CDS complement (869 - 1081)
  /gene="1"
  /product="gp1"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_1"
    /note=Genemark calls start at 1081
    /note=SSC: 1081-869 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_STRAWBERRYJAMM_3 [Microbacterium phage StrawberryJamm]],,NCBI, q1:s1 98.5714% 4.8617E-42 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.906, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_STRAWBERRYJAMM_3 [Microbacterium phage StrawberryJamm]],,QWY80087,97.1429,4.8617E-42 SIF-HHPRED:  SIF-Syn: NKF, homologs have no known function; similar position/neighborhood to StrawberryJamm_3
    /note=Coding potential, GM, Staterator, overlap, scores and BLAST support this start. It is not the longest ORF, but the start that did was investigated and did not have as much compelling evidence. BLAST, HHPRed, and SYN support NKF.

CDS complement (1078 - 1419)
  /gene="2"
  /product="gp2"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_2"
    /note=Original Glimmer call @bp 1419 has strength 11.01; Genemark calls start at 1419
    /note=SSC: 1419-1078 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_STRAWBERRYJAMM_4 [Microbacterium phage StrawberryJamm]],,NCBI, q1:s1 100.0% 2.31928E-65 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.405, -5.8787031795312865, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_STRAWBERRYJAMM_4 [Microbacterium phage StrawberryJamm]],,QWY80088,91.3043,2.31928E-65 SIF-HHPRED:  SIF-Syn: NKF, homologs have no known function; similar position/neighborhood to StrawberryJamm_4 and Teehee_1
    /note=Start 1419 was supported by both Genemark and Glimmer, having coding potential being present. It was the most called on start in starterator and had the most manual annotations. There were multiple 1:1 alignments, but none of them had a known function (all hypothetical proteins). It had the smallest gap at -4, but not the best RBS or LORF. There wasn`t a function known for any of the closely related genes and there wasnt any significant data for the HHPred. The DeepTMHMM had nothing present indicating a membrane.

CDS complement (1416 - 1601)
  /gene="3"
  /product="gp3"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_3"
    /note=Original Glimmer call @bp 1601 has strength 8.15; Genemark calls start at 1601
    /note=SSC: 1601-1416 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_5 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 9.37042E-35 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.953, -4.821320819095688, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_5 [Microbacterium phage Casend] ],,QNL29972,100.0,9.37042E-35 SIF-HHPRED:  SIF-Syn: NKF, homologs have no known function; similar position/neighborhood to Casend_5 and Wheelie_5
    /note=Coding potential, GM, GL, Starterator, RBS scores and BLAST support this start. It also has the smallest overlap. It is not the longest ORF, but that start was investigated and it has a significant overlap and not as much complelling evidence. BLAST, HHPred, and SYN support NKF.

CDS complement (1598 - 1822)
  /gene="4"
  /product="gp4"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_4"
    /note=Original Glimmer call @bp 1822 has strength 9.16; Genemark calls start at 1822
    /note=SSC: 1822-1598 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_6 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 1.95839E-46 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.505, -3.738562143838384, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_6 [Microbacterium phage Casend] ],,QNL29973,100.0,1.95839E-46 SIF-HHPRED:  SIF-Syn: NKF, homologs have no known function; similar position/neighborhood to Casend_6 and Hyperion_5; upstream of a gene that encodes for a histidine triad nucleotide binding protein
    /note=Start 1822 is supported by both Glimmer and Genemark, having coding potential present. There is heavy evidence for it in the starterator report,being the most annotated start. it also has multiple 1 to 1 alignments, the smallest gap value, longest open reading frame, and best ribosomal binding site. There didnt seem to be any functions listed for this gene, and all the functions in similar locations of other genes didnt have a function either. There was also no data found in the Deep TMHMM to indicate a membrane.

CDS complement (1819 - 2184)
  /gene="5"
  /product="gp5"
  /function="histidine triad nucleotide binding protein"
  /locus tag="EverythinBagel_5"
    /note=Original Glimmer call @bp 2184 has strength 6.52; Genemark calls start at 2184
    /note=SSC: 2184-1819 CP: yes SCS: both ST: SS BLAST-Start: [histidine triad nucleotide binding protein [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 1.79896E-83 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.142, -2.417348306996335, yes F: histidine triad nucleotide binding protein SIF-BLAST: ,,[histidine triad nucleotide binding protein [Microbacterium phage Casend] ],,QNL29974,100.0,1.79896E-83 SIF-HHPRED: d.13.1.1 (A:6-144) Histidine triad protein Mfla2506 {Methylobacillus flagellatus [TaxId: 405]},,,d1fita_,79.3388,99.7 SIF-Syn: histidine triad nucleotide binding protein, same pham and position as Casend_7 and Hyperion_6; all are immediately downstream similar genes (share the same pham and position though they are all NKF)
    /note=Start 2184 is supported by Starterator, GeneMark, Glimmer, CP, smallest gap, and most supportive RBS scores. The function, of histidine triad protein was supported through SIF-BLAST, SIF-SYN, and SIF-HHPred

CDS complement (2181 - 2903)
  /gene="6"
  /product="gp6"
  /function="membrane protein"
  /locus tag="EverythinBagel_6"
    /note=Original Glimmer call @bp 2903 has strength 13.31; Genemark calls start at 2903
    /note=SSC: 2903-2181 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Casend]],,NCBI, q1:s1 100.0% 1.42464E-175 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.48, -3.790975366313636, no F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Casend]],,QNL29975,99.5833,1.42464E-175 SIF-HHPRED: DUF6552 ; Family of unknown function (DUF6552),,,PF20189.1,30.4167,98.3 SIF-Syn: NKF, homologs have no function
    /note=Start is supported by: Glimmer, genemark, Starterator, and LORF
    /note=Membrane protein, 3 domains found, both TMHMM and SOUSI is called

CDS complement (2900 - 3142)
  /gene="7"
  /product="gp7"
  /function="membrane protein"
  /locus tag="EverythinBagel_7"
    /note=Original Glimmer call @bp 3142 has strength 8.4; Genemark calls start at 3142
    /note=SSC: 3142-2900 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 9.71611E-46 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.758, -3.0713502170045657, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Casend] ],,QNL29976,100.0,9.71611E-46 SIF-HHPRED:  SIF-Syn: EverythinBagel_8 has same pham and positioning as Casend_9 and Rowlf_5
    /note=Glimmer and genemark both agree with the start, most annotated start, best RBS so gap does not matter
    /note=membrane protein, 2 domains found and called by both TMHMM and SOSUI

CDS complement (3139 - 3324)
  /gene="8"
  /product="gp8"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_8"
    /note=Original Glimmer call @bp 3324 has strength 4.83; Genemark calls start at 3315
    /note=SSC: 3324-3139 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_ZAGIE_10 [Microbacterium phage Zagie] ],,NCBI, q1:s1 100.0% 1.45145E-25 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.773, -5.256359229020349, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ZAGIE_10 [Microbacterium phage Zagie] ],,UVG35363,87.0968,1.45145E-25 SIF-HHPRED:  SIF-Syn: NKF, homologs have no known function.
    /note=Glimmer and genemark both called this gene, but this is the start glimmer called, No MA, best RBS so gap does not matter

CDS complement (3317 - 3622)
  /gene="9"
  /product="gp9"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_9"
    /note=Original Glimmer call @bp 3622 has strength 15.97; Genemark calls start at 3622
    /note=SSC: 3622-3317 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT29_gp011 [Microbacterium phage Squash] ],,NCBI, q1:s1 100.0% 5.04785E-25 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.331, -4.610561041644944, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT29_gp011 [Microbacterium phage Squash] ],,YP_009801750,66.6667,5.04785E-25 SIF-HHPRED:  SIF-Syn: NKF, homologs have no known function.
    /note=Glimmer and genemark both agree with the start, most annotated start, not best RBS but gap is so little it does not matter.
    /note=
    /note=NKF as it is a hypothetical protein.

CDS complement (3619 - 4140)
  /gene="10"
  /product="gp10"
  /function="DprA-like DNA processing chain A"
  /locus tag="EverythinBagel_10"
    /note=Original Glimmer call @bp 4140 has strength 9.76; Genemark calls start at 4122
    /note=SSC: 4140-3619 CP: yes SCS: both-gl ST: SS BLAST-Start: [DprA-like DNA processing chain A [Microbacterium phage Fransoyer]],,NCBI, q2:s4 99.422% 8.34462E-105 GAP: 151 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.004, -4.637072905118042, no F: DprA-like DNA processing chain A SIF-BLAST: ,,[DprA-like DNA processing chain A [Microbacterium phage Fransoyer]],,UUG69575,90.2857,8.34462E-105 SIF-HHPRED: c.129.1.2 (A:1-177) Hypothetical protein YpsA {Bacillus subtilis [TaxId: 1423]},,,d2nx2a1,90.7514,99.8 SIF-Syn: same pham and position as RubyRalph_10 and Fransoyer_10, downstream of helix-turn-helix DNA binding domain protein
    /note=Glimmer and genemark both called this gene, but this is the start glimmer called, most annotated start, not best RBS and gap is fairly big however all evidence points to this start
    /note=
    /note=Function is supported by BLAST hits and SYN.

CDS complement (4292 - 4534)
  /gene="11"
  /product="gp11"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_11"
    /note=Original Glimmer call @bp 4534 has strength 7.03; Genemark calls start at 4534
    /note=SSC: 4534-4292 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT27_gp010 [Microbacterium phage Hyperion] ],,NCBI, q1:s1 100.0% 3.38568E-49 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.089, -4.601664605840989, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT27_gp010 [Microbacterium phage Hyperion] ],,YP_009801552,100.0,3.38568E-49 SIF-HHPRED:  SIF-Syn: Homologs have no known function.
EverythinBagel_12 is similar in pham and position to Hyperion_10, Casend_13, Rudy_10 and Squash_14. All these genes are downstream of a helix-turn-helix DNA binding protein. Upstream of these genes differ
    /note=Start 4534 is supported by Glimmer, GeneMark, and SS (Starterator). The start also has Coding Potential, LORF, and multiple BLAST hits

CDS complement (4531 - 4887)
  /gene="12"
  /product="gp12"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="EverythinBagel_12"
    /note=Original Glimmer call @bp 4887 has strength 5.79; Genemark calls start at 4887
    /note=SSC: 4887-4531 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 1.86793E-80 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.753, -5.220380545373514, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Microbacterium phage Casend] ],,QNL29981,100.0,1.86793E-80 SIF-HHPRED:  SIF-Syn: helix-turn-helix, same pham and position as Casend_14 and Quammi_11.
    /note=Start is supported by: GeneMark,Glimmer, Starterator, CP, and LORF. Multiple Blast hits to helix-turn-helix DNA binding domain proteins. HHPred alignments show that the query has 4 alpha-helices separated by short spacer regions, supporting the helix-turn-helix function.

CDS complement (4880 - 5095)
  /gene="13"
  /product="gp13"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="EverythinBagel_13"
    /note=Original Glimmer call @bp 5038 has strength 7.89; Genemark calls start at 5095
    /note=SSC: 5095-4880 CP: no SCS: both-gm ST: SS BLAST-Start: [helix-turn-helix DNA binding protein [Microbacterium phage Squash] ],,NCBI, q1:s1 100.0% 5.96794E-43 GAP: 61 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.83, -7.134752732491032, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding protein [Microbacterium phage Squash] ],,YP_009801755,100.0,5.96794E-43 SIF-HHPRED:  SIF-Syn: EverythinBagel_14 is in the same pham/ similar position as Hyperion_12, Casend_15, Rudy_12 and Squash_16.

All these genes are upstream of a ribbon-helix-helix DNA binding protein.
    /note=Start is supported by Genemark, Starterator, CP and BLAST hits.
    /note=Function is supported by BLAST hits, HHPred hits, and SYN.

CDS 5157 - 5312
  /gene="14"
  /product="gp14"
  /function="ribbon-helix-helix DNA binding domain"
  /locus tag="EverythinBagel_14"
    /note=Original Glimmer call @bp 5181 has strength 11.2; Genemark calls start at 5157
    /note=SSC: 5157-5312 CP: yes SCS: both-gm ST: SS BLAST-Start: [DNA binding domain protein [Microbacterium phage Hyperion] ],,NCBI, q1:s1 100.0% 6.1774E-28 GAP: 61 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.992, -5.966653499439317, no F: ribbon-helix-helix DNA binding domain SIF-BLAST: ,,[DNA binding domain protein [Microbacterium phage Hyperion] ],,YP_009801555,100.0,6.1774E-28 SIF-HHPRED: Putative; Helicobacter pylori, repressor, transcriptional regulator, DNA-binding, ribbon-helix-helix, HP0564, JHP0511, UNKNOWN FUNCTION, GENE REGULATION; NMR {Helicobacter pylori},,,2K1O_B,78.4314,98.3 SIF-Syn: Synteny suggests that the function is ribbon-helix-helix DNA binding protein. EverythinBagel_15 has the same pham and similar position with Casend_16, Hyperion_13, Rudy_13 and Grassboy_16. 

Downstream gene has NKF except for Rudy_14 (same pham as EverythinBagel_16) with a function of helix-turn-helix DNA binding protein.
    /note=Start is supported by Gm, CP, Starterator, LORF, BLAST and HHPred hits.
    /note=Function is supported by BLAST hits, HHPred hits and Synteny.

CDS 5309 - 6067
  /gene="15"
  /product="gp15"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="EverythinBagel_15"
    /note=Original Glimmer call @bp 5309 has strength 12.2; Genemark calls start at 5309
    /note=SSC: 5309-6067 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA-binding domain protein [Microbacterium phage Rudy] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.575, -3.5925599723783583, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA-binding domain protein [Microbacterium phage Rudy] ],,QQO39196,99.6032,0.0 SIF-HHPRED:  SIF-Syn: EverythinBagel_16 has the same pham/ similar position as Casend_17, Hyperion_14, Rudy_14, and Grassboy_17.

Upstream gene has NKF. Downstream gene is ribbon-helix-helix DNA binding protein.
    /note=Start is supported by Glimmer, GeneMark, CP, Starterator, and has an ideal (-4) gap. Function is supported by BLAST hits and Synteny.

CDS 6069 - 6230
  /gene="16"
  /product="gp16"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_16"
    /note=Genemark calls start at 6069
    /note=SSC: 6069-6230 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_SALLYK_18 [Microbacterium phage SallyK]],,NCBI, q1:s1 100.0% 4.50481E-26 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.906, -2.827683592113848, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_SALLYK_18 [Microbacterium phage SallyK]],,WKW84885,100.0,4.50481E-26 SIF-HHPRED:  SIF-Syn: Homologs have no known function.
Everythinbagel_17 is in the same position and pham as SallyK_18, Babydotz_16, and Gazebo_16 but all of these genes have no known function.
    /note=The start chosen has coding potential, is the supported start in starterator, and is chosen by genemark. It also has a small gap, is the LORF, and has the best RBS values. This gene has NKF and this is supported by evidence from blast, HHpred, and synteny; it is not a membrane protein.

CDS 6227 - 6400
  /gene="17"
  /product="gp17"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_17"
    /note=Original Glimmer call @bp 6227 has strength 7.14; Genemark calls start at 6227
    /note=SSC: 6227-6400 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RUDY_16 [Microbacterium phage Rudy] ],,NCBI, q1:s1 100.0% 2.24351E-33 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.407, -6.526515810972826, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RUDY_16 [Microbacterium phage Rudy] ],,QQO39198,100.0,2.24351E-33 SIF-HHPRED:  SIF-Syn: Homologs have no known function. 
Everythinbagel_17 is in the same pham and position as Babydotz_17, Blab_15, and Gazebo_17 but all of these genes have no known function.
    /note=This start is the supported start in starterator, it has coding potential, and it is the start chosen by glimmer and genemark. Additionally, it has an ideal overlap of -4bp and it is the LORF. For the function, all evidence from blast, HHpred, and synteny point towards no known function and it is not a membrane protein

CDS 6400 - 6774
  /gene="18"
  /product="gp18"
  /function="ribbon-helix-helix DNA binding domain"
  /locus tag="EverythinBagel_18"
    /note=Original Glimmer call @bp 6400 has strength 9.27; Genemark calls start at 6400
    /note=SSC: 6400-6774 CP: yes SCS: both ST: SS BLAST-Start: [DNA binding protein [Microbacterium phage Squash] ],,NCBI, q1:s1 100.0% 1.3065E-81 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.709, -5.24749338024855, no F: ribbon-helix-helix DNA binding domain SIF-BLAST: ,,[DNA binding protein [Microbacterium phage Squash] ],,YP_009801760,100.0,1.3065E-81 SIF-HHPRED:  SIF-Syn: Ribbon-helix-helix DNA binding domain protein.
Everythinbagel_19 is in the same pham and position as Grassboy_20 and Casend_20 which are both ribbon-helix-helix DNA binding domains. All directly upstream to terminase.
    /note=This start has coding potential, is chosen by glimmer and genemark, and it is the supported start in starterator. Additionally, it has a small gap and has blast evidence. For the function, blast and synteny evidence both point towards a ribbon-helix-helix DNA binding domain, and it is not a membrane protein.

CDS 6749 - 8260
  /gene="19"
  /product="gp19"
  /function="terminase"
  /locus tag="EverythinBagel_19"
    /note=Original Glimmer call @bp 6749 has strength 10.88; Genemark calls start at 6749
    /note=SSC: 6749-8260 CP: yes SCS: both ST: SS BLAST-Start: [terminase large subunit [Microbacterium phage Hyperion] ],,NCBI, q1:s1 100.0% 0.0 GAP: -26 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.322, -4.038963679561956, no F: terminase SIF-BLAST: ,,[terminase large subunit [Microbacterium phage Hyperion] ],,YP_009801560,99.6024,0.0 SIF-HHPRED: Gene 2 protein; DNA packaging, terminase, ATPase, nuclease, ATP binding, Magnesium binding, VIRAL PROTEIN; 1.69A {Shigella phage Sf6},,,4IDH_A,90.2584,99.9 SIF-Syn: Terminase
Everythinbagel_20 is in the same pham and  position as BabyDotz_19, Blab_17, and Casend_21, which are all terminases. 
Upstream of helix-turn-helix DNA binding domain protein, and downstream of portal protein
    /note=This start has coding potential, is the supported start in starterator, and it is the start that is chosen by glimmer and genemark, it also has blast evidence and the best RBS values. For function, terminase is supported by blast, HHpred, and synteny, and it is not a membrane protein.

CDS 8257 - 8601
  /gene="20"
  /product="gp20"
  /function="membrane protein"
  /locus tag="EverythinBagel_20"
    /note=Original Glimmer call @bp 8257 has strength 11.17; Genemark calls start at 8257
    /note=SSC: 8257-8601 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Zagie] ],,NCBI, q1:s1 100.0% 3.3142E-67 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.794, -2.996985748252251, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Zagie] ],,UVG35374,98.2143,3.3142E-67 SIF-HHPRED:  SIF-Syn: Same position and pham as BabyDotz_20, Rowlf_17, and Zagie_17 but these genes have no known function.
    /note=This start has coding potential, was chosen by glimmer and genemark, and it is the supported start in starterator. Additionally, it has the ideal overlap of 4 bp, it is the LORF with the beset RBS values, and there is blast evidence pointing towards this start. For function, we know it is a membrane protein because three transmembrane domains were found by both TMHMM and SOSUI. Additionally, blast gives evidence towards a membrane protein.

CDS 8840 - 10666
  /gene="21"
  /product="gp21"
  /function="portal protein"
  /locus tag="EverythinBagel_21"
    /note=Original Glimmer call @bp 8840 has strength 11.39; Genemark calls start at 8840
    /note=SSC: 8840-10666 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Microbacterium phage Teehee] ],,NCBI, q1:s1 99.8355% 0.0 GAP: 238 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.737, -3.196631460098011, no F: portal protein SIF-BLAST: ,,[portal protein [Microbacterium phage Teehee] ],,QWY80406,99.6711,0.0 SIF-HHPRED: Portal protein; Prohead I, icosahedral symmetry, HK97, phage, capsid, VIRUS; 3.6A {Escherichia phage HK97},,,8FQL_D,62.1711,99.9 SIF-Syn: NKF - homologs are NKF
    /note=Starterator supports the selected start at 8840 (37 MA`s) and was chosen by both Glimmer and Genemark; it also has the best RBS and the LORF. The function of the protein is likely to be a portal protein because there many 1:1 matches with other genes that acted as portal proteins. However, no synteny was found when comparing alike genes.

CDS 10666 - 13887
  /gene="22"
  /product="gp22"
  /function="capsid maturation protease"
  /locus tag="EverythinBagel_22"
    /note=Original Glimmer call @bp 10666 has strength 10.08; Genemark calls start at 10666
    /note=SSC: 10666-13887 CP: yes SCS: both ST: SS BLAST-Start: [capsid maturation protease and MuF-like fusion protein [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.019, -4.957272661945414, no F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease and MuF-like fusion protein [Microbacterium phage Casend] ],,QNL29991,96.2617,0.0 SIF-HHPRED:  SIF-Syn: Capsid maturation protease, same position and pham as Casend_24, Gazebo_22, and Judebell_25. All downstream of a portal protein.
    /note=Starterator supports the selected start at position 10666 (35 MA`s) and was chosen by both Glimmer and Genemark; it also has a good RBS and the smallest gap. The function of the protein is likely to be a capsid maturation protease and because there were many 1:1 matches with other genes that acted as capsid maturation protease. Furtheremore, synteny was found between Casend_24, Gazebo_22, and Judebell_25, which all acted as  capsid maturation proteases and were all downstream of a portal protein.

CDS 13891 - 14073
  /gene="23"
  /product="gp23"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_23"
    /note=Original Glimmer call @bp 13924 has strength 10.45; Genemark calls start at 13924
    /note=SSC: 13891-14073 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein HOT29_gp026 [Microbacterium phage Squash] ],,NCBI, q1:s1 100.0% 2.98872E-35 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.559, -3.83711508627892, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT29_gp026 [Microbacterium phage Squash] ],,YP_009801765,100.0,2.98872E-35 SIF-HHPRED:  SIF-Syn: NKF - homologs are NKF, but they share the same pham and position as Squash_26 and Hyperion_23 are all downstream of a capsid maturation protease and upstream of a major capsid hexamer protein.
    /note=Starterator supports the selected start at position 13891 (37 MA`s) although it was not chosen by either Glimmer and Genemark; it also has a the 2nd best RBS, the smallest gap, and the LORF. There is not enough evidence to determine a function for the protein, but it does share synteny with Hyperion_23 and Squash_26, with all of them being downstream of a capsid maturation protease and upstream of a major capsid hexamer protein.

CDS 14211 - 16028
  /gene="24"
  /product="gp24"
  /function="major capsid hexamer protein"
  /locus tag="EverythinBagel_24"
    /note=Original Glimmer call @bp 14211 has strength 12.28; Genemark calls start at 14211
    /note=SSC: 14211-16028 CP: yes SCS: both ST: SS BLAST-Start: [major capsid hexamer protein [Microbacterium phage Namago] ],,NCBI, q1:s1 100.0% 0.0 GAP: 137 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.061, -2.5052746077145835, yes F: major capsid hexamer protein SIF-BLAST: ,,[major capsid hexamer protein [Microbacterium phage Namago] ],,QQO39426,98.1967,0.0 SIF-HHPRED:  SIF-Syn: major capsid hexamer protein, same position and pham as Grassboy_26, and Namago_25. Upstream and downstream of genes that share the same pham and position (although they are NKF)
    /note=Starterator supports the selected start at position 14211 (26 MA`s) and was chosen by both Glimmer and Genemark; it also has the best RBS, the smallest gap (although still pretty big), and the LORF. The function of the protein is likely to be a major capsid hexamer protein because there were many 1:1 matches with other genes that acted as major capsid hexamer protein. Furtheremore, synteny was found between Grassboy_26 and Namago_25, which both act as major capsid hexamer proteins.

