CDS 110 - 667
  /gene="1"
  /product="gp1"
  /function="terminase, small subunit"
  /locus tag="CoffeeBean_1"
    /note=Original Glimmer call @bp 161 has strength 10.97; Genemark calls start at 110
    /note=SSC: 110-667 CP: yes SCS: both-gm ST: NA BLAST-Start: [terminase small subunit [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.83071E-134 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.999, -2.6013996449736907, yes F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Rhodococcus phage Braxoaddie] ],,WIC89623,100.0,1.83071E-134 SIF-HHPRED: Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97},,,6Z6E_C,51.3514,96.7 SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Changed start to fit all cp. This start has better rbs scores and is the most annotated start on starterator.
    /note=Very clear function call on terminase small subunit, NCBI has the best hits but phagesdb and hhpred also show this gene to likely be a terminase small subunit.

CDS 1307 - 2302
  /gene="2"
  /product="gp2"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_2"
    /note=Original Glimmer call @bp 1472 has strength 12.1; Genemark calls start at 1307
    /note=SSC: 1307-2302 CP: yes SCS: both-gm ST: NA BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_2 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 98.4894% 0.0 GAP: 639 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.43, -5.857463951082417, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_2 [Rhodococcus phage Braxoaddie]],,WIC89624,94.5122,0.0 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Changed start. This start now has all cp but has worse rbs scores, and is the most annotated start on starterator.
    /note=No clear hits for function.

CDS 2305 - 2550
  /gene="3"
  /product="gp3"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_3"
    /note=Original Glimmer call @bp 2296 has strength 13.23; Genemark calls start at 2305
    /note=SSC: 2305-2550 CP: yes SCS: both-gm ST: NA BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_3 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 3.77831E-45 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.057, -5.383507109175471, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_3 [Rhodococcus phage Braxoaddie] ],,WIC89625,96.2963,3.77831E-45 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Changed start to avoid massive overlap and better rbs scores. Could possibly call the start before due to the common use of -4 overlaps, but starterator declares our selected start as the most annotated.
    /note=*not all cp is covered, but including more creates overlap. Possibly combine genes? but ruins synteny.
    /note=No clear function, very unlikely call as major capsid hexamer protein.

CDS 2679 - 3497
  /gene="4"
  /product="gp4"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_4"
    /note=Original Glimmer call @bp 2679 has strength 14.61; Genemark calls start at 2679
    /note=SSC: 2679-3497 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_4 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s42 100.0% 0.0 GAP: 128 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.999, -3.1285997640366707, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_4 [Rhodococcus phage Braxoaddie]],,WIC89626,86.262,0.0 SIF-HHPRED: DUF2786 ; Protein of unknown function (DUF2786),,,PF10979.12,14.7059,99.1 SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Kept start. Covers all cp and best rbs scores. Recommended by starterator.
    /note=No clear function call on any database.

CDS 3497 - 3757
  /gene="5"
  /product="gp5"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_5"
    /note=Original Glimmer call @bp 3509 has strength 8.62; Genemark calls start at 3497
    /note=SSC: 3497-3757 CP: yes SCS: both-gm ST: NI BLAST-Start:  GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.054, -4.702334767722353, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: Anomaly in synteny with this gene. Seems to have swapped places with the next gene unlike all other phages in this cluster.
    /note=Changed start for better rbs scores and -1 overlap with ATG start codon. Covers all cp. Could also use start before for slightly better final score.
    /note=No clear function call.

CDS 3759 - 3980
  /gene="6"
  /product="gp6"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_6"
    /note=Original Glimmer call @bp 3774 has strength 15.24; Genemark calls start at 3759
    /note=SSC: 3759-3980 CP: yes SCS: both-gm ST: NA BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_6 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 3.60626E-38 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.943, -2.797947301765889, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_6 [Rhodococcus phage Braxoaddie] ],,WIC89628,93.1507,3.60626E-38 SIF-HHPRED:  SIF-Syn: When compared to other phages in the cluster, this gene seems to have flip-flopped with the previous gene and the gene afterwards is missing.
    /note=Changed start to the earliest possible for better rbs scores and suggestion by starterator. Both the original and new start cover all cp.
    /note=No clear function call.

CDS 3977 - 4231
  /gene="7"
  /product="gp7"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_7"
    /note=Original Glimmer call @bp 3977 has strength 8.96; Genemark calls start at 3977
    /note=SSC: 3977-4231 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_7 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 3.48392E-50 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.27, -4.2553936699841195, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_7 [Rhodococcus phage Braxoaddie] ],,WIC89629,100.0,3.48392E-50 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Kept start. Best rbs scores, covers all cp, approved by starterator.
    /note=No clear function call.

CDS 4336 - 5154
  /gene="8"
  /product="gp8"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_8"
    /note=Original Glimmer call @bp 4336 has strength 20.15; Genemark calls start at 4336
    /note=SSC: 4336-5154 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_8 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 99.2647% 8.96324E-167 GAP: 104 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.999, -2.6013996449736907, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_8 [Rhodococcus phage Braxoaddie]],,WIC89630,91.0072,8.96324E-167 SIF-HHPRED: DUF6378 ; Domain of unknown function (DUF6378),,,PF19905.3,31.6176,99.9 SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Kept start. Covers all cp and best rbs scores. *has most annotated start but we chose not to switch to it because this start has better RBS scores and Braxoaddie calls this selected start.
    /note=No clear function call.

CDS 5151 - 5390
  /gene="9"
  /product="gp9"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_9"
    /note=Original Glimmer call @bp 5151 has strength 13.63; Genemark calls start at 5151
    /note=SSC: 5151-5390 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_9 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 2.13518E-44 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.201, -5.085091778133397, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_9 [Rhodococcus phage Braxoaddie] ],,WIC89631,98.7342,2.13518E-44 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Catches majority of (if not full) coding potential, start is called 5/6 of the time (including on CoffeeBean).
    /note=
    /note=Related phages` BLAST results suggest a hypothetical protein. Phagesdb Function Frequency suggests a tape measure protein, but no substantial evidence/needs more research

CDS 5387 - 5626
  /gene="10"
  /product="gp10"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_10"
    /note=Original Glimmer call @bp 5387 has strength 9.87; Genemark calls start at 5390
    /note=SSC: 5387-5626 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_MASELOP_10 [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 1.0568E-50 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.998, -4.679270584912496, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MASELOP_10 [Rhodococcus phage Maselop]],,WNM64933,98.7342,1.0568E-50 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Some coding potential is not captured but there is no other start that we can move it to. 
    /note=e values in HHPred pretty high so should not use as evidence 
    /note=e values in NCBI really low which is good and calls for hypothetical protein
    /note=does not have most annotated start and is called 95.2% of time when present

CDS 5634 - 6071
  /gene="11"
  /product="gp11"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_11"
    /note=Original Glimmer call @bp 5634 has strength 15.17; Genemark calls start at 5634
    /note=SSC: 5634-6071 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 1.4556E-96 GAP: 7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.678, -4.368212896966963, yes F: Hypothetical Protein SIF-BLAST: ,,[membrane protein [Rhodococcus phage Maselop]],,WNM64934,100.0,1.4556E-96 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Kept suggested start--not the longest ORF, but captures all coding potential. Most annotated start, found 6/6 (100%) of the time.
    /note=
    /note=Currently a hypothetical protein--evidence from related phages in NCBI and PhagesDB BLAST suggest the function may be a membrane protein, but more research needed.

CDS 6068 - 6439
  /gene="12"
  /product="gp12"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_12"
    /note=Original Glimmer call @bp 6068 has strength 16.44; Genemark calls start at 6068
    /note=SSC: 6068-6439 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MASELOP_12 [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 1.01572E-81 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.639, -3.4892599424135016, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MASELOP_12 [Rhodococcus phage Maselop]],,WNM64935,100.0,1.01572E-81 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=not longest ORF but will cover all CP
    /note=most annotated start 
    /note=found 7/7 and called 100% of time

CDS 6432 - 6638
  /gene="13"
  /product="gp13"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_13"
    /note=Original Glimmer call @bp 6432 has strength 14.19; Genemark calls start at 6432
    /note=SSC: 6432-6638 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_13 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.20784E-39 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.155, -2.338663114094478, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_13 [Rhodococcus phage Braxoaddie] ],,WIC89635,100.0,1.20784E-39 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Start chosen because it captures all coding potential (and has better z and final scores)
    /note=
    /note=Evidence from NCBI and PhagesDB BLAST indicate that this gene is most likely a hypothetical protein.

CDS 6650 - 7438
  /gene="14"
  /product="gp14"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_14"
    /note=Original Glimmer call @bp 6650 has strength 12.77; Genemark calls start at 6650
    /note=SSC: 6650-7438 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MASELOP_14 [Rhodococcus phage Maselop]],,NCBI, q1:s6 100.0% 0.0 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.562, -5.114865311845495, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MASELOP_14 [Rhodococcus phage Maselop]],,WNM64937,97.7528,0.0 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Good coding potential but not longest ORF, start should not change bc other has a gap of -4.
    /note=NCBI e value points to hypothetical protein
    /note=Has most annotated start but only called 20% of time

CDS 7506 - 7865
  /gene="15"
  /product="gp15"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_15"
    /note=Original Glimmer call @bp 7506 has strength 17.18; Genemark calls start at 7506
    /note=SSC: 7506-7865 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MASELOP_15 [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 7.70755E-82 GAP: 67 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.155, -2.338663114094478, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MASELOP_15 [Rhodococcus phage Maselop]],,WNM64938,100.0,7.70755E-82 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=good coding potential, longest ORF 
    /note=e values are similar to other genes in NCBI blast

CDS 7870 - 8142
  /gene="16"
  /product="gp16"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_16"
    /note=Original Glimmer call @bp 7870 has strength 14.86; Genemark calls start at 7870
    /note=SSC: 7870-8142 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_16 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 2.12978E-57 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.516, -3.743510309005245, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_16 [Rhodococcus phage Braxoaddie] ],,WIC89638,100.0,2.12978E-57 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Best start: longest ORF, encapsulates all coding potential.
    /note=
    /note=Evidence from PhagesDB BLAST and NCBI BLAST points to this gene being a hypothetical protein.

CDS 8139 - 8681
  /gene="17"
  /product="gp17"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_17"
    /note=Original Glimmer call @bp 8139 has strength 15.73; Genemark calls start at 8139
    /note=SSC: 8139-8681 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MASELOP_17 [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 7.61821E-128 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.999, -2.6814417326944517, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MASELOP_17 [Rhodococcus phage Maselop]],,WNM64940,100.0,7.61821E-128 SIF-HHPRED:  SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=good z and final score, captures all coding potential, longest ORF

CDS 8823 - 9716
  /gene="18"
  /product="gp18"
  /function="ThyX-like thymidylate synthase"
  /locus tag="CoffeeBean_18"
    /note=Original Glimmer call @bp 8823 has strength 14.2; Genemark calls start at 8823
    /note=SSC: 8823-9716 CP: no SCS: both ST: SS BLAST-Start: [ThyX-like thymidylate synthase [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 0.0 GAP: 141 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.075, -2.970161406017234, yes F: ThyX-like thymidylate synthase SIF-BLAST: ,,[ThyX-like thymidylate synthase [Rhodococcus phage Maselop]],,WNM64941,100.0,0.0 SIF-HHPRED: Thymidylate synthase thyX; ThyX, thymidylate synthase, FAD, Flavoprotein, Methyltransferase, Nucleotide biosynthesis, Transferase; HET: FAD; 2.3A {Corynebacterium glutamicum},,,3FNN_A,97.9798,100.0 SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Start chosen because it`s the longest ORF and captures the most coding potential out of any proposed start.
    /note=
    /note=Relatives in the CR cluster have similar functions, and excellent e-values on multiple databases and fellow phages formed substantial evidence for this gene to be a thymidylate synthase.

