CDS 1 - 498
  /gene="1"
  /product="gp1"
  /function="Helix-turn-helix DNA binding domain protein"
  /locus tag="APunk_1"
    /note=
    /note=SSC: 1-498 CP: yes SCS: neither ST: SS BLAST-Start: [helix-turn-helix DNA binding protein [Gordonia phage Verity] ],,NCBI, q1:s1 100.0% 9.26362E-111 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.502, -3.905685530420168, yes F: Helix-turn-helix DNA binding domain protein SIF-BLAST: ,,[helix-turn-helix DNA binding protein [Gordonia phage Verity] ],,YP_010002839,98.7879,9.26362E-111 SIF-HHPRED: TetR-like transcriptional regulator; APC5888, TetR, Rhodococcus sp. RHA1, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: SO4, MSE; 2.4A {Rhodococcus},,,3F1B_A,87.2727,94.3 SIF-Syn: no upstream gene 
downstream gene is terminase

CDS 491 - 3136
  /gene="2"
  /product="gp2"
  /function="terminase"
  /locus tag="APunk_2"
    /note=Original Glimmer call @bp 491 has strength 15.26; Genemark calls start at 491
    /note=SSC: 491-3136 CP: yes SCS: both ST: SS BLAST-Start: [terminase [Gordonia phage Verity] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.324, -6.228980717135431, no F: terminase SIF-BLAST: ,,[terminase [Gordonia phage Verity] ],,YP_010002840,98.2974,0.0 SIF-HHPRED:  SIF-Syn: Location: 491-3136
    /note=Based on what we saw in phagesdb, the BLAST, phamerator, and NCBI.

CDS 3169 - 3375
  /gene="3"
  /product="gp3"
  /function="hypothetical protein"
  /locus tag="APunk_3"
    /note=Original Glimmer call @bp 3169 has strength 4.97; Genemark calls start at 3169
    /note=SSC: 3169-3375 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1766_gp05 [Gordonia phage Bizzy] ],,NCBI, q5:s2 94.1176% 4.65275E-39 GAP: 32 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.865, -6.397849201845283, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1766_gp05 [Gordonia phage Bizzy] ],,YP_010001969,98.4615,4.65275E-39 SIF-HHPRED: DUF6083 ; Family of unknown function (DUF6083),,,PF19561.2,58.8235,95.0 SIF-Syn: Upstream is terminase
downstream is NKF
    /note=-Start: 3169, Stop:3375, forward direction
    /note=-Has coding potential according to GeneMark and all of the coding is included
    /note=-Glimmer and Genemark call it a gene and both of their suggested start sites were chosen
    /note=-Starterator does agreee with glimmer or genemark so it is SS
    /note=-This is the longest possible ORF
    /note=-There is a 32 nucleotide gap
    /note=-Final Score: -6.398 which is not the best score 
    /note=-Phagesbd has no data
    /note=-Blizzy is the best BLAST-start hit with gene J1766_gp05, this has 96.9% identity and a 4.65e-39 e-value; q5:t2
    /note=-Start site was not changed
    /note=-F-Blast: Blizzy gene #5 suggests that it is NKF with an e-value of 2e-33
    /note=-Phamerator shows comparison between Delrey 21 gene #3 in pham 100686, upstream gene is a terminase and downstream gene is NKF
    /note=-F-HHPred: suggests an unknown function with a 95% probability and 58.8% coverage, It comes from the organism Strepomyces and has an e-value of 0.066
    /note=-There is no data in the conserved domain
    /note=-There are zero transmembrane domains comfirmed 
    /note=-Suggested function is NKF based on BLAST and HHPred results

CDS 3372 - 3629
  /gene="4"
  /product="gp4"
  /function="hypothetical protein"
  /locus tag="APunk_4"
    /note=Original Glimmer call @bp 3348 has strength 14.81; Genemark calls start at 3348
    /note=SSC: 3372-3629 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein J1776_gp04 [Gordonia phage Verity] ],,NCBI, q1:s1 100.0% 1.32389E-41 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.842, -5.138684143940787, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1776_gp04 [Gordonia phage Verity] ],,YP_010002842,94.1176,1.32389E-41 SIF-HHPRED:  SIF-Syn: Upstream and downstream are NKF
    /note=- Start: 3348, stop: 4483, forward
    /note=-The gene has coding potential, not all of the coding potential is included in the start and stop because there is an overhang in the front
    /note=-Both Glimmer and Genemark call the start site and both calls were choosen
    /note=-Startorator does agree with Glimmer and genemark so it is SS and the gene is not an orpham
    /note=-It is the longest possible ORF
    /note=-it has a -28 nucleotide overlap
    /note=-Its final score is -5.962 which is not the best score compared to numbers like -4.802
    /note=-Its suggested function on phagesbd is minor tail protein but this is only found in 1 instance so it is not reliable
    /note=-BLAST-start: Ribeye phage was the best hit with gene J1768_gp06; this has 90% identity and an e-value of 8.63e-42, q1:t1
    /note=-The start site was not changed
    /note=-F-BLAST: Ribeye gene #6 with the function NKF and e-value of 2e-43
    /note=-F-Syn: Used phamerator to compare to Delrey21 gene #4 in pham 96308; upstream and downstream genes are NKF
    /note=-F-HHpred: not high enough % to use as evidence 
    /note=-No data for conserved domain
    /note=-Zero transmembrane domains confirmed
    /note=-Suggested function is NKF based on BLAST and phamerator data

CDS 3629 - 4483
  /gene="5"
  /product="gp5"
  /function="hypothetical protein"
  /locus tag="APunk_5"
    /note=Original Glimmer call @bp 3629 has strength 14.32; Genemark calls start at 3629
    /note=SSC: 3629-4483 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1776_gp05 [Gordonia phage Verity] ],,NCBI, q12:s12 96.1268% 2.41586E-146 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.551, -5.79598068500287, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1776_gp05 [Gordonia phage Verity] ],,YP_010002843,73.2523,2.41586E-146 SIF-HHPRED:  SIF-Syn: Upstream and downstream is NKF
    /note=Start: 3629, Stop:4483, forward
    /note=-It has genemark coding potential and all of the potential is included
    /note=-Glimmer and Genemark call the start site and both are chosen
    /note=-Startorator agrees with glimmer and genemark so it is (SS)
    /note=-It is not an orpham
    /note=-It is the longest possible ORF
    /note=-It has an overlap of -1 nucleotides
    /note=-Its final score is -5.796 which is not the best score when compared to -4.156 which was not supported by glimmer or genemark
    /note=-Its suggested function on phagesbd is portal protein but this does not agree with BLAST or phamerator so it is not reliable
    /note=-BLAST-start: Verity gene J1776_gp05 with a 68.9% identity, e-value of 2.42e-146; q12:t12
    /note=-The start site was not changed
    /note=-F-BLAST: Delrey21 gene #5 listed at NKF with an e value of 1e-124
    /note=-F-Syn: Phamerator was used to compare to Delrey21 phage #5 in pham #54566, upstream and downstream genes are NKF
    /note=-F-HHPred: not high enough percentage to use 
    /note=-There is no conserved domain data
    /note=-There are two transmembrane domains which is not comfired by TOPCONS
    /note=-The overall function is determined to be NKF based on BLAST and Phamerator

CDS 4480 - 4596
  /gene="6"
  /product="gp6"
  /function="hypothetical protein"
  /locus tag="APunk_6"
    /note=Original Glimmer call @bp 4480 has strength 10.21; Genemark calls start at 4483
    /note=SSC: 4480-4596 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein J1775_gp06 [Gordonia phage Zipp] ],,NCBI, q2:s1 97.3684% 5.09076E-15 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.848, -3.666652374399734, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp06 [Gordonia phage Zipp] ],,YP_010002755,94.5946,5.09076E-15 SIF-HHPRED:  SIF-Syn: Upstream and downstream are NKF
    /note=Start: 4480, Stop: 4596, FORWARD
    /note=-The gene does have coding potential and not all of the potential is included in the start and stop because the front end of the potential is out of range. 
    /note=-Both Glimmer and Genemark call this gene. Only Glimmer start site was used. 
    /note=-Starterator agrees with the Glimmer stat site, but not the GeneMark start site, so it is marked as suggested start. The gene is not an orpham.
    /note=-Not longest possible ORF because there is a better Glimmer score and BLAST match.
    /note=-overlap: -4
    /note=-There is a final score of -3.667 which is not the best score. The best score is -3.202 for the start site at 4483.
    /note=-No data on phages DB
    /note=-BLAST-start: Zipp gene 1775_gp06 with a 91.89% identity and e-value of 5.09e-15; q2:t1.
    /note=-Start site was not changed
    /note=-F-BLAST: Zipp gene #6 has a NKF with an e-value of 3e-15.
    /note=-F-Syn: Delrey21 gene #6 and pham #4067. Upstream and downstream genes are NKF. 
    /note=-F-HHPred: not high enough %
    /note=-F-CD: no data
    /note=-One predicted TMHMM which is not confirmed by other sites
    /note=-Final function call: NKF due to BLAST and phamerator results

CDS 4554 - 5093
  /gene="7"
  /product="gp7"
  /function="hypothetical protein"
  /locus tag="APunk_7"
    /note=Original Glimmer call @bp 4554 has strength 14.99; Genemark calls start at 4596
    /note=SSC: 4554-5093 CP: no SCS: both-gl ST: SS BLAST-Start: [hypothetical protein J1774_gp07 [Gordonia Phage Zitch] ],,NCBI, q15:s1 92.1788% 1.03686E-100 GAP: -43 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.157, -4.513079314654054, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp07 [Gordonia Phage Zitch] ],,YP_010002665,94.5455,1.03686E-100 SIF-HHPRED:  SIF-Syn: upstream - NKF
downstream - NKF
    /note=- starts at 4596 and ends at 5093
    /note=- it does have coding potential, but it goes over the start location
    /note=- The Genemark call was chosen 
    /note=- Starterator agrees with GeneMark (SS), not an orpham
    /note=- This is not the longest possible orf, but it was chosen due to the coding potential

CDS 5127 - 5408
  /gene="8"
  /product="gp8"
  /function="hypothetical protein"
  /locus tag="APunk_8"
    /note=Original Glimmer call @bp 5127 has strength 6.84; Genemark calls start at 5127
    /note=SSC: 5127-5408 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp08 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.7542E-56 GAP: 33 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.603, -5.692838547509838, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp08 [Gordonia Phage Zitch] ],,YP_010002666,94.6237,1.7542E-56 SIF-HHPRED:  SIF-Syn: - upstream: NKF
- downstream: NKF

CDS 5467 - 5790
  /gene="9"
  /product="gp9"
  /function="hypothetical protein"
  /locus tag="APunk_9"
    /note=Original Glimmer call @bp 5467 has strength 14.94; Genemark calls start at 5467
    /note=SSC: 5467-5790 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp09 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.4283E-70 GAP: 58 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.24, -4.34663776219455, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp09 [Gordonia Phage Zitch] ],,YP_010002667,100.0,1.4283E-70 SIF-HHPRED:  SIF-Syn: Upstream: NKF
Downstream: NFK

