene="68"
  /product="gp68"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_68"
    /note=Original Glimmer call @bp 37036 has strength 4.73; Genemark calls start at 37036
    /note=SSC: 37033-37320 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_61 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 2.77706E-29 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.068, -4.558788117097056, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_61 [Arthrobacter phage LittleTokyo]],,QGZ16953,67.3469,2.77706E-29 SIF-HHPRED:  SIF-Syn: synteny with other phages did not show any functions
    /note=could not conclude final function because there was not enough data in HHPred and BLAST matched it with a hypothetical protein.

CDS 37317 - 37526
  /gene="69"
  /product="gp69"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_69"
    /note=Original Glimmer call @bp 37317 has strength 7.79; Genemark calls start at 37317
    /note=SSC: 37317-37526 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_63 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 1.09387E-9 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.085, -4.522979412939132, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_63 [Arthrobacter phage LittleTokyo]],,QGZ16955,65.7143,1.09387E-9 SIF-HHPRED: DUF4350 ; Domain of unknown function (DUF4350),,,PF14258.12,69.5652,92.4 SIF-Syn: high synteny in pham4740 in almost every phage in AS2. no specific function denoted for any of these proteins

CDS 37523 - 37717
  /gene="70"
  /product="gp70"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_70"
    /note=Genemark calls start at 37523
    /note=SSC: 37523-37717 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_64 [Arthrobacter phage LittleTokyo]],,NCBI, q17:s16 75.0% 1.77471E-18 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.84, -7.134041170973121, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_64 [Arthrobacter phage LittleTokyo]],,QGZ16956,70.3125,1.77471E-18 SIF-HHPRED:  SIF-Syn: high synteny in pham231577 in almost every phage in AS2. no specific function denoted for any of these proteins

CDS 37714 - 38151
  /gene="71"
  /product="gp71"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_71"
    /note=Genemark calls start at 37714
    /note=SSC: 37714-38151 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_LITTLETOKYO_65 [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 4.96922E-73 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLETOKYO_65 [Arthrobacter phage LittleTokyo]],,QGZ16957,85.5172,4.96922E-73 SIF-HHPRED:  SIF-Syn: synteny with only LittleTokyo in pham113116, no other synteny. no specific function denoted for gene in LittleTokyo

CDS 38148 - 38423
  /gene="72"
  /product="gp72"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_72"
    /note=Genemark calls start at 38148
    /note=SSC: 38148-38423 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein [Actinomycetota bacterium]],,NCBI, q4:s3 95.6044% 2.2348E-39 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.156, -4.394706008439538, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Actinomycetota bacterium]],,MDQ5860683,78.7234,2.2348E-39 SIF-HHPRED: Zn_Ribbon_YjdM ; PhnA Zinc-Ribbon,,,PF08274.17,30.7692,97.3 SIF-Syn: synteny with only Cote in pham86460, no other synteny. no specific function denoted for gene in Cote

CDS 38420 - 38548
  /gene="73"
  /product="gp73"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_73"
    /note=
    /note=SSC: 38420-38548 CP: yes SCS: neither ST: NA BLAST-Start: [hypothetical protein SEA_LEONA_65 [Arthrobacter phage Leona]],,NCBI, q1:s1 100.0% 1.81852E-15 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.016, -4.747162315600301, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LEONA_65 [Arthrobacter phage Leona]],,QRI45473,88.0952,1.81852E-15 SIF-HHPRED:  SIF-Syn: 
    /note=Small but coding potential here, but enough with the BLAST matches to call the gene.

CDS 38545 - 38709
  /gene="74"
  /product="gp74"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_74"
    /note=
    /note=SSC: 38545-38709 CP: yes SCS: neither ST: NA BLAST-Start:  GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.145, -2.394485424036831, yes F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Small bit of coding potential here.  BLASTn match to Cygnet

CDS 38706 - 39035
  /gene="75"
  /product="gp75"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_75"
    /note=Genemark calls start at 38706
    /note=SSC: 38706-39035 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein VG1_CDS0075 [Arthrobacter phage Cupello]],,NCBI, q68:s4 38.5321% 1.12188E-14 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.079, -5.125750769048503, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein VG1_CDS0075 [Arthrobacter phage Cupello]],,WPM94399,77.7778,1.12188E-14 SIF-HHPRED:  SIF-Syn: No

When compared to LittleTokyo and Brynnie, gene 76 of Zhuangyuan connects to Brynnie with a light orange line and white background, indicating very low similarity
    /note=No hits with greater than 90% probability or that cover 80% or more of the query; many call RNA-polymerase binding protein 
    /note=
    /note=Top hits are to other related phage that the program is calling hypothetical proteins

CDS 39263 - 39628
  /gene="76"
  /product="gp76"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Zhuangyuan_76"
    /note=
    /note=SSC: 39263-39628 CP: yes SCS: neither ST: NA BLAST-Start: [helix-turn-helix DNA-binding domain protein [Arthrobacter phage Leona]],,NCBI, q1:s1 64.4628% 2.45218E-32 GAP: 227 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.875, -2.8793565916978188, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA-binding domain protein [Arthrobacter phage Leona]],,QRI45475,79.5181,2.45218E-32 SIF-HHPRED: Recombination Directionality Factor RdfS; Excisionase, Recombination Directionality Factor, winged helix-turn-helix, superhelix, DNA BINDING PROTEIN; HET: GOL; 2.45A {Mesorhizobium japonicum R7A},,,8DGL_B,57.0248,98.9 SIF-Syn: 

CDS 39727 - 39909
  /gene="77"
  /product="gp77"
  /function="hypothetical protein"
  /locus tag="Zhuangyuan_77"
    /note=
    /note=SSC: 39727-39909 CP: yes SCS: neither ST: NA BLAST-Start:  GAP: 98 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.39, -4.477782298370688, yes F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Small bit of coding potential here.  BLASTn match to LittleTokyo

CDS 39902 - 40180
  /gene="78"
  /product="gp78"
  /function="HNH endonuclease"
  /locus tag="Zhuangyuan_78"
    /note=
    /note=SSC: 39902-40180 CP: yes SCS: neither ST: NI BLAST-Start: [HNH endonuclease [Arthrobacter phage LittleTokyo]],,NCBI, q1:s1 100.0% 5.92637E-57 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.64, -3.368377069717189, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage LittleTokyo]],,QGZ16965,95.6522,5.92637E-57 SIF-HHPRED: CRISPR-associated endonuclease Cas9; Inhibitor, Complex, VIRAL PROTEIN; HET: NI; 2.097A {Staphylococcus aureus},,,7ENH_A,77.1739,98.3 SIF-Syn: