CDS 1 - 525
  /gene="1"
  /product="gp1"
  /function="hypothetical protein"
  /locus tag="NickSell_1"
    /note=Original Glimmer call @bp 1 has strength 15.82; Genemark calls start at 1
    /note=SSC: 1-525 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PUPPYEGGO_1 [Microbacterium phage PuppyEggo] ],,NCBI, q1:s1 100.0% 1.79345E-121 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.764, -5.135095111895543, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PUPPYEGGO_1 [Microbacterium phage PuppyEggo] ],,AVJ51198,100.0,1.79345E-121 SIF-HHPRED: Prim_Zn_Ribbon ; Zinc-binding domain of primase-helicase,,,PF08273.16,4.5977,21.2 SIF-Syn: PF08273.16

CDS 522 - 1922
  /gene="2"
  /product="gp2"
  /function="terminase"
  /locus tag="NickSell_2"
    /note=Original Glimmer call @bp 522 has strength 15.24; Genemark calls start at 522
    /note=SSC: 522-1922 CP: yes SCS: both ST: SS BLAST-Start: [terminase [Microbacterium phage BeautPeep30]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.911, -4.757883910852364, no F: terminase SIF-BLAST: ,,[terminase [Microbacterium phage BeautPeep30]],,QJD50505,100.0,0.0 SIF-HHPRED: Terminase, large subunit; phage defense, pattern-recognition receptor, nlr, stand, atpase, ANTIVIRAL PROTEIN; HET: ATP;{Salmonella enterica},,,8DGC_F,97.2103,100.0 SIF-Syn: QJD50505
8DGC_F

CDS 1953 - 3350
  /gene="3"
  /product="gp3"
  /function="portal protein"
  /locus tag="NickSell_3"
    /note=Original Glimmer call @bp 1953 has strength 20.32; Genemark calls start at 1953
    /note=SSC: 1953-3350 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Microbacterium phage Martin] ],,NCBI, q1:s1 100.0% 0.0 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.885, -2.5823297389851954, yes F: portal protein SIF-BLAST: ,,[portal protein [Microbacterium phage Martin] ],,AWN03718,100.0,0.0 SIF-HHPRED:  SIF-Syn: QQV93088
7Z4W_L

CDS 3356 - 4024
  /gene="4"
  /product="gp4"
  /function="hypothetical protein"
  /locus tag="NickSell_4"
    /note=Original Glimmer call @bp 3356 has strength 12.6; Genemark calls start at 3356
    /note=SSC: 3356-4024 CP: yes SCS: both ST: SS BLAST-Start: [head morphogenesis [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 5.47301E-162 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.089, -4.645163458565996, no F: hypothetical protein SIF-BLAST: ,,[head morphogenesis [Microbacterium phage Ilzat] ],,YP_009623168,100.0,5.47301E-162 SIF-HHPRED:  SIF-Syn: 

CDS 4108 - 4668
  /gene="5"
  /product="gp5"
  /function="scaffolding protein"
  /locus tag="NickSell_5"
    /note=Original Glimmer call @bp 4108 has strength 13.29; Genemark calls start at 4108
    /note=SSC: 4108-4668 CP: yes SCS: both ST: SS BLAST-Start: [scaffolding protein [Microbacterium phage Martin] ],,NCBI, q1:s1 100.0% 1.89178E-130 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.009, -3.222210725506937, yes F: scaffolding protein SIF-BLAST: ,,[scaffolding protein [Microbacterium phage Martin] ],,AWN03720,100.0,1.89178E-130 SIF-HHPRED:  SIF-Syn: UGL63453
PF10805.12

CDS 4708 - 5634
  /gene="6"
  /product="gp6"
  /function="major capsid protein"
  /locus tag="NickSell_6"
    /note=Original Glimmer call @bp 4708 has strength 19.24; Genemark calls start at 4708
    /note=SSC: 4708-5634 CP: yes SCS: both ST: SS BLAST-Start: [major capsid protein [Microbacterium phage MonChoix] ],,NCBI, q1:s1 100.0% 0.0 GAP: 39 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.177, -2.305049668942183, yes F: major capsid protein SIF-BLAST: ,,[major capsid protein [Microbacterium phage MonChoix] ],,YP_009908645,100.0,0.0 SIF-HHPRED:  SIF-Syn: 

CDS 5631 - 5879
  /gene="7"
  /product="gp7"
  /function="hypothetical protein"
  /locus tag="NickSell_7"
    /note=Original Glimmer call @bp 5631 has strength 9.05; Genemark calls start at 5631
    /note=SSC: 5631-5879 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_GARGOYLE_7 [Microbacterium phage Gargoyle] ],,NCBI, q1:s1 100.0% 3.03897E-47 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.871, -4.9056006736197375, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_GARGOYLE_7 [Microbacterium phage Gargoyle] ],,AWN03462,100.0,3.03897E-47 SIF-HHPRED:  SIF-Syn: There is evidence of synteny for this gene, but closely related phages have no known function.
    /note=This start has 98 manual annotations and is supported by Glimmer and Genemark. It is important to note that there are only 2 possible starts. This start has the LORF, best gap, and best RBS scores. There is no evidence to support a function.

CDS 5942 - 6085
  /gene="8"
  /product="gp8"
  /function="hypothetical protein"
  /locus tag="NickSell_8"
    /note=Original Glimmer call @bp 5951 has strength 18.59; Genemark calls start at 5942
    /note=SSC: 5942-6085 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein H3N90_gp08 [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 2.27622E-25 GAP: 62 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.487, -5.652246897589902, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein H3N90_gp08 [Microbacterium phage Teagan] ],,YP_009908710,100.0,2.27622E-25 SIF-HHPRED:  SIF-Syn: There is evidence of synteny for this gene, but closely related phages have no known function.
    /note=This start is called by both Glimmer and genemark but this is the start genemark called and it contains all of the coding potential. The start is also supported by starterator annotations and a 1:1 ratio on NCBI Blast. It has the smallest gap, the LOF, and the best RBS. There is no known function because similar genes on Blast, HHpred, and Phamerator all have no known function. There is no membrane section.

CDS 6114 - 6527
  /gene="9"
  /product="gp9"
  /function="hypothetical protein"
  /locus tag="NickSell_9"
    /note=Original Glimmer call @bp 6114 has strength 11.1; Genemark calls start at 6114
    /note=SSC: 6114-6527 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TATARKAPM_9 [Microbacterium phage TatarkaPM]],,NCBI, q1:s4 100.0% 8.91315E-96 GAP: 28 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.95, -2.794070146961553, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TATARKAPM_9 [Microbacterium phage TatarkaPM]],,QOC56801,97.8571,8.91315E-96 SIF-HHPRED:  SIF-Syn: There is evidence of synteny for this gene, but closely related phages have no known function.
    /note=Start is called by both Glimmer and Genemark, has the most manual annotations as well as a 1:1 ratio on NCBI Blast, and the best RBS along with the fact that it has the 2nd longest ORF with a decently short overlap and the best final score. Unfortunately no known function, due to similar alignments and closely related phages also having no known functions.

CDS 6493 - 6909
  /gene="10"
  /product="gp10"
  /function="hypothetical protein"
  /locus tag="NickSell_10"
    /note=Original Glimmer call @bp 6493 has strength 12.61; Genemark calls start at 6505
    /note=SSC: 6493-6909 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein PBI_MARTIN_11 [Microbacterium phage Martin] ],,NCBI, q1:s1 100.0% 1.90997E-91 GAP: -35 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.658, -3.0713502170045657, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MARTIN_11 [Microbacterium phage Martin] ],,AWN03725,100.0,1.90997E-91 SIF-HHPRED:  SIF-Syn: There is evidence of synteny but closely related phages have no known function.
    /note=This start is called by both Glimmer and Genemark but this is the start Glimmer called and it contains all of the coding potential. The start is also supported by starterator annotations and a 1:1 ratio on NCBI Blast. It has the smallest overlap and is not the LOF (5th longest) but the best RBS. There is no known function because similar genes on Blast, HHpred, and Phamerator all have no known function. There is no membrane section.

CDS 6906 - 7247
  /gene="11"
  /product="gp11"
  /function="hypothetical protein"
  /locus tag="NickSell_11"
    /note=Original Glimmer call @bp 6906 has strength 13.82; Genemark calls start at 6906
    /note=SSC: 6906-7247 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp11 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 5.64481E-76 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.95, -3.3503726477288405, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp11 [Microbacterium phage Ilzat] ],,YP_009623175,100.0,5.64481E-76 SIF-HHPRED: Minor_capsid_2 ; Minor capsid protein,,,PF11114.12,76.1062,99.5 SIF-Syn: NKF: same pham and position as Ilzat_11 and Bonino_11 which are both hypothetical proteins.
    /note=Start at position 6,906 including all of the coding potential. It is supported by Glimmer, Genemark, and Starterator. There were multiple 1:1 hits with low e-values and high coverage. It has the best gap and is the LO with the best RBS values, all supporting this start. This gene has NKF. There were multiple BLAST hits with low e-values to hypothetical proteins. Looking at Synteny, this gene is in the same pham and position as Ilzat_11 and Bonino_11 which are both hypothetical proteins. Also, TmHmm predicted 0 transmembrane helices. Although HHPred did not support this gene as having NKF (it had multiple hits to different functions with low e-values but low %coverages), all other evidence points towards NKF.

CDS 7250 - 7609
  /gene="12"
  /product="gp12"
  /function="tail terminator"
  /locus tag="NickSell_12"
    /note=Original Glimmer call @bp 7250 has strength 10.91; Genemark calls start at 7250
    /note=SSC: 7250-7609 CP: yes SCS: both ST: SS BLAST-Start: [tail terminator [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 2.49919E-79 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.302, -3.978223840957539, yes F: tail terminator SIF-BLAST: ,,[tail terminator [Microbacterium phage Teagan] ],,YP_009908714,100.0,2.49919E-79 SIF-HHPRED: Tail terminator protein Rcc01690; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_F,57.9832,97.9 SIF-Syn: Tail terminator protein, same Pham and position as Teagan_12 and Ludgate_12.
    /note=The start 11 is supported by genemark, glimmer, starterator (has 120 MA), has an ideal gap of 2 bp, has multiple 1:1 alignments, has coding potential, good RBS score, good BLAST hits, and HHPred hits. The function is tail terminator because the top hits for BLAST and HHpred had the function tail terminator. In SIF-Syn NickSell_12 had the same pham and position as Teagan_12 and Ludgate_12, which had the function tail terminator protein.

CDS 7606 - 7842
  /gene="13"
  /product="gp13"
  /function="hypothetical protein"
  /locus tag="NickSell_13"
    /note=Original Glimmer call @bp 7606 has strength 15.32; Genemark calls start at 7606
    /note=SSC: 7606-7842 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein H3N90_gp13 [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 1.71063E-48 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.103, -2.17469248771465, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein H3N90_gp13 [Microbacterium phage Teagan] ],,YP_009908715,100.0,1.71063E-48 SIF-HHPRED:  SIF-Syn: It has the same pham and position as Teagan_13 and Ilzat_13 which are both hypothetical proteins; downstream of tail terminator and upstream of major tail protein
    /note=Start at position 7,606 includes all of the coding potential. It is supported by Glimmer, Genemark, and Starterator. There were multiple 1:1 hits with low e-values and high coverage. It has the best gap, is the LO, and has the best RBS values. This gene has NKF. There were multiple BLAST hits with low e-values to hypothetical proteins. Looking at Synteny, this gene is in the same pham and position as Teagan_13 and Ilzat_13 which are both hypothetical proteins. Also, TmHmm predicted 0 transmembrane helices

CDS 7855 - 8355
  /gene="14"
  /product="gp14"
  /function="major tail protein"
  /locus tag="NickSell_14"
    /note=Original Glimmer call @bp 7855 has strength 14.51; Genemark calls start at 7855
    /note=SSC: 7855-8355 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 4.15903E-115 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.083, -2.2364030944336752, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Microbacterium phage Ilzat] ],,YP_009623178,100.0,4.15903E-115 SIF-HHPRED: Major tail protein V; gpV, Bacteriophage Lambda, Major tail protein, VIRAL PROTEIN; NMR {Enterobacteria phage lambda},,,2K4Q_A,95.1807,93.5 SIF-Syn: Major tail protein, same pham and postion as Teagan_14, Ilzat_14
    /note=The start 28 is supported by genemark, glimmer, starterator (has 52 MA), has coding potential, has a good gap of 12 bp, has multiple 1:1 alignments, good RBS score, Longest ORF, good BLAST and HHpred hits. The function is a major tail protein because in phamerator the gene had the same pham and postion as Ilzat_14 and Teagan_14 and it also had good and multiple BLAST hits for the function.

CDS 8384 - 8953
  /gene="15"
  /product="gp15"
  /function="tail assembly chaperone"
  /locus tag="NickSell_15"
    /note=Original Glimmer call @bp 8384 has strength 18.13; Genemark calls start at 8384
    /note=SSC: 8384-8953 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 9.71011E-135 GAP: 28 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.95, -2.794070146961553, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Ilzat] ],,YP_009623179,100.0,9.71011E-135 SIF-HHPRED:  SIF-Syn: Closely related phages have NKF
    /note=Start at position 8,384 includes all of the coding potential. It is supported by Glimmer, Genemark, and Starterator with the most manual annotation, HHpred coverage was extremely low around 36% and e-value was high at 190. It has the best RBS values. This gene has tail assembly chaperone as the function. Also, TmHmm predicted 0 transmembrane helices

CDS join(8384..8911,8911..9339)
  /gene="16"
  /product="gp16"
  /function="tail assembly chaperone"
  /locus tag="NickSell_16"
    /note=
    /note=SSC: 8384-9339 CP: no SCS: neither ST: NI BLAST-Start: [tail assembly chaperone [Microbacterium phage Ixel]],,NCBI, q1:s1 100.0% 6.9811E-158 GAP: -570 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.95, -2.794070146961553, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Ixel]],,QKN87717,80.625,6.9811E-158 SIF-HHPRED:  SIF-Syn: 

CDS 9364 - 11634
  /gene="17"
  /product="gp17"
  /function="tape measure protein"
  /locus tag="NickSell_17"
    /note=Original Glimmer call @bp 9364 has strength 21.27; Genemark calls start at 9364
    /note=SSC: 9364-11634 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Microbacterium phage TatarkaPM]],,NCBI, q1:s1 100.0% 0.0 GAP: 23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.177, -1.953940808934884, yes F: tape measure protein SIF-BLAST: ,,[tape measure protein [Microbacterium phage TatarkaPM]],,QOC56809,100.0,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_AF,16.5344,99.9 SIF-Syn: Closely related phages have NKF
    /note=TmHmm predicted 7 domains and SOSUI predicted 6 domains
    /note=Start at position 9,364 includes all of the coding potential. It is supported by Glimmer, Genemark, and Starterator. There were multiple 1:1 hits with low e-values and high coverage. It has the best gap, is the LO, and has the best RBS values. This gene is a tape measure protein. There were multiple BLAST hits with low e-values to tape measure proteins. Looking at Synteny, this gene is in the same pham and position as TatarkaPM_17 and Stanktossa_17 which are both tape measure proteins. HHPred has many hits to tape measure proteins with high probabilities and low e-values.

CDS 11631 - 12404
  /gene="18"
  /product="gp18"
  /function="minor tail protein"
  /locus tag="NickSell_18"
    /note=Original Glimmer call @bp 11631 has strength 17.2; Genemark calls start at 11631
    /note=SSC: 11631-12404 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Martin] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.381, -3.8079208184165134, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Martin] ],,AWN03733,100.0,0.0 SIF-HHPRED: HYPOTHETICAL PROTEIN 19.1; VIRAL PROTEIN, DISTAL TAIL PROTEIN; 2.95A {BACILLUS PHAGE SPP1},,,2X8K_A,99.6109,100.0 SIF-Syn: Minor tail protein, same pham and position as Martin_18 and MillyPhilly_17
    /note=The start 2 is supported by genemark, glimmer, has multiple 1:1 alignments, good BLAST hits, good RBS score, has an ideal gap, good HHPred hits, has good SIF-Syn (have same pham and position as Martin_18 and MillyPhilly_17), and has coding potential. The function is minor tail protein because it has a good SIF-SYN, top BLAST that show the minor tail protein function, even though HHpred top hits are hypothetical protein there`s suffienct evidence that the function is minor tail protein.

CDS 12404 - 14830
  /gene="19"
  /product="gp19"
  /function="minor tail protein"
  /locus tag="NickSell_19"
    /note=Original Glimmer call @bp 12404 has strength 17.95; Genemark calls start at 12404
    /note=SSC: 12404-14830 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage TinSulphur] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.8, -2.7653702713535186, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage TinSulphur] ],,QBZ73127,100.0,0.0 SIF-HHPRED:  SIF-Syn: minor tail protein, same pham and position as TinSulphur_19 and Martin_20 which are both minor tail proteins
    /note=Start at position 12,404 includes all of the coding potential. It is supported by Glimmer, Genemark, and Starterator. There were multiple 1:1 hits with low e-values and high coverage. It has the best gap, is the LO, and the best RBS values. This gene is a minor tail protein. There were multiple BLAST hits with low e-values to minor tail proteins. Looking at Synteny, this gene is in the same pham and position as TinSulphur_19 and Martin_20 which are both minor tail proteins. HHPred has a hit to Tail-Associated Lysin with a high probability, low e-value, and ~39% coverage which is neglegent based on other evidence. Although TmHmm predicted 0 domains, all evidence points to minor tail protein

CDS 14830 - 15015
  /gene="20"
  /product="gp20"
  /function="hypothetical protein"
  /locus tag="NickSell_20"
    /note=Original Glimmer call @bp 14830 has strength 8.98; Genemark calls start at 14830
    /note=SSC: 14830-15015 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp20 [Microbacterium phage Ilzat] ],,NCBI, q1:s2 100.0% 2.98589E-35 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.465, -3.5660483139923818, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp20 [Microbacterium phage Ilzat] ],,YP_009623184,98.3871,2.98589E-35 SIF-HHPRED:  SIF-Syn: 
    /note=Start at position 14,830 includes all of the coding potential. It is supported by Glimmer and Genemark. There were multiple 1:2 and 1:1 hits with low e-values and high coverage. It has the best gap and RBS scores, but is not the LO. However, it is not supported by Starterator as the gene is non-existant. This gene has NKF. There were multiple BLAST hits with low e-values to hypothetical proteins. Looking at Synteny, this gene is non-existant as NickSell_19 jumps to NickSell_21. HHPred showed no significant results. TmHmm predicted 0 domains as well. This gene does not exist

CDS 15012 - 15608
  /gene="21"
  /product="gp21"
  /function="hypothetical protein"
  /locus tag="NickSell_21"
    /note=Original Glimmer call @bp 15012 has strength 12.66; Genemark calls start at 15012
    /note=SSC: 15012-15608 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_MARTIN_22 [Microbacterium phage Martin] ],,NCBI, q1:s1 100.0% 4.64673E-141 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.012, -4.601664605840989, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MARTIN_22 [Microbacterium phage Martin] ],,AWN03736,100.0,4.64673E-141 SIF-HHPRED:  SIF-Syn: 
    /note=Start at 15012 is the ost justified start. It contains all coding potential and is called by both glimmer and genemark. It is supported by starterator, and has multiple 1:1 alignments. It has an optimal overlap of only 4 bp. However this start does not contain the LORF, it has the 2nd best RBS and all other evidence supports this start. This gene has NKF. There is no evidence to support a function for this gene. There was no significant results for HHpred, and all alignments for BLAST were hypothetical.

CDS 15608 - 16096
  /gene="22"
  /product="gp22"
  /function="hypothetical protein"
  /locus tag="NickSell_22"
    /note=Original Glimmer call @bp 15608 has strength 12.76; Genemark calls start at 15608
    /note=SSC: 15608-16096 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein H3N90_gp22 [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 1.12542E-112 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.538, -3.389881189012514, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein H3N90_gp22 [Microbacterium phage Teagan] ],,YP_009908724,100.0,1.12542E-112 SIF-HHPRED:  SIF-Syn: 
    /note=Start agrees with gm + gl, includes all CP (starts ~10 bp upstream), has multiple 1:1 BLAST alignments, is highly conserved in the pham, has the most manual annotations, encodes the longest ORF, and has the best RBS score. No specific function was supported by the SIF, since none of the top BLAST alignments had known functions and synteny was only present with genes of NKF. The top HHPred result was a receptor binding protein, but this is not a listed function on the official function list for phages. It does however somewhat support the result of SOSUI, which detected two transmembrane domains (TMHMM detected none), since receptor binding proteins also typically have transmembrane domains. So this gene likely encodes a membrane protein.

CDS 16096 - 18231
  /gene="23"
  /product="gp23"
  /function="minor tail protein"
  /locus tag="NickSell_23"
    /note=Original Glimmer call @bp 16096 has strength 11.23; Genemark calls start at 16096
    /note=SSC: 16096-18231 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage TatarkaPM]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.992, -4.582905859694018, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage TatarkaPM]],,QOC56815,100.0,0.0 SIF-HHPRED: Chitinase B; GH18, enzyme, inhibitor, chitinase, HYDROLASE; HET: DW0; 1.85A {Clostridium perfringens},,,8C6Z_A,46.4135,99.9 SIF-Syn: Minor tail protein, same pham and position as TinSulphur_23 and Pherferi_23; all are immediately downstream of a gene from pham 743 and upstream of lysin A/endolysin
    /note=Start agrees with gm + gl, includes all CP, is highly conserved in the pham, has the most manual annotations, has many 1:1 BLAST alignments, and has the 2nd best RBS score. Although this start does not encode the longest ORF, the start corresponding to the longest ORF results in a highly unlikely overlap. The function is most likely a minor tail protein, since all of the top BLAST alignments were with minor tail proteins and synteny was present with the minor tail proteins of similar genomes, like TinSulphur_23 and Pherferi_23. The top HHPred hits were all related to chitinase, which differs from the minor tail protein function but is possible and likely indicates that the protein has structural similarities to chitinase, even if it does not actually cleave chitin. It may however have domains that bind to NAG (monomer of chitin). See https://seaphages.org/forums/topic/4941/ for more details. No transmembrane domains were detected by TMHMM or SOSUI.

CDS 18261 - 19067
  /gene="24"
  /product="gp24"
  /function="endolysin"
  /locus tag="NickSell_24"
    /note=Original Glimmer call @bp 18261 has strength 14.82; Genemark calls start at 18261
    /note=SSC: 18261-19067 CP: yes SCS: both ST: SS BLAST-Start: [endolysin [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 0.0 GAP: 29 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.95, -2.5052746077145835, yes F: endolysin SIF-BLAST: ,,[endolysin [Microbacterium phage Teagan] ],,YP_009908726,100.0,0.0 SIF-HHPRED: D,D-dipeptidase/D,D-carboxypeptidase; CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, NIAID; HET: 2D8, LY0, GOL, PE3; 1.364A {Enterococcus faecalis},,,4MUQ_A,40.2985,99.1 SIF-Syn: endolysin, same pham and position as Teagan_24 and Inventa_24; all are immediately downstream of a minor tail protein and upstream of gene from pham 737
    /note=Start agrees with gm + gl, cuts off only ~10 bp of CP, is highly conserved in the pham, has the most manual annotations, has many 1:1 BLAST alignments, and has the best RBS score. Although this start does not encode the longest ORF, the start corresponding to the longest ORF results in a highly unlikely overlap. The function is most likely an endolysin, since all of the top BLAST alignments were with lysins (endolysins or lysin A) and synteny was present with the endolysins of similar genomes, like Teagan_24 and Inventa_24. The top HHPred hits were all related to peptidase, specifically D-ala-D-ala peptidases.This may indicate that the endolysin has a particular peptidase domain, but there is not enough information to know for sure. No transmembrane domains were detected by TMHMM or SOSUI.

CDS 19102 - 19491
  /gene="25"
  /product="gp25"
  /function="membrane protein"
  /locus tag="NickSell_25"
    /note=Original Glimmer call @bp 19102 has strength 13.67; Genemark calls start at 19102
    /note=SSC: 19102-19491 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 4.03977E-88 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.95, -2.970161406017234, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Ilzat] ],,YP_009623189,100.0,4.03977E-88 SIF-HHPRED:  SIF-Syn: 
    /note=Start agrees with gm + gl, cuts off only ~5 bp of CP, is highly conserved in the pham, has the most manual annotations, has many 1:1 BLAST alignments, encodes the longest ORF, and has the best RBS score. The SIF indicates that it is a membrane protein, since all of the top BLAST alignments were with membrane proteins, there was synteny with other membrane proteins from Ilzat_25 and Figueroism_25, and both TMHMM and SOSUI detected a transmembrane domain.

CDS 19496 - 19837
  /gene="26"
  /product="gp26"
  /function="holin"
  /locus tag="NickSell_26"
    /note=Original Glimmer call @bp 19496 has strength 18.76; Genemark calls start at 19496
    /note=SSC: 19496-19837 CP: no SCS: both ST: SS BLAST-Start: [holin [Microbacterium phage Martin] ],,NCBI, q1:s1 100.0% 2.7041E-68 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.083, -2.297359520375101, yes F: holin SIF-BLAST: ,,[holin [Microbacterium phage Martin] ],,AWN03741,100.0,2.7041E-68 SIF-HHPRED:  SIF-Syn: 
    /note=Start agrees with gm + gl, cuts off only ~10 bp of CP, is highly conserved in the pham, has the most manual annotations, has many 1:1 BLAST alignments, and has the best RBS score. Although the start does not encode the longest ORF, the start that does so also introduces a highly improbable overlap. The SIF indicates that it is a holin, since all of the top BLAST alignments were with holins, the top HHPred results were holins from Listeria bacteriophages, and there was synteny with other holins from Martin_27 and Alyxandracam_26. Plus, both TMHMM and SOSUI detected three transmembrane domain, and it is required that at least two transmembrane domains be detected before calling a protein a holin

CDS 19897 - 20307
  /gene="27"
  /product="gp27"
  /function="hypothetical protein"
  /locus tag="NickSell_27"
    /note=Original Glimmer call @bp 19897 has strength 12.41; Genemark calls start at 19897
    /note=SSC: 19897-20307 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein H3N90_gp27 [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 4.99928E-94 GAP: 59 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.065, -4.34663776219455, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein H3N90_gp27 [Microbacterium phage Teagan] ],,YP_009908729,100.0,4.99928E-94 SIF-HHPRED:  SIF-Syn: 
    /note=Start agrees with gm + gl, includes all CP, is highly conserved in the pham, has the most manual annotations, has many 1:1 BLAST alignments, encodes the longest ORF, and has the best RBS score. All SIF failed to indicate any possible functions of the gene, since all BLAST alignments were with genes with NKF, HHPred had no significant hits, and synteny was only found with other genes with NKF. There were no transmembrane domains detected by TMHMM or SOSUI.

CDS complement (20375 - 20563)
  /gene="28"
  /product="gp28"
  /function="hypothetical protein"
  /locus tag="NickSell_28"
    /note=Original Glimmer call @bp 20563 has strength 18.45; Genemark calls start at 20563
    /note=SSC: 20563-20375 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_MARTIN_29 [Microbacterium phage Martin] ],,NCBI, q1:s1 100.0% 2.06578E-36 GAP: 70 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.95, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MARTIN_29 [Microbacterium phage Martin] ],,AWN03743,100.0,2.06578E-36 SIF-HHPRED:  SIF-Syn: 
    /note=Start agrees with gm + gl, is highly conserved in the pham, has the most manual annotations, has many 1:1 BLAST alignments, encodes the longest ORF, and has the best RBS score. Although the start cuts off ~60 bp of CP, there are no other starts that include the area of CP that was cut off. All SIF failed to indicate any possible functions of the gene, since all BLAST alignments were with genes with NKF, HHPred had no significant hits, and synteny was only found with other genes with NKF. There were no transmembrane domains detected by TMHMM or SOSUI.

CDS complement (20634 - 20804)
  /gene="29"
  /product="gp29"
  /function="hypothetical protein"
  /locus tag="NickSell_29"
    /note=Original Glimmer call @bp 20786 has strength 16.11; Genemark calls start at 20786
    /note=SSC: 20804-20634 CP: no SCS: both-cs ST: SS BLAST-Start: [hypothetical protein SEA_MILLYPHILLY_29 [Microbacterium phage MillyPhilly] ],,NCBI, q1:s1 100.0% 8.86233E-34 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.295, -6.354315264641582, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MILLYPHILLY_29 [Microbacterium phage MillyPhilly] ],,QBZ73017,100.0,8.86233E-34 SIF-HHPRED:  SIF-Syn: 
    /note=Start includes all CP, is highly conserved in the pham, has the most manual annotations, has multiple 1:1 BLAST alignments, a 4 bp overlap, and has the 2nd best RBS score. Although the start is not autocalled by gl or gm, the start has other convincing evidence (starterator support, CP, 4 bp overlap, 1:1 BLAST alignments) that makes it more likely than the autocalled start. All SIF failed to indicate any possible functions of the gene, since all BLAST alignments were with genes with NKF, HHPred had no significant hits (all high e-values and hits were hypothetical proteins), and synteny was only found with other genes with NKF. There were no transmembrane domains detected by TMHMM or SOSUI.

CDS complement (20801 - 20959)
  /gene="30"
  /product="gp30"
  /function="hypothetical protein"
  /locus tag="NickSell_30"
    /note=Original Glimmer call @bp 20959 has strength 11.82; Genemark calls start at 20959
    /note=SSC: 20959-20801 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_MARTIN_31 [Microbacterium phage Martin] ],,NCBI, q1:s1 100.0% 6.36916E-28 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.256, -4.075451192669358, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MARTIN_31 [Microbacterium phage Martin] ],,AWN03745,100.0,6.36916E-28 SIF-HHPRED:  SIF-Syn: 
    /note=Start at 20959 is the most justified start for this reverse gene. It contains all of the coding potential and is called by both gene mark and glimmer. It is supported by Starterator. It has multiple 1:1 BLAST alignments and an optimal overlap of only 4 bp. It has the best RBS. This gene has NKF. All BLAST alignments showed hypothetical proteins, and HHPred had no significant results. All closely related phages had NKF for Synteny. There were no transmembrane domains detected by TMHMM or SOSUI.

CDS complement (20956 - 21798)
  /gene="31"
  /product="gp31"
  /function="hypothetical protein"
  /locus tag="NickSell_31"
    /note=Original Glimmer call @bp 21798 has strength 13.76; Genemark calls start at 21798
    /note=SSC: 21798-20956 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TATARKAPM_31 [Microbacterium phage TatarkaPM]],,NCBI, q1:s1 100.0% 0.0 GAP: 43 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.487, -6.242072432500853, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TATARKAPM_31 [Microbacterium phage TatarkaPM]],,QOC56823,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start at 21789 is the most supported start and there are no significant hits or alignments for the gene`s function

CDS complement (21842 - 22180)
  /gene="32"
  /product="gp32"
  /function="membrane protein"
  /locus tag="NickSell_32"
    /note=Original Glimmer call @bp 22180 has strength 5.63; Genemark calls start at 22180
    /note=SSC: 22180-21842 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Rapheph]],,NCBI, q1:s1 100.0% 1.52938E-73 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.093, -2.213540211474171, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Rapheph]],,WNT45506,99.1071,1.52938E-73 SIF-HHPRED:  SIF-Syn: NKF- Closely Related Phages have NKF
    /note=SIF-membrane = Membrane Protein, 1 Domain found by TMHMM, 1 Domain found by SOSUI
    /note=
    /note=Justification = Membrane Protein, aligned with membrane protein on BLASTp, SIF-Mem indicates gene 32 is a membrane protein. No strong evidence on HHpred. Start is highly supported by starterator and RBS score.

CDS complement (22190 - 22432)
  /gene="33"
  /product="gp33"
  /function="membrane protein"
  /locus tag="NickSell_33"
    /note=Original Glimmer call @bp 22432 has strength 16.39; Genemark calls start at 22432
    /note=SSC: 22432-22190 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 1.72304E-49 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.8, -2.9063687850157054, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Teagan] ],,YP_009908735,100.0,1.72304E-49 SIF-HHPRED:  SIF-Syn: NKF (closely related phages have NFK)
    /note=SIF-membrane= Membrane Protein (2 domains found by TMHMM and 1 domain found by SOUSI)
    /note=
    /note=Justification= Start at 22432 is the most supported start and there is significant evidence from NCBI blast SOSUI and TMHMM that the gene codes for a membrane protein

CDS complement (22429 - 24099)
  /gene="34"
  /product="gp34"
  /function="RepA-like helicase"
  /locus tag="NickSell_34"
    /note=Original Glimmer call @bp 24099 has strength 16.02; Genemark calls start at 24099
    /note=SSC: 24099-22429 CP: yes SCS: both ST: SS BLAST-Start: [RepA-like helicase [Microbacterium phage TatarkaPM]],,NCBI, q1:s1 100.0% 0.0 GAP: -25 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.02, -2.4329349954350334, yes F: RepA-like helicase SIF-BLAST: ,,[RepA-like helicase [Microbacterium phage TatarkaPM]],,QOC56826,100.0,0.0 SIF-HHPRED: Regulatory protein repA; replicative DNA helicase structural changes, REPLICATION; HET: SO4; 1.95A {Escherichia coli} SCOP: c.37.1.11,,,1NLF_C,46.9424,99.9 SIF-Syn: NKF- Closely Related Phages have NKF
    /note=RepA-like Helicase, aligned with multiple RepA-like Helicase proteins on BLASTp, HHpred hit to the function with high probability and good e score. Start is highly supported

CDS complement (24075 - 24368)
  /gene="35"
  /product="gp35"
  /function="nuclease"
  /locus tag="NickSell_35"
    /note=Original Glimmer call @bp 24341 has strength 4.01; Genemark calls start at 24368
    /note=SSC: 24368-24075 CP: yes SCS: both-gm ST: SS BLAST-Start: [endonuclease [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 1.47627E-65 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.144, -6.678258492274136, no F: nuclease SIF-BLAST: ,,[endonuclease [Microbacterium phage Ilzat] ],,YP_009623198,100.0,1.47627E-65 SIF-HHPRED: Nuclease; Nuclease, HYDROLASE; HET: SO4; 1.85A {Salmonella phage SETP3} SCOP: c.52.1.35,,,4QBN_A,94.8454,99.8 SIF-Syn: Nuclease (closely related pham is labeled as nuclease)
    /note=Nuclease, aligned with nuclease proteins on BLASTp, HHpred hit and Phamerator hits to nuclease gene function with very high probability and e score

CDS complement (24372 - 25211)
  /gene="36"
  /product="gp36"
  /function="hypothetical protein"
  /locus tag="NickSell_36"
    /note=Original Glimmer call @bp 25211 has strength 18.37; Genemark calls start at 25211
    /note=SSC: 25211-24372 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein H3N90_gp36 [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 0.0 GAP: 32 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.658, -3.2123487306667524, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein H3N90_gp36 [Microbacterium phage Teagan] ],,YP_009908738,100.0,0.0 SIF-HHPRED:  SIF-Syn: NKF- no significant results
    /note=Highest HHpred hit was hypothetical protein but had a low e value. No significant evidence at this time for a function. Start is highly supported and has the lowest gap even through it is over 10 bp

CDS complement (25244 - 25912)
  /gene="37"
  /product="gp37"
  /function="AAA-ATPase"
  /locus tag="NickSell_37"
    /note=Original Glimmer call @bp 25912 has strength 18.47; Genemark calls start at 25912
    /note=SSC: 25912-25244 CP: yes SCS: both ST: NA BLAST-Start: [AAA-ATPase [Microbacterium phage AlexAdler] ],,NCBI, q1:s1 100.0% 7.86121E-162 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.838, -4.9157003279346805, no F: AAA-ATPase SIF-BLAST: ,,[AAA-ATPase [Microbacterium phage AlexAdler] ],,AVO24428,100.0,7.86121E-162 SIF-HHPRED: UPF0273 protein PH0284; RecA superfamily ATPase, Hexamer, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN; HET: ADP; 2.0A {Pyrococcus horikoshii},,,2DR3_D,83.7838,99.2 SIF-Syn: ASCE ATPase, same pham position to related phages and is identified as AAA-ATPase in AlexAdler_37
    /note=The blast hit hinted at ATPase, but it was not specific. The HHpred hit confirmed a function of ASCE ATPase because it hit with high probability and e value to the RecA family.
    /note=
    /note=the function list doesn`t include ASCE ATPase instead only AAA ATPase, but the function for this list is ASCE ATPase

CDS complement (25909 - 27087)
  /gene="38"
  /product="gp38"
  /function="exonuclease"
  /locus tag="NickSell_38"
    /note=Original Glimmer call @bp 27087 has strength 12.52; Genemark calls start at 27096
    /note=SSC: 27087-25909 CP: yes SCS: both-gl ST: SS BLAST-Start: [exonuclease [Microbacterium phage TatarkaPM]],,NCBI, q1:s1 100.0% 0.0 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.379, -3.670670413150579, no F: exonuclease SIF-BLAST: ,,[exonuclease [Microbacterium phage TatarkaPM]],,QOC56830,100.0,0.0 SIF-HHPRED: CRISPR-associated exonuclease, Cas4 family; MCSG, STRUCTURAL GENOMICS, PSI-BIOLOGY, EXONUCLEASE, HYDROLASE, Midwest Center for Structural Genomics; 2.65A {Pyrobaculum calidifontis JCM 11548},,,4R5Q_A,84.949,99.6 SIF-Syn: exonuclease, same pham but different position, identified as exonuclease
    /note=The blast hit to an exonuclease and one of the HHpred hits was the Cas4 Exonuclease that was listed in our functions list. The start is supported.

CDS complement (27074 - 28930)
  /gene="39"
  /product="gp39"
  /function="DNA polymerase I"
  /locus tag="NickSell_39"
    /note=Original Glimmer call @bp 28930 has strength 13.75; Genemark calls start at 28930
    /note=SSC: 28930-27074 CP: yes SCS: both ST: NA BLAST-Start: [DNA polymerase I [Microbacterium phage TatarkaPM]],,NCBI, q1:s46 100.0% 0.0 GAP: 615 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.502, -8.23767798545884, no F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Microbacterium phage TatarkaPM]],,QOC56831,93.2127,0.0 SIF-HHPRED: DNA polymerase I; mycobacteria, DNA polymerase, Flap endonuclease, TRANSFERASE; 2.713A {Mycolicibacterium smegmatis},,,6VDE_B,99.0291,100.0 SIF-Syn: DNA Polymerase I, same pham but different position, identified as DNA polymerase
    /note=DNA Polymerase, function is well supported Blast hit to multiple DNA polymerase and HHpred hit with 100% probability. Start is not supported by Starterator but is backed by both Genemark and Glimmer start

CDS 29546 - 29680
  /gene="40"
  /product="gp40"
  /function="hypothetical protein"
  /locus tag="NickSell_40"
    /note=Genemark calls start at 29564
    /note=SSC: 29546-29680 CP: yes SCS: genemark-cs ST: NA BLAST-Start:  GAP: 615 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.331, -4.4261092987867166, no F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: There are no closely related phage results, unable to compare
    /note=NKF, no significant results in any search along with start given to have a abnormally large BP gap

CDS complement (29140 - 29565)
  /gene="41"
  /product="gp41"
  /function="hypothetical protein"
  /locus tag="NickSell_41"
    /note=Original Glimmer call @bp 29565 has strength 18.94; Genemark calls start at 29565
    /note=SSC: 29565-29140 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp39 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 2.88197E-91 GAP: 170 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.95, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp39 [Microbacterium phage Ilzat] ],,YP_009623203,100.0,2.88197E-91 SIF-HHPRED:  SIF-Syn: NKF - same pham as Alyxandracam_40 and Aubergine_39
    /note=Start is called by both Glimmer and Genemark, start is supported since it has the most MAs, the smallest gap, best score, LORF.  Alignments do not provide evidence for protein function.

CDS complement (29736 - 31124)
  /gene="42"
  /product="gp42"
  /function="DNA helicase"
  /locus tag="NickSell_42"
    /note=Original Glimmer call @bp 31124 has strength 11.42; Genemark calls start at 31124
    /note=SSC: 31124-29736 CP: yes SCS: both ST: SS BLAST-Start: [DNA helicase [Microbacterium phage Nagem] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.06, -4.497860114175419, no F: DNA helicase SIF-BLAST: ,,[DNA helicase [Microbacterium phage Nagem] ],,AVR56369,100.0,0.0 SIF-HHPRED: Transcription regulatory protein SNF2; SWI/SNF remodeling, Swi-Snf complex, nucleosome, DNA BINDING PROTEIN; 2.89A {Saccharomyces cerevisiae S288C},,,7C4J_H,97.1861,100.0 SIF-Syn: DNA helicase, same pham and position as Nagem_41, Inventa_41, and BeautPeep30_41
    /note=Great evidence for start. Both SIF-BLAST and SIF-Syn state DNA Helicase as the most likely function. While HHPred states a different function, I believe there is more evidence for DNA Helicase.

CDS complement (31124 - 31717)
  /gene="43"
  /product="gp43"
  /function="phosphoesterase"
  /locus tag="NickSell_43"
    /note=Original Glimmer call @bp 31717 has strength 15.83; Genemark calls start at 31717
    /note=SSC: 31717-31124 CP: yes SCS: both ST: SS BLAST-Start: [phosphoesterase [Microbacterium phage Bandik] ],,NCBI, q1:s1 100.0% 3.20593E-140 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.948, -4.738143471880277, no F: phosphoesterase SIF-BLAST: ,,[phosphoesterase [Microbacterium phage Bandik] ],,AVR56064,100.0,3.20593E-140 SIF-HHPRED: cyclic phosphodiesterase; ADP-ribose 1``, 2``-cyclic phosphate, RNA processing, 2`, 3`-cyclic nucleotide phosphodiesterase, HYDROLASE; HET: SO4; 1.8A {Arabidopsis thaliana} SCOP: d.61.1.1,,,1JH6_A,63.4518,99.6 SIF-Syn: phosphoesterase, same pham and position as, Bandik_42, Inventa_42,Kurt1_42
    /note=Besides RBS, great evidence for start. Chose phosphoesterase as all three SIF test returned phosphoesterase. Start is called by both Genemark and Glimmer, start is supported since it has the most MAs and smallest gap

CDS complement (31714 - 32010)
  /gene="44"
  /product="gp44"
  /function="hypothetical protein"
  /locus tag="NickSell_44"
    /note=Original Glimmer call @bp 32010 has strength 16.81; Genemark calls start at 32010
    /note=SSC: 32010-31714 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_BANDIK_43 [Microbacterium phage Bandik] ],,NCBI, q1:s1 100.0% 6.29456E-60 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.95, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_BANDIK_43 [Microbacterium phage Bandik] ],,AVR56065,100.0,6.29456E-60 SIF-HHPRED:  SIF-Syn: NKF - Closely related phages have NKF
    /note=Great evidence for start, all tests return NKF. Start is called by both Glimmer and Genemark, start is supported since it has the most MAs, the smallest gap, and best final score.

CDS complement (32010 - 32288)
  /gene="45"
  /product="gp45"
  /function="hypothetical protein"
  /locus tag="NickSell_45"
    /note=Original Glimmer call @bp 32288 has strength 15.19; Genemark calls start at 32288
    /note=SSC: 32288-32010 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_BANDIK_44 [Microbacterium phage Bandik] ],,NCBI, q1:s1 100.0% 7.01866E-61 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.986, -4.59534204625343, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_BANDIK_44 [Microbacterium phage Bandik] ],,AVR56066,100.0,7.01866E-61 SIF-HHPRED:  SIF-Syn: NKF - Closely related phages have NKF
    /note=Great evidence for start, all tests return NKF. Start is called by both Glimmer and Genemark, start is supported since it has the most MAs, the smallest gap, and best final score.

CDS complement (32288 - 33094)
  /gene="46"
  /product="gp46"
  /function="MazG-like nucleotide pyrophosphohydrolase"
  /locus tag="NickSell_46"
    /note=Original Glimmer call @bp 33094 has strength 19.76; Genemark calls start at 33094
    /note=SSC: 33094-32288 CP: yes SCS: both ST: SS BLAST-Start: [MazG-like nucleotide pyrophosphohydrolase [Microbacterium phage TatarkaPM]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.682, -3.1604619823777065, no F: MazG-like nucleotide pyrophosphohydrolase SIF-BLAST: ,,[MazG-like nucleotide pyrophosphohydrolase [Microbacterium phage TatarkaPM]],,QOC56837,100.0,0.0 SIF-HHPRED: putative NTP pyrophosphohydrolase; Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, HYDROLASE; HET: MSE; 1.78A {Exiguobacterium sibiricum 255-15},,,3NL9_A,58.209,100.0 SIF-Syn: MazG-like nucleotide pyrophosphohydrolase, same pham and position as Bandik_45, BeautPeep30_45, TatarkaPM_45
    /note=Great evidence for start it is highly supported in staterator with 117 manual annotations and it is called 100% of the time it is present, it is highly conserved in the cluster within the pham. Additionally, it has the best RBS score, creates the smallest gap, and contains the LORF. Both SIF-BLAST and SIF-Syn state MazG-like nucleotide pyrophosphohydrolase as the most likely function. While HHPred states a different function, I believe there is more evidence for MazG-like nucleotide pyrophosphohydrolase.

CDS complement (33091 - 33816)
  /gene="47"
  /product="gp47"
  /function="hypothetical protein"
  /locus tag="NickSell_47"
    /note=Original Glimmer call @bp 33747 has strength 11.19; Genemark calls start at 33816
    /note=SSC: 33816-33091 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein H3N90_gp46 [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 1.36995E-176 GAP: -23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.267, -6.125680687170574, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein H3N90_gp46 [Microbacterium phage Teagan] ],,YP_009908748,100.0,1.36995E-176 SIF-HHPRED:  SIF-Syn: same pham and position as Bandik_46 and AlexAdler_46 which have NKF
    /note=Start is called only by Genemark, but start is supported since it has the most MAs, the smallest gap, and the LORF.  Alignments do not provide any evidence for a protein function.

CDS complement (33794 - 34375)
  /gene="48"
  /product="gp48"
  /function="thymidylate kinase"
  /locus tag="NickSell_48"
    /note=Original Glimmer call @bp 34375 has strength 14.75; Genemark calls start at 34375
    /note=SSC: 34375-33794 CP: yes SCS: both ST: SS BLAST-Start: [thymidylate kinase [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 5.29122E-142 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.95, -2.583959800616441, yes F: thymidylate kinase SIF-BLAST: ,,[thymidylate kinase [Microbacterium phage Teagan] ],,YP_009908749,100.0,5.29122E-142 SIF-HHPRED: THYMIDYLATE KINASE; NUCLEOTIDE BIOSYNTHESIS, ATP-BINDING, NUCLEOTIDE-BINDING, KINASE, POXVIRUS, TMP KINASE, TRANSFERASE; HET: POP, TYD; 2.4A {VACCINIA VIRUS COPENHAGEN} SCOP: c.37.1.0,,,2V54_A,63.2124,99.5 SIF-Syn: thymidylate kinase, same pham and position as Alyxandracam_46, and BigRedClifford_46. Teagan_46 called AAA-ATPase
    /note=Good evidence for start, it has the best RBS score and contains the LORF. It also covers all coding potential and is highly supported in starterator with a high number of manual annotations (155) and it is called 100% of the time it is present, this start is hightly conserved in the cluster within the pham.  I chose thymidylate kinase because each test results in both thymidylate kinase and AAA-ATPase, which is marked as an innapropirate call in SEA-PHAGES FUNCTIONAL ASSIGNMENTS, therefore I went with thymidylate kinase.

CDS complement (34391 - 35323)
  /gene="49"
  /product="gp49"
  /function="glycosyltransferase"
  /locus tag="NickSell_49"
    /note=Original Glimmer call @bp 35323 has strength 15.63; Genemark calls start at 35323
    /note=SSC: 35323-34391 CP: yes SCS: both ST: SS BLAST-Start: [glycosyltransferase [Microbacterium phage Bandik] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.97, -6.157910251162862, no F: glycosyltransferase SIF-BLAST: ,,[glycosyltransferase [Microbacterium phage Bandik] ],,AVR56070,100.0,0.0 SIF-HHPRED: Putative glycosyltransferase protein; Glycosyltransferase, Protein Structure Initiative II, PSI-II, 12059a, NYSGXRC, Structural Genomics, New York SGX Research Center for; HET: MSE; 2.35A {Bacteroides fragilis},,,3BCV_A,32.5806,99.0 SIF-Syn: glycosyltransferase, same pham as Bandik_48, Inventa_48, all have positional similarity and similar phages have known function of glycosyltransferase
    /note=Start is called by both Genemark and Glimmer, but start is supported since it has the most MAs, the smallest gap, and the LORF.  Alignments provide the most evidence for glycosyltransferase.

CDS complement (35316 - 35549)
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="NickSell_50"
    /note=Original Glimmer call @bp 35450 has strength 8.47
    /note=SSC: 35549-35316 CP: yes SCS: glimmer-cs ST: NA BLAST-Start: [hypothetical protein PBI_PEEP_49 [Microbacterium phage Peep] ],,NCBI, q1:s1 100.0% 7.66734E-51 GAP: 62 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.075, -4.325675514574479, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_PEEP_49 [Microbacterium phage Peep] ],,AUX83135,100.0,7.66734E-51 SIF-HHPRED:  SIF-Syn: Closely related phages have NKF
    /note=Changed start because everything but starterator supports the selected start. The selected start has a best RBS score and contains the LORF. it also creates the smallest gap out of all the start candidates.All tests show NKF

CDS complement (35612 - 35908)
  /gene="51"
  /product="gp51"
  /function="membrane protein"
  /locus tag="NickSell_51"
    /note=Original Glimmer call @bp 35908 has strength 12.25; Genemark calls start at 35908
    /note=SSC: 35908-35612 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein H3N90_gp50 [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 2.43345E-62 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.103, -2.253377680616507, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein H3N90_gp50 [Microbacterium phage Teagan] ],,YP_009908752,100.0,2.43345E-62 SIF-HHPRED:  SIF-Syn: no positional similarity and closely related phages have NKF
    /note=start is called by both glimmer and genemark, has 1:1 blast alignments, and is supported by starterator, has a perfect 4bp overlap
    /note=
    /note=1 TM predicted by TMHMM and SOSUI

CDS complement (35905 - 36672)
  /gene="52"
  /product="gp52"
  /function="thymidylate synthase"
  /locus tag="NickSell_52"
    /note=Original Glimmer call @bp 36672 has strength 14.49; Genemark calls start at 36672
    /note=SSC: 36672-35905 CP: yes SCS: both ST: SS BLAST-Start: [thymidylate synthase [Microbacterium phage Bandik] ],,NCBI, q1:s1 100.0% 0.0 GAP: 119 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.95, -2.523003374675015, yes F: thymidylate synthase SIF-BLAST: ,,[thymidylate synthase [Microbacterium phage Bandik] ],,AVR56073,100.0,0.0 SIF-HHPRED: CMP 5-hydroxymethylase; CMP hydroxymethylase, TRANSFERASE; HET: C5P; 1.65A {Streptomyces rimofaciens},,,5B6D_B,87.8431,100.0 SIF-Syn: No positional similarity and closely related phages have NKF
    /note=Start is called by both, is well supported by MAs, it is not LO and not an ideal gap but good RBS score. NKF because hits were hypothetical proteins.
    /note=
    /note=strong BLAST and hhpred confirmation for thymidylate synthase

CDS complement (36792 - 37022)
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="NickSell_53"
    /note=Original Glimmer call @bp 37004 has strength 10.79; Genemark calls start at 37004
    /note=SSC: 37022-36792 CP: no SCS: both-cs ST: SS BLAST-Start: [hypothetical protein PBI_KNOX_52 [Microbacterium phage Knox] ],,NCBI, q1:s1 100.0% 2.65982E-48 GAP: 60 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.591, -6.672171187999036, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_KNOX_52 [Microbacterium phage Knox] ],,AUX83013,100.0,2.65982E-48 SIF-HHPRED:  SIF-Syn: No positional similarity and closely related phages have NKF
    /note=Start is called by both glimmer and genemark, and it has 1:1 blast alignments

CDS complement (37083 - 37307)
  /gene="54"
  /product="gp54"
  /function="hypothetical protein"
  /locus tag="NickSell_54"
    /note=Original Glimmer call @bp 37307 has strength 20.44; Genemark calls start at 37307
    /note=SSC: 37307-37083 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp52 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 1.32602E-46 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.103, -2.253377680616507, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp52 [Microbacterium phage Ilzat] ],,YP_009623216,100.0,1.32602E-46 SIF-HHPRED:  SIF-Syn: No positional similarity and closely related phages have NKF
    /note=sSart is called by both glimmer and genemark, has 1:1 blast alignments, and is supported by starterator, has best RBS Score

CDS complement (37372 - 37638)
  /gene="55"
  /product="gp55"
  /function="hypothetical protein"
  /locus tag="NickSell_55"
    /note=Original Glimmer call @bp 37638 has strength 19.58; Genemark calls start at 37638
    /note=SSC: 37638-37372 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_BANDIK_54 [Microbacterium phage Bandik] ],,NCBI, q1:s1 100.0% 2.95163E-53 GAP: 71 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.103, -2.1123791669543204, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_BANDIK_54 [Microbacterium phage Bandik] ],,AVR56076,100.0,2.95163E-53 SIF-HHPRED:  SIF-Syn: No positional similarity and closely related phages have NKF
    /note=Start is called by both glimmer and genemark, has coding potential and has 1:1 blast alignments, and is supported by starterator, has best RBS Score

CDS complement (37710 - 38012)
  /gene="56"
  /product="gp56"
  /function="hypothetical protein"
  /locus tag="NickSell_56"
    /note=Original Glimmer call @bp 38012 has strength 17.2; Genemark calls start at 38012
    /note=SSC: 38012-37710 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp54 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 5.99789E-66 GAP: 91 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.038, -2.253486910374644, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp54 [Microbacterium phage Ilzat] ],,YP_009623218,100.0,5.99789E-66 SIF-HHPRED:  SIF-Syn: No positional similarity and closely related phages have NKF
    /note=Start is called by both, is well supported by MAs, it is LO and not an ideal gap but good RBS score. NKF because hits were hypothetical proteins.

CDS complement (38104 - 38298)
  /gene="57"
  /product="gp57"
  /function="hypothetical protein"
  /locus tag="NickSell_57"
    /note=Original Glimmer call @bp 38298 has strength 14.22; Genemark calls start at 38298
    /note=SSC: 38298-38104 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp55 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 2.39308E-39 GAP: 38 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.678, -5.830816207622988, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp55 [Microbacterium phage Ilzat] ],,YP_009623219,100.0,2.39308E-39 SIF-HHPRED:  SIF-Syn: Closely related phages have NKF
    /note=Start is called by both glimmer and genemark, has 1:1 blast alignments, and is supported by starterator, has longest reading frame, 2nd best RBS Score

CDS complement (38337 - 38642)
  /gene="58"
  /product="gp58"
  /function="hypothetical protein"
  /locus tag="NickSell_58"
    /note=Original Glimmer call @bp 38642 has strength 7.93; Genemark calls start at 38642
    /note=SSC: 38642-38337 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp56 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 3.59511E-67 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.41, -4.131070678070218, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp56 [Microbacterium phage Ilzat] ],,YP_009623220,100.0,3.59511E-67 SIF-HHPRED: Alpha- and gamma-adaptin-binding protein p34; protein binding, membrane trafficking, AP Complex, CHAPERONE; HET: PO4; 2.11A {Homo sapiens},,,7TWD_B,30.6931,73.4 SIF-Syn: NKF
    /note=The start is called by both, is well supported by MAs, it is not LO and ideal gap. Good RBS score. NKF because hits were hypothetical proteins.

CDS complement (38639 - 38830)
  /gene="59"
  /product="gp59"
  /function="hypothetical protein"
  /locus tag="NickSell_59"
    /note=Original Glimmer call @bp 38830 has strength 8.03; Genemark calls start at 38830
    /note=SSC: 38830-38639 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_AUBERGINE_57 [Microbacterium phage Aubergine] ],,NCBI, q1:s1 100.0% 5.22569E-38 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.768, -5.047808595116427, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_AUBERGINE_57 [Microbacterium phage Aubergine] ],,AUX82644,100.0,5.22569E-38 SIF-HHPRED:  SIF-Syn: NKF
    /note=start is called by both glimmer and genemark, has 1:1 blast alignments, has a perfect 4bp overlap

CDS complement (38827 - 39558)
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="NickSell_60"
    /note=Original Glimmer call @bp 39558 has strength 13.89; Genemark calls start at 39558
    /note=SSC: 39558-38827 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp58 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 1.75312E-175 GAP: 93 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.038, -2.253486910374644, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp58 [Microbacterium phage Ilzat] ],,YP_009623222,100.0,1.75312E-175 SIF-HHPRED: DUF2786 ; Protein of unknown function (DUF2786),,,PF10979.12,15.6379,99.2 SIF-Syn: NKF
    /note=The start is called by both and is well supported by MAs, it is LO and not an ideal gap but a good RBS score. NKF because hits were hypothetical proteins.

CDS complement (39652 - 40038)
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="NickSell_61"
    /note=Original Glimmer call @bp 39990 has strength 22.38; Genemark calls start at 40038
    /note=SSC: 40038-39652 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein PBI_NAGEM_60 [Microbacterium phage Nagem] ],,NCBI, q1:s1 100.0% 1.57765E-88 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.407, -3.9616183113819163, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_NAGEM_60 [Microbacterium phage Nagem] ],,AVR56388,100.0,1.57765E-88 SIF-HHPRED:  SIF-Syn: NKF
    /note=The start was changed from the original autocalled start. This was because this start has the longest ORF, a better optimal gap at -4, and also has many high confidence BLAST matches. When examining starterator, the autoannotated start was only called 9.6% of the time, the chosen start was called ~90% more often and just as conserved. there is no significant evidence for a start for this gene.

CDS complement (40035 - 40394)
  /gene="62"
  /product="gp62"
  /function="hypothetical protein"
  /locus tag="NickSell_62"
    /note=Original Glimmer call @bp 40364 has strength 5.02; Genemark calls start at 40394
    /note=SSC: 40394-40035 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein PBI_NAGEM_61 [Microbacterium phage Nagem] ],,NCBI, q1:s1 100.0% 1.80613E-78 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.499, -6.393143906827662, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_NAGEM_61 [Microbacterium phage Nagem] ],,AVR56389,100.0,1.80613E-78 SIF-HHPRED:  SIF-Syn: NKF
    /note=The start was changed because chosen start is more conserved and is called ~90% more of the time it is present than the autoannotated start. it also has the optimal gap of -4 and has many significant BLAST results. There is no evidence for a function of this gene.

CDS complement (40391 - 40624)
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="NickSell_63"
    /note=Genemark calls start at 40624
    /note=SSC: 40624-40391 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein PBI_NAGEM_62 [Microbacterium phage Nagem] ],,NCBI, q1:s1 100.0% 4.63564E-50 GAP: 363 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.897, -4.848494831654203, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_NAGEM_62 [Microbacterium phage Nagem] ],,AVR56390,100.0,4.63564E-50 SIF-HHPRED:  SIF-Syn: NKF
    /note=The autoannotated start is the most supported. It has the longest ORF, high confidence BLASt results, and is supported by starterator. It also has the second best RBS scores. The gap was omitted from consideration because all other starts had bigger gaps. There is no evidence for a function for this gene.

CDS 40988 - 41629
  /gene="64"
  /product="gp64"
  /function="hypothetical protein"
  /locus tag="NickSell_64"
    /note=Original Glimmer call @bp 41186 has strength 13.67; Genemark calls start at 41000
    /note=SSC: 40988-41629 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein PBI_MARTIN_64 [Microbacterium phage Martin] ],,NCBI, q1:s1 100.0% 3.02507E-149 GAP: 363 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.986, -5.167948448842958, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MARTIN_64 [Microbacterium phage Martin] ],,AWN03778,100.0,3.02507E-149 SIF-HHPRED: DUF1659 ; Protein of unknown function (DUF1659),,,PF07872.15,16.9014,25.1 SIF-Syn: NKF
    /note=The Start 32 (chosen start) was chosen over the autoannotated start becasue, is marginally less conserved and called 46.5% more of the time when present. It also results in the longest ORF, and has the best gap. Additionally this start has a multitude of 1:1 100% coverage BLAST results. there is no evidence for a function for this gene.