CDS 5832 - 6140
  /gene="10"
  /product="gp10"
  /function="membrane protein"
  /locus tag="APunk_10"
    /note=Original Glimmer call @bp 5832 has strength 13.46; Genemark calls start at 5832
    /note=SSC: 5832-6140 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp10 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.18848E-51 GAP: 41 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.078, -4.810045260256, no F: membrane protein SIF-BLAST: ,,[hypothetical protein J1774_gp10 [Gordonia Phage Zitch] ],,YP_010002668,95.0495,1.18848E-51 SIF-HHPRED:  SIF-Syn: Upstream: NKF
Downstream: NFK

CDS 6211 - 6660
  /gene="11"
  /product="gp11"
  /function="membrane protein"
  /locus tag="APunk_11"
    /note=Original Glimmer call @bp 6211 has strength 14.07; Genemark calls start at 6277
    /note=SSC: 6211-6660 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein J1774_gp11 [Gordonia Phage Zitch] ],,NCBI, q23:s1 85.2349% 1.0816E-83 GAP: 70 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.684, -4.2927322217032575, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein J1774_gp11 [Gordonia Phage Zitch] ],,YP_010002669,99.2126,1.0816E-83 SIF-HHPRED:  SIF-Syn: - F-Syn = APunk, gene 10, pham 20935 (neither upstream nor downstream gene have function listed)
    /note=- Start number 31 was manually annotated 5 times for cluster DE4 (info from Starterator)
    /note=- SSC = 6277-6660 (FOR)
    /note=- CP = all of the gene has coding potential, as seen in the GeneMark graphs, and all coding potential is included 
    /note=- SCS = both programs called, but at different start sites (Glimmer at 6211 and GeneMark at 6277) 
    /note=- ST = SS agrees with GeneMark (gene is 384bp long, and this matches up with the length of the other genes in the same pham). Gene is NOT an orpham, there are 102 other phages with this gene)
    /note=- LO = NOT the longest ORF. Chosen because coding potential matches, gene manually annotated 5 times for other phages in subcluster DE4, better SD score. 
    /note=- GAP = gap of 137 bp between gene 10 and beginning of gene 11, and overlap of 7 bp with beginning of gene 12
    /note=- SD Score = -5.389. Not the best score, best one was -4.293, however the length of the gene was significantly larger than similar genes within the same pham/subcluster. (Other options = -7.116, -5.657, -4.879, -5.082, and -6.164)
    /note=- Phagesdb.org = function unknown (all other functions in the pham, have this gene listed as an unknown function in the pham 20935)
    /note=- BLAST-start = no data available in table
    /note=- No change in start (chose SS from GeneMark)
    /note=- F-BLAST = phage Zitch, protein 11, e value = 7e-72
    /note=-  F-HHPred = mycobacterium membrane protein, probability of 99.8%, organism/hit = mycobacterium, 75.59% coverage, e value = 1.9e-16
    /note=- F-CD = no data available in table
    /note=- F-Mem = 1 TMH. TOPCONS predicts a signal peptide and outside region

CDS 6653 - 6823
  /gene="12"
  /product="gp12"
  /function="hypothetical protein"
  /locus tag="APunk_12"
    /note=Original Glimmer call @bp 6653 has strength 11.28; Genemark calls start at 6662
    /note=SSC: 6653-6823 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein J1774_gp12 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 7.71036E-32 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.649, -5.601721574136733, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp12 [Gordonia Phage Zitch] ],,YP_010002670,100.0,7.71036E-32 SIF-HHPRED:  SIF-Syn: - F-Syn = APunk, gene 11, pham 35112 (neither upstream nor downstream genes have function listed)
    /note=- 6653 – 6823 (FOR)
    /note=- all of the gene has coding potential, as seen in the GeneMark graphs
    /note=- both programs called, but at different start sites (Glimmer at 6653 and GeneMark at 6662)
    /note=- ST = SS agrees with Glimmer (gene is 171bp long, and this matches up with the length of the other genes in the pham). Gene is NOT an orpham, there are 3 other phages with this gene (2 of which are drafts, but the other one is Zitch)
    /note=- Longest ORF
    /note=- GAP = beginning of gene overlaps with 7 bp of gene 11, end of the gene overlaps with 3 bp of gene 13.
    /note=- SD = -5.602, not the best score. Best one was a score of -4.346, however the length of the gene was significantly smaller than 171bp. (Other options = -6.0404, -6.068, and -5.879)
    /note=- Phagesdb.org = function unknown (3 other phages in the pham also have this gene listed as an unknown function, in the pham 35112)
    /note=- BLAST-start = best hit was with phage Zitch, gene 12 (J1774_gp12), 100% identity, e value = 7.71036e-32, (q1:t1)
    /note=- Start not changed
    /note= - F-BLAST = phage Zitch, protein 12, e value = 2e-25
    /note=- no significant information found in HHPRED
    /note=- F-CD = no data available in table
    /note=- F-Mem = not a membrane protein (no predicted TMHMM)
    /note=- final function call = no known function
    /note=- Starterator called the gene 100% of the time (in the cluster DE4)

CDS 6820 - 7002
  /gene="13"
  /product="gp13"
  /function="hypothetical protein"
  /locus tag="APunk_13"
    /note=Original Glimmer call @bp 6820 has strength 18.57; Genemark calls start at 6820
    /note=SSC: 6820-7002 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp13 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.41755E-32 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.264, -4.379101430921652, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp13 [Gordonia Phage Zitch] ],,YP_010002671,100.0,1.41755E-32 SIF-HHPRED:  SIF-Syn: F-Syn = APunk, gene 12, pham 17931 (neither upstream nor downstream genes have function listed)
    /note=- Coding potential located on Starterator
    /note=- Glimmer and GeneMark called the gene (and called the same starting position)
    /note=- Suggested start site agrees with Glimmer and GeneMark
    /note=- PhagesDb shows 8 other phages with this gene in the same pham (17931). no function suggested
    /note=- Longest ORF was not chosen, because coding potential lined up with the data from Starterator. ORF chosen also because of BLAST similarity to phage Zitch (which is in the same subcluster)
    /note=- overlap with previous gene (3 bp), gap of 107 bp between this gene and gene 14
    /note=- SD Score = - 4.379. This is the best score (other options = -7.588, -4.739, -5.115, and -5.071)
    /note=- BLAST-start = best hit was with phage Zitch, gene 13 (J1774_gp13), 100% identity, e value = 1.41755e-32. (q1:t1)
    /note=- no significant information found in HHPRED
    /note=- F-CD = no data available in table
    /note=- F-Mem = not a membrane protein

CDS 7109 - 7426
  /gene="14"
  /product="gp14"
  /function="membrane protein"
  /locus tag="APunk_14"
    /note=Original Glimmer call @bp 7109 has strength 12.73; Genemark calls start at 7109
    /note=SSC: 7109-7426 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp14 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 2.60338E-66 GAP: 106 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.176, -5.778963282823847, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein J1774_gp14 [Gordonia Phage Zitch] ],,YP_010002672,99.0476,2.60338E-66 SIF-HHPRED: DUF1360 ; Protein of unknown function (DUF1360),,,PF07098.14,80.9524,99.9 SIF-Syn: - F-Syn = APunk, gene 13, pham 100417 (upstream gene has no function, downstream gene is likely portal protein)
    /note=- 7109 – 7426 (FOR) 
    /note=- All of the gene has coding potential, as seen in the GeneMark graphs
    /note=- SCS = both programs called the gene at the same start site
    /note=- SS agrees with Glimmer and GeneMark. When looking at Starterator, the gene is called 68.9% of the time when present, and a lot of the phages where this start is called are in the same cluster (and some within the same subcluster as well). Gene is NOT an orpham, as there are 257 total members in the same pham)
    /note=- Longest ORF
    /note=- GAP = gap of 107 bp between end of previous gene and beginning of this gene. Gap of 15bp between end of this gene and start of next gene (gene 15)
    /note=- SD Score = -5.779. not the best. Best one had a value of -4.618, but the length of the gene was halved (Which is not right, in comparison to the length of genes in the same pham in different phages). Other values included -6.416,  -6.577, -4.618, and -5.954.
    /note=- Phagesdb.org = function unknown (256 other phages in the pham also have an unknown function, in the pham 100417)
    /note=- BLAST-start = best hit was with phage Zitch, gene 14 (J1774_gp14), 99.05% identity, e value = 2.60338e-66
    /note=- SS not changed
    /note=- F-BLAST = phage Zitch, protein 14, e value = 3e-58
    /note=- F-HHPred = protein of unknown function, probability of 99.9%, organism/hit = PF07098.14, 80.95% coverage, e value = 1.6e-21
    /note=- F-CD = data in table has low coverage and % identity
    /note=- F-Mem = 3 TMH’s. TOPCONS predicts a portion of the protein to be inside and outside helices.

CDS 7441 - 9111
  /gene="15"
  /product="gp15"
  /function="Portal Protein"
  /locus tag="APunk_15"
    /note=Original Glimmer call @bp 7441 has strength 18.89; Genemark calls start at 7441
    /note=SSC: 7441-9111 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 0.0 GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.09, -5.29832271930559, no F: Portal Protein SIF-BLAST: ,,[portal protein [Gordonia Phage Zitch] ],,YP_010002673,99.1023,0.0 SIF-HHPRED:  SIF-Syn: Up and downstream is NKF
    /note=-Start: 7441; Stop: 9111, FORWARD
    /note=-The gene has coding potential and all of the potential is included within the start and stop. 
    /note=-Glimmer and Genemark call this gene and both start sites were used.
    /note=-Starterator does not agree with Glimmer and Genemark so it is not informative. The gene is not an orpham.
    /note=-It is the longest possible ORF
    /note=-Gap of 14 nucleotides
    /note=-It has a final score of -5.298 which is not the best score. The best score is -4.310 which belongs to the start site at 7771.
    /note=-Phagesdb calls the function portal protein
    /note=-BLAST- start: Zitch gene QKY78462.1 with 98.4% probability and an e-value of zero. Q1:t1
    /note=-Start site was not changed
    /note=-F-BLAST: Zitch gene #15 has a function of portal protein with an e-value of zero.
    /note=-F-Syn: Delrey21 gene #15 pham #16025. Upstream and downstream genes are NKF.
    /note=-F-HHPred: NI
    /note=-F-CD: no data
    /note=-Zero predicted transmembrane domains which is confirmed by other sites
    /note=-Final function call is portal protein based on phagesdb, BLAST, and phamerator

CDS 9108 - 9473
  /gene="16"
  /product="gp16"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="APunk_16"
    /note=Original Glimmer call @bp 9108 has strength 11.21; Genemark calls start at 9108
    /note=SSC: 9108-9473 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp15 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 2.70258E-83 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.528, -3.8362837638757656, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein J1775_gp15 [Gordonia phage Zipp] ],,YP_010002764,100.0,2.70258E-83 SIF-HHPRED:  SIF-Syn: Gene: 56; pham:67705
    /note=NKF

CDS 9454 - 12615
  /gene="17"
  /product="gp17"
  /function="capsid maturation protease and MuF-like fusion protein"
  /locus tag="APunk_17"
    /note=Original Glimmer call @bp 9454 has strength 17.25; Genemark calls start at 9577
    /note=SSC: 9454-12615 CP: yes SCS: both-gl ST: NA BLAST-Start: [MuF-like minor capsid protein [Gordonia phage Keitabear] ],,NCBI, q11:s12 98.9554% 0.0 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.528, -5.07932181256206, no F: capsid maturation protease and MuF-like fusion protein SIF-BLAST: ,,[MuF-like minor capsid protein [Gordonia phage Keitabear] ],,YP_010104512,75.2896,0.0 SIF-HHPRED: Phage_Mu_F ; Phage Mu protein F like protein,,,PF04233.17,16.1444,98.9 SIF-Syn: Gene:16; pham: 20293; up: minor capsid protein; down: unknown

CDS 12612 - 12815
  /gene="18"
  /product="gp18"
  /function="hypothetical protein"
  /locus tag="APunk_18"
    /note=Original Glimmer call @bp 12612 has strength 4.55; Genemark calls start at 12612
    /note=SSC: 12612-12815 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp17 [Gordonia phage Zipp] ],,NCBI, q1:s1 95.5224% 2.62341E-28 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.775, -3.4259484787582526, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp17 [Gordonia phage Zipp] ],,YP_010002766,81.6901,2.62341E-28 SIF-HHPRED:  SIF-Syn: Gene: 59; pham:99210
    /note=NKF

CDS 12842 - 13063
  /gene="19"
  /product="gp19"
  /function="hypothetical protein"
  /locus tag="APunk_19"
    /note=Original Glimmer call @bp 12842 has strength 10.55; Genemark calls start at 12842
    /note=SSC: 12842-13063 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LONELYBOI_34 [Gordonia phage LonelyBoi]],,NCBI, q1:s1 100.0% 5.37946E-33 GAP: 26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.603, -6.139996578852057, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LONELYBOI_34 [Gordonia phage LonelyBoi]],,QZD97552,87.6712,5.37946E-33 SIF-HHPRED: YppF ; YppF-like protein,,,PF14178.9,75.3425,91.9 SIF-Syn: Gene:18; pham: 57238; up: RNA ligase; down: unknown
    /note=NKF

CDS 13215 - 15881
  /gene="20"
  /product="gp20"
  /function="RNA ligase"
  /locus tag="APunk_20"
    /note=Original Glimmer call @bp 13215 has strength 18.39; Genemark calls start at 13311
    /note=SSC: 13215-15881 CP: yes SCS: both-gl ST: SS BLAST-Start: [RNA ligase [Gordonia phage Verity] ],,NCBI, q33:s1 96.3964% 0.0 GAP: 151 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.826, -7.219612433977546, no F: RNA ligase SIF-BLAST: ,,[RNA ligase [Gordonia phage Verity] ],,YP_010002856,93.1684,0.0 SIF-HHPRED: d.61.1.2 (A:) 2`-5` RNA ligase LigT {Thermus thermophilus [TaxId: 274]},,,d1iuha_,14.7523,97.7 SIF-Syn: Gene: 19; pham: 57119; up: unknown; down:unknown

CDS 15881 - 16063
  /gene="21"
  /product="gp21"
  /function="hypothetical protein"
  /locus tag="APunk_21"
    /note=Original Glimmer call @bp 15881 has strength 12.08; Genemark calls start at 15881
    /note=SSC: 15881-16063 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1776_gp19 [Gordonia phage Verity] ],,NCBI, q1:s1 100.0% 1.54913E-24 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.285, -4.6079705234137345, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1776_gp19 [Gordonia phage Verity] ],,YP_010002857,98.3333,1.54913E-24 SIF-HHPRED:  SIF-Syn: Gene:20; pham: 100192; up: unknown; down: RNA ligase
    /note=NKF

CDS 16064 - 16213
  /gene="22"
  /product="gp22"
  /function="hypothetical protein"
  /locus tag="APunk_22"
    /note=Original Glimmer call @bp 16064 has strength 15.19; Genemark calls start at 16064
    /note=SSC: 16064-16213 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp22 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.91867E-25 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.301, -5.133363921001094, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp22 [Gordonia Phage Zitch] ],,YP_010002680,97.9592,1.91867E-25 SIF-HHPRED: DUF4809 ; Domain of unknown function (DUF4809),,,PF16067.8,46.9388,90.6 SIF-Syn: Gene:21; pham: 100628; up: major capsid hexamer protein; down: unknown
    /note=NKF.

CDS 16314 - 18233
  /gene="23"
  /product="gp23"
  /function="major capsid protein"
  /locus tag="APunk_23"
    /note=Original Glimmer call @bp 16314 has strength 15.73; Genemark calls start at 16314
    /note=SSC: 16314-18233 CP: yes SCS: both ST: SS BLAST-Start: [major capsid protein [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 0.0 GAP: 100 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.989, -2.9215542714922735, no F: major capsid protein SIF-BLAST: ,,[major capsid protein [Gordonia Phage Zitch] ],,YP_010002681,98.748,0.0 SIF-HHPRED:  SIF-Syn: Gene:22; pham: 99299; up: unknown; down: unknown

CDS 18327 - 19151
  /gene="24"
  /product="gp24"
  /function="hypothetical protein"
  /locus tag="APunk_24"
    /note=Original Glimmer call @bp 18327 has strength 15.53; Genemark calls start at 18327
    /note=SSC: 18327-19151 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp24 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 0.0 GAP: 93 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.497, -3.9776535502172963, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp24 [Gordonia Phage Zitch] ],,YP_010002682,99.635,0.0 SIF-HHPRED:  SIF-Syn: Gene:23; pham: 100171; up: unknown; down: major capsid hexamer protein
    /note=NKF.

CDS 19157 - 19612
  /gene="25"
  /product="gp25"
  /function="hypothetical protein"
  /locus tag="APunk_25"
    /note=Original Glimmer call @bp 19157 has strength 16.31; Genemark calls start at 19157
    /note=SSC: 19157-19612 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp25 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.54301E-82 GAP: 5 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.882, -3.133663537764895, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp25 [Gordonia Phage Zitch] ],,YP_010002683,80.7018,1.54301E-82 SIF-HHPRED:  SIF-Syn: Gene:24; pham: 98759; up: major tail protein; down: unknown
    /note=NKF

CDS 19766 - 20398
  /gene="26"
  /product="gp26"
  /function="major tail protein"
  /locus tag="APunk_26"
    /note=Original Glimmer call @bp 19766 has strength 14.82; Genemark calls start at 19712
    /note=SSC: 19766-20398 CP: yes SCS: both-gl ST: SS BLAST-Start: [major tail protein [Gordonia Phage Zitch] ],,NCBI, q1:s19 100.0% 7.40001E-149 GAP: 153 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.762, -6.602787046090749, no F: major tail protein SIF-BLAST: ,,[major tail protein [Gordonia Phage Zitch] ],,YP_010002684,92.1053,7.40001E-149 SIF-HHPRED:  SIF-Syn: Gene:25; pham: 54238; up: minor tail protein; down: unknown

CDS 20502 - 21293
  /gene="27"
  /product="gp27"
  /function="head-to-tail adaptor"
  /locus tag="APunk_27"
    /note=Original Glimmer call @bp 20502 has strength 14.0; Genemark calls start at 20502
    /note=SSC: 20502-21293 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail adaptor [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 0.0 GAP: 103 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.988, -4.989602575074527, no F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Gordonia Phage Zitch] ],,YP_010002685,98.8593,0.0 SIF-HHPRED:  SIF-Syn: Upstream gene is NFK, downstream gene is minor tail protein like phages Delrey21, DoctorFroggo, and Verity
    /note=SSC [start 20502, stop 21293], CP [yes], SCS [glimmer/genemark/both called gene], ST [SS], LO [yes], Gap [downstream, 104 bp], overlap [upstream, 3 bp], Blast-start/SIF [Zitch, 27, q1:t1, 100% coverage, e value 0], SIF-Syn [upstream NFK, downstream minor tail protein], F [head-to-tail adaptor]

CDS 21290 - 21388
  /gene="28"
  /product="gp28"
  /function="hypothetical protein"
  /locus tag="APunk_28"
    /note=Genemark calls start at 21290
    /note=SSC: 21290-21388 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein J1774_gp28 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 3.61288E-10 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.617, -3.738562143838384, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp28 [Gordonia Phage Zitch] ],,YP_010002686,100.0,3.61288E-10 SIF-HHPRED:  SIF-Syn: Upstream is NKF, downstream is head-to-tail adaptor
    /note=SSC [start 21290, stop 21388], CP [yes], SCS [GeneMark], ST [SS], Blast-Start/SIF-BLAST [Zitch, gene 28, q1:t1, e value 3.61288e-10, 100% coverage], Gap [upstream, 2 bp], overlap [downstream, 3 bp], LO [no], F [NKF]

CDS 21390 - 21947
  /gene="29"
  /product="gp29"
  /function="hypothetical protein"
  /locus tag="APunk_29"
    /note=Original Glimmer call @bp 21390 has strength 15.83; Genemark calls start at 21390
    /note=SSC: 21390-21947 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp29 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 2.07916E-130 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.731, -6.009847715707425, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp29 [Gordonia Phage Zitch] ],,YP_010002687,100.0,2.07916E-130 SIF-HHPRED:  SIF-Syn: upstream gene is a tail assembly chaperone 
downstream gene is NKF
    /note=Relatives Delrey21 and DoctorFroggo (in Phamerator) which had this gene in common with APunk did not show any function, so we assume this gene in APunk has no function

CDS 21958 - 22368
  /gene="30"
  /product="gp30"
  /function="hypothetical protein"
  /locus tag="APunk_30"
    /note=Original Glimmer call @bp 21958 has strength 17.78; Genemark calls start at 21958
    /note=SSC: 21958-22368 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp30 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 3.84425E-87 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.34, -4.675252546161651, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp30 [Gordonia Phage Zitch] ],,YP_010002688,98.5294,3.84425E-87 SIF-HHPRED: Mu-like prophage FluMu protein gp35, Protein HI1507 in Mu-like prophage FluMu region; structural genomics, Haemophilus influenzae, hypothetical protein, Structure 2 Function Project, S2F, UNKNOWN FUNCTION; NMR {Haemophilus influenzae} SCOP: a.140.3.2, d.344.1.1, l.1.1.1,,,2OUT_A,77.9412,97.3 SIF-Syn: Upstream is tail-assembly chaperone, downstream is NKF similar to phages Delrey21, Verity, and Zipp)
    /note=SSC [start 21958, stop 22668], CP [yes], SCS [Glimmer/GeneMark both call gene], ST [SS], LO [yes], Gap [downstream, 11 bp], overlap [upstream, 16 bp], Blast-start/SIF-BLAST [Gordonia Zitch, 30, q1:t1, 100% coverage, e value 3.84425e-87], F [NKF]

CDS 22352 - 22783
  /gene="31"
  /product="gp31"
  /function="tail assembly chaperone"
  /locus tag="APunk_31"
    /note=Original Glimmer call @bp 22352 has strength 9.48; Genemark calls start at 22352
    /note=SSC: 22352-22783 CP: no SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 3.66331E-93 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.867, -5.089055022229114, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Gordonia phage Zipp] ],,YP_010002778,97.9021,3.66331E-93 SIF-HHPRED:  SIF-Syn: downstream gene is NKF
upstream gene is a tail assembly chaperone
    /note=both phagesdb and phamerator (phages Zipp, DelRey21, and Verity) suggest that the function of this gene in APunk is tail assembly chaperone

CDS 22894 - 23562
  /gene="32"
  /product="gp32"
  /function="tail assembly chaperone"
  /locus tag="APunk_32"
    /note=Original Glimmer call @bp 22894 has strength 15.61; Genemark calls start at 22894
    /note=SSC: 22894-23562 CP: no SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Gordonia Phage Zitch] ],,NCBI, q1:s1 95.045% 5.24256E-138 GAP: 110 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.251, -4.466674028236667, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Gordonia Phage Zitch] ],,YP_010002690,90.5405,5.24256E-138 SIF-HHPRED: Phage_TAC_10 ; Phage tail assembly chaperone,,,PF10963.11,37.3874,96.0 SIF-Syn: downstream gene is a tail assembly chaperone
upstream gene is NKF

CDS 23572 - 24258
  /gene="33"
  /product="gp33"
  /function="hypothetical protein"
  /locus tag="APunk_33"
    /note=Original Glimmer call @bp 23572 has strength 12.54; Genemark calls start at 23572
    /note=SSC: 23572-24258 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp33 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 8.69052E-159 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.994, -5.186767100221219, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp33 [Gordonia Phage Zitch] ],,YP_010002691,99.5614,8.69052E-159 SIF-HHPRED:  SIF-Syn: Downstream gene is a tail assembly chaperone 
Upstream gene is a tape measure protein
    /note=function was determined based on phamerator which did not suggest a function for its relatives (Zitch, DelRey21, DoctorFroggo, Verity, and Zipp)

CDS 24307 - 29232
  /gene="34"
  /product="gp34"
  /function="tape measure protein"
  /locus tag="APunk_34"
    /note=Original Glimmer call @bp 24307 has strength 13.33; Genemark calls start at 24307
    /note=SSC: 24307-29232 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 0.0 GAP: 48 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.431, -5.9550300036610215, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Gordonia Phage Zitch] ],,YP_010002692,99.3301,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_AF,12.4924,100.0 SIF-Syn: Upstream is minor tail protein, downstream NFK, similar to Delrey21, DoctorFroggo, Verity, Zipp, Zitch
    /note=SSC [start 24307, stop 29232], CP [yes], SCS [glimmer/genemark/both called gene], ST [SS], LO [yes], Gap [downstream of 49 bp, upstream of 2 bp], Blast-start/SIF BLAST [Gordonia Zitch, gene 34, q1:t1, 100% coverage, e value 0], F [tape measure protein]

CDS 29234 - 30211
  /gene="35"
  /product="gp35"
  /function="minor tail protein"
  /locus tag="APunk_35"
    /note=Original Glimmer call @bp 29234 has strength 12.33; Genemark calls start at 29234
    /note=SSC: 29234-30211 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 0.0 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.177, -5.000302397801194, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Gordonia Phage Zitch] ],,YP_010002693,99.0769,0.0 SIF-HHPRED:  SIF-Syn: Upstream is a tape measure protein and downstream is minor tail protein
    /note=- has coding potential including stop (30211) and start (29234) [forward direction]
    /note=- Glimmer and GeneMark both support the gene
    /note=- function matches with Phagesdb, NCBI Blasts, and the phages in the same subcluster (Zitch, Delrey21, DoctorFroggo)
    /note=- a gap of 2 nucleotides between upstream gene and no gap/overlap between downstream gene

CDS 30211 - 31833
  /gene="36"
  /product="gp36"
  /function="minor tail protein"
  /locus tag="APunk_36"
    /note=Original Glimmer call @bp 30211 has strength 12.09; Genemark calls start at 30211
    /note=SSC: 30211-31833 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.999, -4.966271270034708, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Gordonia phage Zipp] ],,YP_010002783,100.0,0.0 SIF-HHPRED:  SIF-Syn: upstream is a minor tail protein and downstream is NKF
    /note=- has coding potential including stop (31833) and start (30211) [forward direction]
    /note=- Glimmer and GeneMark both support this gene
    /note=- function matches with Phagesdb, NCBI Blast, and the phages in the same subcluster (Zipp, Delrey21, Verity, DoctorFroggo)
    /note=- 79 nucleotide gap between downstream gene and no gap/overlap between upstream gene

CDS 31858 - 32544
  /gene="37"
  /product="gp37"
  /function="hypothetical protein"
  /locus tag="APunk_37"
    /note=Original Glimmer call @bp 31912 has strength 15.85; Genemark calls start at 31858
    /note=SSC: 31858-32544 CP: no SCS: both-gm ST: SS BLAST-Start: [hypothetical protein J1774_gp37 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.01071E-157 GAP: 24 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.34, -4.148052427098672, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp37 [Gordonia Phage Zitch] ],,YP_010002695,98.69,1.01071E-157 SIF-HHPRED:  SIF-Syn: Upstream and downstream is minor tail protein
    /note=- has coding potential including stop (32544) and start (31912) [foward direction]
    /note=- Glimmer supports the gene
    /note=- function matches with Phagesdb Blast, NCBI Blast, its relative in the same subcluster on Phamerator (Zipp, Zitch, Delrey21, Verity, DoctorFroggo), and HHPred
    /note=- upstream gene overlaps by 3 nucleotides and there is a gap of 3 nucleotides between the downstream gene

CDS 32541 - 33617
  /gene="38"
  /product="gp38"
  /function="minor tail protein"
  /locus tag="APunk_38"
    /note=Original Glimmer call @bp 32541 has strength 17.32; Genemark calls start at 32541
    /note=SSC: 32541-33617 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.999, -4.887586077132851, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Gordonia phage Zipp] ],,YP_010002785,100.0,0.0 SIF-HHPRED:  SIF-Syn: Upstream and downstream are NKF
    /note=- has coding potential including stop (33617) and start (32541) [foward direction]
    /note=- Glimmer and GeneMark both support the gene and both of these start sites are used
    /note=-The start site does agree with Glimmer and Genemark so it is marked as SS. The gene is not an orpham. 
    /note=-It is LORF
    /note=-overlap of 4 nucleotides
    /note=-The final score is -4.888 and this is not the best score. The best score is associated with the start site at 32715 which has a score of -4.689. This is not used due to the values obtained from Glimmer and Genemark. 
    /note=-Phagesdb suggests minor tail protein 
    /note=-NCBI BLAST: Zipp gene QDH93190.1 which has the function of a minor tail protein. It has 100% identity and 0 e-value. Q1:t1
    /note=-F-BLAST: Zipp gene #36 has minor tail protein function and an e-value of 0.
    /note=-F-Syn: Delrey21 gene #36 in pham 96839 has function of minor tail protein. Upstream and downstream genes are NKF. 
    /note=- HHPred: not informative
    /note=-Conserved domain: no data
    /note=-No predicted TMHMM
    /note=-function call is minor tail protein based on phagesdb, BLAST, and phamerator

CDS 33614 - 33886
  /gene="39"
  /product="gp39"
  /function="hypothetical protein"
  /locus tag="APunk_39"
    /note=Original Glimmer call @bp 33614 has strength 12.34; Genemark calls start at 33614
    /note=SSC: 33614-33886 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp39 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 4.97356E-57 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.999, -4.905314844093283, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp39 [Gordonia Phage Zitch] ],,YP_010002697,100.0,4.97356E-57 SIF-HHPRED:  SIF-Syn: Upstream is minor tail protein 
downstream is NKF
    /note=-Start: 33614, Stop: 33886, FORWARD
    /note=-The gene has coding potential and the tail end of the coding potential is not included in the start and stop. 
    /note=-Glimmer and genemark called this gene and both start sites were used.
    /note=-Startorator does agree with the Glimmer and Genemark start site so it is suggested start. The gene is not an orpham. 
    /note=-Not LORF because SD score was better
    /note=-Overlap of 4 nucleotides
    /note=-Final score is -4.905 and this is the best score. 
    /note=-phages bd calls the function integrase
    /note=- NCBI BLAST: Zitch gene J1774_gp39 function NKF, 100% identity, 4.97e-57 e-value, q1:t1
    /note=-F-BLAST: Zitch gene #39, NKF function with an e-value of 3e-50
    /note=-F-Syn: Delrey21 gene #37 in pham #98528 function NKF, upstream and downstream are both NKF
    /note=-HHPRED: not informative
    /note=-Conserved domain: no data
    /note=-No TMHMM predicted
    /note=function call: NKF based off of phamerator and BLAST

CDS 33883 - 34221
  /gene="40"
  /product="gp40"
  /function="hypothetical protein"
  /locus tag="APunk_40"
    /note=Original Glimmer call @bp 33883 has strength 14.19; Genemark calls start at 33883
    /note=SSC: 33883-34221 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp38 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 1.33449E-73 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.966, -2.90473872338446, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp38 [Gordonia phage Zipp] ],,YP_010002787,99.1071,1.33449E-73 SIF-HHPRED:  SIF-Syn: Upstream is NKF
Downstream is Minor tail protein
    /note=-Start: 33883 Stop:34221 FORWARD
    /note=-It does have coding potential and all of the potential is not included within the start and stop because some information goes off of the front and back. 
    /note=-Both Glimmer and genemark call this gene and both of the start sites were used
    /note=-Starterator does agree with both programs so it is marked as SS. The gene is not an orpham. 
    /note=-LORF
    /note=-overlap of 4 nucleotides
    /note=-The final score is -2.905 which is the best score. 
    /note=-Phagesdb calls the function minor tail protein
    /note=-NCBI BLAST: Zipp phage gene J1775_gp38 which has 99.1% identity and an e-value of 1.33e-73 with a function of NKF. Q1:t1
    /note=- F-BLAST: Zipp has the function unknown with gene #38 and e-value of 2e-60.
    /note=- F-Syn: Delrey21 gene #38 pham #45201. Upstream gene is NKF and downstream gene is minor tail protein. 
    /note=-HHPred: not informative
    /note=-F-CD: no data
    /note=- No transmembrane domains
    /note=-function call is NKF based on BLAST and phagesdb

CDS 34218 - 36455
  /gene="41"
  /product="gp41"
  /function="minor tail protein"
  /locus tag="APunk_41"
    /note=Original Glimmer call @bp 34218 has strength 13.66; Genemark calls start at 34218
    /note=SSC: 34218-36455 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.298, -4.373866523711432, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Gordonia phage Zipp] ],,YP_010002788,100.0,0.0 SIF-HHPRED:  SIF-Syn: Upstream is NKF
Downstream is minor tail protien
    /note=-Start: 34218 Stop: 36455, FORWARD
    /note=-The gene has coding potential which is completely included in the start and stop sites. 
    /note=-Glimmer and Genemark both call this gene and both start sites are used. 
    /note=-Starterator agrees with both programs so it is marked as SS. The gene is not an orpham.
    /note=-Not LORF based on better Sd score
    /note=-overlap of 4 nucleotides
    /note=-The final score is -4.374 which is the best score.
    /note=-phagesdb calls the function as minor tail protein
    /note=-NCBI BLAST: Zipp phage gene QDH93193.1 with 100% identity as a minor tail protein function and an e-value of 0. Q1:t1. 
    /note=-F-BLAST: Zipp gene #39 has minor tail protein function with an e-value of 0.
    /note=-F-Syn:Verity gene #39 pham #98490 which a function of minor tail protein. Upstream gene is NKF and downstream gene is minor tail protein.  
    /note=-HHPred- not informative
    /note=-CD: no data
    /note=-No predicted transmembrane domains
    /note=-final function call is minor tail protein based off of phagesdb and BLAST