CDS 9716 - 9913
  /gene="19"
  /product="gp19"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_19"
    /note=Original Glimmer call @bp 9716 has strength 8.53; Genemark calls start at 9716
    /note=SSC: 9716-9913 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_19 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 4.89227E-38 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.442, -3.8360440759163943, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_19 [Rhodococcus phage Braxoaddie] ],,WIC89641,100.0,4.89227E-38 SIF-HHPRED: Amphi-Trp ; Amphi-Trp domain,,,PF20068.3,73.8462,82.1 SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=No evidence of function from HHPred or any other sources. Start at 9716 is supported by GeneMark as well as z and full scores.

CDS 9913 - 10809
  /gene="20"
  /product="gp20"
  /function="lysin B"
  /locus tag="CoffeeBean_20"
    /note=Original Glimmer call @bp 9913 has strength 10.66; Genemark calls start at 9913
    /note=SSC: 9913-10809 CP: yes SCS: both ST: SS BLAST-Start: [lysin B [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.054, -4.702334767722353, no F: lysin B SIF-BLAST: ,,[lysin B [Rhodococcus phage Braxoaddie]],,WIC89642,100.0,0.0 SIF-HHPRED: Gene 12 protein; alpha/beta sandwich, CELL ADHESION; 2.0A {Mycobacterium phage D29},,,3HC7_A,97.3154,99.9 SIF-Syn: Very clear synteny almost perfectly with all phages in the CR cluster except MacGully
    /note=Phagesdb Blast: good e values for phages in the CR cluster which have the function of lysin b
    /note=HHPRED: high probability, coverage and good e value suggesting other than lysin b
    /note=NCBI Blast: high probability and coverage also very good e value for lysin b
    /note=Conserved domain database: low proabability and coverage, also high e value
    /note=Phagesdb Blast and NCBI Blast suggest that function is lysin b

CDS 10806 - 11321
  /gene="21"
  /product="gp21"
  /function="MazG-like nucleotide pyrophosphohydrolase"
  /locus tag="CoffeeBean_21"
    /note=Original Glimmer call @bp 10806 has strength 15.83; Genemark calls start at 10806
    /note=SSC: 10806-11321 CP: yes SCS: both ST: SS BLAST-Start: [MazG-like nucleotide pyrophosphohydrolase [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 6.52821E-120 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.92, -3.1164791313608173, yes F: MazG-like nucleotide pyrophosphohydrolase SIF-BLAST: ,,[MazG-like nucleotide pyrophosphohydrolase [Rhodococcus phage Maselop]],,WNM64944,100.0,6.52821E-120 SIF-HHPRED: Nucleotide pyrophosphohydrolase; MazG, nucleoside triphosphate pyrophosphohydrolase, HYDROLASE; 2.8A {Bacillus cereus} SCOP: a.204.1.2,,,5IE9_B,78.3626,99.2 SIF-Syn: between same two genes and similar poistion in CR cluster phages except MacGully
    /note=Phagesdb Blast: good e value for phages in CR cluster, suggesting MazG-like nucleotide pyrophosphohydrolase
    /note=HHPRED: calls for Nucleotide pyrophosphohydrolase and couple others pretty good e value, probability and coverage
    /note=NCBI Blast: calls for MazG-like nucleotide pyrophosphohydrolase multiple times with very good percent identity, coverage and very low e value
    /note=conserved domain database: bad percent identity and coverage
    /note=base on Phagesdb Blast and NCBI blast function is MazG-like nucleotide pyrophosphohydrolase

CDS 11318 - 11839
  /gene="22"
  /product="gp22"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_22"
    /note=Original Glimmer call @bp 11318 has strength 16.52; Genemark calls start at 11318
    /note=SSC: 11318-11839 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_MASELOP_22 [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 1.79429E-123 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.406, -3.8932062518944837, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MASELOP_22 [Rhodococcus phage Maselop]],,WNM64945,100.0,1.79429E-123 SIF-HHPRED: Conserved hypothetical protein; PUTATIVE THIOESTERASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, HYDROLASE; HET: COA, MSE; 1.91A {Sulfolobus solfataricus} SCOP: d.38.1.1,,,2GF6_A,17.9191,62.5 SIF-Syn: in between same two genes and in similar position in Apiary, Braxoaddie, Maselop and Polyyuki
    /note=Phagesdb Blast: very good e value for CR cluster phages
    /note=HHPRED: low proabbility, coverge and bad e value for called functions
    /note=NCBI Blast: high probability, coverage and very good e value for hypothetical protein called

CDS 11897 - 12580
  /gene="23"
  /product="gp23"
  /function="minor tail protein"
  /locus tag="CoffeeBean_23"
    /note=Original Glimmer call @bp 11897 has strength 11.0; Genemark calls start at 11897
    /note=SSC: 11897-12580 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.31366E-159 GAP: 57 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.819, -3.3252317253000454, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Rhodococcus phage Braxoaddie] ],,WIC89645,100.0,1.31366E-159 SIF-HHPRED: Hyaluronoglucosaminidase; HylP, Lyase, Hyaluronidase, S. pyogenes phage H4489A, Beta-elimination, unsaturated Hyaluronan Octa-saccharides; HET: NAG, GCD, BDP; 3.581A {Streptococcus pyogenes phage H4489A},,,6X3M_E,40.5286,97.2 SIF-Syn: in between same two genes and in similar position in Apiary, Braxoaddie, Maselop, and Polyyuki
    /note=Phagesdb Blast: very good e values for CR cluster phages, suggesting function of minor tail protein
    /note=HHPRED: functions called have high probability but low coverage and high e value
    /note=NCBI Blast: minor tail protein called with high % identity, coverage and very good e values

CDS 12577 - 13254
  /gene="24"
  /product="gp24"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_24"
    /note=Original Glimmer call @bp 12577 has strength 8.09; Genemark calls start at 12577
    /note=SSC: 12577-13254 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_24 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.2195E-148 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.289, -8.367568395056292, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_24 [Rhodococcus phage Braxoaddie] ],,WIC89646,100.0,1.2195E-148 SIF-HHPRED: unc_rv_SF1_Hel-like; uncharacterized domain which connects the Cys/His rich zinc-binding domain (ZBD) and linker to the first helicase domain of ronidovirus SF1 helicase and related proteins.,,,cd21414,7.11111,8.8 SIF-Syn: in between same two genes and similar position in Apiary, Braxoaddie, Maselop, and Polyyuki
    /note=Phagesdb Blast: very good e value for phages in CR cluster, which functions are unknown 
    /note=HHPRED: low probability, coverage and high e value for called function
    /note=NCBI Blast: high probability, coverage and very good e value for called functions of hypothetical protein

CDS 13263 - 13436
  /gene="25"
  /product="gp25"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_25"
    /note=Original Glimmer call @bp 13263 has strength 13.8; Genemark calls start at 13263
    /note=SSC: 13263-13436 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_25 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 3.24432E-29 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.92, -3.8154491356968365, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_25 [Rhodococcus phage Braxoaddie] ],,WIC89647,100.0,3.24432E-29 SIF-HHPRED: E3 ubiquitin-protein ligase TRIM69; coiled-coil domain, oligomerization, Ligase; HET: LMT; 2.152A {Homo sapiens},,,4NQJ_C,31.5789,44.9 SIF-Syn: Surrounding genes match very well with almost all other members of cluster CR.
    /note=Does not have the most annotated start. Start called is called 100% of the time it is found. 
    /note=For function, this gene matches up very well with most of the CR cluster, which calls this as an unknown function. 
    /note=HHPRED called no usable functions, all e-values were much too high. 
    /note=NCBI blast suggests hypothetical protein, similar to several Rhodococcus and Gordonia phages.

CDS 13433 - 13540
  /gene="26"
  /product="gp26"
  /function="membrane protein"
  /locus tag="CoffeeBean_26"
    /note=Genemark calls start at 13433
    /note=SSC: 13433-13540 CP: no SCS: genemark ST: SS BLAST-Start: [membrane protein [Rhodococcus phage Maselop] ],,NCBI, q1:s1 100.0% 2.82809E-15 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.583, -3.5445441946970573, no F: membrane protein SIF-BLAST: ,,[membrane protein [Rhodococcus phage Maselop] ],,WNM64949,100.0,2.82809E-15 SIF-HHPRED: Archaellin; Archaellum, archaellin, Methanocaldococcus villosus, cryoEM, helical reconstruction, PROTEIN FIBRIL; HET: CA, UNL; 3.08A {Methanocaldococcus villosus},,,7OFQ_j,57.1429,82.8 SIF-Syn: Matches with almost all other members of cluster CR.
    /note=Called start is the most annotated, called 100% when present (5/6 in pham). 
    /note=Not the longest possible start, and does not cover all CP, but lengthening would cause major overlap with gene 25. Note, Glimmer did not call this gene at all...
    /note=Also, best z-scores at called start. 
    /note=Function call was Hypothetical protein in all other CR cluster genes here, see Phages DB blast. 
    /note=HHPRED had no good calls, all e-values were bad. 
    /note=NCBI blast calls membrane protein from two Rhodococcus phages with good e-values/coverages, etc. 
    /note=Deep TMHMM found one TMP

CDS 13537 - 13968
  /gene="27"
  /product="gp27"
  /function="HNH endonuclease"
  /locus tag="CoffeeBean_27"
    /note=Original Glimmer call @bp 13537 has strength 5.18; Genemark calls start at 13537
    /note=SSC: 13537-13968 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 4.94517E-100 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.948, -4.783075076578067, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Rhodococcus phage Braxoaddie] ],,WIC89649,100.0,4.94517E-100 SIF-HHPRED: HNH endonuclease; Thermophilic bacteriophage, HNH Endonuclease, DNA nicking, HYDROLASE; 1.52A {Geobacillus virus E2},,,5H0M_A,79.7203,99.2 SIF-Syn: Matches with almost all other members of cluster CR.
    /note=Does not have the most annotated start. Called start is found in 8% of the pham and called 100% of the time it is found. 
    /note=Relatively good z-score, in the top 3, but better scores cut out some CP. 
    /note=Corresponding genes in other CR cluster are all called HNH endonuclease 
    /note=Phages DB blast shows more connection with CR cluster, all call HNH endonuclease. 
    /note=HHPRED: the only good call was from HNH endonuclease Thermophilic bacteriophage found in Geobacillus virus 
    /note=NCBI Blast had strong scores for HNH endonuclease from Rhodococcus phages. 
    /note=Deep TMHMM found no hits
    /note=In approved functions list, only stipulation is it must occur of 30+ aa sequences, which this does.

CDS 13981 - 15654
  /gene="28"
  /product="gp28"
  /function="terminase, large subunit"
  /locus tag="CoffeeBean_28"
    /note=Original Glimmer call @bp 13981 has strength 15.1; Genemark calls start at 13981
    /note=SSC: 13981-15654 CP: yes SCS: both ST: SS BLAST-Start: [terminase large subunit [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 0.0 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.168, -4.6767843745817785, no F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Rhodococcus phage Maselop]],,WNM64951,100.0,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,95.1526,100.0 SIF-Syn: in between same two genes and in similar poition in CR cluster phages
    /note=Phagesdb Blast: good e values for CR cluster pahges, having terminase large subunit function
    /note=HHPRED: couple good function calls but terminase large subunit has best % identity, coverage and e value
    /note=NCBI Blast: has good % identity, coverage and very good e value for called function, terminase large subunit
    /note=conserved domain database: low identity, coverage, but good e value for called function

CDS 15809 - 17398
  /gene="29"
  /product="gp29"
  /function="portal protein"
  /locus tag="CoffeeBean_29"
    /note=Original Glimmer call @bp 15809 has strength 18.67; Genemark calls start at 15809
    /note=SSC: 15809-17398 CP: yes SCS: both ST: NI BLAST-Start: [portal protein [Rhodococcus phage Maselop] ],,NCBI, q1:s1 100.0% 0.0 GAP: 154 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.203, -4.314571574115886, no F: portal protein SIF-BLAST: ,,[portal protein [Rhodococcus phage Maselop] ],,WNM64952,100.0,0.0 SIF-HHPRED: Portal protein; Bacteriophage, SPP1, Portal Protein, Head completion proteins, Connector Complex, DNA Channel, VIRAL PROTEIN; 2.7A {Bacillus subtilis},,,7Z4W_B,85.4442,100.0 SIF-Syn: All phages in CR have the same gene
A lot of synteny with other subclusters too
    /note=Start not changed because coding potential better for current start
    /note=Phagesdb blast, NCBI blast, and HHPRED all suggest portal protein
    /note=Conserved domain also suggests poral protein
    /note=Deep TMHMM N/A

CDS 17395 - 18783
  /gene="30"
  /product="gp30"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_30"
    /note=Original Glimmer call @bp 17395 has strength 8.3; Genemark calls start at 17395
    /note=SSC: 17395-18783 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_MASELOP_30 [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.113, -5.091691163989289, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MASELOP_30 [Rhodococcus phage Maselop]],,WNM64953,99.7835,0.0 SIF-HHPRED: Phage_Mu_F ; Phage Mu protein F like protein,,,PF04233.18,16.8831,97.7 SIF-Syn: Matches function for two phages in cluster CR4 (WhoseManz and Marietta)
    /note=NCBI shows hypothetical protein but HHPRED gives good evidence for MuF-like minor capsid protein
    /note=Function is hypothetical protein, because according to the official function list, MuF-like minor capsid protein should not be used as a function
    /note=Good coding potential, scores, and calls most annotated start on starterator, so start was not changed

CDS 18795 - 19478
  /gene="31"
  /product="gp31"
  /function="scaffolding protein"
  /locus tag="CoffeeBean_31"
    /note=Original Glimmer call @bp 18795 has strength 13.63; Genemark calls start at 18795
    /note=SSC: 18795-19478 CP: yes SCS: both ST: NI BLAST-Start: [scaffolding protein [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 1.11745E-157 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.165, -4.41254625767766, yes F: scaffolding protein SIF-BLAST: ,,[scaffolding protein [Rhodococcus phage Maselop]],,WNM64954,100.0,1.11745E-157 SIF-HHPRED: Scaffold protein; major capsid protein, HK97-like fold, scaffolding protein, procapsid, VIRUS; 3.72A {Staphylococcus phage 80alpha},,,6B0X_b,76.2115,96.2 SIF-Syn: Gene 31 is the same for all the phages in the CR cluster
    /note=Start was not changed becuase selected start has coding potential and other longer ORFs have gaps that are too large
    /note=Phagesdb blast, NCBI blast, and HHPRED all suggest scaffolding protein
    /note=Deep TMHMM and Conserved Domain N/A

CDS 19516 - 19920
  /gene="32"
  /product="gp32"
  /function="capsid decoration protein"
  /locus tag="CoffeeBean_32"
    /note=Original Glimmer call @bp 19516 has strength 12.4; Genemark calls start at 19516
    /note=SSC: 19516-19920 CP: yes SCS: both ST: SS BLAST-Start: [capsid decoration protein [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 2.50106E-93 GAP: 37 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.008, -2.9334385989924945, yes F: capsid decoration protein SIF-BLAST: ,,[capsid decoration protein [Rhodococcus phage Maselop]],,WNM64955,100.0,2.50106E-93 SIF-HHPRED: HDPD ; Bacteriophage lambda head decoration protein D,,,PF02924.18,75.3731,99.4 SIF-Syn: All phages in the CR cluster have this gene
Good synteny with subcluster CR2 and many others
    /note=Phagesdb blast, NCBI blast, and HHPRED all suggest capsid decoration protein
    /note=Also evidence for lamb-like decoration protein, but stronger evidence for capsid decoration protein
    /note=Conserved Domain suggests lambda head decoration protein but with a lower identity
    /note=Start not changed because selected start contains best coding potential, longest ORF, and best gap
    /note=Deep TMHMM N/A

CDS 19964 - 21016
  /gene="33"
  /product="gp33"
  /function="major capsid protein"
  /locus tag="CoffeeBean_33"
    /note=Original Glimmer call @bp 19964 has strength 18.12; Genemark calls start at 19964
    /note=SSC: 19964-21016 CP: yes SCS: both ST: SS BLAST-Start: [major capsid protein [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: 43 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.234, -2.1123791669543204, yes F: major capsid protein SIF-BLAST: ,,[major capsid protein [Rhodococcus phage Braxoaddie] ],,WIC89655,100.0,0.0 SIF-HHPRED: Major head protein; Virus, Virion, Capsid, Major Capsid Protein, Decoration Protein, Icosahedral Virus, Caudovirus, Thermophilic, Bacteriophage; 2.8A {Thermus virus P74-26},,,6O3H_E,97.4286,100.0 SIF-Syn: All phages in CR cluster have the same gene
Also good synteny with subcluster CR2, S, CY1, and others
    /note=Phagesdb blast, NCBI blast, and HHPRED all suggest major capsid protein
    /note=Conserved domain also suggests major capsid protein
    /note=Start not changed because excellent coding potential, longest ORF, good scores, and good starterator data
    /note=Deep TMHMM N/A

CDS 21018 - 21458
  /gene="34"
  /product="gp34"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_34"
    /note=Original Glimmer call @bp 21018 has strength 9.02; Genemark calls start at 21018
    /note=SSC: 21018-21458 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_34 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.74377E-98 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.639, -3.410574749511644, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_34 [Rhodococcus phage Braxoaddie] ],,WIC89656,100.0,1.74377E-98 SIF-HHPRED: YqbF_HeH ; YqbF, HeH motif,,,PF21488.1,21.2329,96.0 SIF-Syn: This gene is in all of the CR phages as either gene 34 or 38.
    /note=Deep TMHMM: N/A
    /note=Phages db Blast: function unknown 
    /note=HHPRED: YqbF_HeH ; YqbF, HeH motif (96%)
    /note=NCBI Blast: Hypothetical protein (100%)

CDS 21507 - 21920
  /gene="35"
  /product="gp35"
  /function="head-to-tail adaptor"
  /locus tag="CoffeeBean_35"
    /note=Original Glimmer call @bp 21507 has strength 13.0; Genemark calls start at 21507
    /note=SSC: 21507-21920 CP: yes SCS: both ST: NI BLAST-Start: [head-to-tail adaptor [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 6.60917E-93 GAP: 48 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.5410833118725082, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Rhodococcus phage Braxoaddie] ],,WIC89657,100.0,6.60917E-93 SIF-HHPRED: Phage_Gp19 ; Phage protein Gp19/Gp15/Gp42,,,PF09355.14,78.1022,99.7 SIF-Syn: This gene is in all of the CR phages as either gene 35 or 39.
    /note=Deep TMHMM: N/A
    /note=Phages db Blast: head-to-tail adaptor
    /note=HHPRED: head-to-tail connector protein (96.5%)
    /note=NCBI Blast: head-to-tail adaptor (100%)

CDS 21929 - 22291
  /gene="36"
  /product="gp36"
  /function="head-to-tail stopper"
  /locus tag="CoffeeBean_36"
    /note=Original Glimmer call @bp 21929 has strength 15.91; Genemark calls start at 21929
    /note=SSC: 21929-22291 CP: yes SCS: both ST: NI BLAST-Start: [head-to-tail stopper [Rhodococcus phage Braxoaddie]],,NCBI, q1:s5 100.0% 1.59695E-83 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.012, -6.8661996368787515, no F: head-to-tail stopper SIF-BLAST: ,,[head-to-tail stopper [Rhodococcus phage Braxoaddie]],,WIC89658,96.7742,1.59695E-83 SIF-HHPRED: Minor_capsid_1 ; Minor capsid protein,,,PF10665.13,90.0,99.3 SIF-Syn: This gene is in all of the CR phages as either gene 36 or 40
    /note=Deep TMHMM: N/A
    /note=Phages db Blast: head-to-tail stopper
    /note=HHPRED: minor capsid protein (99.3%)
    /note=NCBI Blast: head-to-tail stopper (100%)

CDS 22291 - 22698
  /gene="37"
  /product="gp37"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_37"
    /note=Original Glimmer call @bp 22291 has strength 9.87; Genemark calls start at 22288
    /note=SSC: 22291-22698 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_37 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.35026E-93 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.998, -4.759312672633257, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_37 [Rhodococcus phage Braxoaddie] ],,WIC89659,100.0,1.35026E-93 SIF-HHPRED: Minor_capsid_2 ; Minor capsid protein,,,PF11114.12,72.5926,98.6 SIF-Syn: This gene is in all CR phages as either gene 37 or 41.
    /note=Deep TMHMM: N/A
    /note=Phages db Blast: function unknown
    /note=HHPRED: minor capsid protein (98.6%), family of unknown function (98.6%)
    /note=NCBI Blast: Hypothetical protein (100%)

CDS 22695 - 23129
  /gene="38"
  /product="gp38"
  /function="tail terminator"
  /locus tag="CoffeeBean_38"
    /note=Original Glimmer call @bp 22695 has strength 10.99; Genemark calls start at 22695
    /note=SSC: 22695-23129 CP: yes SCS: both ST: NI BLAST-Start: [tail terminator [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 2.41352E-101 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.802, -5.14847875699779, no F: tail terminator SIF-BLAST: ,,[tail terminator [Rhodococcus phage Braxoaddie] ],,WIC89660,100.0,2.41352E-101 SIF-HHPRED: TAIL-TO-HEAD JOINING PROTEIN GP17; VIRAL PROTEIN, VIRAL INFECTION, TAILED BACTERIOPHAGE, SIPHOVIRIDAE, SPP1, VIRAL ASSEMBLY, HEAD-TO-TAIL INTERFACE, DNA GATEKEEPER, ALLOSTERIC MECHANISM; 7.2A {BACILLUS PHAGE SPP1},,,5A21_G,93.0556,99.5 SIF-Syn: This gene is found on all CR phages as either gene 38 or 42.
    /note=Deep TMHMM: N/A
    /note=Phages db Blast: tail terminator
    /note=HHPRED: TAIL-TO-HEAD JOINING PROTEIN (99.5%); tail terminator (99.4%)
    /note=NCBI Blast: tail terminator (100%)

CDS 23172 - 23840
  /gene="39"
  /product="gp39"
  /function="major tail protein"
  /locus tag="CoffeeBean_39"
    /note=Original Glimmer call @bp 23172 has strength 15.21; Genemark calls start at 23172
    /note=SSC: 23172-23840 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 7.07259E-162 GAP: 42 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.234, -2.1123791669543204, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Rhodococcus phage Braxoaddie] ],,WIC89661,100.0,7.07259E-162 SIF-HHPRED: YSD1_22 major tail protein; Bacteriophage tail, helical assembly, VIRAL PROTEIN; 3.5A {Bacteriophage sp.},,,6XGR_M,86.9369,97.7 SIF-Syn: Very High synteny with other phages in cluster CR
    /note=Deep TMHMM: N/A
    /note=Phage db Blast: major tail protein
    /note=HHPRED: major tail protein (97.7%)
    /note=NCBI Blast: major tail protein (100%)

CDS 23984 - 24250
  /gene="40"
  /product="gp40"
  /function="hypothetical protein"
  /locus tag="CoffeeBean_40"
    /note=Original Glimmer call @bp 23984 has strength 11.47; Genemark calls start at 23984
    /note=SSC: 23984-24250 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_MASELOP_40 [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 1.06601E-50 GAP: 143 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.168, -4.4057176022952405, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MASELOP_40 [Rhodococcus phage Maselop]],,WNM64963,94.3182,1.06601E-50 SIF-HHPRED:  SIF-Syn: High synteny
    /note=Start kept due to good RBS, captures all CP and most annotated start
    /note=No viable functions from HHPRED or from Blast besides Hypothetical protein

CDS 24265 - 24576
  /gene="41"
  /product="gp41"
  /function="tail assembly chaperone"
  /locus tag="CoffeeBean_41"
    /note=Original Glimmer call @bp 24265 has strength 14.03; Genemark calls start at 24265
    /note=SSC: 24265-24576 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.5733E-67 GAP: 14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.262, -4.271082485841055, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Rhodococcus phage Braxoaddie] ],,WIC89663,100.0,1.5733E-67 SIF-HHPRED: GP24_25 ; Mycobacteriophage tail assembly protein,,,PF17388.6,94.1748,93.5 SIF-Syn: High synteny
    /note=Start kept for good RBS, CP, and most annotated start in starterator
    /note=Great scores in Blast for tail assembly chaperone

CDS complement (24573 - 24725)
  /gene="42"
  /product="gp42"
  /locus tag="CoffeeBean_42"
    /note=Original Glimmer call @bp 24725 has strength 7.89
    /note=SSC: 24725-24573 CP: no SCS: glimmer ST: NI BLAST-Start:  GAP: 12 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.166, -2.253486910374644, yes F:  SIF-BLAST:  SIF-HHPRED: E3 ubiquitin-protein ligase HUWE1; Ubiquitin Binding Motif, Protein binding; NMR {Homo sapiens},,,2MUL_A,48.0,72.1 SIF-Syn: No synteny due to no presence in other phages
    /note=Suggest for deletion due to poor CP, massive overlap, and no viable functions or matches with other phages.

CDS 24738 - 25088
  /gene="43"
  /product="gp43"
  /function="tail assembly chaperone"
  /locus tag="CoffeeBean_43"
    /note=Original Glimmer call @bp 24738 has strength 14.88; Genemark calls start at 24738
    /note=SSC: 24738-25088 CP: no SCS: both ST: NA BLAST-Start: [tail assembly chaperone [Rhodococcus phage Maselop]],,NCBI, q1:s159 100.0% 1.33254E-72 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.754, -7.323698656036769, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Rhodococcus phage Maselop]],,WNM64965,42.3358,1.33254E-72 SIF-HHPRED: DUF5361 ; Family of unknown function (DUF5361),,,PF17318.6,30.1724,98.1 SIF-Syn: 
    /note=Found slippery sequence at base pair 24566 (A) more likely 24563 (A)
    /note=The amino acid sequence changed from GGK in one reading frame to RGL in another reading frame
    /note=Guy Fagieri was also used to give an idea of where the slippery sequence would be because Guy Fagieri is a very similar phage to CoffeeBean

CDS 25156 - 30366
  /gene="44"
  /product="gp44"
  /function="tape measure protein"
  /locus tag="CoffeeBean_44"
    /note=Original Glimmer call @bp 25156 has strength 16.02; Genemark calls start at 25156
    /note=SSC: 25156-30366 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Rhodococcus phage Maselop]],,NCBI, q1:s1 100.0% 0.0 GAP: 67 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.659, -3.368377069717189, yes F: tape measure protein SIF-BLAST: ,,[tape measure protein [Rhodococcus phage Maselop]],,WNM64966,100.0,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BF,11.4055,100.0 SIF-Syn: Gene is found in exact same location in all CR phage genomes.
    /note=Start is called in every single phage with pham. Blast and HHPRED almost unanimously indicated tape measure protein as function.
    /note=
    /note=Contains transmembrane domain.

CDS 30363 - 31289
  /gene="45"
  /product="gp45"
  /function="minor tail protein"
  /locus tag="CoffeeBean_45"
    /note=Original Glimmer call @bp 30399 has strength 14.06; Genemark calls start at 30363
    /note=SSC: 30363-31289 CP: yes SCS: both-gm ST: NI BLAST-Start: [minor tail protein [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.597, -5.5114639437351745, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Rhodococcus phage Braxoaddie] ],,WIC89666,100.0,0.0 SIF-HHPRED:  SIF-Syn: Gene is in same location for all CR phages.
    /note=ORIGINAL START (30399): Not all CP contained, called in a few CR phages but not all, slightly better scores.
    /note=
    /note=NEW START (30363): All CP contained, LORF, called 96.6% of the time when start is present, slightly worse scores. 
    /note=
    /note=For now start is changed to LORF, but should be further reviewed. 
    /note=
    /note=Blast and HHPRED results heavily suggest that this gene functions as a minor tail protein.

CDS 31300 - 32874
  /gene="46"
  /product="gp46"
  /function="minor tail protein"
  /locus tag="CoffeeBean_46"
    /note=Original Glimmer call @bp 31300 has strength 16.56; Genemark calls start at 31300
    /note=SSC: 31300-32874 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.822, -3.494990588194529, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Rhodococcus phage Braxoaddie] ],,WIC89667,100.0,0.0 SIF-HHPRED: Sipho_Gp37 ; Siphovirus ReqiPepy6 Gp37-like protein,,,PF14594.10,88.1679,99.9 SIF-Syn: Found in exact same place in all CR phage genomes.
    /note=Suggested Start called due to LORF, contains all CP, best scores, and synteny with other CR phages. 
    /note=
    /note=Blast and HHPRED all strongly suggest that function is minor tail protein.

CDS 32905 - 34011
  /gene="47"
  /product="gp47"
  /function="minor tail protein"
  /locus tag="CoffeeBean_47"
    /note=Original Glimmer call @bp 32905 has strength 13.73; Genemark calls start at 32905
    /note=SSC: 32905-34011 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.719, -3.708850054194189, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Rhodococcus phage Braxoaddie] ],,WIC89668,100.0,0.0 SIF-HHPRED: Pulmonary surfactant-associated protein D; collectin, c-type lectin, alpha-helical coiled coil, carbohydrate recognition domain, SIGNALING PROTEIN; HET: GLC; 1.4A {Homo sapiens} SCOP: h.1.1.1, d.169.1.1,,,1PWB_A,4.61957,70.9 SIF-Syn: Yes, synteny with other CR phages.
    /note=No start change due to covering all coding potential, Longest ORF, good scores, and Starterator. Function is a minor tail protein due to direct matches to other phages in CR cluster using BLAST.

CDS 34013 - 34354
  /gene="48"
  /product="gp48"
  /function="membrane protein"
  /locus tag="CoffeeBean_48"
    /note=Original Glimmer call @bp 34013 has strength 16.5; Genemark calls start at 34013
    /note=SSC: 34013-34354 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_47 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.9015E-74 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.273, -4.759359944890645, no F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_47 [Rhodococcus phage Braxoaddie] ],,WIC89669,100.0,1.9015E-74 SIF-HHPRED:  SIF-Syn: Yes, with other phages in CR cluster.
    /note=BLAST q1:t1 hit reveals hypothetical membrane protein with 100% Identity. HHPRED does not suggest alternative function, and DeepTMHMM predicts presence of transmembrane protein.

CDS 34358 - 35335
  /gene="49"
  /product="gp49"
  /function="minor tail protein"
  /locus tag="CoffeeBean_49"
    /note=Original Glimmer call @bp 34358 has strength 16.09; Genemark calls start at 34358
    /note=SSC: 34358-35335 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.075, -2.794070146961553, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Rhodococcus phage Braxoaddie] ],,WIC89670,100.0,0.0 SIF-HHPRED:  SIF-Syn: Yes, with phages in cluster CR.
    /note=BLAST reveals q1:t1 hit for minor tail protein for phages in same cluster (CR), and start called in every single phage with pham. HHPRED does not suggest different function.

CDS 35344 - 35664
  /gene="50"
  /product="gp50"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_50"
    /note=Original Glimmer call @bp 35344 has strength 11.79; Genemark calls start at 35344
    /note=SSC: 35344-35664 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_49 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.35707E-69 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.168, -4.4057176022952405, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_49 [Rhodococcus phage Braxoaddie] ],,WIC89671,100.0,1.35707E-69 SIF-HHPRED: DUF1314 ; Protein of unknown function (DUF1314),,,PF07013.15,49.0566,68.0 SIF-Syn: Gene is in same location as other CR cluster phages that contain this gene.
    /note=No good results for function.
    /note=
    /note=Start ALMOST included all CP, but missed a small amount at the start. This start is the LORF, so still the best possible start when it comes to CP.

CDS 35651 - 36994
  /gene="51"
  /product="gp51"
  /function="lysin A"
  /locus tag="CoffeeBean_51"
    /note=Original Glimmer call @bp 35651 has strength 10.99; Genemark calls start at 35651
    /note=SSC: 35651-36994 CP: yes SCS: both ST: SS BLAST-Start: [lysin A [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.899, -4.946058559219759, no F: lysin A SIF-BLAST: ,,[lysin A [Rhodococcus phage Braxoaddie] ],,WIC89672,100.0,0.0 SIF-HHPRED: N-acetylmuramoyl-L-alanine amidase amiD; ZINC AMIDASE, PGRP, Peptidoglycan Recognizing Protein, AmpD, N-ACETYLMURAMYL-L-ALANINE AMIDASE, Cell wall biogenesis/degradation, Hydrolase, Lipoprotein, Membrane, Metal-binding; HET: GOL, AH0; 1.75A {Escherichia coli},,,3D2Y_A,54.1387,99.7 SIF-Syn: Shares gene location with CR phages like Apiary and Braxoaddie.
    /note=Start kept same due to good scores, Starterator evidence, good CP, and it being the Longest ORF. BLAST results provide evidence for this gene`s function being a lysin A.

CDS 36991 - 37221
  /gene="52"
  /product="gp52"
  /function="holin"
  /locus tag="CoffeeBean_52"
    /note=Original Glimmer call @bp 36991 has strength 8.25; Genemark calls start at 36991
    /note=SSC: 36991-37221 CP: yes SCS: both ST: SS BLAST-Start: [holin [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.71919E-45 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.752, -6.097136544885063, no F: holin SIF-BLAST: ,,[holin [Rhodococcus phage Braxoaddie] ],,WIC89673,100.0,1.71919E-45 SIF-HHPRED: Phage_holin_7_1 ; Mycobacterial 2 TMS Phage Holin (M2 Hol) Family,,,PF16081.9,69.7368,98.5 SIF-Syn: Gene present in same location as all other CR cluster phages containing gene.
    /note=LORF start present in all phages of PHAM and only start that contains all CP
    /note=
    /note=Multiple Q1:T1 matches with holin protein in other phages suggest that this ORF codes for a holin protein.

CDS complement (37302 - 37472)
  /gene="53"
  /product="gp53"
  /function="membrane protein"
  /locus tag="CoffeeBean_53"
    /note=Original Glimmer call @bp 37472 has strength 15.92; Genemark calls start at 37472
    /note=SSC: 37472-37302 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_52 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 2.09239E-33 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.075, -3.095100142625534, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_52 [Rhodococcus phage Braxoaddie] ],,WIC89674,100.0,2.09239E-33 SIF-HHPRED: d.58.58.1 (A:) Cas2 {Escherichia coli K-12 MG1655 [TaxId: 511145]} | CLASS: Alpha and beta proteins (a+b), FOLD: Ferredoxin-like, SUPFAM: CRISPR associated protein Cas2-like, FAM: CRISPR associated protein Cas2-like,,,SCOP_d4maka_,30.3571,55.0 SIF-Syn: Gene in same location as all other phages in cluster.
    /note=LORF start present in all phages with pham, contains all CP, best scores.
    /note=
    /note=No good results for function in BLAST/HHPRED, But DeepTHMM detected a transmembrane domain.

CDS complement (37459 - 40059)
  /gene="54"
  /product="gp54"
  /function="DNA primase/polymerase"
  /locus tag="CoffeeBean_54"
    /note=Original Glimmer call @bp 40059 has strength 17.94; Genemark calls start at 40059
    /note=SSC: 40059-37459 CP: yes SCS: both ST: SS BLAST-Start: [DNA primase/polymerase [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.589, -3.513874779476501, no F: DNA primase/polymerase SIF-BLAST: ,,[DNA primase/polymerase [Rhodococcus phage Braxoaddie] ],,WIC89675,100.0,0.0 SIF-HHPRED: DNA primase; Helicase, DNA binding, AMPPNP, REPLICATION; HET: ANP; 3.1A {Staphylococcus aureus},,,7OM0_D,41.6859,100.0 SIF-Syn: Gene present in same location as all other CR cluster phages containing gene.
    /note=LORF start is called in all other CR phages, only start containing all CP, best scores.
    /note=
    /note=Multiple Q1:T1 results with DNA primase/polymerase listed as function, all with very good E-values.

CDS complement (40064 - 40477)
  /gene="55"
  /product="gp55"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_55"
    /note=Original Glimmer call @bp 40477 has strength 12.0; Genemark calls start at 40477
    /note=SSC: 40477-40064 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_54 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 2.77887E-97 GAP: 28 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.075, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_54 [Rhodococcus phage Braxoaddie] ],,WIC89676,100.0,2.77887E-97 SIF-HHPRED:  SIF-Syn: Good synteny
    /note=Start kept: good RBS, full CP, and most annotated start
    /note=No other options for functions because poor e-values in HHPRED and no results for TMHMM

CDS complement (40506 - 40766)
  /gene="56"
  /product="gp56"
  /function="WhiB family transcription factor"
  /locus tag="CoffeeBean_56"
    /note=Original Glimmer call @bp 40748 has strength 9.77; Genemark calls start at 40733
    /note=SSC: 40766-40506 CP: yes SCS: both-cs ST: NI BLAST-Start: [WhiB family transcription factor [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 100.0% 2.06757E-56 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.018, -5.544484265892628, no F: WhiB family transcription factor SIF-BLAST: ,,[WhiB family transcription factor [Rhodococcus phage Braxoaddie]],,WIC89677,100.0,2.06757E-56 SIF-HHPRED:  SIF-Syn: Yes, with CR cluster
    /note=BLAST q1:t1 hit calls for WhiB family transcription factor with 100% identity. HHPred hits support with corresponding low e-values.

CDS complement (40763 - 41053)
  /gene="57"
  /product="gp57"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_57"
    /note=Original Glimmer call @bp 41053 has strength 12.46; Genemark calls start at 41017
    /note=SSC: 41053-40763 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_56 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.32528E-60 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.847, -5.132255893439239, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_56 [Rhodococcus phage Braxoaddie] ],,WIC89678,100.0,1.32528E-60 SIF-HHPRED:  SIF-Syn: Good synteny
    /note=Start kept due to good RBS, full CP, and most annotated start
    /note=No good functions besides hypothetical protein (no good results from HHPRED)

CDS complement (41057 - 41485)
  /gene="58"
  /product="gp58"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="CoffeeBean_58"
    /note=Original Glimmer call @bp 41485 has strength 13.9; Genemark calls start at 41485
    /note=SSC: 41485-41057 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding protein [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.35445E-96 GAP: 64 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.075, -2.583959800616441, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding protein [Rhodococcus phage Braxoaddie] ],,WIC89679,100.0,1.35445E-96 SIF-HHPRED: AM32; Repressor, Protein-DNA complex, Type IV secretion system, DNA BINDING PROTEIN; HET: EPE; 1.93A {Enterococcus faecalis},,,6G1T_A,88.0282,99.7 SIF-Syn: The gene aligns well with the other genes in the cluster.
    /note=It is the longest ORF and has the best scores and the CP is good. The NCBI Blast and the PhagesDB blast shows the gene is a helix-turn-helix DNA-binding domain protein. HHPred has other hits that are higher but still have hits that are helix-turn-helix. Conserved domain also has hits with good e-value calling it to helix-turn-helix DNA-binding domain protein.

CDS complement (41550 - 42290)
  /gene="59"
  /product="gp59"
  /function="RuvC-like resolvase"
  /locus tag="CoffeeBean_59"
    /note=Original Glimmer call @bp 42290 has strength 12.87; Genemark calls start at 42290
    /note=SSC: 42290-41550 CP: yes SCS: both ST: SS BLAST-Start: [RuvC-like resolvase [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 2.17267E-180 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.29, -6.211012262215628, no F: RuvC-like resolvase SIF-BLAST: ,,[RuvC-like resolvase [Rhodococcus phage Braxoaddie] ],,WIC89680,100.0,2.17267E-180 SIF-HHPRED: c.55.3.6 (A:) RuvC resolvase {Escherichia coli [TaxId: 562]} | CLASS: Alpha and beta proteins (a/b), FOLD: Ribonuclease H-like motif, SUPFAM: Ribonuclease H-like, FAM: RuvC resolvase,,,SCOP_d1hjra_,72.7642,99.7 SIF-Syn: The gene is in a very similar spot to other genes in the CR cluster
    /note=Longest ORF was not use because of overlap. Recommended start has decent scores and good CP. HHpred and NCBI blast have high e-values that point to the gene being RuvC-like resolvase. One hit with Holliday junction resolvase however, the approved function list state if RuvC or RusA are present the call don`t call it as Holliday junction resolvase

CDS complement (42292 - 45708)
  /gene="60"
  /product="gp60"
  /function="DnaE-like DNA polymerase III (alpha)"
  /locus tag="CoffeeBean_60"
    /note=Original Glimmer call @bp 45708 has strength 19.78; Genemark calls start at 45627
    /note=SSC: 45708-42292 CP: yes SCS: both-gl ST: SS BLAST-Start: [DnaE-like DNA polymerase III alpha [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 100.0% 0.0 GAP: 24 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.589, -3.5316035464369326, no F: DnaE-like DNA polymerase III (alpha) SIF-BLAST: ,,[DnaE-like DNA polymerase III alpha [Rhodococcus phage Braxoaddie]],,WIC89681,100.0,0.0 SIF-HHPRED: DNA polymerase III alpha subunit; Pol-beta-like Nucleotidyltransferase fold, TRANSFERASE; 3.0A {Thermus aquaticus},,,2HPI_A,99.6485,100.0 SIF-Syn: The gene was in a similar spot as all the other genes in its cluster.
    /note=It is the longest ORF and has good scores and CP. All Blast hits and HHpred had great e-values and pointed to the function being DnaE-like DNA polymerase III (alpha). The conserved domain also had hits with good e-values for DnaE-like DNA polymerase III (alpha) as well.

CDS complement (45733 - 45879)
  /gene="61"
  /product="gp61"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_61"
    /note=Original Glimmer call @bp 45879 has strength 10.21; Genemark calls start at 45945
    /note=SSC: 45879-45733 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_60 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s23 100.0% 3.36268E-25 GAP: 62 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.454, -7.112152760602187, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_60 [Rhodococcus phage Braxoaddie] ],,WIC89682,68.5714,3.36268E-25 SIF-HHPRED:  SIF-Syn: This gene is not in any phages in the same cluster but is in some that are not in the same cluster, and it is in a similar spot to those genes.
    /note=It is not the longest ORF, but it has an okay score with decent length. Starterator has the start that is currently selected in 13 of 20 and is called 100 percent of the time so we are changing the start to the one selected. The HHPred has bad hits with the e-value, but there are NCBI blasts that say that it is a hypothetical protein.

CDS complement (45942 - 46340)
  /gene="62"
  /product="gp62"
  /function="thioredoxin"
  /locus tag="CoffeeBean_62"
    /note=Original Glimmer call @bp 46340 has strength 16.87; Genemark calls start at 46340
    /note=SSC: 46340-45942 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_61 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.55659E-91 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.92, -3.2925703904164987, yes F: thioredoxin SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_61 [Rhodococcus phage Braxoaddie] ],,WIC89683,100.0,1.55659E-91 SIF-HHPRED: Thioredoxin domain protein; APC92103, thioredoxin, Desulfitobacterium hafniense DCB, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: MSE; 1.99A {Desulfitobacterium hafniense DCB-2} SCOP: c.47.1.0, l.1.1.1,,,3GNJ_D,82.5758,99.8 SIF-Syn: Very similar locations in all phages in CR. varies between 60-62, with the only outlier being MacGully where it is located at 70.
    /note=Strong hits in HHPred genes. and called in MacGully on phages DB. Start: 46340, End: 45942. Best Z score, not best final. This start has the least amount of overlap and good CP.

CDS complement (46337 - 46531)
  /gene="63"
  /product="gp63"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_63"
    /note=Original Glimmer call @bp 46531 has strength 8.75; Genemark calls start at 46531
    /note=SSC: 46531-46337 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_62 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.13813E-39 GAP: 59 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.999, -2.6814417326944517, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_62 [Rhodococcus phage Braxoaddie] ],,WIC89684,100.0,1.13813E-39 SIF-HHPRED: DUF5832 ; Family of unknown function (DUF5832),,,PF19150.4,53.125,95.0 SIF-Syn: Very similar location across all CR phages. Range from 62-64, with only outlier being 72 in MacGully.
    /note=Hits in HHPred, and PhagesDB all point to hypothetical protein. Good CP, not best final score, but best Z-score. Start:46531, End: 46337.

CDS complement (46591 - 47454)
  /gene="64"
  /product="gp64"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_64"
    /note=Original Glimmer call @bp 47454 has strength 18.85; Genemark calls start at 47454
    /note=SSC: 47454-46591 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_63 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: 41 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.999, -2.6814417326944517, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_63 [Rhodococcus phage Braxoaddie] ],,WIC89685,100.0,0.0 SIF-HHPRED: DUF669 ; Protein of unknown function (DUF669),,,PF05037.17,28.223,98.7 SIF-Syn: 

CDS complement (47496 - 48347)
  /gene="65"
  /product="gp65"
  /function="ASCE ATPase"
  /locus tag="CoffeeBean_65"
    /note=Original Glimmer call @bp 48347 has strength 15.76; Genemark calls start at 48347
    /note=SSC: 48347-47496 CP: yes SCS: both ST: SS BLAST-Start: [RecA-like DNA recombinase [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: 47 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.642, -3.3418724531147843, yes F: ASCE ATPase SIF-BLAST: ,,[RecA-like DNA recombinase [Rhodococcus phage Braxoaddie] ],,WIC89686,100.0,0.0 SIF-HHPRED: Protein recA; Alpha and beta proteins (a/b, a+b), ATP-binding, Cytoplasm, DNA damage, DNA recombination, DNA repair, DNA-binding, Nucleotide-binding; 1.95A {Thermotoga maritima},,,3HR8_A,65.371,99.2 SIF-Syn: Shows up in all CR cluster phages from genes 63-65. Only outlier is MacGully where it is at 73.
    /note=Longest ORF best Z and final score. Good CP. Reverse. Start:48347, End: 47496
    /note=Blast and HHpred strongly point to RecA-like DNA recombinase, but now called ASCE ATPase.

CDS complement (48395 - 48628)
  /gene="66"
  /product="gp66"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_66"
    /note=Original Glimmer call @bp 48628 has strength 13.51; Genemark calls start at 48625
    /note=SSC: 48628-48395 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_65 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 2.42887E-45 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.153, -4.436903688233993, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_65 [Rhodococcus phage Braxoaddie] ],,WIC89687,100.0,2.42887E-45 SIF-HHPRED: b.107.1.1 (A:1-70) Urease metallochaperone UreE, N-terminal domain {Klebsiella aerogenes [TaxId: 28451]} | CLASS: All beta proteins, FOLD: Urease metallochaperone UreE, N-terminal domain, SUPFAM: Urease metallochaperone UreE, N-terminal domain, FAM: Urease metallochaperone UreE, N-terminal domain,,,SCOP_d1gmua1,57.1429,55.4 SIF-Syn: Gene 66 in this phage is nearly identical to gene 65 in several other members of the pham, and the arrangement/order of genes is very similar between the phages.
    /note=CP: good, all included; LO: no, but longest doesn`t add any coding potential and has a large overlap; Gap: -4; RBS: close to best score; no conserved domains or transmembrane domains; HHPred: insignificant results

CDS complement (48625 - 48849)
  /gene="67"
  /product="gp67"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_67"
    /note=Original Glimmer call @bp 48849 has strength 10.89; Genemark calls start at 48849
    /note=SSC: 48849-48625 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_66 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 2.39238E-45 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.645, -5.4744737427355155, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_66 [Rhodococcus phage Braxoaddie] ],,WIC89688,100.0,2.39238E-45 SIF-HHPRED: BRX_N ; Transcription factor BRX N-terminal domain,,,PF13713.10,36.4865,42.9 SIF-Syn: Gene 67 in this phage is nearly identical to gene 66 in several other members of the pham, and the arrangement/order of genes is very similar between the phages.
    /note=CP: good, all included; LO: yes; Gap: 0; RBS: close to best score; no conserved domains or transmembrane domains; HHPred: insignificant results

CDS complement (48850 - 50013)
  /gene="68"
  /product="gp68"
  /function="Cas4 exonuclease"
  /locus tag="CoffeeBean_68"
    /note=Original Glimmer call @bp 50013 has strength 18.84; Genemark calls start at 50013
    /note=SSC: 50013-48850 CP: yes SCS: both ST: SS BLAST-Start: [Cas4 exonuclease [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.155, -2.356391881054909, yes F: Cas4 exonuclease SIF-BLAST: ,,[Cas4 exonuclease [Rhodococcus phage Braxoaddie] ],,WIC89689,100.0,0.0 SIF-HHPRED: ATP-dependent helicase/deoxyribonuclease subunit B; Helicase, nuclease, Double strand DNA repair, Protein-DNA complex, HYDROLASE-DNA complex; 2.8A {Bacillus subtilis},,,3U4Q_B,90.9561,99.8 SIF-Syn: Gene 68 in this phage is nearly identical to gene 67 in several other members of the pham, and the arrangement/order of genes is very similar between the phages.
    /note=CP: good, all included; LO: no, but longest doesn`t add a substantial amount of coding potential; Gap: -4; RBS: close to best score; no transmembrane domains; conserved domain from nuclease superfamily, HHPred hit to same nuclease superfamily

CDS complement (50010 - 50336)
  /gene="69"
  /product="gp69"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_69"
    /note=Original Glimmer call @bp 50336 has strength 7.35; Genemark calls start at 50336
    /note=SSC: 50336-50010 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_68 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 5.61321E-73 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.09, -4.488477140305168, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_68 [Rhodococcus phage Braxoaddie] ],,WIC89690,100.0,5.61321E-73 SIF-HHPRED: DUF3039 ; Protein of unknown function (DUF3039),,,PF11238.12,50.9259,90.3 SIF-Syn: Gene 69 in this phage is nearly identical to gene 68 in several other members of the pham, and the arrangement/order of genes is very similar between the phages.
    /note=CP: good, all included; LO: yes; Gap: -4; RBS: close to best score; no conserved domains or transmembrane domains

CDS complement (50333 - 50521)
  /gene="70"
  /product="gp70"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_70"
    /note=Original Glimmer call @bp 50521 has strength 18.34; Genemark calls start at 50521
    /note=SSC: 50521-50333 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_69 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.3748E-37 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.572, -3.54831954703195, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_69 [Rhodococcus phage Braxoaddie] ],,WIC89691,100.0,1.3748E-37 SIF-HHPRED: b.84.5.1 (A:113-184) V1 ATP synthase A subunit, bulge domain {Thermus thermophilus HB8 [TaxId: 300852]} | CLASS: All beta proteins, FOLD: Barrel-sandwich hybrid, SUPFAM: V1 ATP synthase A subunit, bulge domain-like, FAM: V1 ATP synthase A subunit, bulge domain-like,,,SCOP_d3gqba3,33.871,56.9 SIF-Syn: Yes. It is the same pharm as Gene 70 in Braxoaddie which also appears in the same region.
    /note=Good coding potential. Captures the longest possible ORF. The currently selected start is the best start because it has the smallest gap and RBS score. Phagesdb blast lists phages with unknown function. Blasts to Sea_Polyyuki_69 and Sea_Maselop_69 (both Rhodococus phages in cluster CR ) with q1:t1 and hypothetical protein function.

CDS complement (50523 - 50726)
  /gene="71"
  /product="gp71"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_71"
    /note=Original Glimmer call @bp 50726 has strength 27.25; Genemark calls start at 50726
    /note=SSC: 50726-50523 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_70 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 9.65723E-40 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.999, -2.6814417326944517, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_70 [Rhodococcus phage Braxoaddie] ],,WIC89692,100.0,9.65723E-40 SIF-HHPRED: b.34.20.1 (A:7-71) Uncharacterized protein YorP {Bacillus subtilis [TaxId: 1423]} | CLASS: All beta proteins, FOLD: SH3-like barrel, SUPFAM: YorP-like, FAM: YorP-like,,,SCOP_d2heqa1,49.2537,93.1 SIF-Syn: Yes. It is the same pharm as Gene 70 in Braxoaddie which also appears in the same region.
    /note=Good coding potential. Captures the longest possible ORF. The currently selected start is the best start because it has the smallest gap and RBS score. No Transmembrane domain. No conserved domain. Phagesdb blast lists phages with unknown function. Blasts to Sea_Polyyuki_70 ( Rhodococus phage in cluster CR ) with q1:t1 and hypothetical protein function.

CDS complement (50726 - 50995)
  /gene="72"
  /product="gp72"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_72"
    /note=Original Glimmer call @bp 50995 has strength 16.53; Genemark calls start at 50995
    /note=SSC: 50995-50726 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_71 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.39886E-56 GAP: 58 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.999, -2.7423981586358774, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_71 [Rhodococcus phage Braxoaddie] ],,WIC89693,100.0,1.39886E-56 SIF-HHPRED: PENICILLIN-BINDING PROTEIN 4; PENICILLIN-BINDING PROTEIN; HET: GOL, DXF; 1.804A {LISTERIA MONOCYTOGENES},,,3ZG9_A,17.9775,35.4 SIF-Syn: Yes. It is the same pharm as Gene 71 in Braxoaddie which also appears in the same region.
    /note=Good coding potential. Captures the longest possible ORF. The currently selected start is the best start because it has the smallest gap and RBS score. No Transmembrane domain. No conserved domain. Phagesdb blast lists Phage Braxoaddie with unknown function. Blasts to Sea_Maselop_71  and 	 Sea_Braxoaddie_71(both Rhodococus phages in cluster CR ) with q1:t1 and hypothetical protein function.

tRNA 51669 - 51732
  /gene="73"
  /product="tRNA-Ala(tgc)"
  /locus tag="COFFEEBEAN_73"
    /note=tRNA-Ala(tgc)

CDS complement (51054 - 53090)
  /gene="74"
  /product="gp74"
  /function="DNA helicase"
  /locus tag="CoffeeBean_74"
    /note=Original Glimmer call @bp 53090 has strength 15.28; Genemark calls start at 53090
    /note=SSC: 53090-51054 CP: no SCS: both ST: NA BLAST-Start: [DNA helicase [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.234, -2.1924212546750814, yes F: DNA helicase SIF-BLAST: ,,[DNA helicase [Rhodococcus phage Braxoaddie] ],,WIC89694,100.0,0.0 SIF-HHPRED: Chromatin-remodeling ATPase INO80; chromatin remodeler, transcription, replication, DNA repair, DNA BINDING PROTEIN; HET: ADP;{Homo sapiens},,,7ZI4_G,78.6136,100.0 SIF-Syn: Yes. It is in the same pharm as Gene 72 in Braxoaddie which also appears in the same region.
    /note=Start: The currently selected start is the best start because it has the smallest overlap and RBS score. Good coding potential. Does not capture the longest possible ORF.
    /note=Phagesdb blast lists Phage Braxoaddie with function as DNA helicase. Blasts to Sea_Polyyuki_72 and 	 Sea_Braxoaddie_72(both Rhodococus phages in cluster CR) with q1:t1 and with function as DNA helicase.
    /note= No Transmembrane domain. Conserved domain is found: DEXQc_arch_SWI2_SNF2 which are members of DEAD-like helicase superfamily.

CDS complement (53090 - 53365)
  /gene="75"
  /product="gp75"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_75"
    /note=Original Glimmer call @bp 53365 has strength 6.17; Genemark calls start at 53365
    /note=SSC: 53365-53090 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_73 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 7.33823E-60 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.643, -4.3905925537939225, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_73 [Rhodococcus phage Braxoaddie] ],,WIC89695,100.0,7.33823E-60 SIF-HHPRED: b.62.1.1 (A:5-159) Putative cyclophilin PFE0505w {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]} | CLASS: All beta proteins, FOLD: Cyclophilin-like, SUPFAM: Cyclophilin-like, FAM: Cyclophilin (peptidylprolyl isomerase),,,SCOP_d2fu0a1,30.7692,61.6 SIF-Syn: High levels of synteny with Apiary and Braxoaddie with adjacent genes all being nearly identical.
    /note=Most annotated start (seen in every pham that has this start)

CDS complement (53362 - 53562)
  /gene="76"
  /product="gp76"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_76"
    /note=Original Glimmer call @bp 53562 has strength 15.4; Genemark calls start at 53562
    /note=SSC: 53562-53362 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_74 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.06653E-38 GAP: 44 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.434, -4.602200557842397, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_74 [Rhodococcus phage Braxoaddie] ],,WIC89696,100.0,1.06653E-38 SIF-HHPRED: DpnD-PcfM ; DpnD/PcfM-like protein,,,PF14207.10,42.4242,95.5 SIF-Syn: High synteny- near identical genes seen surrounding this pham in other phage genomes (such as Braxoaddie).
    /note=Not most annotated start, but start is seen in other similar phages in same cluster. 
    /note=This pham is most likely a hypothetical protein as all matches point to it being such, and there is no evidence suggesting a known function.

CDS complement (53607 - 54818)
  /gene="77"
  /product="gp77"
  /function="rtcB-like RNA ligase"
  /locus tag="CoffeeBean_77"
    /note=Original Glimmer call @bp 54818 has strength 15.77; Genemark calls start at 54818
    /note=SSC: 54818-53607 CP: yes SCS: both ST: SS BLAST-Start: [RtcB-like RNA ligase [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: 14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.999, -2.6013996449736907, yes F: rtcB-like RNA ligase SIF-BLAST: ,,[RtcB-like RNA ligase [Rhodococcus phage Braxoaddie] ],,WIC89697,100.0,0.0 SIF-HHPRED: d.261.1.1 (A:2-481) automated matches {Pyrococcus horikoshii [TaxId: 53953]} | CLASS: Alpha and beta proteins (a+b), FOLD: Hypothetical protein PH1602, SUPFAM: Hypothetical protein PH1602, FAM: Hypothetical protein PH1602,,,SCOP_d4dwra1,97.0223,100.0 SIF-Syn: The surrounding genes in phage Braxoaddie are nearly identical to those seen in Coffeebean, implying a high level of synteny.
    /note=Great coding potential. Not most annotated start, but shares start with five other phages in its cluster. This gene has striking resemblance to several other phages in its cluster, particularly Braxoaddie, Polyyuki, and Maselop. Due to this, and high synteny with Braxoaddie, it has been determined that this gene is most likely an rtcB-like RNA ligase.

CDS complement (54833 - 55213)
  /gene="78"
  /product="gp78"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_78"
    /note=Original Glimmer call @bp 55213 has strength 16.45; Genemark calls start at 55213
    /note=SSC: 55213-54833 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_76 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 3.58644E-87 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.075, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_76 [Rhodococcus phage Braxoaddie] ],,WIC89698,100.0,3.58644E-87 SIF-HHPRED: DUF6319 ; Family of unknown function (DUF6319),,,PF19844.3,16.6667,61.8 SIF-Syn: It has a similar start to 8 out of the 135 phages in that phage, and this start was called in these phages 100% of the time when it was present.
    /note=Not most annotated start, but shares start with several 5 other phages in same cluster. Has the best Z-Score and final score. CP is good. No significant hits in NCBI Blast or HHPred.

CDS complement (55210 - 55554)
  /gene="79"
  /product="gp79"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_79"
    /note=Original Glimmer call @bp 55554 has strength 8.94; Genemark calls start at 55554
    /note=SSC: 55554-55210 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_77 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s13 100.0% 1.53844E-78 GAP: 32 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.645, -5.9375763810740265, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_77 [Rhodococcus phage Braxoaddie] ],,WIC89699,90.4762,1.53844E-78 SIF-HHPRED: DUF3797 ; Domain of unknown function (DUF3797),,,PF12677.11,46.4912,69.5 SIF-Syn: Shares synteny with fellow phages in CR group; Polyyuki and Braxoaddie. And shares similar synteny with phages GuyFagieri, MacGully and Maselop.
    /note=Changing the start to 55590 would increase the Z-score and final score slightly. Additionally, CoffeeBean contains the most annotated start, but does not call it. However, changing the start would result in an overlap of 4, which would be worse as a gap is preferred. NCBI Blast and PhagesDB Blast suggest a hypothetical protein.

CDS complement (55587 - 56525)
  /gene="80"
  /product="gp80"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_80"
    /note=Original Glimmer call @bp 56525 has strength 19.55; Genemark calls start at 56525
    /note=SSC: 56525-55587 CP: yes SCS: both ST: SS BLAST-Start: [DNA binding protein [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 0.0 GAP: 49 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.075, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[DNA binding protein [Rhodococcus phage Braxoaddie] ],,WIC89700,100.0,0.0 SIF-HHPRED: DUF6551 ; Family of unknown function (DUF6551),,,PF20188.2,26.6026,98.5 SIF-Syn: This gene has the most annotated start for this pham, and calls it.
    /note=Start had ok CP, the end aligns a bit less with the cut off of the stop. If another start was selected, the gap would be too wide and scores would be lower. Strong evidence for DNA binding protein, however HHPred results of protein sequence showed no signs of helix turn helix.
    /note=Yes, the turn of any of the possible HTH`s is just a little too long (at least 8 residues)

CDS complement (56575 - 56913)
  /gene="81"
  /product="gp81"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_81"
    /note=Original Glimmer call @bp 56913 has strength 9.63; Genemark calls start at 56913
    /note=SSC: 56913-56575 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_79 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.29693E-78 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.322, -1.9310779259753799, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_79 [Rhodococcus phage Braxoaddie] ],,WIC89701,100.0,1.29693E-78 SIF-HHPRED: PUTATIVE NICKEL-RESPONSIVE REGULATOR; TRANSCRIPTION FACTOR, TRANSCRIPTION REGULATION, RHH, NIKR, DNA-BINDING, TRANSCRIPTION, METAL-BINDING, METALLOREGULATOR; HET: FMT, SO4, GOL; 1.6A {HELICOBACTER PYLORI} SCOP: a.43.1.0, d.58.18.0,,,2WVF_A,48.2143,70.3 SIF-Syn: Shares synteny with phages Braxoaddi, Polyyuki, GuyFagieri and MacGully, which are other phages in the CR cluster
    /note=Starterator hits towards the suggested start. Selected start has the best Z and final scores with minimal gaps. There were many HHPred hits to nickel-responsive regulator transcription factor, however the scores were not significant. NCBI Blast suggest hypothetical protein.

CDS complement (56924 - 57085)
  /gene="82"
  /product="gp82"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_82"
    /note=Original Glimmer call @bp 57085 has strength 10.64; Genemark calls start at 57085
    /note=SSC: 57085-56924 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_80 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.36777E-29 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.639, -3.4283035164720754, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_80 [Rhodococcus phage Braxoaddie] ],,WIC89702,100.0,1.36777E-29 SIF-HHPRED: Dsc3_C ; DSC E3 ubiquitin ligase complex subunit 3, C-terminal domain,,,PF13373.10,35.8491,48.1 SIF-Syn: It has, and calls the most annotated start in the pham, though the pham is small, but shares strong synteny with other members of the CR cluster.
    /note=Start that was selected seemed the most optimal. This start has a small enough overlap and CP. This start also has the best RBS scores. No strong hits for any specific function.

CDS complement (57085 - 58026)
  /gene="83"
  /product="gp83"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_83"
    /note=Original Glimmer call @bp 58488 has strength 11.41; Genemark calls start at 58026
    /note=SSC: 58026-57085 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_81 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s155 100.0% 0.0 GAP: 810 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.168, -4.4057176022952405, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_81 [Rhodococcus phage Braxoaddie]],,WIC89703,67.0236,0.0 SIF-HHPRED: DUF6422 ; Family of unknown function (DUF6422),,,PF19986.3,8.30671,57.4 SIF-Syn: Shares similar synteny with Polyyuki.
    /note=Some phages in the CR cluster selected the longer start (start 58488) while others selected a shorter start (start 58026). When the shorter start is selected in similar phages, another reverse gene was discovered in the gap. Our coding potential does suggest changing our start to the shorter start, however there is no coding potential which suggest another gene to be present in the gap. (Bring in Gordonia phages to compare - Patio, Lolipop, Ennea). Reviewed synteny in previously mentioned phages, displayed no overlap. This led to us making the decision to shorten the gene to reflect the coding potential.

CDS 58837 - 59151
  /gene="84"
  /product="gp84"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_84"
    /note=Original Glimmer call @bp 58837 has strength 8.21; Genemark calls start at 58837
    /note=SSC: 58837-59151 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_83 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.20842E-66 GAP: 810 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.754, -3.170856472917156, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_83 [Rhodococcus phage Braxoaddie] ],,WIC89705,100.0,1.20842E-66 SIF-HHPRED: Uncharacterized protein; Protein, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, UNKNOWN FUNCTION; NMR {Agrobacterium tumefaciens str. C58},,,2KPQ_A,33.6538,46.1 SIF-Syn: It has the most annotated start for the pham and calls it, shows similarity within the CR cluster
    /note=The chosen start has good CP and the best RBS values. Gene does not hit any specific function in HHPred or Blast.

CDS 59256 - 59912
  /gene="85"
  /product="gp85"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_85"
    /note=Original Glimmer call @bp 59256 has strength 7.12; Genemark calls start at 59256
    /note=SSC: 59256-59912 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_84 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.41365E-153 GAP: 104 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.754, -3.170856472917156, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_84 [Rhodococcus phage Braxoaddie] ],,WIC89706,100.0,1.41365E-153 SIF-HHPRED: UPF0339 protein SO_3888; solution NMR structure, STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG; NMR {Shewanella oneidensis} SCOP: d.348.1.1, l.1.1.1,,,2K49_A,37.6147,64.0 SIF-Syn: It has the most annotated start in the pham and it calls it, shares similarity with the members of the CR cluster
    /note=This start has the best scores, good coding potential, and matches the most annotated start in the pham for this gene. There are no strong hits for any specific function.

CDS 59909 - 60178
  /gene="86"
  /product="gp86"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_86"
    /note=Original Glimmer call @bp 59909 has strength 7.04; Genemark calls start at 59909
    /note=SSC: 59909-60178 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_85 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 3.74266E-54 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.006, -4.741344217713455, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_85 [Rhodococcus phage Braxoaddie] ],,WIC89707,100.0,3.74266E-54 SIF-HHPRED: Lipoprotein_15 ; Secreted repeat of unknown function,,,PF03640.19,17.9775,48.8 SIF-Syn: Has the same start as 6 out of the 7 members of this gene`s pham, and this start is called 100% of the time when present.
    /note=We considered another start that had similar but slightly better scores that would start at 59957, but this would make the gap bigger and would not include some coding potential, and is unlikely due to the synteny witnessed for the current start in this gene`s pham. No strong hits for any specific function, HHPred had some results but with low e-values.

CDS 60263 - 60703
  /gene="87"
  /product="gp87"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_87"
    /note=Original Glimmer call @bp 60263 has strength 12.84; Genemark calls start at 60263
    /note=SSC: 60263-60703 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_86 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 100.0% 1.9038E-98 GAP: 84 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.754, -3.2495416658190135, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_86 [Rhodococcus phage Braxoaddie]],,WIC89708,100.0,1.9038E-98 SIF-HHPRED: MATERNAL EFFECT PROTEIN OSKAR; PROTEIN BINDING, OST-HTH DOMAIN, DIMER, WINGED HELIX-TURN-HELIX, VASA, PROTEIN BINDING INTERACTION, GERM PLASM; 2.098A {DROSOPHILA MELANOGASTER},,,5A49_C,16.4384,27.6 SIF-Syn: Has same start as four other phages in its cluster
    /note=Good CP. Original start has best values. No strong hits for any specific function

CDS 60796 - 61506
  /gene="88"
  /product="gp88"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_88"
    /note=Original Glimmer call @bp 60796 has strength 11.46; Genemark calls start at 60796
    /note=SSC: 60796-61506 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_MASELOP_87 [Rhodococcus phage Maselop] ],,NCBI, q1:s1 100.0% 3.2898E-163 GAP: 92 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.754, -3.2495416658190135, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MASELOP_87 [Rhodococcus phage Maselop] ],,WNM65010,99.5763,3.2898E-163 SIF-HHPRED: DUF732 ; Protein of unknown function (DUF732),,,PF05305.18,30.0847,96.9 SIF-Syn: Has the most annotated start and calls it, shared with members of the CR cluster and phages from other clusters.
    /note=Chosen start has best RBS values and CP.  No significant hits for any function in NCBI Blast or HHpred.

CDS 61550 - 62035
  /gene="89"
  /product="gp89"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_89"
    /note=Original Glimmer call @bp 61550 has strength 7.34; Genemark calls start at 61550
    /note=SSC: 61550-62035 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_APIARY_88 [Rhodococcus phage Apiary]],,NCBI, q1:s1 100.0% 3.80865E-99 GAP: 43 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.754, -3.170856472917156, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_APIARY_88 [Rhodococcus phage Apiary]],,WNM69896,93.9394,3.80865E-99 SIF-HHPRED: DUF6152 ; Family of unknown function (DUF6152),,,PF19649.3,36.646,44.5 SIF-Syn: This gene does not have the most annotated start, but the start it does have is selected 100% of the time it is present. It is present in 6 out of the 32 genes in this pham.
    /note=This was the best start, had the best scores and strong synteny in the gene`s pham, and good coding potential. There were no strong hits for any particular function.

CDS 62131 - 62601
  /gene="90"
  /product="gp90"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_90"
    /note=Original Glimmer call @bp 62239 has strength 7.3; Genemark calls start at 62239
    /note=SSC: 62131-62601 CP: yes SCS: both-cs ST: NA BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_89 [Rhodococcus phage Braxoaddie] ],,NCBI, q1:s1 100.0% 1.1447E-92 GAP: 95 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.452, -3.799245402967468, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_89 [Rhodococcus phage Braxoaddie] ],,WIC89711,91.0256,1.1447E-92 SIF-HHPRED: PHP_HisPPase; Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase.,,,cd07432,19.8718,29.6 SIF-Syn: This gene is an orpham, no clear synteny.
    /note=This start has the best scores, though we did note it has a larger gap which could be considered as evidence to lengthen the start. However, since it is an orpham and the coding potential was covered by this better start and hits no specific function, so we don`t think the evidence is convincing enough to have us change the start.

CDS 62598 - 62903
  /gene="91"
  /product="gp91"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_91"
    /note=Original Glimmer call @bp 62598 has strength 5.32; Genemark calls start at 62598
    /note=SSC: 62598-62903 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_90 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 100.0% 4.8369E-61 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.242, -4.699481771036304, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_90 [Rhodococcus phage Braxoaddie]],,WIC89712,100.0,4.8369E-61 SIF-HHPRED: c.52.1.0 (A:2-180) automated matches {Escherichia coli K-12 [TaxId: 83333]} | CLASS: Alpha and beta proteins (a/b), FOLD: Restriction endonuclease-like, SUPFAM: Restriction endonuclease-like, FAM: automated matches,,,SCOP_d3c0ua1,28.7129,42.0 SIF-Syn: Five other phages from different clusters have this gene at the same start.
    /note=Chosen start has the best possible RBS scores and CP. No significant hits for function.

CDS 62960 - 63250
  /gene="92"
  /product="gp92"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_92"
    /note=Original Glimmer call @bp 63041 has strength 8.06; Genemark calls start at 62960
    /note=SSC: 62960-63250 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_91 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 100.0% 8.05318E-60 GAP: 56 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.754, -3.170856472917156, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_91 [Rhodococcus phage Braxoaddie]],,WIC89713,100.0,8.05318E-60 SIF-HHPRED: Outer capsid protein sigma-1; cell attachment protein, reovirus sigma1, coiled coil, beta-spiral repeat, VIRAL PROTEIN; 2.15A {Mammalian orthoreovirus 3 Dearing},,,6GAP_A,47.9167,76.4 SIF-Syn: This start is the most annotated start in the gene`s pham and is called 100% of the time it is present.
    /note=The start was changed from 63041 to 62960, as it had better scores, is the longest ORF, has less of a gap, and is the most annotated start for this gene`s pham. Additionally, the prior start would not have included all the coding potential. This mainly hits hypothetical protein functions and does not have any hits that suggest a more specific function.

CDS 63343 - 64737
  /gene="93"
  /product="gp93"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_93"
    /note=Original Glimmer call @bp 63343 has strength 13.25; Genemark calls start at 63343
    /note=SSC: 63343-64737 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_92 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 100.0% 0.0 GAP: 92 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.754, -3.170856472917156, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_92 [Rhodococcus phage Braxoaddie]],,WIC89714,99.3534,0.0 SIF-HHPRED: Probable ferredoxin,Putative cytochrome P450 143; M. tuberculosis, cytochrome P450, redox partner, ferredoxin, Rv1786, Rv1785c, fusion, chimera, OXIDOREDUCTASE; HET: HEM; 1.6A {Mycobacterium tuberculosis H37Rv},,,8AMQ_A,11.6379,28.9 SIF-Syn: 
    /note=Chosen start has good CP and RBS numbers. Five other phages have this gene and two of them have the same start. There were no significant hits for function.

CDS 64861 - 66057
  /gene="94"
  /product="gp94"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_94"
    /note=Original Glimmer call @bp 64861 has strength 13.91; Genemark calls start at 64861
    /note=SSC: 64861-66057 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_POLYYUKI_92 [Rhodococcus phage Polyyuki]],,NCBI, q1:s1 100.0% 0.0 GAP: 123 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.754, -3.170856472917156, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_POLYYUKI_92 [Rhodococcus phage Polyyuki]],,WNM67476,95.4887,0.0 SIF-HHPRED: ABC_ATPase ; P-loop domain,,,PF09818.13,23.1156,78.1 SIF-Syn: Five other phages have the same start.
    /note=Start has good CP and RBS values. No good hits for a function.

CDS 66128 - 66325
  /gene="95"
  /product="gp95"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_95"
    /note=Original Glimmer call @bp 66128 has strength 6.67; Genemark calls start at 66128
    /note=SSC: 66128-66325 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_94 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 100.0% 2.80598E-37 GAP: 70 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.754, -3.170856472917156, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_94 [Rhodococcus phage Braxoaddie]],,WIC89716,100.0,2.80598E-37 SIF-HHPRED: DNA-directed RNA polymerase subunit P; Transcription, DNA-directed RNA polymerase; HET: ZN; 3.5A {Thermococcus kodakarensis},,,4QIW_W,13.8462,72.5 SIF-Syn: It has the most suggested start in its gene`s pham and continues to show a strong similarity with other phages in the CR cluster, like Apiary and GuyFagieri.
    /note=This start has the best scores and has good coding potential, additionally, it is the most annotated start for this gene`s pham although there are a small number of genomes in it. Doesn`t have strong hits for any specific function.

CDS 66328 - 66642
  /gene="96"
  /product="gp96"
  /function="Hypothetical Protein"
  /locus tag="CoffeeBean_96"
    /note=Original Glimmer call @bp 66328 has strength 7.78; Genemark calls start at 66328
    /note=SSC: 66328-66642 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BRAXOADDIE_95 [Rhodococcus phage Braxoaddie]],,NCBI, q1:s1 100.0% 1.06931E-70 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.754, -3.170856472917156, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BRAXOADDIE_95 [Rhodococcus phage Braxoaddie]],,WIC89717,100.0,1.06931E-70 SIF-HHPRED: c.47.1.23 (A:4-89) Hypothetical protein Atu0228 {Agrobacterium tumefaciens [TaxId: 358]} | CLASS: Alpha and beta proteins (a/b), FOLD: Thioredoxin fold, SUPFAM: Thioredoxin-like, FAM: Selenoprotein W-related,,,SCOP_d2fa8a1,38.4615,51.8 SIF-Syn: coincides with others in CR cluster
    /note=Went with suggested start. CP is good. Decided that this was a hypothetical protein because all proposed functions from HHPred and Phages DB. Frequency were inconsistent, and functions in HHPred had low e-values, so it was concluded that this was a hypothetical protein.