CDS 16093 - 16827
  /gene="25"
  /product="gp25"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_25"
    /note=Original Glimmer call @bp 16093 has strength 11.28; Genemark calls start at 16093
    /note=SSC: 16093-16827 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT29_gp028 [Microbacterium phage Squash] ],,NCBI, q1:s1 100.0% 3.5742E-170 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.47, -3.670670413150579, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT29_gp028 [Microbacterium phage Squash] ],,YP_009801767,98.7705,3.5742E-170 SIF-HHPRED:  SIF-Syn: NKF - homologs are NKF, but they share the same pham and position as Squash_28 and Nike_26 and are all downstream of a major capsid hexamer protein
    /note=Starterator supports the selected start at position 16093 (38 MA`s) and was chosen by both Glimmer and Genemark; it also has the best RBS, and the second smallest gap. There is not enough evidence to determine a function for the protein, but it does share synteny with Squash_28 and Nike_26, with all of them being downstream of a major capsid hexamer protein

CDS 16837 - 17403
  /gene="26"
  /product="gp26"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_26"
    /note=Original Glimmer call @bp 16837 has strength 14.01; Genemark calls start at 16837
    /note=SSC: 16837-17403 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_28 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 8.69766E-117 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.308, -2.0111200136961407, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_28 [Microbacterium phage Casend] ],,QNL29995,98.4043,8.69766E-117 SIF-HHPRED:  SIF-Syn: NKF - homologs are NKF, but they share the same pham and position as Casend_28 and Phabia_27 which are all upstream of a major tail protein
    /note=Starterator supports the selected start at position 16837 (38 MA`s) and was chosen by both Glimmer and Genemark; it also has the best RBS, and the smallest gap, and the LORF.  There is not enough evidence to determine a function for the protein, but it does share synteny with Casend_28 and Phabia_27, which are all upstream of a major tail protein

CDS 17434 - 18381
  /gene="27"
  /product="gp27"
  /function="major tail protein"
  /locus tag="EverythinBagel_27"
    /note=Original Glimmer call @bp 17458 has strength 11.09; Genemark calls start at 17458
    /note=SSC: 17434-18381 CP: yes SCS: both-cs ST: SS BLAST-Start: [major tail protein [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 0.0 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.39, -3.8366550365551095, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Microbacterium phage Casend] ],,QNL29996,100.0,0.0 SIF-HHPRED:  SIF-Syn: Major Tail Protein, same pham and position as Casend/ Grassboy.
    /note=Glimmer and Genemark call this Start, High Coding Potential and Best Start accordung to RBS. Otherwise Function, E-values, Coverage and Probability from multiple sources pointed to Major Tail Protein as function.

CDS 18505 - 19386
  /gene="28"
  /product="gp28"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_28"
    /note=Original Glimmer call @bp 18505 has strength 11.32; Genemark calls start at 18505
    /note=SSC: 18505-19386 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Microbacterium phage Judebell]],,NCBI, q1:s1 100.0% 0.0 GAP: 123 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.906, -3.59360038608048, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Microbacterium phage Judebell]],,XCG97245,100.0,0.0 SIF-HHPRED:  SIF-Syn: NKF - Homologous have no know function
    /note=Glimmer and Genemark call this start, High CP and Best Start according to RBS.  In addition to that there are High Probabilities and Coverage as well as low E-values from BLAST results, other evidence inconclusive. Evidence points toward a gene with no known protein function.

CDS 19389 - 20927
  /gene="29"
  /product="gp29"
  /function="Phosphoesterase"
  /locus tag="EverythinBagel_29"
    /note=Original Glimmer call @bp 19389 has strength 10.93; Genemark calls start at 19389
    /note=SSC: 19389-20927 CP: yes SCS: both ST: SS BLAST-Start: [phosphoesterase [Microbacterium phage Judebell]],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.81, -5.69021729366323, no F: Phosphoesterase SIF-BLAST: ,,[phosphoesterase [Microbacterium phage Judebell]],,XCG97246,99.2188,0.0 SIF-HHPRED: c.1.18.3 (A:1-240) Glycerophosphodiester phosphodiesterase UgpQ {Agrobacterium tumefaciens [TaxId: 358]},,,d1zcca1,46.2891,100.0 SIF-Syn: phosphoesterase, same pham and position as Judebell/ Namago. Both upstream from head to tail adaptor.
    /note=This start is called by Glitter and Genemark, High CP. SIF-Blast and HHPred have Low e-values and high Probability. Synteny evidence supports with similar Phams and Position.  Evidence points towards the function being a Phosphoesterase.

CDS 20958 - 21806
  /gene="30"
  /product="gp30"
  /function="head-to-tail adaptor"
  /locus tag="EverythinBagel_30"
    /note=Original Glimmer call @bp 20958 has strength 9.23; Genemark calls start at 20958
    /note=SSC: 20958-21806 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail adaptor [Microbacterium phage BabyDotz]],,NCBI, q1:s1 100.0% 0.0 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.044, -3.005970110175159, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Microbacterium phage BabyDotz]],,WNT45285,99.6454,0.0 SIF-HHPRED: Head completion protein; Neck, Portal, T5, VIRUS, VIRAL PROTEIN; 3.2A {Escherichia phage DT57C},,,8HQO_R,80.8511,98.5 SIF-Syn: Head-to-tail adaptor, same pham and position as BabyDotz_30, Hyperion_30, SallyK_32 and Sqush_33. 
All are immediately upstream of phosphoesterase. The first and second genes downstream of this pham has NKF
    /note=This start is called by Glitter and Genemark, High CP and best start according to RBS. The function is a Head-to-Tail Adaptor protein based on the HHPred, SIF-BLAST, and SIF-SYN evidence. High Probabilites and Coverages as well as Low E-values. Synteny evidence supports Pham and position based on similar phages.

CDS 21806 - 22336
  /gene="31"
  /product="gp31"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_31"
    /note=Original Glimmer call @bp 21806 has strength 11.41; Genemark calls start at 21806
    /note=SSC: 21806-22336 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_33 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 7.37671E-124 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.664, -3.2669815101762634, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_33 [Microbacterium phage Casend] ],,QNL30000,100.0,7.37671E-124 SIF-HHPRED:  SIF-Syn: NKF, same pham as Casend_33, Lonelysoil_31,  Phabia_32, similar locations
    /note=This start is called by Glitter and Genemark, with high CP and best start according to RBS. HHPred and SIF-BLAST yielded high e-values and low probabilities, and SIF-SYN showed similar genes, but with no known function. Gene is present, function unknown

CDS 22338 - 22736
  /gene="32"
  /product="gp32"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_32"
    /note=Original Glimmer call @bp 22338 has strength 7.63; Genemark calls start at 22338
    /note=SSC: 22338-22736 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Microbacterium phage Judebell]],,NCBI, q1:s1 100.0% 4.53422E-86 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.319, -4.045036357814993, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Microbacterium phage Judebell]],,XCG97249,97.7612,4.53422E-86 SIF-HHPRED:  SIF-Syn: NKF - homologs have no known function
    /note=Start is predicted by Genemark and Glimmer, called by both, and supported by Starterator. Start is also supported by BLAST and has favorable RBS scores. There is no known function due to conflicting information from BLAST, HHPred, and SIF-SYN.

CDS 22779 - 23237
  /gene="33"
  /product="gp33"
  /function="tail assembly chaperone"
  /locus tag="EverythinBagel_33"
    /note=Original Glimmer call @bp 22779 has strength 8.82; Genemark calls start at 22788
    /note=SSC: 22779-23237 CP: yes SCS: both-gl ST: SS BLAST-Start: [tail assembly chaperone [Microbacterium phage Namago] ],,NCBI, q1:s1 100.0% 4.88702E-94 GAP: 42 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.758, -3.133663537764895, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Namago] ],,QQO39435,94.7368,4.88702E-94 SIF-HHPRED: Phage_TAC_10 ; Phage tail assembly chaperone,,,PF10963.11,57.8947,94.7 SIF-Syn: tail assembly chaperone, same pham as Judebell_36, Phabia_34, SallyK,35, similar location
    /note=Start is predicted by Genemark and Glimmer, called by Glimmer, and supported by Starterator. Start is also supported by BLAST and has favorable RBS scores. The function is tail assembly chaperone which is supported by BLAST, HHPred, and SIF-SYN.

CDS join(22779..23198,23198..23431)
  /gene="34"
  /product="gp34"
  /function="tail assembly chaperone"
  /locus tag="EverythinBagel_34"
    /note=
    /note=SSC: 22779-23431 CP: yes SCS: neither ST: SS BLAST-Start: [tail assembly chaperone [Microbacterium phage Namago]],,NCBI, q1:s1 100.0% 9.54972E-144 GAP: -459 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.758, -3.133663537764895, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Namago]],,QQO39436,95.8525,9.54972E-144 SIF-HHPRED:  SIF-Syn: tail assembly chaperone, same pham as Judebell_36, Phabia_34, SallyK,35, similar location
    /note=Start is predicted by Genemark and Glimmer, called by Glimmer, and supported by Starterator. Start is also supported by BLAST and has favorable RBS scores. The function is tail assembly chaperone which is supported by BLAST, HHPred, and SIF-SYN.

CDS 23440 - 26616
  /gene="35"
  /product="gp35"
  /function="tape measure protein"
  /locus tag="EverythinBagel_35"
    /note=Original Glimmer call @bp 23440 has strength 9.43; Genemark calls start at 23440
    /note=SSC: 23440-26616 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Microbacterium phage Namago] ],,NCBI, q1:s1 100.0% 0.0 GAP: 7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.154, -4.4057176022952405, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Microbacterium phage Namago] ],,QQO39437,100.0,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BF,5.67108,96.5 SIF-Syn: Tape measure protein, same pham and position as Casend_37, Jehoshaphat_38, Namago_36 and Wheelie_35
    /note=Start is predicted by Genemark and Glimmer, called by both, and supported by Starterator. Start is also supported by BLAST and has favorable RBS scores. The function is tape measure protein which is supported by BLAST, HHPred, and SIF-SYN.

CDS 26625 - 27968
  /gene="36"
  /product="gp36"
  /function="minor tail protein"
  /locus tag="EverythinBagel_36"
    /note=Original Glimmer call @bp 26625 has strength 11.84; Genemark calls start at 26625
    /note=SSC: 26625-27968 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage SallyK]],,NCBI, q1:s1 100.0% 0.0 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.154, -4.4057176022952405, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage SallyK]],,WKW84904,96.868,0.0 SIF-HHPRED:  SIF-Syn: minor tail protein, same pham and position as Hyperion_37, Jehoshaphat_40, Namago_38 and SallyK_39
    /note=Start is predicted by Genemark and Glimmer, called by both, and supported by Starterator. Start is also supported by BLAST and has favorable RBS scores. The function is minor tail protein which is supported by BLAST and SIF-SYN.

CDS 27988 - 30915
  /gene="37"
  /product="gp37"
  /function="minor tail protein"
  /locus tag="EverythinBagel_37"
    /note=Original Glimmer call @bp 27988 has strength 7.91; Genemark calls start at 27988
    /note=SSC: 27988-30915 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage SallyK]],,NCBI, q1:s1 100.0% 0.0 GAP: 19 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.548, -3.649482460397077, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage SallyK]],,WKW84905,99.5897,0.0 SIF-HHPRED:  SIF-Syn: minor tail protein, same pham and position as Casend_39, Jehoshaphat_40, Judebell_40 and SallyK_39.
 Gene downstream and upstream are both minor tail protein.
    /note=Start 27988 is supported by annotations, blast, synteny. called 35 times and 100% of the time when present. function is minor tail protein, supported by blast and synteny. HHPred links to contractile proteins but they are not phage proteins.

CDS 30915 - 32066
  /gene="38"
  /product="gp38"
  /function="minor tail protein"
  /locus tag="EverythinBagel_38"
    /note=Original Glimmer call @bp 30915 has strength 10.92; Genemark calls start at 30915
    /note=SSC: 30915-32066 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.603, -3.3937592014038303, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Casend] ],,QNL30007,100.0,0.0 SIF-HHPRED: Tail protein, 43 kDa; tail protein, structural genomics, PSI, MCSG, Protein Structure Initiative, Midwest Center for Structural Genomics, UNKNOWN FUNCTION; 2.1A {Neisseria meningitidis MC58} SCOP: b.106.1.1,,,3D37_B,91.1227,99.0 SIF-Syn: minor tail protein, same pham and position as Casend_40, Jehoshaphat_41, Nike_39.
Downstream function unknown, upstream function is minor tail protein.
    /note=Start 30915 is supported by annotations, blast, synteny. called 77 times and 95% of the time when present. Function is minor tail protein, supported by HHPred and blast

CDS 32066 - 32827
  /gene="39"
  /product="gp39"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_39"
    /note=Original Glimmer call @bp 32066 has strength 9.12; Genemark calls start at 32066
    /note=SSC: 32066-32827 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_41 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 2.338E-179 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.47, -3.8116689268127657, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_41 [Microbacterium phage Casend] ],,QNL30008,100.0,2.338E-179 SIF-HHPRED:  SIF-Syn: NKF, same pham as Casend_41, Lonelysoil_39, Phabia_40, similar locations
    /note=Start 32066 is supported by annotations, blast, synteny. called 35 times and 100% of the time when present. Function unknown

CDS 32839 - 33102
  /gene="40"
  /product="gp40"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_40"
    /note=Original Glimmer call @bp 32839 has strength 11.21; Genemark calls start at 32839
    /note=SSC: 32839-33102 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_42 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 5.61904E-54 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.142, -2.2763497933341483, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_42 [Microbacterium phage Casend] ],,QNL30009,98.8506,5.61904E-54 SIF-HHPRED:  SIF-Syn: NKF - homologs have no known function
    /note=Start 32,839 is supported by both glimmer and gene mark. It is supported by the starterator as well and is highly conserved within the genome. There are multiple 1:1 alignments and a fairly small gap of 11 bp. It was investigated and all other evidence point to this start. While it isn`t the LORF, it contains the best RBS. This gene has NKF. BLAST alignments were stated as hypothetical proteins and both HHPred and SYN had NKF.

CDS 33176 - 33640
  /gene="41"
  /product="gp41"
  /function="membrane protein"
  /locus tag="EverythinBagel_41"
    /note=Original Glimmer call @bp 33176 has strength 8.89; Genemark calls start at 33176
    /note=SSC: 33176-33640 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Hyperion] ],,NCBI, q1:s1 100.0% 5.03226E-106 GAP: 73 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.153, -2.394485424036831, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Hyperion] ],,YP_009801583,100.0,5.03226E-106 SIF-HHPRED:  SIF-Syn: Same pham as casend_43 and hyperion_41
    /note=SIF-Mem: membrane protein, 1 domain found by both TMHMM and SOSUI. Start 33,176 has coding potential, chosen by glimmer and genemark, it is the supported start with the most manual annotations and called 98% of the time when present, and it has a 1:1 hit on blast. It is the LORF, and it has the most favorable RBS values. It is a membrane protein because blast shows a 1:1 hit with a membrane protein and HHpred did not have any significant results and this gene`s homologs have not been given a function. Therefore there is no evidence towards any other functions and TMHMM and SOSUI both showed evidence towards this being a membrane protein

CDS 33630 - 33827
  /gene="42"
  /product="gp42"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_42"
    /note=Original Glimmer call @bp 33630 has strength 11.42; Genemark calls start at 33630
    /note=SSC: 33630-33827 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT27_gp042 [Microbacterium phage Hyperion] ],,NCBI, q1:s1 100.0% 4.87859E-39 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.985, -3.2535385006449706, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT27_gp042 [Microbacterium phage Hyperion] ],,YP_009801584,100.0,4.87859E-39 SIF-HHPRED:  SIF-Syn: Same pham and gene neighbourhood as Casend_43 and Hyperion_41. These homologs have no known function.
    /note=This start has coding potential and it is the start chosen by glimmer and GeneMark. It is also the supported start in Starterator and the one with the most manual annotations and it is called 98% of the time that it is present. There is a 1:1 alignment with this blast start. There is an 11 bp overlap and while this is not ideal, it is the smallest gap/overlap of all of the starts. This start also is the LORF and has the most favorable RBS values. For function, the protein has NKF becasue the blast results show a hit with hypothetical proteins which does not provide any indication of a specific function. Additionally, the HHpred did not show any significant results and the homologs of this gene have no known function. It is also not a membrane protein.

CDS 33832 - 34569
  /gene="43"
  /product="gp43"
  /function="membrane protein"
  /locus tag="EverythinBagel_43"
    /note=Original Glimmer call @bp 33832 has strength 15.97; Genemark calls start at 33832
    /note=SSC: 33832-34569 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 4.99774E-174 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.454, -5.8568091738896655, no F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Casend] ],,QNL30012,100.0,4.99774E-174 SIF-HHPRED:  SIF-Syn: Homologs of this gene have no known function.
    /note=This start has coding potential, it is the start that has been chosen by Glimmer and GeneMark, and it was the supported start on Starterator with the most manual annotations and it is most conserved in the cluster. The blast shows that this start does have 1:1 alignments. It has a gap of 4 bp which is the smallest gap of the other starts and it is the LORF. Additionally, this start does not have the best RBS values but they are the second best and all of the other evidence points towards this start. The function membrane protein was assigned because the blast results are for a membrane protein. The HHpred showed no significant results and the homologues of this gene have NKF so we have no evidence pointing towards any other functions. This start was selected because it has coding potential, it is the start that has been chosen by Glimmer and GeneMark, and it was the supported start on Starterator with the most manual annotations and it is most conserved in the cluster. The blast shows that this start does have 1:1 alignments. It has a gap of 4 bp which is the smallest gap of the other starts and it is the LORF. Additionally, this start does not have the best RBS values but they are the second best and all of the other evidence points towards this start. In terms of function, I chose membrane protein because the blast results are for a membrane protein. The TMHMM results indicate the protein has five transmembrane domains and the SOSUI results found 3 transmembrane domains.

CDS 34639 - 35460
  /gene="44"
  /product="gp44"
  /function="endolysin"
  /locus tag="EverythinBagel_44"
    /note=Original Glimmer call @bp 34639 has strength 14.19; Genemark calls start at 34639
    /note=SSC: 34639-35460 CP: yes SCS: both ST: SS BLAST-Start: [endolysin [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 0.0 GAP: 69 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.319, -4.045036357814993, no F: endolysin SIF-BLAST: ,,[endolysin [Microbacterium phage Casend] ],,QNL30013,100.0,0.0 SIF-HHPRED:  SIF-Syn: Endolysin, same pham and position as Casend_46 and Gazebo_44; all are upstream of DNA J-like chaperonins and downstream of minor tall protein with about 5 genes in between.
    /note=This start because has coding potential and it is the start chosen by Glimmer and GeneMark. It is also the supported start in Starterator with the most manual annotations and it is called 100% of the time when present in this cluster. There is a 1:1 alignment with this blast start. There is a 69 bp overlap and while this is not ideal, it is the smallest gap/overlap of all of the starts. This start also is the LORF and has the most favorable RBS values. For function, endolysin was chosen because the blast results show a hit with an endolysin. The HHpred hit was for a hydrolase which have known to be associated with lysins in the database but this hit also had low coverage. Additionally, similar genes have the function of an endolysin.

CDS complement (35530 - 36042)
  /gene="45"
  /product="gp45"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_45"
    /note=Original Glimmer call @bp 36048 has strength 8.13; Genemark calls start at 35937
    /note=SSC: 36042-35530 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_47 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 2.00005E-116 GAP: -32 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.906, -3.1164791313608173, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_47 [Microbacterium phage Casend] ],,QNL30014,100.0,2.00005E-116 SIF-HHPRED:  SIF-Syn: NKF, homologs have no known function
    /note=To start off, I did change the start in PECAAN to a different start than the one originally chosen. This start was not the start chosen by Glimmer or Genemark. However, I have chosen to change this start for multiple reasons. This start was the most conserved in the cluster and it had the most manual annotations. It has a 32 bp overlap and while this is a large number it is the smallest of all of the other gaps and overlaps of the other starts. Additionally, it does have a 1:1 hit on blast. While it is not the LORF, it also has the best ribosome binding site values. I chose NKF because the top blast hits are with a hypothetical protein. The HHpred section came up with a hit of a probable DNA packing protein which I assume the term "probable" should not be an indication of function, and the other hits had non-significant e-values as well as this hit having a very low coverage so I chose not to take the HHpred results into consideration when determining function. Additionally, the similar homologue genes did not have a known function. These results give no indication to what the function may be and it is not a membrane protein.

CDS complement (36011 - 36313)
  /gene="46"
  /product="gp46"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_46"
    /note=Original Glimmer call @bp 36313 has strength 3.44; Genemark calls start at 36313
    /note=SSC: 36313-36011 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_48 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 1.59516E-63 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.906, -2.9063687850157054, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_48 [Microbacterium phage Casend] ],,QNL30015,100.0,1.59516E-63 SIF-HHPRED:  SIF-Syn: NKF, homologs have no known function
    /note=This start has coding potential, it was chosen by Glimmer and Genemark, it is the supported start with the most manual annotations and called 93% of the time that it is present, and it has 1:1 alignments in blast. It is the LORF and it has the most ideal overlap of 4 bp and has the best RBS values. In terms of the gap, it is larger than 10 bp but it is still the smallest of all of the start options. For the function, the blast results only show hypothetical proteins which does not give us much information, there are no significant results in HHpred, and the homologs have no known function. Additionally, it is not a membrane protein. There is no evidence pointing towards any function so I chose NKF.

CDS complement (36310 - 36942)
  /gene="47"
  /product="gp47"
  /function="chaperonin, DnaJ-like"
  /locus tag="EverythinBagel_47"
    /note=Original Glimmer call @bp 36942 has strength 10.98; Genemark calls start at 36942
    /note=SSC: 36942-36310 CP: yes SCS: both ST: SS BLAST-Start: [DnaJ-like chaperonin [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 1.83303E-149 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.219, -4.2529836510151195, no F: chaperonin, DnaJ-like SIF-BLAST: ,,[DnaJ-like chaperonin [Microbacterium phage Casend] ],,QNL30016,100.0,1.83303E-149 SIF-HHPRED: a.2.3.1 (A:) Large T antigen, the N-terminal J domain {Murine polyomavirus [TaxId: 10634]},,,d1fafa_,26.6667,98.6 SIF-Syn: DnaJ-like chaperonin, same pham and position as Casend_49, Jehosaphat_50, and Lonelysoil_47. Most directly upstream and downstream genes do not have known functions
    /note=Start 36942 chosen by GeneMark/Glimmer.  CP, -4 gap, SS. Found in 35 of 74 ( 47.3% ) of genes in pham.  Manual Annotations of this start: 17 of 60.  Called 71.4% of time when present.  F = chaperonin, DnaJ-like.  Called DnaJ-like chaperonin by NCBI blast.  The HHpred section also showed a hit for an N-terminal J domain which is in the family of chaperone J-domain so this could be an indication for the function DnaJ-like chaperonin. Additionally the similar homologue genes are all DnaJ-like chaperonins. It is also not a membrane protein.

CDS complement (36939 - 37280)
  /gene="48"
  /product="gp48"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_48"
    /note=Original Glimmer call @bp 37280 has strength 10.32; Genemark calls start at 37280
    /note=SSC: 37280-36939 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_50 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 2.49163E-76 GAP: 21 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.061, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_50 [Microbacterium phage Casend] ],,QNL30017,100.0,2.49163E-76 SIF-HHPRED:  SIF-Syn: NKF, homologs have no known function
    /note=Start 37,280 is supported by both glimmer and gene mark. It is a reverse gene and also supported by starterator. There are multiple 1:1 alignments and has a base pair gap of 21. This start does contain the LORF and has the best RBS. From the results of BLAST, HHPred, and Synteny there is no significant results and concluded in no known function. It is also not a membrane protein.

CDS complement (37302 - 39539)
  /gene="49"
  /product="gp49"
  /function="Cas4 exonuclease"
  /locus tag="EverythinBagel_49"
    /note=Original Glimmer call @bp 39539 has strength 10.41; Genemark calls start at 39539
    /note=SSC: 39539-37302 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_51 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.575, -3.513874779476501, no F: Cas4 exonuclease SIF-BLAST: ,,[hypothetical protein SEA_CASEND_51 [Microbacterium phage Casend] ],,QNL30018,99.8658,0.0 SIF-HHPRED: Uncharacterized protein; Cas4, CRISPR, MCSG, Exonuclease, PSI-Biology, STRUCTURAL GENOMICS, UNKNOWN FUNCTION, Midwest Center for Structural Genomics; HET: MN, MSE, SF4; 2.35A {Sulfolobus solfataricus},,,4IC1_H,26.3087,98.6 SIF-Syn: Cas4 Family Exonuclease, same pham and position as Jehoshaphat_52 and Phabia_50; all are downstream(2) of DNAJ-like chaperonin and upstream of a DNA recombinase.
    /note=Start 39,539 is supporte by both glimmer and gene mark. It is a reverse gene and also supported by the starterator.  Found in 41 of 52 ( 78.8% ) of genes in pham.  Manual Annotations of this start: 27 of 38.  Called 92.7% of time when present. There are multiple 1:1 alignments and has an optimal one base pair overlap. While it doens`t have the LORF, it does have the best RBS, and has coding potential. From the results of BLAST, HHPred, and Syteny it points that the function of this gene is noted to be Cas4 Family Exonuclease. Some of top hits were NKF though. It is also not a membrane protein.  Cas4 exonuclease as Cas4 Family Exonuclease not a option

CDS complement (39539 - 40555)
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_50"
    /note=Original Glimmer call @bp 40555 has strength 8.19; Genemark calls start at 40555
    /note=SSC: 40555-39539 CP: yes SCS: both ST: SS BLAST-Start: [DNA recombinase [Microbacterium phage StrawberryJamm]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.964, -2.707694805492614, no F: hypothetical protein SIF-BLAST: ,,[DNA recombinase [Microbacterium phage StrawberryJamm]],,QWY80134,97.9532,0.0 SIF-HHPRED: d.50.1.3 (A:) The homologous-pairing domain of Rad52 recombinase {Human (Homo sapiens) [TaxId: 9606]},,,d1kn0a_,43.4911,99.9 SIF-Syn: Same position, pham and gene neighborhood as Phage_StrawberryJamm_54 and Phage_Zagie.  Casend_52 is Same position, pham and gene neighborhood with RecA-like DNA recombinase.
    /note=Start 36942 chosen by GeneMark/Glimmer.  CP, -4 gap. Best RBS, SS, Found in 38 of 41 ( 92.7% ) of genes in pham.  Manual Annotations of this start: 27 of 30.  Called 100.0% of time when present.  DNA recombinase was 1st pick from NCBI/HHPred, but DNA recombinase is not on function list.  NCBI/HHPred also have RecA-like DNA recombinase, in phamerator, Casend_52 is Same position, pham and gene neighborhood with RecA-like DNA recombinase. The information on the forums and evidence in HHPred does not support calling this gene RecA-like DNA recombinase or ASCE ATPase, so we`re leaving it as NKF.

CDS complement (40552 - 41085)
  /gene="51"
  /product="gp51"
  /function="HNH endonuclease"
  /locus tag="EverythinBagel_51"
    /note=Original Glimmer call @bp 41085 has strength 10.15; Genemark calls start at 41085
    /note=SSC: 41085-40552 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Microbacterium phage SallyK]],,NCBI, q1:s1 100.0% 4.80559E-124 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.794, -3.077027835973012, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Microbacterium phage SallyK]],,WKW84919,98.3051,4.80559E-124 SIF-HHPRED: zf-His_Me_endon ; Zinc-binding loop region of homing endonuclease,,,PF05551.14,45.1977,99.4 SIF-Syn: HNH Endonuclease, Same pham, position and gene neighborhood as Phage_SallyK and Phage_Gazebo
    /note=Start 41085 chosen by GeneMark/Glimmer.  CP, -4 gap. Best RBS, SS.  HNH Endonuclease because  NCBI/HHPred had HNH Endonuclease or Zinc Binding Loop of HNH Endonuclease, a type of HNH Endonuclease.  It is also not a membrane protein.

CDS complement (41082 - 41660)
  /gene="52"
  /product="gp52"
  /function="RuvC-like resolvase"
  /locus tag="EverythinBagel_52"
    /note=Original Glimmer call @bp 41660 has strength 8.78; Genemark calls start at 41660
    /note=SSC: 41660-41082 CP: yes SCS: both ST: SS BLAST-Start: [RuvC-like resolvase [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 9.10269E-137 GAP: 28 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.808, -3.7960205838585104, yes F: RuvC-like resolvase SIF-BLAST: ,,[RuvC-like resolvase [Microbacterium phage Casend] ],,QNL30021,99.4792,9.10269E-137 SIF-HHPRED: c.55.3.6 (A:) RuvC resolvase {Escherichia coli [TaxId: 562]},,,d1hjra_,85.4167,99.9 SIF-Syn: Ruvc Revolvase, Same pham, position and gene neighborhood as casend and Rudy(are Ruvc Revolvase), 1 downstream of HNH Endonuclease.
    /note=Start 41660 chosen by GeneMark/Glimmer.  CP, Best RBS.  While startarator stats were not best: Found in 122 of 801 ( 15.2% ) of genes in pham.  Manual Annotations of this start: 35 of 708.  Called 39.3% of time when present.  None of the other proposed starts were better.  NCBI/HHPred had HNH RuvC-like resolvase or similar.  It is also not a membrane protein.

CDS complement (41689 - 41961)
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_53"
    /note=Original Glimmer call @bp 41961 has strength 12.37; Genemark calls start at 41961
    /note=SSC: 41961-41689 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_55 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 3.05427E-58 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.47, -3.75071250087134, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_55 [Microbacterium phage Casend] ],,QNL30022,100.0,3.05427E-58 SIF-HHPRED:  SIF-Syn: NKF same position and pham as Casend_56 and Rudy_53; homologs have NKF
    /note=I agree with the start; supported by glimmer, genemark, and phamerator; has coding potential; even though it does not have LORF, only a gap of -1bp; NKF found through Blast, HHPred, and MEM; NKF

CDS complement (41961 - 42158)
  /gene="54"
  /product="gp54"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_54"
    /note=Original Glimmer call @bp 42158 has strength 14.3; Genemark calls start at 42158
    /note=SSC: 42158-41961 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_56 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 2.03015E-36 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.625, -3.4283035164720754, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_56 [Microbacterium phage Casend] ],,QNL30023,100.0,2.03015E-36 SIF-HHPRED:  SIF-Syn: NKF same position and pham as Casend_56 and Rudy_53; homologs have NKF
    /note=I agree with the start; supported by glimmer, genemark, and phamerator; has coding potential; has the LORF and best RBS scores; no significant findings from Blast, HHPred, and MEM; NKF

CDS complement (42158 - 42550)
  /gene="55"
  /product="gp55"
  /function="MazG-like nucleotide pyrophosphohydrolase"
  /locus tag="EverythinBagel_55"
    /note=Original Glimmer call @bp 42550 has strength 11.81; Genemark calls start at 42550
    /note=SSC: 42550-42158 CP: yes SCS: both ST: SS BLAST-Start: [MazG-like nucleotide pyrophosphohydrolase [Microbacterium phage Rudy] ],,NCBI, q1:s1 100.0% 7.85763E-91 GAP: 129 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.643, -3.3732766706951867, no F: MazG-like nucleotide pyrophosphohydrolase SIF-BLAST: ,,[MazG-like nucleotide pyrophosphohydrolase [Microbacterium phage Rudy] ],,QQO39236,100.0,7.85763E-91 SIF-HHPRED: a.204.1.2 (A:1-98) Hypothetical protein YpjD {Bacillus subtilis [TaxId: 1423]},,,d2gtaa1,80.0,99.2 SIF-Syn: MAzG-like nucleotid has the same pham and position as Rudy and Phabia
    /note=NKF, NCBI, d2gtaa1, 80, prob= 99.2%
    /note=I agree with the start; supprted and called for on Pecaan, glimmer, and genemark; starterater had another start that looked much better, but all of the phages included were in a different pham and were not being considered as a start; had the LORF and a gap of 11 bp; MazG-like nucleotide pyrophosphohydrolase

CDS complement (42680 - 43393)
  /gene="56"
  /product="gp56"
  /function="SSB protein"
  /locus tag="EverythinBagel_56"
    /note=Original Glimmer call @bp 43393 has strength 5.99; Genemark calls start at 43393
    /note=SSC: 43393-42680 CP: yes SCS: both ST: SS BLAST-Start: [ssDNA binding protein [Microbacterium phage Grassboy]],,NCBI, q1:s1 100.0% 2.90305E-155 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.906, -2.827683592113848, yes F: SSB protein SIF-BLAST: ,,[ssDNA binding protein [Microbacterium phage Grassboy]],,UVG34317,98.7288,2.90305E-155 SIF-HHPRED: b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]},,,d1qvca_,44.7257,99.9 SIF-Syn: ssDNA binding protein; same position and pham (function) as Casend_58 and Rudy_55
    /note=ssDNA binding protein, Escherichia coli [Taxld:562], NCBI, d1qvca low coverage =  44.7, prob = 99.9%
    /note=I agree with tthe start; supported by glimmer, genemark, and Phamerator; had the LORF and best RBS scores; ssDNA binding protein on blast and HHPred; no membrane protein on MEM

CDS complement (43395 - 43574)
  /gene="57"
  /product="gp57"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_57"
    /note=Original Glimmer call @bp 43574 has strength 17.35; Genemark calls start at 43574
    /note=SSC: 43574-43395 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_GRASSBOY_61 [Microbacterium phage Grassboy]],,NCBI, q1:s1 100.0% 1.38384E-34 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.061, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_GRASSBOY_61 [Microbacterium phage Grassboy]],,UVG34318,100.0,1.38384E-34 SIF-HHPRED:  SIF-Syn: NKF, Same Pham and Similar Gene Neighborhood as Phage_Grassboy and Phage_Fizzles
    /note=I agree with the start; supported by genemark, glimmer, and phamerator; did not have the LORFbut had the smallest gap of 11bp; had best RBS scores; no significant data found in HHPred or Blast; NKF

CDS complement (43586 - 43774)
  /gene="58"
  /product="gp58"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_58"
    /note=Original Glimmer call @bp 43774 has strength 9.08; Genemark calls start at 43774
    /note=SSC: 43774-43586 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_60 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 4.67503E-13 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.762, -5.200997464701116, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_60 [Microbacterium phage Casend] ],,QNL30027,70.7692,4.67503E-13 SIF-HHPRED: Inhibitor_I78 ; Peptidase inhibitor I78 family,,,PF11720.11,24.1935,76.2 SIF-Syn: NKF - homologs have no known function
    /note=I agree with the start site called for, 44007, because this aligned with both glimmer and genemark, had coding potential, supported evidence from starterator, and had the best RBS. However, it did not have the longest ORF and a large gap of + 71 but all other data points to a start of 44007. This gene had a unknown function SIF blast had no strong alignments, and SIF-SYN had  no significant evidence to support a function. HHPred also had hits with a low coverage and high e-value.

CDS complement (43771 - 44007)
  /gene="59"
  /product="gp59"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_59"
    /note=Original Glimmer call @bp 44007 has strength 10.5; Genemark calls start at 44007
    /note=SSC: 44007-43771 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_61 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 3.18285E-45 GAP: 71 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.297, -1.953940808934884, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_61 [Microbacterium phage Casend] ],,QNL30028,94.8718,3.18285E-45 SIF-HHPRED: a.60.7.1 (A:183-305) T4 RNase H {Bacteriophage T4 [TaxId: 10665]},,,d1tfra1,24.359,48.2 SIF-Syn: NKF - homologs have no known function
    /note=I agree with the start site called for, 44007, because this aligned with both glimmer and genemark, had coding potential, supported evidence from starterator, and had the best RBS. However, it did not have the longest ORF and a large gap of + 71 but all other data points to a start of 44007. This gene had a unknown function SIF blast had no strong alignments, and SIF-SYN had  no significant evidence to support a function. HHPred also had hits with a low coverage and high e-value.

CDS complement (44079 - 44189)
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_60"
    /note=Original Glimmer call @bp 44231 has strength 3.03; Genemark calls start at 44189
    /note=SSC: 44189-44079 CP: no SCS: both-gm ST: SS BLAST-Start: [hypothetical protein [Microbacterium phage Judebell]],,NCBI, q2:s4 97.2222% 7.46987E-14 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.537, -4.057188185093195, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Microbacterium phage Judebell]],,XCG97275,89.4737,7.46987E-14 SIF-HHPRED: DUF3046 ; Protein of unknown function (DUF3046),,,PF11248.11,44.4444,73.5 SIF-Syn: NFK, homologs have no known functions
    /note=I agree with the start site called for, 44189, because this aligned with genemark, had coding potential, supported evidence from starterator, and had a small overlap of 8. However, it did not have the longest ORF, had the 2nd best RBS, and was not called for by glimmer, but all other data points to a start of 44189. This gene had a unknown function SIF blast had no strong alignments, and SIF-SYN had  no significant evidence to support a function. HHPred also had hits with a low coverage and high e-value.

CDS complement (44182 - 44508)
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_61"
    /note=Original Glimmer call @bp 44508 has strength 4.46; Genemark calls start at 44508
    /note=SSC: 44508-44182 CP: no SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_ALUMINUMJESUS_59 [Microbacterium phage AluminumJesus]],,NCBI, q1:s1 51.8519% 1.00781E-9 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.549, -4.0338999058337315, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ALUMINUMJESUS_59 [Microbacterium phage AluminumJesus]],,UJD20794,53.4091,1.00781E-9 SIF-HHPRED: zf_C2H2_ZHX ; Zinc-fingers and homeoboxes C2H2 finger domain,,,PF18387.4,7.40741,62.2 SIF-Syn: I agree with the start site called for, 44508, because this aligned with both glimmer and genemark, had coding potential, and had an ideal overlap of 4, had the longest ORF and the best RBS. However, it was not supported by starterator, but all other data points to a start of 44508.This gene had a unknown function SIF blast had no strong alignments, and SIF-SYN had  no significant evidence to support a function. HHPred also had hits with a low coverage and high e-value.
    /note=NKF - homologs have no known function

CDS complement (44505 - 44756)
  /gene="62"
  /product="gp62"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_62"
    /note=Original Glimmer call @bp 44756 has strength 5.77; Genemark calls start at 44756
    /note=SSC: 44756-44505 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ZAGIE_64 [Microbacterium phage Zagie]],,NCBI, q1:s1 100.0% 4.10513E-49 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.547, -5.646677400615975, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ZAGIE_64 [Microbacterium phage Zagie]],,UVG35417,98.7952,4.10513E-49 SIF-HHPRED: b.34.1.2 (A:1-75) Hypothetical protein PA4359 {Pseudomonas aeruginosa [TaxId: 287]},,,d2h3ja1,80.7229,71.8 SIF-Syn: NKF - homologs have no known function.
    /note=I agree with the start site called for, 44756, because this aligned with both glimmer and genemark, had coding potential, supported evidence from starterator, and had an ideal overlap of 4. However, it did not have the longest ORF or best RBS, but all other data points to a start of 44756.This gene had a unknown function SIF blast had no strong alignments, and SIF-SYN had  no significant evidence to support a function. HHPred also had hits with a low coverage and high e-value.

CDS complement (44753 - 44926)
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_63"
    /note=Original Glimmer call @bp 44926 has strength 4.93; Genemark calls start at 44926
    /note=SSC: 44926-44753 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_CASEND_65 [Microbacterium phage Casend] ],,NCBI, q2:s3 98.2456% 4.35608E-23 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.423, -4.867713808513585, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_65 [Microbacterium phage Casend] ],,QNL30032,84.4828,4.35608E-23 SIF-HHPRED:  SIF-Syn: Homologous genes (Casend_65, Jehoshaphat_66, and Phabia_64) are all hypothetical proteins with no known function.
    /note=The selected start, although not supported by starterator, results in a 4 bp overlap, indicating and operon, and creates the best alignment with homologous genes. All NCBI alignments were to hypothetical proteins and HHPred yielded no significant hits, meaning no specific function could be assigned to this gene.

CDS complement (44923 - 45018)
  /gene="64"
  /product="gp64"
  /function="membrane protein"
  /locus tag="EverythinBagel_64"
    /note=Genemark calls start at 45015
    /note=SSC: 45018-44923 CP: yes SCS: genemark-cs ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_66 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 6.25863E-10 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.392, -3.8308929311341546, no F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_66 [Microbacterium phage Casend] ],,QNL30033,96.875,6.25863E-10 SIF-HHPRED:  SIF-Syn: Homologous genes are either labeled as membrane proteins or hypothetical proteins, positional similarity and all part of the same operon
    /note=Start is supported by staterator and creates a 4 bp overlap, indicating an operon. NCBI blast shows 1:1 alignment with genes in closely related phages. Blast alignments are to hypothetical proteins, but TMHMM and SOSUI identify one transmembrane domain.

CDS complement (45015 - 45299)
  /gene="65"
  /product="gp65"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_65"
    /note=Original Glimmer call @bp 45299 has strength 10.17; Genemark calls start at 45299
    /note=SSC: 45299-45015 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_67 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 2.00895E-60 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.773, -5.466930120988581, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_67 [Microbacterium phage Casend] ],,QNL30034,100.0,2.00895E-60 SIF-HHPRED:  SIF-Syn: All homologs have no known function, but high positional similarity, with most being located in the same operon with the same surrounding genes.
    /note=The selected start creates 4 bp overlap, is supported by staterator, and creates 1:1 alignment to genes in the same pham. NCBI blast yields high alignment to other hypothetical proteins, and HHPred showed no significant hits, so no protein function can be assigned at the moment.

CDS complement (45296 - 45622)
  /gene="66"
  /product="gp66"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_66"
    /note=Original Glimmer call @bp 45622 has strength 10.88; Genemark calls start at 45622
    /note=SSC: 45622-45296 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_68 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 1.16404E-71 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.597, -5.5603199455171834, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_68 [Microbacterium phage Casend] ],,QNL30035,100.0,1.16404E-71 SIF-HHPRED:  SIF-Syn: All homologs have no known function, with a similar gap, surrounded by similar genes.
    /note=The selected start, despite not having the best RBS or LORF, creates best alignments, with multiple 1:1, 100% identity hits and has the most manual annotations. With all NCBI hits to hypothetical proteins and no significant HHPred hits, no function can be assigned to this gene.

CDS complement (45619 - 45765)
  /gene="67"
  /product="gp67"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_67"
    /note=Original Glimmer call @bp 45765 has strength 8.79; Genemark calls start at 45765
    /note=SSC: 45765-45619 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_69 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 4.92954E-25 GAP: 522 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.061, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_69 [Microbacterium phage Casend] ],,QNL30036,100.0,4.92954E-25 SIF-HHPRED: DUF5395 ; Family of unknown function (DUF5395),,,PF17373.5,50.0,77.0 SIF-Syn: NKF - homologs have no known function
    /note=Start 45765 is supported by gene mark and glimmer. This start in starterator is highly conserved, has the most manual annotations and the most calls. There are multiple 1:1 blast results. There is a 129bp gap, which seems fine as this appears to be the end of an operon and the next gene is really large. This contains the best RBS. There exists no evidence to determine a function.

CDS complement (46288 - 48156)
  /gene="68"
  /product="gp68"
  /function="DNA primase/helicase"
  /locus tag="EverythinBagel_68"
    /note=Original Glimmer call @bp 48156 has strength 10.25; Genemark calls start at 48156
    /note=SSC: 48156-46288 CP: yes SCS: both ST: SS BLAST-Start: [DNA primase/helicase [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.294, -6.188708875567495, no F: DNA primase/helicase SIF-BLAST: ,,[DNA primase/helicase [Microbacterium phage Casend] ],,QNL30037,99.8392,0.0 SIF-HHPRED: DNA primase/helicase; helicase, ATPase, hexamer, DNA replication, HYDROLASE, TRANSFERASE-DNA complex; HET: TTP; 3.2A {Enterobacteria phage T7},,,6N7I_C,57.8778,99.9 SIF-Syn: DNA primase/helicase, same pham and position as AluminumJesus_67
    /note=Start 48516 is supported by gene mark and glimmer. This start in starterator is highly conserved, has the most manual annotations and the most calls. There is a 3bp gap, this is the longest open reading frame, and this contains the best RBS. There are many 1:1 blast results with the assigned function of DNA primase/helicase. HHPred also has many significant results with the assigned function DNA primase/helicase and the local gene neighborhood of this gene is very similar to othere genes in this pham.

CDS complement (48160 - 48321)
  /gene="69"
  /product="gp69"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_69"
    /note=Original Glimmer call @bp 48321 has strength 0.27
    /note=SSC: 48321-48160 CP: no SCS: glimmer ST: NA BLAST-Start:  GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.078, -5.5322921015977995, no F: hypothetical protein SIF-BLAST:  SIF-HHPRED: c.47.1.10 (A:) Thiol peroxidase Tpx {Mycobacterium tuberculosis [TaxId: 1773]},,,d1xvqa_,47.1698,56.5 SIF-Syn: NKF - no positional similarity with closely-related phages
    /note=No real evidence for a gene here. Low CP, high e-values, etc.

CDS complement (48335 - 49828)
  /gene="70"
  /product="gp70"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_70"
    /note=Original Glimmer call @bp 49828 has strength 8.64; Genemark calls start at 49828
    /note=SSC: 49828-48335 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_WAYNE3_72 [Microbacterium phage Wayne3]],,NCBI, q1:s33 100.0% 0.0 GAP: 136 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.964, -3.1725816037952645, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_WAYNE3_72 [Microbacterium phage Wayne3]],,WNM75589,93.7618,0.0 SIF-HHPRED: DUF3153 ; Protein of unknown function (DUF3153),,,PF11353.11,4.62777,72.9 SIF-Syn: NKF - no positional similarity with closely-related phages
    /note=Starterator shows 2 possible starts for this pham, with start number 12 (49927) manually annotated 15 times and start number 20 (49828) manually annotated 13 times. Since 49828 was called by both genemark and glimmer, and has many manual annotations, we went with that as the supported start. NCBI blast hits were to hypothetical protein - there is no known function, HHPred yielded high evalue and extremely low probability and percent coverage, phamerator showed no known function, not a membrane protein, good RBS scores, large gap, phamerator reveals no function upstream or downstream of gene, genes of the same pham have no known function

CDS complement (49965 - 50243)
  /gene="71"
  /product="gp71"
  /function="ribbon-helix-helix DNA binding domain"
  /locus tag="EverythinBagel_71"
    /note=Original Glimmer call @bp 50243 has strength 12.88; Genemark calls start at 50243
    /note=SSC: 50243-49965 CP: yes SCS: both ST: SS BLAST-Start: [ribbon-helix-helix DNA binding domain protein [Microbacterium phage Blab]],,NCBI, q1:s1 100.0% 5.05127E-56 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.061, -2.523003374675015, no F: ribbon-helix-helix DNA binding domain SIF-BLAST: ,,[ribbon-helix-helix DNA binding domain protein [Microbacterium phage Blab]],,QXN73995,95.6522,5.05127E-56 SIF-HHPRED: Putative; Helicobacter pylori, repressor, transcriptional regulator, DNA-binding, ribbon-helix-helix, HP0564, JHP0511, UNKNOWN FUNCTION, GENE REGULATION; NMR {Helicobacter pylori},,,2K1O_B,47.8261,97.9 SIF-Syn: Ribbon-helix-helix binding protein, same pham and position as Phabia_71 and Blab_69, upstream and downstream of genes with no known function.
    /note=Starterator, glimmer, and genemark all call the same start, 50243, which has 25 mannual annotations. ideal gap, insufficient evalue, HHPred showed low probability but high coverage, phamerator revealed ribbon-helix-helix binding domain protein

CDS complement (50240 - 50512)
  /gene="72"
  /product="gp72"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_72"
    /note=Original Glimmer call @bp 50410 has strength 14.79; Genemark calls start at 50410
    /note=SSC: 50512-50240 CP: yes SCS: both-cs ST: NA BLAST-Start: [hypothetical protein SEA_BABYDOTZ_70 [Microbacterium phage BabyDotz]],,NCBI, q1:s17 100.0% 1.67011E-55 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.582, -6.816815313181799, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BABYDOTZ_70 [Microbacterium phage BabyDotz]],,WNT45323,83.9623,1.67011E-55 SIF-HHPRED:  SIF-Syn: NKF - homologs have no known functions
    /note=I choose start 50512 changing it from 50410. There is more Blast 1:1 alignments for 50512 compared to 50410, EverythinBagel_72 is placed in the wrong pham, should be placed in pham 194160. The phages that EverythinBagel_72 aligned with all comes from pham 194160, are reversed, and has an overlap. I believe there is no function for EverythinBagel_72 as there is a lack of evidence from HHPred, SIF-BLAST, and SIF-SYN.

CDS complement (50496 - 50675)
  /gene="73"
  /product="gp73"
  /function="membrane protein"
  /locus tag="EverythinBagel_73"
    /note=Original Glimmer call @bp 50675 has strength 8.61; Genemark calls start at 50675
    /note=SSC: 50675-50496 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 1.47566E-32 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.741, -3.2495416658190135, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Casend] ],,QNL30041,100.0,1.47566E-32 SIF-HHPRED:  SIF-Syn: Hyperion_73 and Phabia_73 have the same pham and position as EverythinBagel_74, both have NKF, upstream and downstream of genes with no known function.
    /note=Start 50,675 is the best start for this gene because gl and gm both call this start and starerator supports it. The best ribosome binding site and LORF. I called this gene`s function a membrane protein because TMTHMM hit 2 membrane domain and there is SIF-Blast to other phages similar to EverythinBagel_75 that are membrane protein.
    /note=
    /note=membrane protein, 2 domains found by TMHMM (SOSUI down)

CDS complement (50659 - 51000)
  /gene="74"
  /product="gp74"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_74"
    /note=Original Glimmer call @bp 51000 has strength 12.45; Genemark calls start at 51000
    /note=SSC: 51000-50659 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_75 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 2.11955E-75 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.47, -4.197870532213559, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_75 [Microbacterium phage Casend] ],,QNL30042,100.0,2.11955E-75 SIF-HHPRED:  SIF-Syn: NFK, homologs have no known functions
    /note=The start 51000 is supported by Starterator, genemark, and glimmer, it has 38 mannual annotations. Blast showed 1:1 alignments, 100% coverage, low evalue. Function of this gene is NFK due to HHPred showing low probability and % coverage, e-value is high and insufficient, not a membrane protein, phamerator reveals no function upstream or downstream of gene, genes of the same pham have no known function

CDS complement (50993 - 51307)
  /gene="75"
  /product="gp75"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_75"
    /note=Original Glimmer call @bp 51307 has strength 14.81; Genemark calls start at 51307
    /note=SSC: 51307-50993 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_NAMAGO_77 [Microbacterium phage Namago]],,NCBI, q1:s1 99.0385% 5.20293E-67 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.913, -4.887586077132851, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NAMAGO_77 [Microbacterium phage Namago]],,QQO39478,99.0291,5.20293E-67 SIF-HHPRED:  SIF-Syn: NFK, homologs have no known functions
    /note=Start 51,307 is the start for this gene because it includes all coding potential, both genemark and glimmer call this start and starterator supports this start. This start also has a good gap, loongest open reading frame and the best ribosome binding site. The function of this gene is no known function because the NCBI blast hits are all for hypothetical proteins and the HHPred hits have no significant results.

CDS complement (51300 - 51560)
  /gene="76"
  /product="gp76"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_76"
    /note=Original Glimmer call @bp 51560 has strength 12.92; Genemark calls start at 51560
    /note=SSC: 51560-51300 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_NAMAGO_78 [Microbacterium phage Namago]],,NCBI, q1:s1 100.0% 6.11853E-53 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.906, -3.2925703904164987, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NAMAGO_78 [Microbacterium phage Namago]],,QQO39479,100.0,6.11853E-53 SIF-HHPRED:  SIF-Syn: NFK, homologs have no known functions
    /note=Start 51560 is supported by ideal -4 overlap, called by both gl & gm, good RBS score, 1:1 blast alignments. I called this gene function NFK because not enough information given by SIF-BLAST, HHPRED, SYN to call a function.

CDS complement (51557 - 51811)
  /gene="77"
  /product="gp77"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_77"
    /note=Original Glimmer call @bp 51811 has strength 13.56; Genemark calls start at 51811
    /note=SSC: 51811-51557 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_NAMAGO_80 [Microbacterium phage Namago] ],,NCBI, q1:s1 94.0476% 1.10481E-21 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.139, -4.497860114175419, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NAMAGO_80 [Microbacterium phage Namago] ],,QQO39481,71.4286,1.10481E-21 SIF-HHPRED:  SIF-Syn: There is a similarity with the neighborhood of Sallyk gene 81.
    /note=Both Glimmer and Genemark called it a gene, and the function is unknown, HHPred showed a low probability.

CDS complement (51811 - 52140)
  /gene="78"
  /product="gp78"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_78"
    /note=Original Glimmer call @bp 52140 has strength 12.14; Genemark calls start at 52140
    /note=SSC: 52140-51811 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ZAGIE_82 [Microbacterium phage Zagie]],,NCBI, q1:s1 100.0% 2.65706E-73 GAP: 24 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.061, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ZAGIE_82 [Microbacterium phage Zagie]],,UVG35435,100.0,2.65706E-73 SIF-HHPRED:  SIF-Syn: FrankDeliGuy_80 has the same Pham and position as EverythinBagel_80
    /note=NKF, all 1:1 alignments are with hypothetical proteins, and HHPred produced no significant results. All evidence supports called start and function.

CDS complement (52165 - 52416)
  /gene="79"
  /product="gp79"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_79"
    /note=Original Glimmer call @bp 52416 has strength 9.9; Genemark calls start at 52416
    /note=SSC: 52416-52165 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BLAB_79 [Microbacterium phage Blab]],,NCBI, q1:s1 100.0% 6.51612E-51 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.179, -6.488768851164151, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BLAB_79 [Microbacterium phage Blab]],,QXN74005,98.8095,6.51612E-51 SIF-HHPRED:  SIF-Syn: Blab_79 has the same Pham and position as EverythinBagel_81
    /note=NKF, all 1:1 alignments are with hypothetical proteins, and HHPred produced no significant results. All evidence supports called start and function.

CDS complement (52413 - 52919)
  /gene="80"
  /product="gp80"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_80"
    /note=Original Glimmer call @bp 52919 has strength 12.28; Genemark calls start at 52919
    /note=SSC: 52919-52413 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MASHLEY_83 [Microbacterium phage Mashley]],,NCBI, q1:s1 100.0% 7.14822E-106 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.061, -3.3503726477288405, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MASHLEY_83 [Microbacterium phage Mashley]],,QED11899,95.2381,7.14822E-106 SIF-HHPRED:  SIF-Syn: Mashley_83 has the same Pham and position as EverythinBagel_82
    /note=NKF, all 1:1 alignments are with hypothetical proteins, and HHPred produced no significant results. All evidence supports called start and function.

CDS complement (52922 - 53419)
  /gene="81"
  /product="gp81"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_81"
    /note=Original Glimmer call @bp 53419 has strength 11.0; Genemark calls start at 53419
    /note=SSC: 53419-52922 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BLAB_81 [Microbacterium phage Blab]],,NCBI, q1:s1 100.0% 2.03925E-51 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.151, -4.332504169956899, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BLAB_81 [Microbacterium phage Blab]],,QXN74007,67.6923,2.03925E-51 SIF-HHPRED:  SIF-Syn: FrankDeliGuy_83 has the same Pham and position as EverythinBagel_83
    /note=Start called 100% of time when present and most annotated in pham. Supported by genemark, glimmer, BLAST, and starterator. Doesn`t have LORF but does have a gap of-4 and the best RBS score. No valid HHPred hits and is similar to other NKF proteins in similar phages.

CDS complement (53416 - 53604)
  /gene="82"
  /product="gp82"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_82"
    /note=Original Glimmer call @bp 53604 has strength 9.34; Genemark calls start at 53604
    /note=SSC: 53604-53416 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_CASEND_85 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 7.09396E-38 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.121, -4.744199388040119, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_85 [Microbacterium phage Casend] ],,QNL30052,100.0,7.09396E-38 SIF-HHPRED:  SIF-Syn: Casend_85 has the same Pham and position as EverythinBagel_84
    /note=genemark, starterator, BLAST, and glimmer both call this start, best gap, good RBS. No HHPred results and matches other hypothetical proteins in other phages.

CDS complement (53601 - 53924)
  /gene="83"
  /product="gp83"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_83"
    /note=Original Glimmer call @bp 53924 has strength 12.05; Genemark calls start at 53933
    /note=SSC: 53924-53601 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_86 [Microbacterium phage Casend] ],,NCBI, q1:s1 100.0% 7.69782E-74 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.502, -3.666183879767567, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_86 [Microbacterium phage Casend] ],,QNL30053,100.0,7.69782E-74 SIF-HHPRED:  SIF-Syn: NFK, homologs have no known function
    /note=start position is supported & evidence supports that there`s NKF

CDS complement (53921 - 54241)
  /gene="84"
  /product="gp84"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_84"
    /note=Original Glimmer call @bp 54241 has strength 11.99; Genemark calls start at 54241
    /note=SSC: 54241-53921 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ALUMINUMJESUS_83 [Microbacterium phage AluminumJesus]],,NCBI, q1:s1 100.0% 8.49456E-68 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.153, -2.7806870294376242, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ALUMINUMJESUS_83 [Microbacterium phage AluminumJesus]],,UJD20818,99.0566,8.49456E-68 SIF-HHPRED:  SIF-Syn: NFK, homologs have no known function
    /note=start position is strongly supported & evidence supports that there`s NKF

CDS complement (54250 - 54822)
  /gene="85"
  /product="gp85"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_85"
    /note=Original Glimmer call @bp 54822 has strength 12.06; Genemark calls start at 54822
    /note=SSC: 54822-54250 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PHABIA_87 [Microbacterium phage Phabia] ],,NCBI, q1:s1 100.0% 7.69347E-131 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.47, -3.75071250087134, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PHABIA_87 [Microbacterium phage Phabia] ],,QQO39596,100.0,7.69347E-131 SIF-HHPRED:  SIF-Syn: NFK, homologs have no known function
    /note=start position is strongly supported & evidence supports that there`s NKF

CDS complement (54819 - 55436)
  /gene="86"
  /product="gp86"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_86"
    /note=Original Glimmer call @bp 55436 has strength 14.36; Genemark calls start at 55397
    /note=SSC: 55436-54819 CP: yes SCS: both-gl ST: SS BLAST-Start:  GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.177, -6.3511191392333295, no F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: NFK, homologs have no known funciton
    /note=start position is strongly supported & evidence supports that there`s NKF

CDS complement (55433 - 55681)
  /gene="87"
  /product="gp87"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_87"
    /note=Original Glimmer call @bp 55681 has strength 11.84; Genemark calls start at 55681
    /note=SSC: 55681-55433 CP: yes SCS: both ST: NI BLAST-Start:  GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.636, -5.47994862755136, no F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: NFK, homologs have no known function
    /note=start position is supported & evidence supports that there`s NKF

CDS complement (55681 - 56157)
  /gene="88"
  /product="gp88"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_88"
    /note=Original Glimmer call @bp 56157 has strength 11.48; Genemark calls start at 56157
    /note=SSC: 56157-55681 CP: yes SCS: both ST: SS BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.718, -3.296037457437639, yes F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: NFK, homologs have no known function
    /note=This start is supported by both genemark and glimmer. It has the most manual annotations. It is the LORF, has the best final score, and overlap of -4. Blast, HHPred, Synteny and Membrane lack evidence for a known function.

CDS complement (56154 - 56723)
  /gene="89"
  /product="gp89"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_89"
    /note=Original Glimmer call @bp 56723 has strength 8.97; Genemark calls start at 56723
    /note=SSC: 56723-56154 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TEEHEE_92 [Microbacterium phage Teehee] ],,NCBI, q1:s1 100.0% 5.88399E-130 GAP: 112 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.044, -2.5410833118725082, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TEEHEE_92 [Microbacterium phage Teehee] ],,QWY80475,99.4709,5.88399E-130 SIF-HHPRED:  SIF-Syn: NKF - homologs have no known function
    /note=This start is supported by genemark and glimmer. It is the LORF and has the best final score. It has 1:1 alignments and has the most manual annotations. Blast, HHpred, Synteny and Membrane all do not contain evidence for a function.

CDS complement (56836 - 57009)
  /gene="90"
  /product="gp90"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_90"
    /note=Original Glimmer call @bp 57009 has strength 7.63; Genemark calls start at 57009
    /note=SSC: 57009-56836 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein HOT27_gp091 [Microbacterium phage Hyperion] ],,NCBI, q1:s1 100.0% 1.84609E-33 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.505, -3.738562143838384, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT27_gp091 [Microbacterium phage Hyperion] ],,YP_009801633,100.0,1.84609E-33 SIF-HHPRED:  SIF-Syn: NKF - homologs have no known function
    /note=Start is supported by both genemark and glimmer, has the most most manual annotations, is the LORF, has the best final score, has an overlap of -4, 1:1 alignments. Blast, Synteny, HHPred and Membrane do not have evidence for function.

CDS complement (57006 - 57233)
  /gene="91"
  /product="gp91"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_91"
    /note=Original Glimmer call @bp 57233 has strength 12.04; Genemark calls start at 57233
    /note=SSC: 57233-57006 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASEND_94 [Microbacterium phage Casend]],,NCBI, q1:s1 100.0% 2.72515E-45 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.061, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASEND_94 [Microbacterium phage Casend]],,QNL30061,98.6667,2.72515E-45 SIF-HHPRED:  SIF-Syn: NKF - homologs have no known function
    /note=The start is supported by glimmer and genemark, is the LORF, has the best final score, has 1:1 alignment, has the most Manual annotations. Blast, HHPred, SYN and Mem have no evidence for a function.

CDS complement (57226 - 57390)
  /gene="92"
  /product="gp92"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_92"
    /note=Original Glimmer call @bp 57390 has strength 11.03; Genemark calls start at 57390
    /note=SSC: 57390-57226 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_NIKE_92 [Microbacterium phage Nike] ],,NCBI, q1:s1 100.0% 2.01833E-27 GAP: 50 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.061, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NIKE_92 [Microbacterium phage Nike] ],,QIQ63672,100.0,2.01833E-27 SIF-HHPRED:  SIF-Syn: NKF - homologs have no known function
    /note=Start supported by glimmer and genemark. has the most manual annotations, has the best final score. It has a slightly larger gap and it is not the LORF, but still seems like the best choice. Blast, SYN, HHPred, and Mem say NKF.

CDS complement (57441 - 57764)
  /gene="93"
  /product="gp93"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_93"
    /note=Original Glimmer call @bp 57764 has strength 12.56; Genemark calls start at 57764
    /note=SSC: 57764-57441 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_STRAWBERRYJAMM_101 [Microbacterium phage StrawberryJamm]],,NCBI, q1:s1 96.2617% 3.51357E-67 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.159, -4.455662434380964, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_STRAWBERRYJAMM_101 [Microbacterium phage StrawberryJamm]],,QWY80179,79.5276,3.51357E-67 SIF-HHPRED:  SIF-Syn: NKF - homologs have no known function
    /note=Start supported by glimmer and genemark, Manual annotations, LORF, -4 overlap, best final score. HHPred, Blast, SYN, and Mem all say NKF.

CDS complement (57761 - 57898)
  /gene="94"
  /product="gp94"
  /function="membrane protein"
  /locus tag="EverythinBagel_94"
    /note=Original Glimmer call @bp 57898 has strength 15.03; Genemark calls start at 57898
    /note=SSC: 57898-57761 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage StrawberryJamm] ],,NCBI, q1:s1 100.0% 1.89533E-16 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.122, -4.532304881730868, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage StrawberryJamm] ],,QWY80180,95.5556,1.89533E-16 SIF-HHPRED:  SIF-Syn: Gene is located in the same operon surrounded by the same genes, most phages call this gene a membrane protein, and some have NKF.
    /note=The start is supported by all resources. The genes align with many hypothetical proteins and membrane proteins. Additionally, it has 2 membrane regions, so I called this gene a membrane protein. DeepTMHMM predicts 2 membrane regions, while SOSUI predicts 1 region. HHpred had no reliable results.

CDS complement (57895 - 58326)
  /gene="95"
  /product="gp95"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_95"
    /note=Original Glimmer call @bp 58326 has strength 9.64; Genemark calls start at 58326
    /note=SSC: 58326-57895 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Microbacterium phage Judebell]],,NCBI, q1:s1 100.0% 1.10966E-98 GAP: 33 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.499, -4.43822993146257, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Microbacterium phage Judebell]],,XCG97310,100.0,1.10966E-98 SIF-HHPRED:  SIF-Syn: NKF; homologs have no known functions
    /note=The start is supported by all resources. The genes align with many hypothetical proteins, all homologs also have NKF, and it has no membrane regions - NKF.

CDS complement (58360 - 58641)
  /gene="96"
  /product="gp96"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_96"
    /note=Original Glimmer call @bp 58641 has strength 13.31; Genemark calls start at 58641
    /note=SSC: 58641-58360 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Microbacterium phage Judebell]],,NCBI, q1:s1 100.0% 2.73188E-62 GAP: 37 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.741, -3.1085431521568267, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Microbacterium phage Judebell]],,XCG97311,100.0,2.73188E-62 SIF-HHPRED:  SIF-Syn: NKF, all homologs are hypothetical proteins, located in same gene neighborhood
    /note=The start is called by Genemark and glimmer, is supported by Starterator, aligns with Judebell, has the best RBS, and has a fine gap. The gene did not align with any functional genes and doesn`t have any membrane regions - NKF.

CDS complement (58679 - 59029)
  /gene="97"
  /product="gp97"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_97"
    /note=Original Glimmer call @bp 59029 has strength 14.23; Genemark calls start at 59029
    /note=SSC: 59029-58679 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT29_gp102 [Microbacterium phage Squash] ],,NCBI, q1:s1 100.0% 5.53696E-79 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.49, -3.6907860541164537, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT29_gp102 [Microbacterium phage Squash] ],,YP_009801841,100.0,5.53696E-79 SIF-HHPRED:  SIF-Syn: NKF, all homologs in the same gene neighborhood have no known function
    /note=The start was called by Genemark and Gimmber, supported by Starterator, and has the best RBS, the LORF, and a -4 gap. All alignments had no known function and no membrane regions - NKF.

CDS complement (59026 - 59490)
  /gene="98"
  /product="gp98"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_98"
    /note=Original Glimmer call @bp 59490 has strength 10.28; Genemark calls start at 59490
    /note=SSC: 59490-59026 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Microbacterium phage Judebell]],,NCBI, q1:s1 100.0% 1.72138E-106 GAP: 44 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.741, -3.1085431521568267, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Microbacterium phage Judebell]],,XCG97313,100.0,1.72138E-106 SIF-HHPRED:  SIF-Syn: NKF, all homologs in same gene neighborhood have no know function
    /note=The start was called by Genemark and glimmer, has CP, was supported by Starterator, has LORF, and best RBS. The gene is aligned with hypothetical proteins and has no membrane regions - NKF.

CDS complement (59535 - 59624)
  /gene="99"
  /product="gp99"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_99"
    /note=Genemark calls start at 59624
    /note=SSC: 59624-59535 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein [Microbacterium phage Judebell]],,NCBI, q1:s1 100.0% 6.29273E-11 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.361, -4.996601827017273, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Microbacterium phage Judebell]],,XCG97314,100.0,6.29273E-11 SIF-HHPRED:  SIF-Syn: NKF - same pham as Judebell_101 and Phabia_102, homologs have no known function.
    /note=All data points favorably to the slected start. No significant hits therefore NKF

CDS complement (59624 - 59770)
  /gene="100"
  /product="gp100"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_100"
    /note=Original Glimmer call @bp 59770 has strength 9.72; Genemark calls start at 59770
    /note=SSC: 59770-59624 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RUDY_102 [Microbacterium phage Rudy] ],,NCBI, q1:s1 100.0% 9.07448E-26 GAP: 21 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.741, -3.635743271219807, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RUDY_102 [Microbacterium phage Rudy] ],,QQO39284,100.0,9.07448E-26 SIF-HHPRED:  SIF-Syn: NKF - same pham as Namago_105, homologs have no known function.
    /note=All data points favorably to the selected start. No significant hits therefore NKF

CDS complement (59792 - 59905)
  /gene="101"
  /product="gp101"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_101"
    /note=Original Glimmer call @bp 59905 has strength 3.75
    /note=SSC: 59905-59792 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein SEA_NAMAGO_105 [Microbacterium phage Namago]],,NCBI, q1:s1 100.0% 6.65187E-18 GAP: 36 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.643, -3.3910054376556182, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NAMAGO_105 [Microbacterium phage Namago]],,QQO39506,100.0,6.65187E-18 SIF-HHPRED:  SIF-Syn: NKF - same pham as Namago_105, homologs have no known function.
    /note=All data points favorably to the selected start. No significant hits therefore NKF

CDS complement (59942 - 60253)
  /gene="102"
  /product="gp102"
  /function="membrane protein"
  /locus tag="EverythinBagel_102"
    /note=Original Glimmer call @bp 60253 has strength 7.1; Genemark calls start at 60253
    /note=SSC: 60253-59942 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage StrawberryJamm] ],,NCBI, q1:s1 100.0% 6.03387E-66 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.908, -4.897971560974249, no F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage StrawberryJamm] ],,QWY80188,99.0291,6.03387E-66 SIF-HHPRED:  SIF-Syn: NKF - same pham as Jehoshaphat_105, StrawberryJamm_111, Teehee_104, homologs have no known function.
    /note=All data points favorably to the slected start. Sif-SYN domain found therefore membrane protein

CDS complement (60250 - 60465)
  /gene="103"
  /product="gp103"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_103"
    /note=Original Glimmer call @bp 60465 has strength 5.3; Genemark calls start at 60465
    /note=SSC: 60465-60250 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_STRAWBERRYJAMM_112 [Microbacterium phage StrawberryJamm] ],,NCBI, q1:s1 100.0% 4.39675E-38 GAP: 185 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.753, -5.238109312333945, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_STRAWBERRYJAMM_112 [Microbacterium phage StrawberryJamm] ],,QWY80189,98.5916,4.39675E-38 SIF-HHPRED:  SIF-Syn: NKF - same pham as Jehoshaphat_106, StrawberryJamm_112, Teehee_105, homologs have no known function.
    /note=All data points favorably to the slected start. No significant hits therefore NKF

CDS complement (60651 - 61346)
  /gene="104"
  /product="gp104"
  /function="hypothetical protein"
  /locus tag="EverythinBagel_104"
    /note=Original Glimmer call @bp 61346 has strength 9.56; Genemark calls start at 61346
    /note=SSC: 61346-60651 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_MASHLEY_104 [Microbacterium phage Mashley]],,NCBI, q1:s1 100.0% 9.50974E-157 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.891, -5.699697059098805, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MASHLEY_104 [Microbacterium phage Mashley]],,QED11920,99.5671,9.50974E-157 SIF-HHPRED:  SIF-Syn: NKF - same pham as Mashley_104, Gazebo_106, homologs have no known function.
    /note=All data points favorably to the slected start. No significant hits therefore NKF