CDS 36455 - 37051
  /gene="42"
  /product="gp42"
  /function="minor tail protein"
  /locus tag="APunk_42"
    /note=Original Glimmer call @bp 36455 has strength 13.38; Genemark calls start at 36455
    /note=SSC: 36455-37051 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 3.19535E-132 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.233, -6.410083658262294, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Gordonia phage Zipp] ],,YP_010002789,100.0,3.19535E-132 SIF-HHPRED:  SIF-Syn: upstream is minor tail protein 
downstream is lysin A
    /note=- Start: 36455 Stop: 37051, FORWARD
    /note=-The gene has coding potential and the front end of the coding potential goes outside of the start site.  
    /note=-Glimmer and genemark both call this gene and both start sites are used
    /note=-The start site does agree with Glimmer and Genemark so it is marked as SS. The gene is not an orpham. 
    /note=-Not the LORF because the overlap is the smallest
    /note=-overlap of 1 nucleotide
    /note=-The final score is -6.410 and this is not the best score. The best score is associated with the start site at 36569 which has a score of -5.259. This is not used due to the values obtained from Glimmer and Genemark. 
    /note=-phagesdb calls the function minor tail protein
    /note=-NCBI BLAST: Zipp gene QDH93194 which has the function of a minor tail protein. It has 100% identity and 3.19e-132 e-value. Q1:t1
    /note=-F-BLAST: Zipp gene #40 has minor tail protein function and an e-value of 1e-106.
    /note=-F-Syn: Verity phage gene #40 has minor tail protein function in pham #99183. Upstream gene is minor tail protein and downstream gene is lysin A. 
    /note=-HHPred: not informative
    /note=-no data in conserved domain
    /note=-No predicted TMHMM
    /note=-Final function call is a minor tail protein based on phagesdb and BLAST

CDS 37152 - 38765
  /gene="43"
  /product="gp43"
  /function="lysin A"
  /locus tag="APunk_43"
    /note=Original Glimmer call @bp 37152 has strength 9.54; Genemark calls start at 37167
    /note=SSC: 37152-38765 CP: yes SCS: both-gl ST: SS BLAST-Start: [lysin A [Gordonia phage Verity] ],,NCBI, q1:s1 100.0% 0.0 GAP: 100 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.03, -5.114865311845495, no F: lysin A SIF-BLAST: ,,[lysin A [Gordonia phage Verity] ],,YP_010002879,97.3881,0.0 SIF-HHPRED:  SIF-Syn: upstream is minor tail protein
downstream is NKF
    /note=-Start: 37152 Stop: 38765, FORWARD
    /note=-The gene has coding potential and some of the coding potential is hanging outside of the stop site. 
    /note=-Both Glimmer and genemark call this gene, but only the Glimmer start site was used based off of starterator results. 
    /note=-The start site on starterator agrees with only Glimmer but not Genemark so it is marked as SS. The gene is not an orpham. 
    /note=-LORF
    /note=-gap of 100 nucleotides
    /note=-The final score is -5.115  and this is not the best score. The best score is associated with the start site at 37644 which has a score of -2.742. This is not used due to the values obtained from Glimmer and starterator.
    /note=-phagesdb calls the function lysin a
    /note=-NCBI BLAST: Verity gene QDH93527.1 which has the function of a lysin A. It has 95% identity and 0 e-value. Q1:t1
    /note=-F-BLAST: Delrey21 gene #41 has lysin a function and an e-value of 0.
    /note=- F-syn: Delrey21 gene #41 in pham 100803 has function of lysin a. Upstream gene is minor tail protein and downstream gene is HNH endonuclease (this is not the downstream gene for Apunk) 
    /note=-HHpred: not informative
    /note=-CD: no data
    /note=-No TMHMM predicted
    /note=-final function call is lysin a based on phagesdb and BLAST

CDS 38782 - 39267
  /gene="44"
  /product="gp44"
  /function="holin"
  /locus tag="APunk_44"
    /note=Original Glimmer call @bp 38782 has strength 16.61; Genemark calls start at 38782
    /note=SSC: 38782-39267 CP: yes SCS: both ST: SS BLAST-Start: [holin [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.73765E-107 GAP: 16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.276, -4.274735973818826, no F: holin SIF-BLAST: ,,[holin [Gordonia Phage Zitch] ],,YP_010002704,100.0,1.73765E-107 SIF-HHPRED:  SIF-Syn: 

CDS 39354 - 39626
  /gene="45"
  /product="gp45"
  /function="hypothetical protein"
  /locus tag="APunk_45"
    /note=Original Glimmer call @bp 39390 has strength 11.86; Genemark calls start at 39354
    /note=SSC: 39354-39626 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein J1774_gp47 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.03931E-56 GAP: 86 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.827, -3.2616920228519697, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp47 [Gordonia Phage Zitch] ],,YP_010002705,100.0,1.03931E-56 SIF-HHPRED:  SIF-Syn: 

CDS 39623 - 40141
  /gene="46"
  /product="gp46"
  /function="hypothetical protein"
  /locus tag="APunk_46"
    /note=Original Glimmer call @bp 39623 has strength 14.7; Genemark calls start at 39623
    /note=SSC: 39623-40141 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp48 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 6.16426E-122 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.078, -4.810045260256, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp48 [Gordonia Phage Zitch] ],,YP_010002706,100.0,6.16426E-122 SIF-HHPRED: DUF4407 ; Domain of unknown function (DUF4407),,,PF14362.9,93.0233,86.0 SIF-Syn: 

CDS 40146 - 40871
  /gene="47"
  /product="gp47"
  /function="lysin B"
  /locus tag="APunk_47"
    /note=Original Glimmer call @bp 40146 has strength 16.15; Genemark calls start at 40146
    /note=SSC: 40146-40871 CP: yes SCS: both ST: SS BLAST-Start: [lysin B [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 4.35168E-170 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.934, -3.108788982793736, no F: lysin B SIF-BLAST: ,,[lysin B [Gordonia Phage Zitch] ],,YP_010002707,100.0,4.35168E-170 SIF-HHPRED:  SIF-Syn: 

CDS 40958 - 41353
  /gene="48"
  /product="gp48"
  /function="hypothetical protein"
  /locus tag="APunk_48"
    /note=Original Glimmer call @bp 40958 has strength 19.18; Genemark calls start at 40958
    /note=SSC: 40958-41353 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp50 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 3.76181E-64 GAP: 86 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.03, -4.843798539558957, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp50 [Gordonia Phage Zitch] ],,YP_010002708,85.4962,3.76181E-64 SIF-HHPRED:  SIF-Syn: 

CDS 41353 - 41601
  /gene="49"
  /product="gp49"
  /function="hypothetical protein"
  /locus tag="APunk_49"
    /note=Original Glimmer call @bp 41353 has strength 13.06; Genemark calls start at 41353
    /note=SSC: 41353-41601 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein J1774_gp51 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.24301E-53 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.073, -4.820269098574683, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp51 [Gordonia Phage Zitch] ],,YP_010002709,100.0,1.24301E-53 SIF-HHPRED: DUF6083 ; Family of unknown function (DUF6083),,,PF19561.2,91.4634,98.5 SIF-Syn: F-Syn = APunk, gene 49, pham = 96513. Upstream gene has no gene function listed, and downstream gene has no known function listed
    /note=- 41353 – 41601 (FOR) (info from Glimmer and GeneMark off of PECAAN)
    /note=- CP = has coding potential in accordance with graphs from GeneMark. All coding potential is included within the start and stop (info from Host-Trained GeneMark)
    /note=- SCS = both programs called the gene and called them at the same place (info from PECAAN)
    /note=- ST = SS agrees with Glimmer and GeneMark. Gene is NOT an orpham, as there are 94 members in the pham (info from Starterator and phagesdb)
    /note=- longest possible ORF (info from PECAAN)
    /note=- GAP = no gap or overlap with previous gene. Gap of 35 nucleotides between end of gene 49 and start of gene 50 (info from PECAAN and phamerator)
    /note=- SD Score = -4.820. Yes, this is the best score. Only other option was -6.389 (info from PECAAN)
    /note=- Phagesdb.org = no function suggested from phagesdb.org. One phage with a gene in this pham (96513) calls it as a DNA binding protein; however, this phage is in a different subcluster (DE2), and it is only 1 out of 102 genes within the pham that have a function listed on phagesdb.org
    /note=- BLAST-start = best hit was with phage Zitch, gene 51 (J1774_gp51), with 100% identity and an e value of 1.24301e-53. (q1:t1) (info from PECAAN BLAST)
    /note=- F_BLAST = phage Zitch, protein number 51, e value = 5e-42 (info from PECAAN)
    /note=- F-HHPred = family of unknown function (DUF6083), probability of 98.5% and coverage of 91.46%. E value = 4.6e-7 (info from PECAAN)
    /note=- F-CD = no information available in data table
    /note=- F-Mem = no predicted TMH`s (data from PECAAN)

CDS 41636 - 41869
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="APunk_50"
    /note=Original Glimmer call @bp 41636 has strength 16.15; Genemark calls start at 41636
    /note=SSC: 41636-41869 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp52 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 1.02045E-36 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.784, -4.174392870950849, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp52 [Gordonia Phage Zitch] ],,YP_010002710,97.4026,1.02045E-36 SIF-HHPRED:  SIF-Syn: - F-Syn = APunk, gene 50, pham = 99711. Upstream gene has no gene function listen, and downstream gene is likely an exonuclease gene
    /note=- SSC = 41636 – 41869 (FOR)
    /note=- CP =  has coding potential in accordance with graphs from GeneMark. All coding potential is included within the start and stop
    /note=- SCS = both programs called the gene and called it at the same place
    /note=- ST = SS agrees with Glimmer and GeneMark. Gene is NOT an orpham, as there are 9 members in the pham, 4 of which are drafts)
    /note=- longest possible ORF
    /note=- GAP = gap of 35 nucleotides between end of upstream gene and start of gene 50. Overlap of 3 nucleotides with downstream gene and end of gene 50
    /note=- SD Score = -4.174. Yes, this is the best score. Other SD scores for potential start sites include -5.918, -7.682, and -6.067.
    /note=- Phagesdb.org = no function from phagesdb.org. Phagesdb Function Frequency from PECAAN listys major capsid hexamer protein, but the pham does not match, and the phages listed when the pham is looked at more closely are not in the same cluster or subcluster. Additionally, the length of these genes are 10 times the length of gene 50 in APunk
    /note=- BLAST-start = best hit was with phage Zitch, gene 52 (J1774_gp52), with 96.1% identity and an e value of 1.02045e-36. (q1:t1)
    /note=- F-BLAST = phage Zitch, protein number 52, e value = 5e-34
    /note=-  F-HHPred = no significant information found in HHPred 
    /note=- F-CD = no information available in data table
    /note=- no predicted TMH`s

CDS 41866 - 43041
  /gene="51"
  /product="gp51"
  /function="exonuclease"
  /locus tag="APunk_51"
    /note=Original Glimmer call @bp 41866 has strength 19.21; Genemark calls start at 41866
    /note=SSC: 41866-43041 CP: yes SCS: both ST: SS BLAST-Start: [RecE-like endonuclease [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.073, -4.759312672633257, no F: exonuclease SIF-BLAST: ,,[RecE-like endonuclease [Gordonia Phage Zitch] ],,YP_010002711,99.4885,0.0 SIF-HHPRED: Uncharacterized protein R354; MIMIVIRE, Cas4-like, nuclease, R354, NUCLEAR PROTEIN; 2.806A {Acanthamoeba polyphaga mimivirus},,,5YET_B,88.7468,100.0 SIF-Syn: 

CDS 43066 - 44106
  /gene="52"
  /product="gp52"
  /function="RecT-like ssDNA binding protein"
  /locus tag="APunk_52"
    /note=Original Glimmer call @bp 43066 has strength 18.03; Genemark calls start at 43066
    /note=SSC: 43066-44106 CP: yes SCS: both ST: SS BLAST-Start: [RecT-like ssDNA binding protein [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 0.0 GAP: 24 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.18, -2.8298788511194775, yes F: RecT-like ssDNA binding protein SIF-BLAST: ,,[RecT-like ssDNA binding protein [Gordonia Phage Zitch] ],,YP_010002712,98.5591,0.0 SIF-HHPRED: RecT ; RecT family,,,PF03837.17,55.4913,100.0 SIF-Syn: F-Syn = APunk, gene 52, pham 101056. Upstream gene is an exonuclease gene, downstream gene has no known function
    /note=SSC = 43066 – 44106 (FOR)
    /note=CP = has coding potential in accordance with graphs from GeneMark. All coding potential is included within the start and stop
    /note=SCS = both programs called the gene and called it at the same place
    /note=ST = SS agrees with Glimmer and GeneMark. Gene is NOT an orpham, as there are 211 other members in the pham (pham 101056)
    /note=- longest orf possible
    /note=GAP = gap of 25 nucleotides between end of upstream gene and start of gene 52. Gap of 25 nucleotides between end of gene 52 and start of downstream gene
    /note=- SD Score = -2.830. Yes, this is the best score. Other SD scores for potential start included -4.856, -4.631, and -6.259
    /note=- phagesdb.org = suggestion of RecT-like ssDNA binding protein from phagesdb.org, based on the other phages in the pham. Other phages with a gene in this pham, along with being in the DE4 cluster, have a gene homologous to this called as a RecT-like ssDNA binding protein. 
    /note=- BLAST-start = best hit was with phage Zitch, gene “RecT-like ssDNA binding protein”, with 98.6% identity, and an e value of 0. (q1:t1)
    /note=- F-BLAST = phage Zitch, protein number 54, e value = 0
    /note=Phage Zipp, protein number 52, e value = 0
    /note=Phage Delrey21, protein number 51, e value = 0
    /note=Phage DoctorFroggo, protein number 51, e value = 0
    /note=Phage Verity, protein number 51, e value = 0
    /note=
    /note=- F-HHPreD = RecT family, probability of 100%, coverage of 55.5%, e value = 1.2e-31, 
    /note=- F-CD = no significant information available in data table
    /note=- F-Mem = no predicted TMH’s
    /note=- Final Function Call = exonuclease (size of the gene better matched with Zipp, Verity, and DoctorFroggo, which all call the gene as an exonuclease. Zitch called it as a RecE-like exonuclease, but its gene is smaller in comparison)
    /note=52 = RecT-like ssDNA binding protein (size matches genes in the same pham and in the same subcluster that have the same function)

CDS 44131 - 44613
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="APunk_53"
    /note=Original Glimmer call @bp 44131 has strength 14.75; Genemark calls start at 44131
    /note=SSC: 44131-44613 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1597_gp49 [Gordonia phage Dexdert] ],,NCBI, q4:s3 95.625% 4.73896E-60 GAP: 24 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.078, -5.719125610937132, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1597_gp49 [Gordonia phage Dexdert] ],,YP_010001429,79.0541,4.73896E-60 SIF-HHPRED:  SIF-Syn: - F-Syn = APunk, gene 53, pham 56157. Upstream gene is a RecT-like ssDNA binding protein, downstream gene has no known function
    /note=- SSC = 44161 – 44613 (FOR)
    /note=- CP = has coding potential in accordance with graphs from GeneMark. All coding potential is included within the start and stop
    /note=- SCS = both programs called the gene and called it at the same place
    /note=- ST = SS agrees with Glimmer and GeneMark. Gene is NOT an orpham, as there are 94 other members in the pham (pham 56157)
    /note=- Longest possible ORF
    /note=- GAP = gap of 25 nucleotides between the end of upstream gene and start of gene 52. Gap of 53 nucleotides between end of gene 53 and beginning of downstream 
    /note=- SD = -5.719. Yes, this is the best score. Other SD scores for potential starts included -6.321, -6.984, and -6.015
    /note=- Phagesdb.org = no function suggestion from phagesdb.org. Phagesdb function frequency from PECAAN gives an option of tape measure protein, but this is for a different cluster (G1) and different pham (95098). Additionally, the gene is not large enough to be a tape measure protein
    /note=- BLAST-start = best hit was with phage Epsilon15, gene “3J40”, with 92.9% identity, and an e value of 1.4 (information therefore not significant, because e value is too large). (q52:t48)
    /note=- F-BLAST = phage Ali17, protein number 48, e value = 9e-54
    /note=Phage Hans, protein number 52, e value = 9e-54
    /note=- F-HHPred = no significant information found in HHPred 
    /note=- F-CD = no information available in data table
    /note=- F-Mem = no predicted TMH`s

CDS 44576 - 44821
  /gene="54"
  /product="gp54"
  /function="hypothetical protein"
  /locus tag="APunk_54"
    /note=Original Glimmer call @bp 44666 has strength 6.7; Genemark calls start at 44666
    /note=SSC: 44576-44821 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein J1774_gp56 [Gordonia Phage Zitch] ],,NCBI, q31:s1 62.963% 2.24538E-28 GAP: -38 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.625, -5.632249746582413, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp56 [Gordonia Phage Zitch] ],,YP_010002714,100.0,2.24538E-28 SIF-HHPRED:  SIF-Syn: - F-Syn = APunk, gene 54, pham 100732. Upstream gene has no known function, and downstream gene is likely helix-turn-helix-DNA-binding protein.
    /note=- SSC = 44666 – 44821 (FOR)
    /note=- CP = has coding potential in accordance with graphs from GeneMark. All coding potential is included within the start and stop
    /note=- SCS = both programs called the gene and called it at the same place
    /note=- ST = SS agrees with Glimmer and GeneMark. Gene is NOT an orpham, as there are 57 other members in the pham (pham 100732)
    /note=- LO = no, NOT longest possible ORF. Reason being the size of the gene in the LORF is larger than homologous genes in the same pham and subcluster (gene with LORF would be about 100bp too long, in comparison with the homologous genes in the same pham/subcluster). Additionally, the coding potential maps better to the gene being 156bp long, versus 246bp long. Matches with phagesdb.
    /note=- GAP = gap of 53 nucleotides between the end of upstream gene and start of gene 54. Overlap of 3 nucleotides with downstream gene and end of gene 54.
    /note=- SD = -6.268. No, not the best score (best score was -5.632, but the length of the gene did not match to homologous genes in other phages in the same subcluster/other genes in the same pham. Other SD scores for potential start sites included -5.632 (LORF) and -6.157.
    /note=- Phagesdb.org = no function suggestion from phagesdb.org. Phagesdb function frequency from PECAAN gives an option of helix-turn-helix dna binding protein, but this is for a different cluster (DE2), and a different pham (34343). Additionally, the genes in pham 34343 are double the length of this gene (gene 54 in APunk).
    /note=- BLAST-Start = best hit was with phage Zitch, gene J1774_gp56, with 100% identity, and a e value of 5.17274e-29. (q1:t1)
    /note=- F-BLAST = phage Zitch, protein number 56, e value = 2e-26
    /note=phage Zipp, protein number 54, e value = 5e-26
    /note=
    /note=- F-HHPred = no significant information found in HHPred
    /note=- F-CD = no information available in data table
    /note=- F-Mem = no predicted TMH`s

CDS 44818 - 45009
  /gene="55"
  /product="gp55"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="APunk_55"
    /note=Original Glimmer call @bp 44818 has strength 9.33; Genemark calls start at 44818
    /note=SSC: 44818-45009 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Gordonia Phage Zitch] ],,NCBI, q1:s1 95.2381% 2.17929E-33 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.161, -4.585118207934747, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Gordonia Phage Zitch] ],,YP_010002715,86.5672,2.17929E-33 SIF-HHPRED: Regulatory protein cox; helix-turn-helix, DNA binding, VIRAL PROTEIN; 2.401A {Enterobacteria phage P2},,,4LHF_A,88.8889,99.1 SIF-Syn: 

CDS 45016 - 45216
  /gene="56"
  /product="gp56"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="APunk_56"
    /note=Original Glimmer call @bp 45016 has strength 9.8; Genemark calls start at 45016
    /note=SSC: 45016-45216 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Gordonia phage Dexdert] ],,NCBI, q5:s9 86.3636% 3.50791E-8 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.251, -6.392711655555888, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Gordonia phage Dexdert] ],,YP_010001432,59.375,3.50791E-8 SIF-HHPRED: Regulatory protein cox; helix-turn-helix, DNA binding, VIRAL PROTEIN; 2.401A {Enterobacteria phage P2},,,4LHF_A,86.3636,98.9 SIF-Syn: Gene: 56; pham:67705

CDS 45213 - 46196
  /gene="57"
  /product="gp57"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="APunk_57"
    /note=Original Glimmer call @bp 45213 has strength 9.92; Genemark calls start at 45213
    /note=SSC: 45213-46196 CP: yes SCS: both ST: NI BLAST-Start: [helix-turn-helix DNA binding protein [Gordonia phage Walrus] ],,NCBI, q1:s1 94.4954% 1.07065E-91 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.198, -2.583959800616441, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding protein [Gordonia phage Walrus] ],,YP_010101719,63.8629,1.07065E-91 SIF-HHPRED:  SIF-Syn: Gene: 57; pham:101311

CDS 46202 - 46435
  /gene="58"
  /product="gp58"
  /locus tag="APunk_58"
    /note=
    /note=SSC: 46202-46435 CP: no SCS: neither ST: NI BLAST-Start: [hypothetical protein J1775_gp58 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 1.25552E-44 GAP: 5 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.036, -2.9063687850157054, yes F:  SIF-BLAST: ,,[hypothetical protein J1775_gp58 [Gordonia phage Zipp] ],,YP_010002807,96.1039,1.25552E-44 SIF-HHPRED:  SIF-Syn: 

CDS 46515 - 46763
  /gene="59"
  /product="gp59"
  /function="hypothetical protein"
  /locus tag="APunk_59"
    /note=Original Glimmer call @bp 46515 has strength 3.17; Genemark calls start at 46515
    /note=SSC: 46515-46763 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp59 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 9.07427E-53 GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.934, -7.468955032295226, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp59 [Gordonia phage Zipp] ],,YP_010002808,100.0,9.07427E-53 SIF-HHPRED: YjdM_Zn_Ribbon ; PhnA Zinc-Ribbon,,,PF08274.15,32.9268,95.1 SIF-Syn: Gene: 59; pham:99210

CDS 46791 - 47549
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="APunk_60"
    /note=Original Glimmer call @bp 46791 has strength 14.2; Genemark calls start at 46791
    /note=SSC: 46791-47549 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp60 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 6.23707E-175 GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.24, -4.34663776219455, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp60 [Gordonia phage Zipp] ],,YP_010002809,98.4127,6.23707E-175 SIF-HHPRED: DUF5678 ; Family of unknown function (DUF5678),,,PF18929.3,17.8571,84.6 SIF-Syn: Gene: 60; pham:101321
    /note=NKF

CDS 47561 - 47935
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="APunk_61"
    /note=Original Glimmer call @bp 47561 has strength 11.12; Genemark calls start at 47591
    /note=SSC: 47561-47935 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein J1774_gp62 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 3.0539E-84 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.999, -5.92650414316322, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp62 [Gordonia Phage Zitch] ],,YP_010002720,100.0,3.0539E-84 SIF-HHPRED:  SIF-Syn: Gene: 61; pham:10023
    /note=NKF

CDS 47932 - 48282
  /gene="62"
  /product="gp62"
  /function="ASC-1 transcription coactivator"
  /locus tag="APunk_62"
    /note=Original Glimmer call @bp 47932 has strength 14.54; Genemark calls start at 47932
    /note=SSC: 47932-48282 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp62 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 7.29201E-78 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.937, -3.103539494358988, yes F: ASC-1 transcription coactivator SIF-BLAST: ,,[hypothetical protein J1775_gp62 [Gordonia phage Zipp] ],,YP_010002811,100.0,7.29201E-78 SIF-HHPRED: Activating signal cointegrator; NP_814290.1, Activating signal cointegrator, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2; HET: CAC, MSE; 1.58A {Enterococcus faecalis V583},,,3IUW_B,61.2069,99.1 SIF-Syn: upstream gene: unknown
downstream gene: unknown

CDS 48279 - 48725
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="APunk_63"
    /note=Original Glimmer call @bp 48279 has strength 5.87; Genemark calls start at 48279
    /note=SSC: 48279-48725 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp63 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 4.41789E-104 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.073, -4.820269098574683, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp63 [Gordonia phage Zipp] ],,YP_010002812,100.0,4.41789E-104 SIF-HHPRED:  SIF-Syn: upstream gene: no known function 
downstream gene: ASC-1 transcription coactivator

CDS 48715 - 49200
  /gene="64"
  /product="gp64"
  /function="hypothetical protein"
  /locus tag="APunk_64"
    /note=Original Glimmer call @bp 48898 has strength 12.53; Genemark calls start at 48898
    /note=SSC: 48715-49200 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein J1776_gp63 [Gordonia phage Verity] ],,NCBI, q29:s1 82.6087% 1.05096E-45 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.423, -4.511281919781824, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1776_gp63 [Gordonia phage Verity] ],,YP_010002901,77.8626,1.05096E-45 SIF-HHPRED:  SIF-Syn: upstream gene: no known function 
downstream gene: no known function

CDS 49264 - 49710
  /gene="65"
  /product="gp65"
  /function="hypothetical protein"
  /locus tag="APunk_65"
    /note=Original Glimmer call @bp 49399 has strength 17.02; Genemark calls start at 49399
    /note=SSC: 49264-49710 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein J1776_gp64 [Gordonia phage Verity] ],,NCBI, q1:s6 100.0% 4.66499E-93 GAP: 63 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.528, -5.380351808226041, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1776_gp64 [Gordonia phage Verity] ],,YP_010002902,91.5033,4.66499E-93 SIF-HHPRED:  SIF-Syn: upstream gene: Ruv-C like resolvase 
downstream gene: no known function

CDS 49707 - 50354
  /gene="66"
  /product="gp66"
  /function="RuvC-like resolvase"
  /locus tag="APunk_66"
    /note=Original Glimmer call @bp 49707 has strength 14.99; Genemark calls start at 49707
    /note=SSC: 49707-50354 CP: yes SCS: both ST: SS BLAST-Start: [RuvC-like resolvase [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 2.83616E-151 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.03, -4.904754965500383, no F: RuvC-like resolvase SIF-BLAST: ,,[RuvC-like resolvase [Gordonia Phage Zitch] ],,YP_010002726,99.5349,2.83616E-151 SIF-HHPRED: c.55.3.6 (A:) RuvC resolvase {Thermus thermophilus [TaxId: 300852]},,,d4ep4a_,81.3953,99.9 SIF-Syn: upstream gene: no known function
downstream gene: no known function

CDS 50351 - 50623
  /gene="67"
  /product="gp67"
  /function="hypothetical protein"
  /locus tag="APunk_67"
    /note=Original Glimmer call @bp 50351 has strength 15.58; Genemark calls start at 50351
    /note=SSC: 50351-50623 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1776_gp66 [Gordonia phage Verity] ],,NCBI, q1:s1 100.0% 1.06462E-55 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.521, -3.7893453046823904, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1776_gp66 [Gordonia phage Verity] ],,YP_010002904,96.6667,1.06462E-55 SIF-HHPRED:  SIF-Syn: Gene:66; pham: 21671; up: RuvC-like resolvase; down: unknown

CDS 50616 - 51281
  /gene="68"
  /product="gp68"
  /function="hypothetical protein"
  /locus tag="APunk_68"
    /note=Original Glimmer call @bp 50616 has strength 13.63; Genemark calls start at 50616
    /note=SSC: 50616-51281 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp70 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 3.23946E-134 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.515, -3.8622971487145565, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp70 [Gordonia Phage Zitch] ],,YP_010002728,83.5341,3.23946E-134 SIF-HHPRED:  SIF-Syn: Gene: 67; pham: 10361; up: unknown; down: unknown

CDS 51316 - 52536
  /gene="69"
  /product="gp69"
  /function="hypothetical protein"
  /locus tag="APunk_69"
    /note=Original Glimmer call @bp 51316 has strength 16.69; Genemark calls start at 51316
    /note=SSC: 51316-52536 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp71 [Gordonia Phage Zitch] ],,NCBI, q1:s1 99.7537% 0.0 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.343, -2.156361006712914, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp71 [Gordonia Phage Zitch] ],,YP_010002729,73.0361,0.0 SIF-HHPRED:  SIF-Syn: Gene: 68; pham: 101050; up: unknown; down: unknown

CDS 52521 - 53081
  /gene="70"
  /product="gp70"
  /function="hypothetical protein"
  /locus tag="APunk_70"
    /note=Original Glimmer call @bp 52629 has strength 17.78; Genemark calls start at 52629
    /note=SSC: 52521-53081 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein J1775_gp71 [Gordonia phage Zipp] ],,NCBI, q37:s1 80.6452% 1.87389E-97 GAP: -16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.487, -6.496397267647118, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp71 [Gordonia phage Zipp] ],,YP_010002820,97.3333,1.87389E-97 SIF-HHPRED:  SIF-Syn: Gene: 69; pham: 9709; up: unknown; down: unknown

CDS 53143 - 53451
  /gene="71"
  /product="gp71"
  /function="hypothetical protein"
  /locus tag="APunk_71"
    /note=Original Glimmer call @bp 53143 has strength 10.23; Genemark calls start at 53164
    /note=SSC: 53143-53451 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein J1775_gp72 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 3.52764E-67 GAP: 61 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.596, -5.690017942720486, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp72 [Gordonia phage Zipp] ],,YP_010002821,99.0196,3.52764E-67 SIF-HHPRED: g.37.1.2 (A:3-36) U-shaped transcription factor, different fingers {Fruit fly (Drosophila melanogaster) [TaxId: 7227]},,,d1fu9a1,26.4706,96.1 SIF-Syn: Gene: 70; pham: 3617; up: unknown; down: unknown.

CDS 53448 - 53717
  /gene="72"
  /product="gp72"
  /function="hypothetical protein"
  /locus tag="APunk_72"
    /note=Original Glimmer call @bp 53448 has strength 17.2; Genemark calls start at 53448
    /note=SSC: 53448-53717 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein J1775_gp73 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 1.14231E-55 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.119, -2.7423981586358774, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp73 [Gordonia phage Zipp] ],,YP_010002822,97.7528,1.14231E-55 SIF-HHPRED:  SIF-Syn: Gene: 71; pham: 19675; up: helix-turn-helix DNA binding domain; down: unknown

CDS 53717 - 53935
  /gene="73"
  /product="gp73"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="APunk_73"
    /note=Original Glimmer call @bp 53717 has strength 14.93; Genemark calls start at 53717
    /note=SSC: 53717-53935 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1776_gp74 [Gordonia phage Verity] ],,NCBI, q1:s1 100.0% 4.44449E-25 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.919, -5.336604134363396, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein J1776_gp74 [Gordonia phage Verity] ],,YP_010002912,86.1111,4.44449E-25 SIF-HHPRED:  SIF-Syn: Upstream NKF, downstream NKF
    /note=SSC [start 53717, stop 53935], CP [yes], SCS [glimmer/genemark/both], ST [SS], LO [no], Gap [no], Overlap [downstream 1 bp, upstream 3 bp], Blast-start/SIF-BLAST [Gordonia DoctorFroggo, 74, q1:t1, 100%, e value -25], SIF-Syn [upstream NKF, downstream NKF], F [helix-turn-helix DNA binding domain protein similar to DoctorFroggo in PhagesDB]

CDS 53932 - 54042
  /gene="74"
  /product="gp74"
  /function="hypothetical protein"
  /locus tag="APunk_74"
    /note=Genemark calls start at 53932
    /note=SSC: 53932-54042 CP: yes SCS: genemark ST: SS BLAST-Start:  GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.547, -3.7369320822071384, yes F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: Upstream NKF, downstream helix-turn-helix DNA binding domain
    /note=SSC [start 53932, stop 54042], CP [yes], SCS [genemark called gene], ST [SS], LO [no], Overlap [upstream 15 bp and downstream 3 bp], Gap [no], Blast-start/SIF-BLAST [no significant BLAST alignments, NKF], SIF-Syn [upstream NKF, downstream helix-turn-helix DNA binding domain], F [NKF]

CDS 54027 - 54182
  /gene="75"
  /product="gp75"
  /function="hypothetical protein"
  /locus tag="APunk_75"
    /note=Original Glimmer call @bp 54027 has strength 15.47; Genemark calls start at 54027
    /note=SSC: 54027-54182 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Mycolicibacter sp. MYC098] ],,NCBI, q5:s1 90.1961% 3.69003E-10 GAP: -16 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.931, -7.028016035428936, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Mycolicibacter sp. MYC098] ],,WP_225406331,17.3077,3.69003E-10 SIF-HHPRED:  SIF-Syn: Upstream is NKF, downstream is NKF
    /note=SSC [start 54027, stop 54182], CP [yes], SCS [glimmer/genemark/both], ST [NI], LO [no], Gap [no], Overlap [downstream 15 bp, upstream 13 bp], Blast-Start/SF-BLAST [no significant BLAST alignments, NKF], SIF-Syn [upstream NKF, downstream NKF], F [NKF]

CDS 54169 - 54375
  /gene="76"
  /product="gp76"
  /function="hypothetical protein"
  /locus tag="APunk_76"
    /note=Original Glimmer call @bp 54169 has strength 7.5; Genemark calls start at 54169
    /note=SSC: 54169-54375 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1771_gp78 [Gordonia phage MelBins] ],,NCBI, q1:s1 100.0% 5.93205E-33 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.497, -5.885962410576086, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1771_gp78 [Gordonia phage MelBins] ],,YP_010002466,92.7536,5.93205E-33 SIF-HHPRED: PriA_CRR ; PriA DNA helicase Cys-rich region (CRR) domain,,,PF18319.4,44.1176,96.7 SIF-Syn: Upstream NKF, downstream NKF
    /note=SSC [start 54169, stop 54375], CP [yes, includes start], SCS [glimmer/genemark/both], ST [SS], LO [no], Gap [no], Overlap [downstream 13 bp, upstream 3 bp], Blast-start/SIF-BLAST [Gordonia Melbins, 78, q1:t1, 100% coverage, e value 5.93205e-33], SIF-Syn [upstream NKF, downstream NKF], F [NKF]

CDS 54372 - 54731
  /gene="77"
  /product="gp77"
  /function="hypothetical protein"
  /locus tag="APunk_77"
    /note=Original Glimmer call @bp 54372 has strength 16.06; Genemark calls start at 54372
    /note=SSC: 54372-54731 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1771_gp79 [Gordonia phage MelBins] ],,NCBI, q1:s1 100.0% 1.61524E-57 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.276, -4.354778061539587, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1771_gp79 [Gordonia phage MelBins] ],,YP_010002467,82.3529,1.61524E-57 SIF-HHPRED: PGDYG ; PGDYG protein,,,PF14083.9,25.2101,99.2 SIF-Syn: Upstream NKF, downstream NKF
    /note=SSC [start 54372, stop 54731], CP [yes], SCS [glimmer/genemark/both called gene], ST [SS], LO [no], Overlap [downstream 3 bp], Gap [upstream 52 bp], Blast-start/SIF-BLAST [Gordonia Melbins, 79, q1:t1, 100% coverage, e value 1.61524e-57], SIF-Syn [upstream NKF, downstream NKF], F [NKF]

CDS 54783 - 55109
  /gene="78"
  /product="gp78"
  /function="hypothetical protein"
  /locus tag="APunk_78"
    /note=Original Glimmer call @bp 54783 has strength 11.45; Genemark calls start at 54783
    /note=SSC: 54783-55109 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp78 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 9.88676E-68 GAP: 51 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.343, -2.5074698667202133, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp78 [Gordonia phage Zipp] ],,YP_010002827,96.2963,9.88676E-68 SIF-HHPRED:  SIF-Syn: Upstream NKF, downstream NKF
    /note=SSC [start 54783, stop 55109], CP [yes], SCS [glimmer/genemark/both call gene], ST [SS], LO [yes], Gap [downstream 52 bp], Overlap [upstream 3 bp], Blast-Start/SIF-BLAST [Gordonia Zipp, 78, 100% coverage, q1:t1, e value 9.88676e-68; Gordonia Zitch, 79, 100% coverage, q1:t1, e value 3.61097e-67], SIF-Syn [upstream NKF, downstream NKF], F [NKF]

CDS 55106 - 55579
  /gene="79"
  /product="gp79"
  /function="hypothetical protein"
  /locus tag="APunk_79"
    /note=Original Glimmer call @bp 55106 has strength 13.06; Genemark calls start at 55106
    /note=SSC: 55106-55579 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp79 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 1.40725E-75 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.684, -3.5268154277366257, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp79 [Gordonia phage Zipp] ],,YP_010002828,86.5385,1.40725E-75 SIF-HHPRED:  SIF-Syn: downstream gene is NKF
upstream gene is NKF
    /note=the close relatives of APunk in Phamerator do not suggest a function for this gene they have in common, so we conclude that it is NKF, since there is not enough information to suggest otherwise

CDS 55576 - 55845
  /gene="80"
  /product="gp80"
  /function="hypothetical protein"
  /locus tag="APunk_80"
    /note=Original Glimmer call @bp 55576 has strength 12.14; Genemark calls start at 55576
    /note=SSC: 55576-55845 CP: yes SCS: both ST: SS BLAST-Start:  GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.663, -3.586741874491512, yes F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: downstream gene is NKF 
upstream gene is DnaQ-like DNA polymerase III
    /note=close relatives of APunk in phamerator do not suggest a function for this gene they have in common, phagesdb does not suggest a function either, so we conclude that the gene is NKF

CDS 55842 - 56555
  /gene="81"
  /product="gp81"
  /function="DnaQ-like (DNA polymerase III subunit)"
  /locus tag="APunk_81"
    /note=Original Glimmer call @bp 55857 has strength 14.91; Genemark calls start at 55857
    /note=SSC: 55842-56555 CP: yes SCS: both-cs ST: SS BLAST-Start: [DNA polymerase III subunit [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 9.76492E-156 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.999, -3.1896562502401133, yes F: DnaQ-like (DNA polymerase III subunit) SIF-BLAST: ,,[DNA polymerase III subunit [Gordonia Phage Zitch] ],,YP_010002740,94.9367,9.76492E-156 SIF-HHPRED:  SIF-Syn: downstream gene is NKF
upstream gene is NKF
    /note=DoctorFroggo, Verity, and Zipp in phamerator assign this gene (that they have in common with APunk) the function of DnaQ-like DNA polymerase III. Phagesdb also suggests this function.

CDS 56552 - 57142
  /gene="82"
  /product="gp82"
  /function="hypothetical protein"
  /locus tag="APunk_82"
    /note=Original Glimmer call @bp 56552 has strength 12.96; Genemark calls start at 56552
    /note=SSC: 56552-57142 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1775_gp82 [Gordonia phage Zipp] ],,NCBI, q1:s1 100.0% 8.8406E-69 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.596, -5.690017942720486, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1775_gp82 [Gordonia phage Zipp] ],,YP_010002831,65.8163,8.8406E-69 SIF-HHPRED:  SIF-Syn: downstream gene is a DNA Q-like DNA polymerase III 
upstream gene is NKF
    /note=relatives in phamerator do not suggest a function for this gene they have in common with APunk, so we conclude that the gene is NKF

CDS 57139 - 57345
  /gene="83"
  /product="gp83"
  /function="hypothetical protein"
  /locus tag="APunk_83"
    /note=Original Glimmer call @bp 57139 has strength 14.2; Genemark calls start at 57124
    /note=SSC: 57139-57345 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein J1774_gp85 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 4.45725E-40 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.753, -3.678676728259483, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp85 [Gordonia Phage Zitch] ],,YP_010002743,100.0,4.45725E-40 SIF-HHPRED:  SIF-Syn: downstream gene is NKF
upstream gene is NKF
    /note=Since the relatives of APunk in phamerator do not have a suggested function for the gene they have in common, and phagesdb does not give any results about the function either, we conclude that this gene is NKF

CDS 57342 - 57623
  /gene="84"
  /product="gp84"
  /function="hypothetical protein"
  /locus tag="APunk_84"
    /note=Original Glimmer call @bp 57342 has strength 7.62; Genemark calls start at 57342
    /note=SSC: 57342-57623 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp86 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 2.81625E-59 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.09, -4.787182377296497, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp86 [Gordonia Phage Zitch] ],,YP_010002744,100.0,2.81625E-59 SIF-HHPRED:  SIF-Syn: upstream is NKF, downstream is NKF
    /note=- has coding potential includes only the stop (57623); start is located at 57342 [forward direction]
    /note=- Glimmer and GeneMark both support this gene
    /note=- function matches with Phagesdb Blast, NCBI Blast, and its relatives in the same subcluster on Phamerator (Zitch, Delrey21, DoctorFroggo, Verity, Zipp)
    /note=- there is a 3 nucleotide gap between the upstream gene and a 3 nucleotide overlap between the downstream gene

CDS 57620 - 58039
  /gene="85"
  /product="gp85"
  /function="hypothetical protein"
  /locus tag="APunk_85"
    /note=Original Glimmer call @bp 57620 has strength 12.75; Genemark calls start at 57620
    /note=SSC: 57620-58039 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp87 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 8.29324E-94 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.764, -3.368377069717189, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp87 [Gordonia Phage Zitch] ],,YP_010002745,100.0,8.29324E-94 SIF-HHPRED:  SIF-Syn: upstream is NKF, downstream is NKF
    /note=- has coding potential including stop (58039) and start (57620) [forward direction]
    /note=- Glimmer and GeneMark both support this gene
    /note=- functions match with Phagesdb, NCBI Blast, its relative in the same subcluster on Phamerator (Zitch)
    /note=- upstream gene overlaps by 3 nucleotides and downstream gene overlaps by 3 nucleotides

CDS 58036 - 58491
  /gene="86"
  /product="gp86"
  /function="hypothetical protein"
  /locus tag="APunk_86"
    /note=Original Glimmer call @bp 58036 has strength 15.92; Genemark calls start at 58036
    /note=SSC: 58036-58491 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp88 [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 3.02948E-73 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.24, -4.487636275856737, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp88 [Gordonia Phage Zitch] ],,YP_010002746,80.3922,3.02948E-73 SIF-HHPRED:  SIF-Syn: upstream is NKF, downstream is NKF
    /note=- has coding potential including stop (58391) and start (58036) [foward direction]
    /note=- Glimmer and GeneMark both support this gene
    /note=- function matches Phagesdb and F-Blast (Delrey21, DoctorFroggo, Verity, Zipp)
    /note=- upstream gene overlap by 3 nucleotides and there is a gap of 91 nucleotides between the downstream gene

CDS 58482 - 58658
  /gene="87"
  /product="gp87"
  /function="hypothetical protein"
  /locus tag="APunk_87"
    /note=Original Glimmer call @bp 58482 has strength 9.33; Genemark calls start at 58482
    /note=SSC: 58482-58658 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J1774_gp89 [Gordonia Phage Zitch] ],,NCBI, q1:s1 98.2759% 7.87902E-33 GAP: -10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.03, -5.672013520732137, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J1774_gp89 [Gordonia Phage Zitch] ],,YP_010002747,98.2759,7.87902E-33 SIF-HHPRED:  SIF-Syn: upstream is NKF, downstream is helix-turn-helix DNA binding domain
    /note=- has coding potential including stop (58658) and start (58482) [forward gene]
    /note=- Glimmer and GeneMark support the gene
    /note=- function matches with Phagesdb, NCBI Blast, its relative in the same subcluster on Phameratory (Zitch, Delrey21, DoctorFroggo, Verity, Zipp)
    /note=- there is a 9 nucleotide gap between the upstream gene and a 56 nucleotide gap between the downstream gene

CDS 58714 - 58983
  /gene="88"
  /product="gp88"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="APunk_88"
    /note=Original Glimmer call @bp 58714 has strength 14.28; Genemark calls start at 58714
    /note=SSC: 58714-58983 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Gordonia Phage Zitch] ],,NCBI, q1:s1 100.0% 4.45792E-55 GAP: 55 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.937, -2.9625409806968013, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Gordonia Phage Zitch] ],,YP_010002748,97.7528,4.45792E-55 SIF-HHPRED: Redirecting phage packaging protein C (RppC); Redirecting packaging protein, DNA Binding protein, Homo-dimer, phage interference; HET: MSE; 2.42A {Escherichia coli},,,6HLK_A,85.3933,98.5 SIF-Syn: upstream is unknown, no downstream gene
    /note=- has coding potential including stop (58983) and start (58714) [forward direction]
    /note=- Glimmer and GeneMark suppot this gene
    /note=- Function matches with Phagesdb, NCBI blast, and its relative in the same subcluster on Phamerator (Zitch and Doctor Froggo)
    /note=- Upstream gene has a 56 nucleotide gap and there is no downstream gene

CDS join(59113. .59154;1. .498)
  /gene="89"
  /product="gp89"
  /locus tag="APunk_89"
    /note=Original Glimmer call @bp 59113 has strength 17.5; Genemark calls start at 1
    /note=SSC: 59113-498 CP: no SCS: both-gl ST: NI BLAST-Start: [helix-turn-helix DNA binding protein [Gordonia phage Verity] ],,NCBI, q15:s1 92.1788% 6.84695E-110 GAP: 129 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.82, -6.009111938462203, no F:  SIF-BLAST: ,,[helix-turn-helix DNA binding protein [Gordonia phage Verity] ],,YP_010002839,98.7879,6.84695E-110 SIF-HHPRED:  SIF-Syn: