CDS 1 - 645 /gene="1" /product="gp1" /function="terminase, small subunit" /locus tag="Yeti_1" /note=Original Glimmer call @bp 1 has strength 6.39; Genemark calls start at 1 /note=SSC: 1-645 CP: no SCS: both ST: SS BLAST-Start: [terminase small subunit [Microbacterium phage Phorgeous]],,NCBI, q1:s1 100.0% 6.35048E-152 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.887, -3.2925703904164987, no F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Microbacterium phage Phorgeous]],,UVK63182,99.5327,6.35048E-152 SIF-HHPRED: Phage_term_sma ; Putative bacteriophage terminase small subunit,,,PF07141.15,88.3178,99.2 SIF-Syn: Found upstream of Terminase as in Honeyfin. /note=NOTE /note=Current Gene Number: 1 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 2.887 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All evidence matches /note= /note=FUNCTION /note=Synteny: Terminase Small Subunit /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 642 - 914 /gene="2" /product="gp2" /function="hypothetical protein" /locus tag="Yeti_2" /note=Original Glimmer call @bp 642 has strength 11.13; Genemark calls start at 654 /note=SSC: 642-914 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein HOT30_gp02 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 7.62858E-59 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.987, -4.778071418780228, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp02 [Microbacterium phage Paschalis] ],,YP_009801849,100.0,7.62858E-59 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 2 /note=Did the start site stay the same or change: Change /note=Do the Glimmer and Genemark start sites agree? No /note=What about Starterator? Yes, agree w Glimmer Start /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: No /note=Is there a 1:1 alignment on blast and with which phage? Yes, Brazzle PHS, Cranjis, Crazy Rich, Crisis, EarickHC, Hermeonysus, Jollipop, KaiHai Dragon, Kowalski, NoodlelyBoi, Paschalis, Phorgeous, PierreOrion, Piperis, Ramiel05, Shotgun /note=Z score = 1.987 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 911 - 2533 /gene="3" /product="gp3" /function="terminase, large subunit" /locus tag="Yeti_3" /note=Original Glimmer call @bp 911 has strength 12.34; Genemark calls start at 911 /note=SSC: 911-2533 CP: yes SCS: both ST: SS BLAST-Start: [terminase large subunit [Microbacterium phage Shotgun] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.056, -5.402017758808125, no F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Microbacterium phage Shotgun] ],,YP_010751475,100.0,0.0 SIF-HHPRED: Terminase, large subunit; phage defense, pattern-recognition receptor, nlr, stand, atpase, ANTIVIRAL PROTEIN; HET: ATP;{Salmonella enterica},,,8DGC_F,87.037,100.0 SIF-Syn: Found downstream of terminase, small subunit as in Honeyfin /note=NOTE /note=Current Gene Number: 3 /note=Did the start site stay the same or change: change 911. /note=Do the Glimmer and Genemark start sites agree? yes. /note=What about Starterator? yes. /note=Is the ORF chosen the longest ORF: no. /note=Is all of the coding potential captured on GeneMark file: yes, captures more. /note=Is there a 1:1 alignment on blast and with which phage? Yes, Jollipop /note=Z score = 2.056 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: Terminase /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 2608 - 2841 /gene="4" /product="gp4" /function="hypothetical protein" /locus tag="Yeti_4" /note=Original Glimmer call @bp 2608 has strength 19.25; Genemark calls start at 2608 /note=SSC: 2608-2841 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp04 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 4.46722E-46 GAP: 74 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.104, -4.39472476044006, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp04 [Microbacterium phage Paschalis] ],,YP_009801851,100.0,4.46722E-46 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 4 /note=Did the start site stay the same or change: change, starts at 2608. /note=Do the Glimmer and Genemark start sites agree? yes. /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? BrazzalePHS /note=Z score = 2.104 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 2838 - 3254 /gene="5" /product="gp5" /function="hypothetical protein" /locus tag="Yeti_5" /note=Original Glimmer call @bp 2838 has strength 13.75; Genemark calls start at 2838 /note=SSC: 2838-3254 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PIPERIS_5 [Microbacterium phage Piperis] ],,NCBI, q1:s1 100.0% 6.59999E-92 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.79, -3.875201829906135, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PIPERIS_5 [Microbacterium phage Piperis] ],,QCW22563,100.0,6.59999E-92 SIF-HHPRED: a.4.5.0 (A:3-130) automated matches {Mycobacterium tuberculosis [TaxId: 1773]} | CLASS: All alpha proteins, FOLD: DNA/RNA-binding 3-helical bundle, SUPFAM: `Winged helix` DNA-binding domain, FAM: automated matches,,,SCOP_d2o03a1,32.6087,91.7 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 5 /note=Did the start site stay the same or change: changed to 2838. /note=Do the Glimmer and Genemark start sites agree? yes. /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: no, it starts at about 2850 instead of 2838. /note=Is there a 1:1 alignment on blast and with which phage? Phorgeous /note=Z score = 2.79 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 3254 - 3418 /gene="6" /product="gp6" /function="hypothetical protein" /locus tag="Yeti_6" /note=Original Glimmer call @bp 3254 has strength 7.52; Genemark calls start at 3254 /note=SSC: 3254-3418 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA06_gp06 [Microbacterium phage Shotgun] ],,NCBI, q1:s1 100.0% 4.132E-32 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.887, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA06_gp06 [Microbacterium phage Shotgun] ],,YP_010751478,100.0,4.132E-32 SIF-HHPRED: HalOD2 ; Halobacterial output domain 2,,,PF18547.5,38.8889,94.9 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 6 /note=Did the start site stay the same or change: change to 3254. /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes. /note=Is the ORF chosen the longest ORF: yes. /note=Is all of the coding potential captured on GeneMark file: no it does not capture from 3254 to 3418. /note=Is there a 1:1 alignment on blast and with which phage? no. /note=Z score = 2.887 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 3479 - 4219 /gene="7" /product="gp7" /function="hypothetical protein" /locus tag="Yeti_7" /note=Original Glimmer call @bp 3479 has strength 15.75; Genemark calls start at 3479 /note=SSC: 3479-4219 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp08 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 1.67662E-176 GAP: 60 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.006, -5.425375072945052, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp08 [Microbacterium phage Quhwah] ],,YP_009803206,100.0,1.67662E-176 SIF-HHPRED: DUF2786 ; Protein of unknown function (DUF2786),,,PF10979.12,15.4472,99.2 SIF-Syn: NKF /note=Current Gene Number: 7 /note=Did the start site stay the same or change: change to 3479 /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: no /note=Is there a 1:1 alignment on blast and with which phage? none /note=Z score = 2.006 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 4216 - 4377 /gene="8" /product="gp8" /function="hypothetical protein" /locus tag="Yeti_8" /note=Original Glimmer call @bp 4216 has strength 8.69; Genemark calls start at 4219 /note=SSC: 4216-4377 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein HOT47_gp09 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 3.92443E-31 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.551, -3.9917022260392767, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp09 [Microbacterium phage Quhwah] ],,YP_009803207,100.0,3.92443E-31 SIF-HHPRED: g.41.14.1 (A:97-125) NADH pyrophosphatase intervening domain {Escherichia coli [TaxId: 562]} | CLASS: Small proteins, FOLD: Rubredoxin-like, SUPFAM: NADH pyrophosphatase intervening domain, FAM: NADH pyrophosphatase intervening domain,,,SCOP_d2gb5a2,52.8302,93.5 SIF-Syn: NKF /note=Current Gene Number: 8 /note=Did the start site stay the same or change: changed to 4126 /note=Do the Glimmer and Genemark start sites agree? no /note=What about Starterator? agrees with glimmer start /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? no /note=Z score = 2.551 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 4389 - 4703 /gene="9" /product="gp9" /function="hypothetical protein" /locus tag="Yeti_9" /note=Original Glimmer call @bp 4389 has strength 8.32; Genemark calls start at 4389 /note=SSC: 4389-4703 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp10 [Microbacterium phage Quhwah] ],,NCBI, q1:s5 100.0% 2.63324E-68 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.113, -6.454543007120014, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp10 [Microbacterium phage Quhwah] ],,YP_009803208,96.2963,2.63324E-68 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 9 /note=Did the start site stay the same or change: changes to 4389 /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: no but almost all is captured. /note=Is there a 1:1 alignment on blast and with which phage? yes, PierreOrion_Draft /note=Z score = 1.113 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 4700 - 5074 /gene="10" /product="gp10" /function="hypothetical protein" /locus tag="Yeti_10" /note=Original Glimmer call @bp 4700 has strength 11.79; Genemark calls start at 4700 /note=SSC: 4700-5074 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp11 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 1.30574E-84 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.887, -3.4175091270247986, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp11 [Microbacterium phage Honeyfin] ],,YP_010751392,100.0,1.30574E-84 SIF-HHPRED: DUF6758 ; Family of unknown function (DUF6758),,,PF20544.2,22.5806,90.8 SIF-Syn: NKF /note=Current Gene Number: 10 /note=Did the start site stay the same or change: changed to 4,700 /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: no but almost all is captured /note=Is there a 1:1 alignment on blast and with which phage? yes, Piperis /note=Z score = 2.887 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 5144 - 5356 /gene="11" /product="gp11" /function="hypothetical protein" /locus tag="Yeti_11" /note=Original Glimmer call @bp 5144 has strength 13.55; Genemark calls start at 5144 /note=SSC: 5144-5356 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp12 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 2.18757E-43 GAP: 69 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.042, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp12 [Microbacterium phage Honeyfin] ],,YP_010751393,100.0,2.18757E-43 SIF-HHPRED: SIF-Syn: NKF /note=NOTES /note=Current Gene Number: 11 /note=Did the start site stay the same or change: Change /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Cranjis /note=Z score = 3.042 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 5365 - 5763 /gene="12" /product="gp12" /function="hypothetical protein" /locus tag="Yeti_12" /note=Original Glimmer call @bp 5365 has strength 14.42; Genemark calls start at 5365 /note=SSC: 5365-5763 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp13 [Microbacterium phage Honeyfin] ],,NCBI, q1:s5 100.0% 4.23259E-91 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.816, -5.056409918993686, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp13 [Microbacterium phage Honeyfin] ],,YP_010751394,97.0588,4.23259E-91 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 12 /note=Did the start site stay the same or change: changes to 5365 /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? Piperis /note=Z score = 1.816 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 5763 - 6131 /gene="13" /product="gp13" /function="hypothetical protein" /locus tag="Yeti_13" /note=Original Glimmer call @bp 5763 has strength 15.19; Genemark calls start at 5763 /note=SSC: 5763-6131 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp14 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 2.07416E-81 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.967, -4.820269098574683, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp14 [Microbacterium phage Honeyfin] ],,YP_010751395,100.0,2.07416E-81 SIF-HHPRED: GumN; poorly characterized family of proteins related to gumN pathogenicity factor of Xanthomonas.,,,cd14788,35.2459,92.5 SIF-Syn: NKF /note=NOTES /note=Current Gene Number: 13 /note=Did the start site stay the same or change: Stay /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Honeyfin /note=Z score = 1.967 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 6128 - 6358 /gene="14" /product="gp14" /function="hypothetical protein" /locus tag="Yeti_14" /note=Original Glimmer call @bp 6128 has strength 6.83; Genemark calls start at 6134 /note=SSC: 6128-6358 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein QDA05_gp15 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 6.9655E-49 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.82, -5.047808595116427, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp15 [Microbacterium phage Honeyfin] ],,YP_010751396,100.0,6.9655E-49 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 14 /note=Did the start site stay the same or change: changes to 6128 /note=Do the Glimmer and Genemark start sites agree? no /note=What about Starterator? agrees with Glimmer start. /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: no not all the potential is recorded. /note=Is there a 1:1 alignment on blast and with which phage? Piperis /note=Z score = 1.82 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 6355 - 6699 /gene="15" /product="gp15" /function="hypothetical protein" /locus tag="Yeti_15" /note=Original Glimmer call @bp 6355 has strength 16.07; Genemark calls start at 6355 /note=SSC: 6355-6699 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp16 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 6.41792E-73 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.411, -3.8970005018578204, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp16 [Microbacterium phage Honeyfin] ],,YP_010751397,100.0,6.41792E-73 SIF-HHPRED: SIF-Syn: NKF /note=NOTES /note=Current Gene Number: 15 /note=Did the start site stay the same or change: Change /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Honeyfin /note=Z score = 2.411 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 6792 - 7337 /gene="16" /product="gp16" /function="hypothetical protein" /locus tag="Yeti_16" /note=Original Glimmer call @bp 6792 has strength 14.76; Genemark calls start at 6792 /note=SSC: 6792-7337 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp18 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 2.0038E-125 GAP: 92 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.161, -4.337049294579155, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp18 [Microbacterium phage Quhwah] ],,YP_009803216,100.0,2.0038E-125 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 16 /note= /note=Did the start site stay the same or change: Stayed the same /note= /note=Do the Glimmer and Genemark start sites agree? Yes. Both Glimmer and Genemark agree /note= /note=What about Starterator? Starterator also agrees. /note= /note=Is the ORF chosen the longest ORF: The chosen ORF is the longest at 546 codons. /note= /note=Is all of the coding potential captured on GeneMark file: Yes /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, honeyfin /note= /note=Z score = 2.161 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION : No known function /note= /note=Synteny: Yes /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Honeyfin (4e^-98) /note= /note=Blast NCBI function match with E value should be 10^-7 or less: Honeyfin (2.0038e^-125) /note= /note=HHPRED Match with > 90% probability: N/A /note= /note=Conserved Domain: None CDS 7403 - 7573 /gene="17" /product="gp17" /function="hypothetical protein" /locus tag="Yeti_17" /note=Original Glimmer call @bp 7403 has strength 8.86; Genemark calls start at 7403 /note=SSC: 7403-7573 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp16 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 9.78509E-34 GAP: 65 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.541, -4.536085090614939, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp16 [Microbacterium phage Paschalis] ],,YP_009801863,100.0,9.78509E-34 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 17 /note= /note=Did the start site stay the same or change: Same /note= /note=Do the Glimmer and Genemark start sites agree? Yes /note= /note=What about Starterator? Yes; 87.1% /note= /note=Is the ORF chosen the longest ORF: It is the longest ORF. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, it is aligned with the Honeyfin /note=Z score = 2.541 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: No Known Function /note=Synteny: Yes; Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: BrazzlePHS (1e^-29) /note=Blast NCBI function match with E value should be 10^-7 or less: Honeyfin (9.79^-34) /note=HHPRED Match with > 90% probability: No; 63.3% /note=Conserved Domain: None CDS 7576 - 7995 /gene="18" /product="gp18" /function="hypothetical protein" /locus tag="Yeti_18" /note=Original Glimmer call @bp 7576 has strength 9.3; Genemark calls start at 7588 /note=SSC: 7576-7995 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein HOT30_gp17 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 2.77901E-95 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.462, -3.790975366313636, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp17 [Microbacterium phage Paschalis] ],,YP_009801864,100.0,2.77901E-95 SIF-HHPRED: DUF1360 ; Protein of unknown function (DUF1360),,,PF07098.15,85.6115,99.9 SIF-Syn: NKF /note=Current Gene Number: 18… Issue /note= /note=Did the start site stay the same or change: Changed /note= /note=Do the Glimmer and Genemark start sites agree? No. /note= /note=What about Starterator? Yes; 75.9% /note= /note=Is the ORF chosen the longest ORF: No. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? N/A /note=Z score = 2.406 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We adjusted the start site to 7588… /note= /note=FUNCTION: No Known Function /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 7992 - 8213 /gene="19" /product="gp19" /function="hypothetical protein" /locus tag="Yeti_19" /note=Original Glimmer call @bp 7992 has strength 7.4; Genemark calls start at 7992 /note=SSC: 7992-8213 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLEFORTUNE_20 [Microbacterium phage LittleFortune]],,NCBI, q1:s1 100.0% 5.22473E-43 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.664, -3.2297885750240023, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLEFORTUNE_20 [Microbacterium phage LittleFortune]],,WNM67723,100.0,5.22473E-43 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 19 /note= /note=Did the start site stay the same or change: Same /note= /note=Do the Glimmer and Genemark start sites agree? Yes. /note= /note=What about Starterator? Starterator agrees /note= /note=Is the ORF chosen the longest ORF: No. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, it was aligned with LittleFortune /note= /note=Z score = 2.664 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note= /note=FUNCTION: No Known Function /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: LittleFortune (9e^-41) /note=Blast NCBI function match with E value should be 10^-7 or less: LittleFortune (5.22e^-43) /note=HHPRED Match with > 90% probability: No; 70% /note=Conserved Domain: N/A CDS 8441 - 10147 /gene="20" /product="gp20" /function="portal protein" /locus tag="Yeti_20" /note=Original Glimmer call @bp 8450 has strength 18.26; Genemark calls start at 8441 /note=SSC: 8441-10147 CP: yes SCS: both-gm ST: NI BLAST-Start: [portal protein [Microbacterium phage LittleFortune]],,NCBI, q1:s1 100.0% 0.0 GAP: 227 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.189, -7.346845867616434, no F: portal protein SIF-BLAST: ,,[portal protein [Microbacterium phage LittleFortune]],,WNM67724,100.0,0.0 SIF-HHPRED: Portal protein; Prohead I, icosahedral symmetry, HK97, phage, capsid, VIRUS; 3.6A {Escherichia phage HK97},,,8FQL_L,70.0704,100.0 SIF-Syn: Found upstream of capsid maturation protease as in honeyfin /note=Current Gene Number: 20 /note= /note=Did the start site stay the same or change: Same /note= /note=Do the Glimmer and Genemark start sites agree? No. /note= /note=What about Starterator? No; 7.3% /note= /note=Is the ORF chosen the longest ORF: No /note= /note=Is all of the coding potential captured on GeneMark file: Yes /note= /note=Is there a 1:1 alignment on blast and with which phage? No, but there is a 99% alignment with LittleFortune /note=Z score = 1.435 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: Portal Protein /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: LittleFortune; 0 /note=Blast NCBI function match with E value should be 10^-7 or less: LittleFortune; 0 /note=HHPRED Match with > 90% probability: HK97; 100% /note=Conserved Domain: None CDS 10144 - 10590 /gene="21" /product="gp21" /function="hypothetical protein" /locus tag="Yeti_21" /note=Original Glimmer call @bp 10144 has strength 13.76; Genemark calls start at 10144 /note=SSC: 10144-10590 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp20 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 3.99464E-103 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.055, -4.847583656344026, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp20 [Microbacterium phage Paschalis] ],,YP_009801867,100.0,3.99464E-103 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 21 /note= /note=Did the start site stay the same or change: Same /note= /note=Do the Glimmer and Genemark start sites agree? Yes. /note= /note=What about Starterator? yes: 92.6% /note= /note=Is the ORF chosen the longest ORF: Yes. /note= /note=Is all of the coding potential captured on GeneMark file: Yes /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, it is aligned with Honeyfin /note=Z score = 2.055 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: No Known Function /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: None; 2.5 /note=Blast NCBI function match with E value should be 10^-7 or less: Honeyfin (3.99e^-103 /note=HHPRED Match with > 90% probability: no; 80.2% /note=Conserved Domain: None CDS 10571 - 10669 /gene="22" /product="gp22" /function="hypothetical protein" /locus tag="Yeti_22" /note=Genemark calls start at 10571 /note=SSC: 10571-10669 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_PIPERSANSNOM_22 [Microbacterium phage PiperSansNom] ],,NCBI, q1:s1 100.0% 1.37553E-13 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.163, -7.656470508679953, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PIPERSANSNOM_22 [Microbacterium phage PiperSansNom] ],,QDP45415,100.0,1.37553E-13 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 22 /note= /note=Did the start site stay the same or change: Yes /note= /note=Do the Glimmer and Genemark start sites agree? N/A /note= /note=What about Starterator? 77.8% /note= /note=Is the ORF chosen the longest ORF: Yes. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, it is aligned with LittleFortune /note=Z score = 1.163 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: No Known Function /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: LittleFortune (1e^-13) /note=Blast NCBI function match with E value should be 10^-7 or less: LittleFortune (1.38^-13) /note=HHPRED Match with > 90% probability: no; 88.8% /note=Conserved Domain: None CDS 10662 - 11465 /gene="23" /product="gp23" /function="hypothetical protein" /locus tag="Yeti_23" /note=Original Glimmer call @bp 10662 has strength 13.89; Genemark calls start at 10662 /note=SSC: 10662-11465 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.133, -2.3158002311349737, yes F: hypothetical protein SIF-BLAST: ,,[portal protein [Microbacterium phage Paschalis] ],,YP_009801869,100.0,0.0 SIF-HHPRED: Phage_Mu_F ; Phage Mu protein F like protein,,,PF04233.18,52.4345,99.5 SIF-Syn: NKF /note=Current Gene Number: 23 /note= /note=Did the start site stay the same or change: Same /note= /note=Do the Glimmer and Genemark start sites agree? Yes. /note= /note=What about Starterator? Yes; 90.7% /note= /note=Is the ORF chosen the longest ORF: No. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, it is aligned with Honeyfin /note=Z score = 3.133 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note= /note=FUNCTION: NKF /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Honeyfin; 1e^-151 /note=Blast NCBI function match with E value should be 10^-7 or less: Honeyfin; 0 /note=HHPRED Match with > 90% probability: 99.5% /note=Conserved Domain: <10% CDS 11541 - 11825 /gene="24" /product="gp24" /function="hypothetical protein" /locus tag="Yeti_24" /note=Original Glimmer call @bp 11541 has strength 16.69; Genemark calls start at 11541 /note=SSC: 11541-11825 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp23 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 1.0064E-62 GAP: 75 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.142, -4.314663920718777, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp23 [Microbacterium phage Paschalis] ],,YP_009801870,100.0,1.0064E-62 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 24 /note= /note=Did the start site stay the same or change: Same /note= /note=Do the Glimmer and Genemark start sites agree? Yes. /note= /note=What about Starterator? Yes; 97.6% /note= /note=Is the ORF chosen the longest ORF: Yes. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, it is aligned with Piperis /note=Z score = 2.142 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: No Known Function /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Piperis: 7e^-51 /note=Blast NCBI function match with E value should be 10^-7 or less: Piperis; 1.01^-62 /note=HHPRED Match with > 90% probability: 24.5% /note=Conserved Domain: None CDS 11944 - 13413 /gene="25" /product="gp25" /function="capsid maturation protease" /locus tag="Yeti_25" /note=Original Glimmer call @bp 11944 has strength 18.6; Genemark calls start at 11944 /note=SSC: 11944-13413 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 0.0 GAP: 118 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.887, -5.895904363400588, no F: capsid maturation protease SIF-BLAST: ,,[portal protein [Microbacterium phage Paschalis] ],,YP_009801871,100.0,0.0 SIF-HHPRED: Peptidase_S78 ; Caudovirus prohead serine protease,,,PF04586.21,37.8323,99.2 SIF-Syn: Upstream of major capsid hexamer protein as found in honeyfin /note=Current Gene Number: 25 /note= /note=Did the start site stay the same or change: Same. /note= /note=Do the Glimmer and Genemark start sites agree? Yes. /note= /note=What about Starterator? Yes; 86% /note= /note=Is the ORF chosen the longest ORF: Yes. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, it is aligned with Piperis /note=Z score = 1.887 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: capsid maturation protease /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Piperis; 0 /note=Blast NCBI function match with E value should be 10^-7 or less: Piperis; 0 /note=HHPRED Match with > 90% probability: 99.2% /note=Conserved Domain: None CDS 13410 - 13652 /gene="26" /product="gp26" /function="hypothetical protein" /locus tag="Yeti_26" /note=Original Glimmer call @bp 13410 has strength 10.84; Genemark calls start at 13410 /note=SSC: 13410-13652 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp25 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 1.02672E-47 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.313, -3.9584221859736637, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp25 [Microbacterium phage Paschalis] ],,YP_009801872,100.0,1.02672E-47 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 26 /note= /note=Did the start site stay the same or change: Same /note= /note=Do the Glimmer and Genemark start sites agree? Yes. /note= /note=What about Starterator? No; 77.4% /note= /note=Is the ORF chosen the longest ORF: No. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? /note=Yes, it is aligned with Piperis /note=Z score = 2.313 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: No Known Function /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Piperis; 3e^-38 /note=Blast NCBI function match with E value should be 10^-7 or less: Piperis; 1.03^-47 /note=HHPRED Match with > 90% probability: No; 43.7% /note=Conserved Domain: None CDS 13790 - 15646 /gene="27" /product="gp27" /function="major capsid hexamer protein" /locus tag="Yeti_27" /note=Original Glimmer call @bp 13790 has strength 15.46; Genemark calls start at 13790 /note=SSC: 13790-15646 CP: yes SCS: both ST: SS BLAST-Start: [major capsid hexamer protein [Microbacterium phage PiperSansNom]],,NCBI, q1:s1 100.0% 0.0 GAP: 137 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.966, -2.66371296573402, yes F: major capsid hexamer protein SIF-BLAST: ,,[major capsid hexamer protein [Microbacterium phage PiperSansNom]],,QDP45420,100.0,0.0 SIF-HHPRED: SIF-Syn: Found downstream of capsid maturation protease found in honeyfin /note=Current Gene Number: 27 /note= /note=Did the start site stay the same or change: Same /note= /note=Do the Glimmer and Genemark start sites agree? Yes. /note= /note=What about Starterator? No; 22.5% /note= /note=Is the ORF chosen the longest ORF: Yes. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, It is aligned PiperSansNom /note=Z score = 2.966 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: major capsid hexamer protein /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: PiperSansNom; 0 /note=Blast NCBI function match with E value should be 10^-7 or less: PiperSansNom; 0 /note=HHPRED Match with > 90% probability: 36.8% /note=Conserved Domain: None CDS 15862 - 16509 /gene="28" /product="gp28" /function="hypothetical protein" /locus tag="Yeti_28" /note=Original Glimmer call @bp 15862 has strength 13.79; Genemark calls start at 15862 /note=SSC: 15862-16509 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein EARICKHC_28 [Microbacterium phage EarickHC]],,NCBI, q1:s1 100.0% 2.89953E-155 GAP: 215 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.498, -6.483014150123188, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein EARICKHC_28 [Microbacterium phage EarickHC]],,UVG34503,100.0,2.89953E-155 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 28 /note= /note=Did the start site stay the same or change: Same. /note= /note=Do the Glimmer and Genemark start sites agree? Yes. /note= /note=What about Starterator? No; 0.4% /note= /note=Is the ORF chosen the longest ORF: No. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? It has a 99% alignment with Earick /note= /note=Z score = 1.498 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: Major capsid pentamer protein /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Earick; 1e^-122 /note=Blast NCBI function match with E value should be 10^-7 or less: Earick; 2.9^-155 /note=HHPRED Match with > 90% probability: 9.2% /note=Conserved Domain: None CDS 16506 - 17300 /gene="29" /product="gp29" /function="hypothetical protein" /locus tag="Yeti_29" /note=Original Glimmer call @bp 16506 has strength 14.47; Genemark calls start at 16506 /note=SSC: 16506-17300 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp32 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 1.4118E-180 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.411, -3.8970005018578204, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp32 [Microbacterium phage Quhwah] ],,YP_009803230,100.0,1.4118E-180 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 29 /note= /note=Did the start site stay the same or change: Same. /note= /note=Do the Glimmer and Genemark start sites agree? Yes. /note= /note=What about Starterator? No; 73.8% /note= /note=Is the ORF chosen the longest ORF: No. /note= /note=Is all of the coding potential captured on the GeneMark file: Yes. /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, it is aligned with Quhwah /note=Z score = 2.411 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=We kept the start site because the codons align with other similar genes numbers from different phages. /note= /note=FUNCTION: No Known Function /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Quhwah; 1e^-151 /note=Blast NCBI function match with E value should be 10^-7 or less: Quhwah; 1.41^-180 /note=HHPRED Match with > 90% probability: 77.4% /note=Conserved Domain: No; 5.33% CDS 17302 - 17982 /gene="30" /product="gp30" /function="major tail protein" /locus tag="Yeti_30" /note=Original Glimmer call @bp 17302 has strength 14.83; Genemark calls start at 17302 /note=SSC: 17302-17982 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 1.32115E-161 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.817, -4.9912573797770525, no F: major tail protein SIF-BLAST: ,,[major tail protein [Microbacterium phage Paschalis] ],,YP_009801876,100.0,1.32115E-161 SIF-HHPRED: SIF-Syn: Found upstream of head-to-tail adapter as in Busephilis. /note=NOTE /note=Current Gene Number: 30 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Y /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Y /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? Y /note=Z score = 1.817 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All sources agree /note= /note=FUNCTION - Major tail protein /note=Synteny: Y Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 17991 - 18905 /gene="31" /product="gp31" /function="head-to-tail adaptor" /locus tag="Yeti_31" /note=Original Glimmer call @bp 17991 has strength 12.9; Genemark calls start at 17991 /note=SSC: 17991-18905 CP: yes SCS: both ST: NI BLAST-Start: [head-tail adaptor [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 0.0 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.803, -3.4668782168002776, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-tail adaptor [Microbacterium phage Quhwah] ],,YP_009803232,99.6711,0.0 SIF-HHPRED: Neck 1 protein, gp14; Myophage, redox trigger, VIRUS; 4.5A {Agrobacterium phage Milano},,,8FXR_i,44.7368,98.6 SIF-Syn: Found downstream of major tail protein as in Busephilis. /note=NOTE /note=Current Gene Number: 31 /note=Did the start site stay the same or change: stay the same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? Does not agree with other programs /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes /note=Z score = 2.803 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Everything but Starterator agrees. /note= /note=FUNCTION /note=Synteny: head-to-tail adaptor /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 18915 - 19379 /gene="32" /product="gp32" /function="hypothetical protein" /locus tag="Yeti_32" /note=Original Glimmer call @bp 18915 has strength 12.07; Genemark calls start at 18915 /note=SSC: 18915-19379 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp31 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 5.26065E-109 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.07, -4.465043966605421, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp31 [Microbacterium phage Paschalis] ],,YP_009801878,100.0,5.26065E-109 SIF-HHPRED: a.4.5.79 (A:1-80) Alkylmercury lyase MerB {Escherichia coli [TaxId: 562]} | CLASS: All alpha proteins, FOLD: DNA/RNA-binding 3-helical bundle, SUPFAM: `Winged helix` DNA-binding domain, FAM: MerB N-terminal domain-like,,,SCOP_d3f0pa1,36.3636,23.0 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 32 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 2.07 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=The genes are the same /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 19382 - 19786 /gene="33" /product="gp33" /function="hypothetical protein" /locus tag="Yeti_33" /note=Original Glimmer call @bp 19382 has strength 14.11; Genemark calls start at 19382 /note=SSC: 19382-19786 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp32 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 7.35675E-91 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.992, -6.768399669413642, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp32 [Microbacterium phage Paschalis] ],,YP_009801879,100.0,7.35675E-91 SIF-HHPRED: HK97-gp10_like ; Bacteriophage HK97-gp10, putative tail-component,,,PF04883.16,47.7612,99.1 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 33 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 0.992 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=This is the start because all of the programs agree with each other. /note= /note=FUNCTION /note=Synteny: /note=NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 19819 - 20247 /gene="34" /product="gp34" /function="tail assembly chaperone" /locus tag="Yeti_34" /note=Original Glimmer call @bp 19819 has strength 14.79; Genemark calls start at 19819 /note=SSC: 19819-20247 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp33 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 6.06647E-97 GAP: 32 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.105, -5.441385232411999, no F: tail assembly chaperone SIF-BLAST: ,,[hypothetical protein HOT30_gp33 [Microbacterium phage Paschalis] ],,YP_009801880,100.0,6.06647E-97 SIF-HHPRED: Phage_TAC_10 ; Phage tail assembly chaperone,,,PF10963.12,62.6761,97.3 SIF-Syn: Found upstream of tail assembly chaperone as in Busephilis. /note=Current Gene Number: 34 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 2.105 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the programs agree with each other /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 20313 - 20537 /gene="35" /product="gp35" /function="tail assembly chaperone" /locus tag="Yeti_35" /note=Original Glimmer call @bp 20313 has strength 8.63; Genemark calls start at 20313 /note=SSC: 20313-20537 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp34 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 9.349E-47 GAP: 65 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.697, -7.672378599604343, no F: tail assembly chaperone SIF-BLAST: ,,[hypothetical protein HOT30_gp34 [Microbacterium phage Paschalis] ],,YP_009801881,100.0,9.349E-47 SIF-HHPRED: SIF-Syn: Found upstream of tape measure protein as in Busephilis. /note=Current Gene Number: 35 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 0.697 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All the programs agree /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 20633 - 23500 /gene="36" /product="gp36" /function="tape measure protein" /locus tag="Yeti_36" /note=Original Glimmer call @bp 20633 has strength 12.76; Genemark calls start at 20633 /note=SSC: 20633-23500 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Microbacterium phage Selwyn23]],,NCBI, q1:s1 100.0% 0.0 GAP: 95 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.402, -4.301170562178417, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Microbacterium phage Selwyn23]],,QWY84817,100.0,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BF,13.1937,100.0 SIF-Syn: Found upstream of minor tail protein as in Busephilis. /note=Current Gene Number: 36 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 2.402 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=The data matches in the sources /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 23497 - 25449 /gene="37" /product="gp37" /function="minor tail protein" /locus tag="Yeti_37" /note=Original Glimmer call @bp 23497 has strength 16.06; Genemark calls start at 23497 /note=SSC: 23497-25449 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Busephilis] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.82, -2.90473872338446, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Busephilis] ],,QDF19051,100.0,0.0 SIF-HHPRED: Endo-1,4-beta-xylanase C; Binding Site, Carbohydrates, Enzyme Stability, Substrate Specificity, Endo-1, 4-beta-xylanase, Xylan-binding domain, Thermophilic enzymes, Thermostabilizing Domains, sugar; HET: CA, GOL; 2.43A {Paenibacillus barcinonensis},,,4XUP_D,71.8462,99.3 SIF-Syn: Found upstream of minor tail protein as in Busephilis. /note=Current Gene Number: 37 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 2.82 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All the sources agree /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 25463 - 27652 /gene="38" /product="gp38" /function="minor tail protein" /locus tag="Yeti_38" /note=Original Glimmer call @bp 25463 has strength 16.41; Genemark calls start at 25463 /note=SSC: 25463-27652 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 0.0 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.122, -2.338663114094478, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Honeyfin] ],,YP_010751420,100.0,0.0 SIF-HHPRED: Receptor-type tyrosine-protein phosphatase F; Fibronectin type-III, adhesion protein, CELL ADHESION; HET: SO4; 2.9A {Homo sapiens},,,6TPW_A,37.7229,99.4 SIF-Syn: Found upstream of minor tail protein as in Busephilis. /note=NOTE /note=Current Gene Number: 38 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 3.122 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=This is the start because all of the programs agree with each other. /note= /note=FUNCTION /note=Synteny: Honeyfin /note=minor tail protein /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 27652 - 28854 /gene="39" /product="gp39" /function="minor tail protein" /locus tag="Yeti_39" /note=Original Glimmer call @bp 27652 has strength 17.59; Genemark calls start at 27652 /note=SSC: 27652-28854 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Selwyn23] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.585, -3.3937592014038303, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Selwyn23] ],,QWY84820,100.0,0.0 SIF-HHPRED: Sipho_Gp37 ; Siphovirus ReqiPepy6 Gp37-like protein,,,PF14594.10,91.0,99.9 SIF-Syn: Found upstream of minor tail protein as in Busephilis. /note=NOTE /note=Current Gene Number: 39 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 2.585 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=This is the start because all of the programs agree with each other. /note= /note=FUNCTION /note=Synteny: Honeyfin /note=minor tail protein /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 28827 - 29423 /gene="40" /product="gp40" /function="minor tail protein" /locus tag="Yeti_40" /note=Original Glimmer call @bp 28854 has strength 13.56; Genemark calls start at 28854 /note=SSC: 28827-29423 CP: yes SCS: both-cs ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Honeyfin] ],,NCBI, q10:s1 95.4545% 1.0488E-134 GAP: -28 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.662, -7.392947760790533, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Honeyfin] ],,YP_010751422,100.0,1.0488E-134 SIF-HHPRED: SIF-Syn: Found downstream of minor tail protein as in Busephilis. /note=NOTE /note=Current Gene Number: 40 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Not informative /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 0.662 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=This is the start because all of the programs agree with each other. /note= /note=FUNCTION /note=Synteny: Honeyfin /note=minor tail protein /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 29434 - 29724 /gene="41" /product="gp41" /function="hypothetical protein" /locus tag="Yeti_41" /note=Original Glimmer call @bp 29434 has strength 11.43; Genemark calls start at 29434 /note=SSC: 29434-29724 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp44 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 1.21535E-59 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.122, -2.356391881054909, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp44 [Microbacterium phage Quhwah] ],,YP_009803242,100.0,1.21535E-59 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 41 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 3.122 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=This is the start because all of the programs agree with each other. /note= /note=FUNCTION /note=Synteny: Hypothetical Protein /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 29721 - 30014 /gene="42" /product="gp42" /function="hypothetical protein" /locus tag="Yeti_42" /note=Original Glimmer call @bp 29721 has strength 18.52; Genemark calls start at 29721 /note=SSC: 29721-30014 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JEFE_42 [Microbacterium phage Jefe]],,NCBI, q1:s1 100.0% 4.94927E-58 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.332, -4.572111470246742, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_JEFE_42 [Microbacterium phage Jefe]],,WBF79190,100.0,4.94927E-58 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 42 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Not Informative /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 2.332 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All sources agree /note= /note=FUNCTION /note=Synteny: Hypothetical Protein /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 30007 - 30912 /gene="43" /product="gp43" /function="lysin A" /locus tag="Yeti_43" /note=Original Glimmer call @bp 30007 has strength 15.28; Genemark calls start at 30007 /note=SSC: 30007-30912 CP: yes SCS: both ST: SS BLAST-Start: [lysin A [Microbacterium phage Piperis] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.887, -3.4175091270247986, no F: lysin A SIF-BLAST: ,,[lysin A [Microbacterium phage Piperis] ],,QCW22601,100.0,0.0 SIF-HHPRED: D,D-dipeptidase/D,D-carboxypeptidase; CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, NIAID; HET: 2D8, LY0, GOL, PE3; 1.364A {Enterococcus faecalis},,,4MUQ_A,48.1728,99.4 SIF-Syn: Found upstream of lysin A as in Honeyfin. /note=Current Gene Number: 43 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Not Informative /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 2.887 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All sources agree /note= /note=FUNCTION /note=Synteny: Lysin A /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 30909 - 31409 /gene="44" /product="gp44" /function="membrane protein" /locus tag="Yeti_44" /note=Original Glimmer call @bp 30909 has strength 11.31; Genemark calls start at 30909 /note=SSC: 30909-31409 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Selwyn23]],,NCBI, q1:s1 100.0% 9.40667E-114 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.926, -4.904754965500383, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Selwyn23]],,QWY84825,100.0,9.40667E-114 SIF-HHPRED: SIF-Syn: Found downstream of lysin A as in Honeyfin. /note=NOTE /note=Current Gene Number: 44 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Not informative /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 1.926 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=This is the start because all of the programs agree with each other. /note= /note=FUNCTION /note=Synteny: Selwyn23 /note=Tape measure protein /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 31372 - 31794 /gene="45" /product="gp45" /function="membrane protein" /locus tag="Yeti_45" /note=Original Glimmer call @bp 31372 has strength 11.76; Genemark calls start at 31381 /note=SSC: 31372-31794 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_PIPERIS_45 [Microbacterium phage Piperis] ],,NCBI, q1:s1 100.0% 2.72061E-94 GAP: -38 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.122, -2.338663114094478, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_PIPERIS_45 [Microbacterium phage Piperis] ],,QCW22603,99.2857,2.72061E-94 SIF-HHPRED: DUF2570 ; Protein of unknown function (DUF2570),,,PF10828.12,87.1429,97.5 SIF-Syn: Found upstream of Gene 46 as in Selwyn23 /note=Current Gene Number: 45 /note=Did the start site stay the same or change: change /note=Do the Glimmer and Genemark start sites agree? no /note=What about Starterator? yes, 88% /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? No 97.1429% /note=Z score = 2.202 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=GeneMark Start Chosen. The Genemark file showed that both were applicable. The Z-score was the deciding factor that the GeneMark start was more accurate. /note= /note=FUNCTION /note=Synteny: Yes; Selwyn23 /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2e-74 /note=Blast NCBI function match with E value should be 10^-7 or less: 7.81775e-92 /note=HHPRED Match with > 90% probability: 97.2% /note=Conserved Domain: n/a CDS 31806 - 32207 /gene="46" /product="gp46" /function="membrane protein" /locus tag="Yeti_46" /note=Original Glimmer call @bp 31806 has strength 15.57; Genemark calls start at 31806 /note=SSC: 31806-32207 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Jefe]],,NCBI, q1:s1 100.0% 5.61959E-85 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.18, -2.2364030944336752, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Jefe]],,WBF79194,100.0,5.61959E-85 SIF-HHPRED: SIF-Syn: Found downstream of Gene 46 as in Jefe /note=NOTE /note=Current Gene Number: 46 /note=Did the start site stay the same or change: stay /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? no, 43.8% /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: no /note=Is there a 1:1 alignment on blast and with which phage? Yes /note=Z score = 3.18 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=The Z Score and LORF support the start above the start that we choose, however, there is a 112 overlap between these genes if that is the true start. In conclusion, 31806 is the true start of this gene. /note=FUNCTION /note=Synteny: Yes; Jefe /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2e-69 /note=Blast NCBI function match with E value should be 10^-7 or less: yes, 5.61959e-85 /note=HHPRED Match with > 90% probability: no, 84.6% /note=Conserved Domain: n/a CDS 32280 - 32426 /gene="47" /product="gp47" /function="membrane protein" /locus tag="Yeti_47" /note=Original Glimmer call @bp 32280 has strength 12.14; Genemark calls start at 32280 /note=SSC: 32280-32426 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp48 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 5.70012E-26 GAP: 72 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.646, -3.618090370183562, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein QDA05_gp48 [Microbacterium phage Honeyfin] ],,YP_010751429,100.0,5.70012E-26 SIF-HHPRED: T-cell surface glycoprotein CD4; Protein, Cell membrane, Disulfide bond, Glycoprotein, Host-virus interaction, Immune response, Immunoglobulin domain, Lipoprotein, Membrane, Palmitate, Polymorphism; NMR {Homo sapiens},,,2KLU_A,60.4167,93.2 SIF-Syn: Found upstream of Gene 48 as in Honeyfin /note=Current Gene Number: 47 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes /note=Z score = 2.646 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Gene Mak and Glimmer both agree with the start. Furthermore, the Z score is 2.6 which is somewhat close to 2. /note=FUNCTION /note=Synteny: Yes; Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2e-21 /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: 93.2% /note=Conserved Domain: n/a CDS 32507 - 33580 /gene="48" /product="gp48" /function="exonuclease" /locus tag="Yeti_48" /note=Original Glimmer call @bp 32507 has strength 18.32; Genemark calls start at 32507 /note=SSC: 32507-33580 CP: yes SCS: both ST: SS BLAST-Start: [RecE-like recombination exonuclease [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 0.0 GAP: 80 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.957, -5.227904825154088, no F: exonuclease SIF-BLAST: ,,[RecE-like recombination exonuclease [Microbacterium phage Paschalis] ],,YP_009801894,100.0,0.0 SIF-HHPRED: c.52.1.13 (A:) lambda exonuclease {Bacteriophage lambda [TaxId: 10710]} | CLASS: Alpha and beta proteins (a/b), FOLD: Restriction endonuclease-like, SUPFAM: Restriction endonuclease-like, FAM: lambda exonuclease,,,SCOP_d3sm4a_,61.0644,99.9 SIF-Syn: Found upstream of exonuclease as in Honeyfin /note=Current Gene Number: 48 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes, 85% /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, with Selwyn23 /note=Z score = 1.957 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start. /note=FUNCTION /note=Synteny: Yes; Selwyn23 /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: 99.9 /note=Conserved Domain: n/a CDS 33634 - 34449 /gene="49" /product="gp49" /function="ERF family DNA pairing protein" /locus tag="Yeti_49" /note=Original Glimmer call @bp 33634 has strength 18.88; Genemark calls start at 33634 /note=SSC: 33634-34449 CP: yes SCS: both ST: SS BLAST-Start: [ERF family ssDNA binding protein [Microbacterium phage PiperSansNom] ],,NCBI, q1:s1 100.0% 0.0 GAP: 53 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.161, -4.801936092881806, no F: ERF family DNA pairing protein SIF-BLAST: ,,[ERF family ssDNA binding protein [Microbacterium phage PiperSansNom] ],,QDP45442,100.0,0.0 SIF-HHPRED: ERF ; ERF superfamily,,,PF04404.16,45.3875,99.9 SIF-Syn: Found upstream of ERF family ssDNA Binding Protein as in Honeyfin /note=Current Gene Number: 49 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes, 81.8% /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, Cranjis & PiperSansNom /note=Z score = 2.161 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start. /note=FUNCTION /note=Synteny: Yes; PiperSansNom /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-155 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: 99.9 /note=Conserved Domain: n/a CDS 34449 - 34784 /gene="50" /product="gp50" /function="hypothetical protein" /locus tag="Yeti_50" /note=Original Glimmer call @bp 34449 has strength 16.25; Genemark calls start at 34449 /note=SSC: 34449-34784 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp53 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 2.72015E-73 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.869, -5.024743752121617, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp53 [Microbacterium phage Quhwah] ],,YP_009803251,100.0,2.72015E-73 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 50 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes, 78.6% /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, Quhwah /note=Z score = 1.869 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start. /note= /note=FUNCTION /note=Synteny: Yes; Quhwah /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2e-57 /note=Blast NCBI function match with E value should be 10^-7 or less: 2.72-73 /note=HHPRED Match with > 90% probability: 79.6 /note=Conserved Domain: n/a CDS 34774 - 35142 /gene="51" /product="gp51" /function="hypothetical protein" /locus tag="Yeti_51" /note=Original Glimmer call @bp 34774 has strength 13.82; Genemark calls start at 34774 /note=SSC: 34774-35142 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PIPERIS_51 [Microbacterium phage Piperis] ],,NCBI, q1:s1 100.0% 6.69565E-82 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.887, -3.2925703904164987, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PIPERIS_51 [Microbacterium phage Piperis] ],,QCW22609,100.0,6.69565E-82 SIF-HHPRED: Recombination protein uvsY; recombination, DNA binding, homo-heptamer, asymmetry, alpha barrel, VIRAL PROTEIN; 2.351A {Enterobacteria phage T4},,,4ZWQ_D,84.4262,94.1 SIF-Syn: NKF /note=Current Gene Number: 51 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? no, 10.2% /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, Phorgeous & PiperSansNom & Piperis /note=Z score = 2.887 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start with the exception of starterator. However, we concluded that with the rest of the information, the predetermined start is the correct start. /note=FUNCTION /note=Synteny: Yes; Piperis /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 5e-63 /note=Blast NCBI function match with E value should be 10^-7 or less: 6.70e-82 /note=HHPRED Match with > 90% probability: 94.1% /note=Conserved Domain: n/a CDS 35142 - 35396 /gene="52" /product="gp52" /function="helix-turn-helix DNA binding domain" /locus tag="Yeti_52" /note=Original Glimmer call @bp 35142 has strength 13.35; Genemark calls start at 35142 /note=SSC: 35142-35396 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 6.27028E-54 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.996, -4.970213310205538, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Microbacterium phage Honeyfin] ],,YP_010751434,100.0,6.27028E-54 SIF-HHPRED: Chromosomal replication initiator protein dnaA; Helix-turn-Helix motif, Interacting with DnaA-box, DnaA-box, DNA BINDING PROTEIN-DNA complex; 2.0A {Mycobacterium tuberculosis},,,3PVV_B,89.2857,97.2 SIF-Syn: found upstream of helix-turn-helix DNA binding domain in Honeyfin. /note=Current Gene Number: 52 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes, 100% /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, Honeyfin /note=Z score = 1.996 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start. /note=FUNCTION /note=Synteny: Yes; Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 3e-42 /note=Blast NCBI function match with E value should be 10^-7 or less: 6.27e-54 /note=HHPRED Match with > 90% probability: 97.2 /note=Conserved Domain: n/a CDS 35398 - 35691 /gene="53" /product="gp53" /function="hypothetical protein" /locus tag="Yeti_53" /note=Original Glimmer call @bp 35398 has strength 5.24; Genemark calls start at 35398 /note=SSC: 35398-35691 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp54 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 4.04643E-66 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.39, -3.940982341616414, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp54 [Microbacterium phage Honeyfin] ],,YP_010751435,100.0,4.04643E-66 SIF-HHPRED: INSULINOMA-ASSOCIATED PROTEIN 1; OXIDOREDUCTASE-PEPTIDE COMPLEX, DEMETHYLASE, TRANSCRIPTION FACTOR, CHROMATIN; HET: FAD; 2.96A {HOMO SAPIENS},,,3ZMS_C,63.9175,95.5 SIF-Syn: NKF /note=Current Gene Number: 53 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes, 100% /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, Honeyfin & Piperis & Phorgeous & Selwyn23 & Busephilis & Phrancesco /note=Z score = 2.39 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start. /note=FUNCTION /note=Synteny: Yes; Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 3e-56 /note=Blast NCBI function match with E value should be 10^-7 or less: 4.05e-66 /note=HHPRED Match with > 90% probability: 95.5 /note=Conserved Domain: n/a CDS 35678 - 36130 /gene="54" /product="gp54" /function="HNH endonuclease" /locus tag="Yeti_54" /note=Original Glimmer call @bp 35678 has strength 1.69 /note=SSC: 35678-36130 CP: yes SCS: glimmer ST: NI BLAST-Start: [HNH endonuclease [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 1.83986E-100 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.193, -6.429065907148427, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Microbacterium phage Honeyfin] ],,YP_010751436,100.0,1.83986E-100 SIF-HHPRED: 5-methylcytosine-specific restriction enzyme A; HNH ENDONUCLEASE, MODIFICATION DEPENDENT RESTRICTION, 5-METHYLCYTOSINE, 5MC, 5-HYDROXYMETHYLCYTOSINE, 5HMC, BBA-ME NUCLEASE, ScoMcrA, HYDROLASE; 2.85A {Escherichia coli (strain K12)},,,6GHC_A,42.6667,96.3 SIF-Syn: found upstream of HNH endonuclease as in Honeyfin. /note=Current Gene Number: 54 /note=Did the start site stay the same or change: /note=Do the Glimmer and Genemark start sites agree? /note=What about Starterator? /note=Is the ORF chosen the longest ORF: /note=Is all of the coding potential captured on GeneMark file: /note=Is there a 1:1 alignment on blast and with which phage? /note=Z score = /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 36327 - 36509 /gene="55" /product="gp55" /function="hypothetical protein" /locus tag="Yeti_55" /note= /note=SSC: 36327-36509 CP: yes SCS: neither ST: NI BLAST-Start: [hypothetical protein SEA_PIPERIS_55 [Microbacterium phage Piperis]],,NCBI, q1:s1 100.0% 2.09145E-29 GAP: 196 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.981, -6.791262552373147, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PIPERIS_55 [Microbacterium phage Piperis]],,QCW22613,96.6667,2.09145E-29 SIF-HHPRED: SIF-Syn: NKF CDS 36481 - 36672 /gene="56" /product="gp56" /function="hypothetical protein" /locus tag="Yeti_56" /note=Original Glimmer call @bp 36481 has strength 5.92; Genemark calls start at 36481 /note=SSC: 36481-36672 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp56 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 2.49188E-37 GAP: -29 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.357, -3.9301544432541915, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp56 [Microbacterium phage Honeyfin] ],,YP_010751437,100.0,2.49188E-37 SIF-HHPRED: TRAF2_zf ; TRAF2, second zinc finger,,,PF21341.1,15.873,91.2 SIF-Syn: NKF /note=Current Gene Number: 55 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes, 96.6% /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, Honeyfin /note=Z score = 2.357 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start. /note=FUNCTION /note=Synteny: Yes; Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2e-32 /note=Blast NCBI function match with E value should be 10^-7 or less: 2.49e-37 /note=HHPRED Match with > 90% probability: 91.2 /note=Conserved Domain: n/a CDS 36762 - 36983 /gene="57" /product="gp57" /function="hypothetical protein" /locus tag="Yeti_57" /note=Original Glimmer call @bp 36762 has strength 7.72; Genemark calls start at 36762 /note=SSC: 36762-36983 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT74_gp57 [Microbacterium phage KaiHaiDragon] ],,NCBI, q1:s1 100.0% 9.94879E-44 GAP: 89 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.332, -3.919972614575461, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT74_gp57 [Microbacterium phage KaiHaiDragon] ],,YP_009807079,100.0,9.94879E-44 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 56 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes, 85.7% /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, KaiHaiDragon & Honeyfin & EarickHC /note=Z score = 2.332 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start. /note=FUNCTION /note=Synteny: Yes; Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 4e-37 /note=Blast NCBI function match with E value should be 10^-7 or less: 9.95e-44 /note=HHPRED Match with > 90% probability: n/a /note=Conserved Domain: n/a CDS 37061 - 37231 /gene="58" /product="gp58" /function="hypothetical protein" /locus tag="Yeti_58" /note=Original Glimmer call @bp 37061 has strength 12.8; Genemark calls start at 37052 /note=SSC: 37061-37231 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein HOT30_gp57 [Microbacterium phage Paschalis] ],,NCBI, q1:s4 100.0% 9.87301E-32 GAP: 77 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.887, -3.1164791313608173, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp57 [Microbacterium phage Paschalis] ],,YP_009801904,94.9153,9.87301E-32 SIF-HHPRED: DUF4177 ; Domain of unknown function (DUF4177),,,PF13783.10,53.5714,98.3 SIF-Syn: NKF /note=Current Gene Number: 57 /note=Did the start site stay the same or change: /note=Do the Glimmer and Genemark start sites agree? /note=What about Starterator? /note=Is the ORF chosen the longest ORF: /note=Is all of the coding potential captured on GeneMark file: /note=Is there a 1:1 alignment on blast and with which phage? /note=Z score = /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 37298 - 38293 /gene="59" /product="gp59" /function="hypothetical protein" /locus tag="Yeti_59" /note=Original Glimmer call @bp 37298 has strength 14.81; Genemark calls start at 37298 /note=SSC: 37298-38293 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp58 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 0.0 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.161, -4.337049294579155, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp58 [Microbacterium phage Paschalis] ],,YP_009801905,100.0,0.0 SIF-HHPRED: DUF932 ; Domain of unknown function (DUF932),,,PF06067.15,70.997,99.9 SIF-Syn: NKF /note=Current Gene Number: 58 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? no, 68.9% /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, Paschalis & Quhwah & KaiHaiDragon & Honeyfin &Shotgun & ClearAsMud & Noodlely & Piperis & Busephilis & PiperSansNom /note=Z score = 2.161 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start. /note=FUNCTION /note=Synteny: Yes; Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: 99.9% /note=Conserved Domain: n/a CDS 38447 - 38917 /gene="60" /product="gp60" /function="hypothetical protein" /locus tag="Yeti_60" /note=Original Glimmer call @bp 38447 has strength 11.27; Genemark calls start at 38447 /note=SSC: 38447-38917 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 6.43815E-106 GAP: 153 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.898, -5.650622440084484, no F: hypothetical protein SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Microbacterium phage Honeyfin] ],,YP_010751441,100.0,6.43815E-106 SIF-HHPRED: PUTATIVE TRANSCRIPTIONAL REGULATOR; TRANSCRIPTION, MARR-FAMILY, WINGED HELIX MOTIF; HET: EDO, SAL; 1.95A {STREPTOMYCES COELICOLOR},,,3ZMD_C,70.5128,99.6 SIF-Syn: NKF /note=Current Gene Number: 59 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? no, 44.9% /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, Honeyfin /note=Z score = 1.898 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start except for starterator. However, the rest of the evidence does agree with the predetermined start. /note=FUNCTION /note=Synteny: Yes; Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-84 /note=Blast NCBI function match with E value should be 10^-7 or less: 6.44e-106 /note=HHPRED Match with > 90% probability: 99.6% /note=Conserved Domain: n/a CDS 38914 - 39282 /gene="61" /product="gp61" /function="hypothetical protein" /locus tag="Yeti_61" /note=Original Glimmer call @bp 38914 has strength 13.81; Genemark calls start at 38914 /note=SSC: 38914-39282 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT30_gp61 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 2.17922E-83 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.466, -5.861263335174037, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp61 [Microbacterium phage Paschalis] ],,YP_009801908,100.0,2.17922E-83 SIF-HHPRED: SIF-Syn: NKF Found downstream of helix-turn-helix DNA binding domain protein as in honeyfin. /note=Current Gene Number: 60 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? 81.6% yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes, Paschalis & Busephilis & Scumberland /note=Z score = 1.466 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=All of the data supports the predetermined start. The Z score is a little bit low, however, the rest of the information agrees. The GeneMark file shows that the gene needs to be larger so the better Z score starts are disqualified. /note=FUNCTION /note=Synteny: Yes; Scumberland /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-64 /note=Blast NCBI function match with E value should be 10^-7 or less: 2.18e-83 /note=HHPRED Match with > 90% probability: n/a /note=Conserved Domain: n/a CDS 39279 - 39911 /gene="62" /product="gp62" /function="hypothetical protein" /locus tag="Yeti_62" /note=Original Glimmer call @bp 39279 has strength 19.42; Genemark calls start at 39279 /note=SSC: 39279-39911 CP: yes SCS: both ST: SS BLAST-Start: [DNA ligase [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 1.95056E-149 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.869, -2.944818356413908, no F: hypothetical protein SIF-BLAST: ,,[DNA ligase [Microbacterium phage Paschalis] ],,YP_009801909,100.0,1.95056E-149 SIF-HHPRED: Collagen alpha-1(VII) chain; vWFA, collagen VII, VWA, structural protein; HET: EDT; 2.0A {Mus musculus},,,6S4C_A,88.0952,99.5 SIF-Syn: NKF found upstream of DNA ligase as in KaiHaiDragon. /note=NOTE /note=Current Gene Number: 61 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? Yes. 1MF7_A, SCOP_D1MF7A1. /note=Z score = 2.869 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site: Everything agreed. CDS 39908 - 40378 /gene="63" /product="gp63" /function="hypothetical protein" /locus tag="Yeti_63" /note=Original Glimmer call @bp 39908 has strength 12.77; Genemark calls start at 39908 /note=SSC: 39908-40378 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PHORGEOUS_62 [Microbacterium phage Phorgeous]],,NCBI, q1:s1 100.0% 5.15847E-107 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.966, -2.66371296573402, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PHORGEOUS_62 [Microbacterium phage Phorgeous]],,UVK63242,100.0,5.15847E-107 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 62 /note=Did the start site stay the same or change: Same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? No. /note=Z score = 2.966 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Everything agreed. CDS 40378 - 40533 /gene="64" /product="gp64" /function="hypothetical protein" /locus tag="Yeti_64" /note=Original Glimmer call @bp 40378 has strength 16.96; Genemark calls start at 40378 /note=SSC: 40378-40533 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT74_gp65 [Microbacterium phage KaiHaiDragon] ],,NCBI, q1:s1 100.0% 8.2918E-26 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.887, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT74_gp65 [Microbacterium phage KaiHaiDragon] ],,YP_009807087,98.0392,8.2918E-26 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 63 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? no /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes. /note=Is there a 1:1 alignment on blast and with which phage? no /note=Z score = 2.887 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site: Glimmer and genemark agree. The Z score is same for LORF and the chosen start. Full coding capacity is used. CDS 40535 - 41041 /gene="65" /product="gp65" /function="SSB protein" /locus tag="Yeti_65" /note=Original Glimmer call @bp 40535 has strength 13.99; Genemark calls start at 40535 /note=SSC: 40535-41041 CP: yes SCS: both ST: SS BLAST-Start: [SSB protein [Microbacterium phage Hermeonysus]],,NCBI, q1:s1 100.0% 1.34994E-118 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.53, -5.650089995820535, no F: SSB protein SIF-BLAST: ,,[SSB protein [Microbacterium phage Hermeonysus]],,WKW87010,100.0,1.34994E-118 SIF-HHPRED: Single-stranded DNA-binding protein 2; Single-stranded DNA-binding protein, Streptomyces Coelicolor, DNA damage, DNA repair, DNA replication, DNA-binding, Phosphoprotein, DNA BINDING PROTEIN; 2.141A {Streptomyces coelicolor} SCOP: b.40.4.3,,,3EIV_A,99.4048,99.9 SIF-Syn: Found Downstream of terminase as in Honeyfin /note=NOTE /note=Current Gene Number: 64 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? No /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? Yes, 7F5Y_B /note=Z score = 1.53 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Glimmer and genemark agreed. It also had the longest ORF, despite starterator possibly disagreeing. /note=Synteny: No /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 41253 - 41378 /gene="66" /product="gp66" /function="hypothetical protein" /locus tag="Yeti_66" /note=Original Glimmer call @bp 41253 has strength 11.44; Genemark calls start at 41253 /note=SSC: 41253-41378 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PIPERIS_66 [Microbacterium phage Piperis]],,NCBI, q1:s1 100.0% 1.35971E-20 GAP: 211 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.161, -4.274735973818826, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PIPERIS_66 [Microbacterium phage Piperis]],,QCW22624,100.0,1.35971E-20 SIF-HHPRED: DUF6724 ; Family of unknown function (DUF6724),,,PF20485.2,92.6829,89.8 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 65 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? Yes, /note=What about Starterator? Yes. /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: No? only about 100 base pairs long. only found in 3rd start of the last (64) gene. /note=Is there a 1:1 alignment on blast and with which phage? Yes, PF20458.2 /note=Z score = 2.161 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Needs review. because of Genemark file. CDS 41362 - 41655 /gene="67" /product="gp67" /function="DNA binding protein" /locus tag="Yeti_67" /note=Original Glimmer call @bp 41362 has strength 11.49; Genemark calls start at 41362 /note=SSC: 41362-41655 CP: yes SCS: both ST: SS BLAST-Start: [DNA binding protein [Microbacterium phage KaiHaiDragon] ],,NCBI, q1:s1 100.0% 9.4772E-61 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.792, -3.0425830684175623, yes F: DNA binding protein SIF-BLAST: ,,[DNA binding protein [Microbacterium phage KaiHaiDragon] ],,YP_009807090,98.9691,9.4772E-61 SIF-HHPRED: Putative excisionase; excisionase, DNA binding, wHTH motif, Structural Genomics, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-2, Protein Structure Initiative; NMR {Klebsiella pneumoniae},,,2KVV_A,75.2577,98.1 SIF-Syn: Found downstream of minor Tail protein /note=NOTE /note=Current Gene Number: 66 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? No. /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? Yes. 2KVV_A /note=Z score = 2.792 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Everything seems to agree /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 41652 - 42485 /gene="68" /product="gp68" /function="helix-turn-helix DNA binding domain" /locus tag="Yeti_68" /note=Original Glimmer call @bp 41652 has strength 7.61; Genemark calls start at 41907 /note=SSC: 41652-42485 CP: yes SCS: both-gl ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.411, -3.8970005018578204, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Microbacterium phage Honeyfin] ],,YP_010751449,99.278,0.0 SIF-HHPRED: a.4.5.3 (A:4-78) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus stearothermophilus [TaxId: 1422]} | CLASS: All alpha proteins, FOLD: DNA/RNA-binding 3-helical bundle, SUPFAM: `Winged helix` DNA-binding domain, FAM: Arginine repressor (ArgR), N-terminal DNA-binding domain,,,SCOP_d1b4aa1,19.1336,94.0 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 67 /note=Did the start site stay the same or change: Change /note=Do the Glimmer and Genemark start sites agree? No. 41652, and 41907 /note=What about Starterator? yes. (which one?) /note=Is the ORF chosen the longest ORF: Yes. /note=Is all of the coding potential captured on GeneMark file: No. /note=Is there a 1:1 alignment on blast and with which phage? yes. SCOP_D6HN7B1, 8DGL_A, PF06806.16 /note=Z score = 2.792 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=genemark, and glimmer did not agree. the genemark file was an issue. May not be a gene. CDS 42478 - 42672 /gene="69" /product="gp69" /function="helix-turn-helix DNA binding domain" /locus tag="Yeti_69" /note=Original Glimmer call @bp 42478 has strength 8.11; Genemark calls start at 42478 /note=SSC: 42478-42672 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 4.97361E-38 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.541, -3.54831954703195, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Microbacterium phage Honeyfin] ],,YP_010751450,100.0,4.97361E-38 SIF-HHPRED: VIRAL PROTEIN F93; VIRAL PROTEIN-WINGED HELIX COMPLEX, WINGED HELIX, DNA-BINDING, HTH, WHTH, F93, DISULFIDE BOND, STIV, SULFOLOBUS TURRETED ICOSAHEDRAL; 2.2A {SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS} SCOP: a.4.5.48, l.1.1.1,,,2CO5_A,73.4375,91.4 SIF-Syn: Found downstream of small terminase subunit /note=NOTE /note=Current Gene Number: 68 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes. /note=What about Starterator? yes. /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes (?) /note=Is there a 1:1 alignment on blast and with which phage? no. /note=Z score = 2.541 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Everything seems to agree /note=Synteny: 1:1 /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 42669 - 42968 /gene="70" /product="gp70" /function="hypothetical protein" /locus tag="Yeti_70" /note=Original Glimmer call @bp 42669 has strength 17.83; Genemark calls start at 42669 /note=SSC: 42669-42968 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp70 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 2.87731E-64 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.142, -4.394706008439538, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp70 [Microbacterium phage Honeyfin] ],,YP_010751451,100.0,2.87731E-64 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 69 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes. /note=Is the ORF chosen the longest ORF: No. /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? No /note=Z score = 1.847 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Everything seems to agree despite ORF not being longest. CDS 42968 - 43210 /gene="71" /product="gp71" /function="hypothetical protein" /locus tag="Yeti_71" /note=Original Glimmer call @bp 42968 has strength 5.1; Genemark calls start at 42968 /note=SSC: 42968-43210 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage KaiHaiDragon] ],,NCBI, q1:s1 100.0% 9.0962E-51 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.737, -6.06547858538777, no F: hypothetical protein SIF-BLAST: ,,[membrane protein [Microbacterium phage KaiHaiDragon] ],,YP_009807094,100.0,9.0962E-51 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 70 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: No /note=Is there a 1:1 alignment on blast and with which phage? No /note=Z score = 1.737 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=things seem to agree. the Z score for LORF and chosen are same. But genemark file has confusion. May not be a gene.. CDS 43207 - 43383 /gene="72" /product="gp72" /function="membrane protein" /locus tag="Yeti_72" /note=Original Glimmer call @bp 43207 has strength 14.83; Genemark calls start at 43207 /note=SSC: 43207-43383 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp72 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 8.7939E-32 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.042, -2.5052746077145835, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein QDA05_gp72 [Microbacterium phage Honeyfin] ],,YP_010751453,100.0,8.7939E-32 SIF-HHPRED: SIF-Syn: Membrane protein as found downstream of protein binding in Honeyfin. /note=NOTE /note=Current Gene Number: 71 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: No /note=Is there a 1:1 alignment on blast and with which phage? No /note=Z score = 1.379 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Problem gene. Genemark file has issues. CDS 43380 - 43748 /gene="73" /product="gp73" /function="hypothetical protein" /locus tag="Yeti_73" /note=Original Glimmer call @bp 43380 has strength 15.99; Genemark calls start at 43362 /note=SSC: 43380-43748 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein QDA05_gp73 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 5.15867E-81 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.406, -4.867713808513585, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp73 [Microbacterium phage Honeyfin] ],,YP_010751454,100.0,5.15867E-81 SIF-HHPRED: DUF6085 ; Family of unknown function (DUF6085),,,PF19563.3,63.9344,99.9 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 72 /note=Did the start site stay the same or change: change /note=Do the Glimmer and Genemark start sites agree? No. 43380, and 43362. /note=What about Starterator? Most annotated /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: Yes, for the third start. /note=Is there a 1:1 alignment on blast and with which phage? No /note=Z score = 2.406 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Nothing agrees at all. CDS 43735 - 43983 /gene="74" /product="gp74" /function="hypothetical protein" /locus tag="Yeti_74" /note=Original Glimmer call @bp 43735 has strength 12.89; Genemark calls start at 43735 /note=SSC: 43735-43983 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp78 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 6.19673E-51 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.887, -2.827683592113848, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp78 [Microbacterium phage Quhwah] ],,YP_009803276,100.0,6.19673E-51 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 73 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? No /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: Yes, first start. /note=Is there a 1:1 alignment on blast and with which phage? No /note=Z score = 1.182 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Things disagree. Review needed. /note= /note=FUNCTION: NKF /note=Synteny: 1:1 /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 43980 - 44462 /gene="75" /product="gp75" /function="hypothetical protein" /locus tag="Yeti_75" /note=Original Glimmer call @bp 43980 has strength 12.12; Genemark calls start at 43980 /note=SSC: 43980-44462 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp75 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 5.60912E-112 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.722, -3.170856472917156, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp75 [Microbacterium phage Honeyfin] ],,YP_010751456,100.0,5.60912E-112 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 74 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: yes, third start (?) /note=Is there a 1:1 alignment on blast and with which phage? No /note=Z score = 1.962 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Most things agree, but LORF does not. needs review. /note= /note=FUNCTION: NKF /note=Synteny: No /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 44531 - 45139 /gene="76" /product="gp76" /function="hypothetical protein" /locus tag="Yeti_76" /note=Original Glimmer call @bp 44531 has strength 14.43; Genemark calls start at 44531 /note=SSC: 44531-45139 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp81 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 8.05754E-147 GAP: 68 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.774, -5.160958035523474, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp81 [Microbacterium phage Quhwah] ],,YP_009803279,100.0,8.05754E-147 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 75 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes, second start /note=Is there a 1:1 alignment on blast and with which phage? No /note=Z score = 1.774 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Most things agree. ORF need review. /note= /note=FUNCTION: NKF /note=Synteny: No /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 45136 - 45345 /gene="77" /product="gp77" /function="hypothetical protein" /locus tag="Yeti_77" /note=Original Glimmer call @bp 45136 has strength 6.58; Genemark calls start at 45172 /note=SSC: 45136-45345 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein HOT30_gp78 [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 1.62582E-42 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.411, -4.408140843866914, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT30_gp78 [Microbacterium phage Paschalis] ],,YP_009801925,100.0,1.62582E-42 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 76 /note= /note=Did the start site stay the same or change: Stay the same /note= /note=Do the Glimmer and Genemark start sites agree? No /note= /note=What about Starterator? Agrees with glimmer start site /note= /note=Is the ORF chosen the longest ORF: No /note= /note=Is all of the coding potential captured on GeneMark file: Yes /note= /note=Is there a 1:1 alignment on blast and with which phage? Yes, YP_009801925 /note= /note=Z score = 2.411 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Kept auto-annotated start site because the phamerator start site agreed, the z-score was closest to 2, and all of the coding potential was captured on the genemark file. /note= /note=FUNCTION /note=Synteny: Yes /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Cranjis, Ganondorf_draft /note= /note=Blast NCBI function match with E value should be 10^-7 or less: YP_009801925 /note= /note=HHPRED Match with > 90% probability: None /note= /note=Conserved Domain: None CDS 45338 - 45625 /gene="78" /product="gp78" /function="hypothetical protein" /locus tag="Yeti_78" /note=Original Glimmer call @bp 45338 has strength 14.05; Genemark calls start at 45338 /note=SSC: 45338-45625 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp83 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 1.93079E-63 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.887, -2.827683592113848, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp83 [Microbacterium phage Quhwah] ],,YP_009803281,100.0,1.93079E-63 SIF-HHPRED: DUF6283 ; Family of unknown function (DUF6283),,,PF19800.3,81.0526,99.8 SIF-Syn: NKF /note=Current Gene Number: /note=77 /note= /note=Did the start site stay the same or change: /note=stay the same /note= /note=Do the Glimmer and Genemark start sites agree? /note=yes /note= /note=What about Starterator? /note=yes /note= /note=Is the ORF chosen the longest ORF: /note=yes /note= /note=Is all of the coding potential captured on GeneMark file: /note=yes /note= /note=Is there a 1:1 alignment on blast and with which phage? /note=yes /note= /note=Z score = /note=2.887 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Everything agreed /note= /note=Synteny: yes /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Hermeonysus, Honeyfin /note= /note=Blast NCBI function match with E value should be 10^-7 or less: /note=YP_009803281 /note= /note=HHPRED Match with > 90% probability: /note=PF19800.3 /note= /note=Conserved Domain: /note=no CDS 45628 - 46191 /gene="79" /product="gp79" /function="hypothetical protein" /locus tag="Yeti_79" /note=Original Glimmer call @bp 45628 has strength 11.48; Genemark calls start at 45628 /note=SSC: 45628-46191 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT47_gp84 [Microbacterium phage Quhwah] ],,NCBI, q1:s1 100.0% 9.5228E-135 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.142, -4.455662434380964, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT47_gp84 [Microbacterium phage Quhwah] ],,YP_009803282,100.0,9.5228E-135 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: /note=78 /note= /note=Did the start site stay the same or change: /note=stayed the same /note= /note=Do the Glimmer and Genemark start sites agree? /note=yes /note= /note=What about Starterator? /note=yes /note= /note=Is the ORF chosen the longest ORF: /note=no /note= /note=Is all of the coding potential captured on GeneMark file: /note=no /note= /note=Is there a 1:1 alignment on blast and with which phage? /note=yes, YP_009803282 /note= /note=Z score = /note=2.142 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=everything agreed /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: BrazzalePHS, Hermeonysus /note=Blast NCBI function match with E value should be 10^-7 or less: YP_009803282 /note=HHPRED Match with > 90% probability: none /note=Conserved Domain: none /note= /note=review note: LCN /note=LORF should be yes. /note=Potential gene capacity should be yes. CDS 46191 - 46721 /gene="80" /product="gp80" /function="hypothetical protein" /locus tag="Yeti_80" /note=Original Glimmer call @bp 46191 has strength 10.15; Genemark calls start at 46191 /note=SSC: 46191-46721 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_SCUMBERLAND_82 [Microbacterium phage Scumberland] ],,NCBI, q1:s1 100.0% 4.40861E-127 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.541, -3.5660483139923818, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_SCUMBERLAND_82 [Microbacterium phage Scumberland] ],,QOC58104,100.0,4.40861E-127 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 79 /note=Did the start site stay the same or change: Stay the same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? Yes /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? QOC58104 /note=Z score = 2.541 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Kept, most evidence agrees. /note=*Z-score for start 46473 is closer to 2* /note= /note=FUNCTION NKF /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Cranjis, phorgeous /note=Blast NCBI function match with E value should be 10^-7 or less: QOC58104 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None /note= /note=Review note: LCN /note=Z-score is wrong, should be 2.541 CDS 46796 - 48121 /gene="81" /product="gp81" /function="membrane protein" /locus tag="Yeti_81" /note=Original Glimmer call @bp 46796 has strength 13.95; Genemark calls start at 46796 /note=SSC: 46796-48121 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PHORGEOUS_81 [Microbacterium phage Phorgeous]],,NCBI, q1:s1 100.0% 0.0 GAP: 74 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.161, -4.337049294579155, no F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_PHORGEOUS_81 [Microbacterium phage Phorgeous]],,UVK63261,100.0,0.0 SIF-HHPRED: RCR ; Chitin synthesis regulation, resistance to Congo red,,,PF12273.12,6.57596,91.4 SIF-Syn: Found upstream of ParB-like nuclease domain as in Savannah /note=NOTE /note=Current Gene Number: 80 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: Yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes UVK63261 /note=Z score = 2.161 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=They agree /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Phorgeous, Jefe /note=Blast NCBI function match with E value should be 10^-7 or less: UVK63261 /note=HHPRED Match with > 90% probability: PF12273.12 /note=Conserved Domain: PRK10263 /note= /note=Two z scores are the same CDS 48206 - 48439 /gene="82" /product="gp82" /function="DNA binding protein" /locus tag="Yeti_82" /note=Original Glimmer call @bp 48206 has strength 12.12; Genemark calls start at 48206 /note=SSC: 48206-48439 CP: yes SCS: both ST: SS BLAST-Start: [DNA binding protein [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 2.94296E-46 GAP: 84 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.355, -4.52522946659989, yes F: DNA binding protein SIF-BLAST: ,,[DNA binding protein [Microbacterium phage Honeyfin] ],,YP_010751463,100.0,2.94296E-46 SIF-HHPRED: Uncharacterized protein Rv2667; ClpC2, CymA, N-terminal domain, Transcription factor, DNA BINDING PROTEIN; 1.996A {Mycobacterium tuberculosis H37Rv},,,8ADA_A,37.6623,98.4 SIF-Syn: Found upstream of ParB-like nuclease domain protein as in Honeyfin /note=NOTE /note=Current Gene Number: 81 /note=Did the start site stay the same or change: stay the same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes YP_010751463 /note=Z score = 2.355 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=they all agree /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Hermeonysus, Honeyfin /note=Blast NCBI function match with E value should be 10^-7 or less: YP_010751463 /note=HHPRED Match with > 90% probability: 8ADA_A /note=Conserved Domain: PRK14050 CDS 48436 - 49095 /gene="83" /product="gp83" /function="ParB-like nuclease domain" /locus tag="Yeti_83" /note=Original Glimmer call @bp 48436 has strength 21.22; Genemark calls start at 48436 /note=SSC: 48436-49095 CP: no SCS: both ST: SS BLAST-Start: [ParB-like partition protein [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 2.45755E-156 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.627, -3.4470622626190464, yes F: ParB-like nuclease domain SIF-BLAST: ,,[ParB-like partition protein [Microbacterium phage Paschalis] ],,YP_009801931,100.0,2.45755E-156 SIF-HHPRED: ParB family protein; DNA-binding protein, CTP, Myxococcus, DNA-segregation, DNA BINDING PROTEIN; HET: UFQ, GOL; 1.7A {Myxococcus xanthus (strain DK 1622)},,,7BNR_B,80.3653,99.7 SIF-Syn: Found downstream of DNA binding protein as in Honeyfin /note=NOTE /note=Current Gene Number: 82 /note=Did the start site stay the same or change: stay the same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes, first start /note=Is there a 1:1 alignment on blast and with which phage? YP_009801931 /note=Z score = 2.627 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=They all agreed /note=FUNCTION /note=Synteny: no /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Antares, BrazzalePHS /note=Blast NCBI function match with E value should be 10^-7 or less: YP_009801931 /note=HHPRED Match with > 90% probability: 7BNR_B /note=Conserved Domain: cd16402 /note= /note=Review Note: LCN /note=gene capacity should be yes. CDS 49092 - 49322 /gene="84" /product="gp84" /function="hypothetical protein" /locus tag="Yeti_84" /note=Original Glimmer call @bp 49092 has strength 13.7; Genemark calls start at 49092 /note=SSC: 49092-49322 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA06_gp83 [Microbacterium phage Shotgun] ],,NCBI, q1:s1 100.0% 1.36291E-42 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.607, -3.4892599424135016, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA06_gp83 [Microbacterium phage Shotgun] ],,YP_010751555,98.6842,1.36291E-42 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 83 /note=Did the start site stay the same or change: yes /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? yes YP_010751555 /note=Z score = 2.607 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=They all agreed /note=FUNCTION /note=Synteny: yes in regards to gene 83 /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: CrazyRich, Jefe /note=Blast NCBI function match with E value should be 10^-7 or less: yes YP_010751555 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: none /note= /note=Review Note: LCN /note=gene capacity in notes should be no. File shows gap of no data from 49092-49100 in chosen ORF. CDS 49312 - 50052 /gene="85" /product="gp85" /function="glycosyltransferase" /locus tag="Yeti_85" /note=Original Glimmer call @bp 49312 has strength 12.45; Genemark calls start at 49357 /note=SSC: 49312-50052 CP: yes SCS: both-gl ST: NI BLAST-Start: [glycosyltransferase [Microbacterium phage Shotgun] ],,NCBI, q1:s1 100.0% 2.53635E-178 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.617, -3.389881189012514, yes F: glycosyltransferase SIF-BLAST: ,,[glycosyltransferase [Microbacterium phage Shotgun] ],,YP_010751556,100.0,2.53635E-178 SIF-HHPRED: GT2_RfbC_Mx_like; Myxococcus xanthus RfbC like proteins are required for O-antigen biosynthesis. The rfbC gene encodes a predicted protein of 1,276 amino acids, which is required for O-antigen biosynthesis in Myxococcus xanthus.,,,cd04184,74.7967,99.8 SIF-Syn: Found downstream of UDP-glucose dehydrogenase as in Honeyfin /note=NOTE /note=Current Gene Number: 84 /note=Did the start site stay the same or change: change /note=Do the Glimmer and Genemark start sites agree? no /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes, regards to the 1st /note=Is there a 1:1 alignment on blast and with which phage? yes, YP_010751556 /note=Z score = -3.390 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=The glimmer start and score did not agree, was not the longest ORF, /note=FUNCTION /note=Synteny: Yes, CrazyRich /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Ganandorf_Draft, Shotgun /note=Blast NCBI function match with E value should be 10^-7 or less: YP_010751556 /note=HHPRED Match with > 90% probability: cd04184, 3BCV_A /note=Conserved Domain: none /note= /note=Review Notes: LCN /note=coding capacity should be yes. /note=Z score should be 2.617 /note=Recommended start stay the same. CDS 50049 - 50831 /gene="86" /product="gp86" /function="UDP-glucose dehydrogenase" /locus tag="Yeti_86" /note=Original Glimmer call @bp 50064 has strength 13.96; Genemark calls start at 50064 /note=SSC: 50049-50831 CP: yes SCS: both-cs ST: SS BLAST-Start: [UDP-glucose dehydrogenase [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.607, -4.398340293094632, yes F: UDP-glucose dehydrogenase SIF-BLAST: ,,[UDP-glucose dehydrogenase [Microbacterium phage Paschalis] ],,YP_009801933,100.0,0.0 SIF-HHPRED: Sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family; STRUCTURAL GENOMICS, OXIDOREDUCTASE, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC; HET: UGA; 1.7A {Porphyromonas gingivalis},,,3GG2_A,96.9231,100.0 SIF-Syn: Found upstream of AAA-ATPase as in Honeyfin /note=NOTE /note=Current Gene Number: 85 /note=Did the start site stay the same or change: stay the same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes /note=Is there a 1:1 alignment on blast and with which phage? none /note=Z score = 2.416 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=they all agreed /note=FUNCTION /note=Synteny: Yes, Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: BrazzlePHS, Busephilis /note=Blast NCBI function match with E value should be 10^-7 or less: YP_009801933 /note=HHPRED Match with > 90% probability: 2Y0E_D, 4A7P_B /note=Conserved Domain: TIGR03026 CDS 50877 - 51497 /gene="87" /product="gp87" /function="AAA-ATPase" /locus tag="Yeti_87" /note=Original Glimmer call @bp 50877 has strength 17.55; Genemark calls start at 50877 /note=SSC: 50877-51497 CP: yes SCS: both ST: SS BLAST-Start: [AAA-ATPase [Microbacterium phage Paschalis] ],,NCBI, q1:s1 100.0% 2.87756E-152 GAP: 45 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.142, -4.665772780726076, no F: AAA-ATPase SIF-BLAST: ,,[AAA-ATPase [Microbacterium phage Paschalis] ],,YP_009801934,100.0,2.87756E-152 SIF-HHPRED: AAA ATPase, central region; STRUCTURAL GENOMICS, ATPASE, PSI-2, PROTEIN STRUCTURE INITIATIVE, New York SGX Research Center for Structural Genomics, NYSGXRC; HET: ACT, GOL; 2.09A {Enterococcus faecium} SCOP: l.1.1.1, a.80.1.2,,,2R9G_I,79.6116,100.0 SIF-Syn: Found downstream of UDP-glucose dehydrogenase as in Honeyfin /note=NOTE /note=Current Gene Number: 86 /note=Did the start site stay the same or change: stay the same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? YP_009801934 /note=Z score = 2.142 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=They all agree /note=FUNCTION /note=Synteny: Yes, HoneyFin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Antares, BrazzlePHS /note=Blast NCBI function match with E value should be 10^-7 or less: yes, YP_009801934 /note=HHPRED Match with > 90% probability: 2R9G_I, 3BGE_A /note=Conserved Domain: none CDS 51490 - 51732 /gene="88" /product="gp88" /function="hypothetical protein" /locus tag="Yeti_88" /note=Original Glimmer call @bp 51490 has strength 8.16; Genemark calls start at 51490 /note=SSC: 51490-51732 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LITTLEFORTUNE_89 [Microbacterium phage LittleFortune]],,NCBI, q1:s1 97.5% 1.18849E-49 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.231, -4.192397292939198, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LITTLEFORTUNE_89 [Microbacterium phage LittleFortune]],,WNM67791,96.25,1.18849E-49 SIF-HHPRED: g.39.1.18 (A:169-201) Uncharacterized protein Ta1109 {Thermoplasma acidophilum [TaxId: 2303]} | CLASS: Small proteins, FOLD: Glucocorticoid receptor-like (DNA-binding domain), SUPFAM: Glucocorticoid receptor-like (DNA-binding domain), FAM: FwdE C-terminal domain-like,,,SCOP_d2gvia2,67.5,93.1 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 87 /note=Did the start site stay the same or change: stay the same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: Yes /note=Is there a 1:1 alignment on blast and with which phage? yes WNM67791, QXN74880 /note=Z score = 2.231 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=They all agreed /note=FUNCTION /note=Synteny: Yes, HoneyFin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: PierreOrion_Draft, LittleFortune /note=Blast NCBI function match with E value should be 10^-7 or less: WNM67791, QXN74880 /note=HHPRED Match with > 90% probability: SCOP_d2gvia2 /note=Conserved Domain: none CDS 51725 - 52039 /gene="89" /product="gp89" /function="hypothetical protein" /locus tag="Yeti_89" /note=Original Glimmer call @bp 51725 has strength 11.06; Genemark calls start at 51725 /note=SSC: 51725-52039 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp87 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 9.48878E-70 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.172, -4.3323003410763175, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp87 [Microbacterium phage Honeyfin] ],,YP_010751468,99.0385,9.48878E-70 SIF-HHPRED: YjdM_Zn_Ribbon ; PhnA Zinc-Ribbon,,,PF08274.16,25.9615,97.3 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 88 /note=Did the start site stay the same or change: Yes /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes, in regards to 2nd /note=Is there a 1:1 alignment on blast and with which phage? yes YP_010751468 /note=Z score = 2.172 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=The starting site stayed the same /note=FUNCTION /note=Synteny: yes, HoneyFin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: CrazyRich, Honeyfin /note=Blast NCBI function match with E value should be 10^-7 or less: YP_010751468 /note=HHPRED Match with > 90% probability: PF08274.16 , SCOP_d2akla2 /note=Conserved Domain: None CDS 52036 - 52302 /gene="90" /product="gp90" /function="hypothetical protein" /locus tag="Yeti_90" /note=Original Glimmer call @bp 52036 has strength 13.53; Genemark calls start at 52036 /note=SSC: 52036-52302 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp88 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 3.71368E-57 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.887, -2.9063687850157054, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp88 [Microbacterium phage Honeyfin] ],,YP_010751469,100.0,3.71368E-57 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 89 /note=Did the start site stay the same or change: The same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes, in regards to 1st /note=Is there a 1:1 alignment on blast and with which phage? Yes YP_010751469 /note=Z score = 2.887 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=The starting sites agreed so everything stayed the same /note=FUNCTION /note=Synteny: Yes, HoneyFin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Honeyfin , Crisis_Draft /note=Blast NCBI function match with E value should be 10^-7 or less: YP_010751469 /note=HHPRED Match with > 90% probability: No /note=Conserved Domain: cd04444 CDS 52299 - 52631 /gene="91" /product="gp91" /function="hypothetical protein" /locus tag="Yeti_91" /note=Original Glimmer call @bp 52299 has strength 9.23; Genemark calls start at 52299 /note=SSC: 52299-52631 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp89 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 1.30739E-73 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.462, -3.790975366313636, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp89 [Microbacterium phage Honeyfin] ],,YP_010751470,100.0,1.30739E-73 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 90 /note=Did the start site stay the same or change: stay the same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes 3rd /note=Is there a 1:1 alignment on blast and with which phage? YP_010751470 /note=Z score = 2.462 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Everything stayed the same and agreed /note=FUNCTION /note=Synteny: yes, honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Honeyfin , Phorgeous /note=Blast NCBI function match with E value should be 10^-7 or less: YP_010751470 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None CDS 52628 - 52972 /gene="92" /product="gp92" /function="hypothetical protein" /locus tag="Yeti_92" /note=Original Glimmer call @bp 52628 has strength 11.66; Genemark calls start at 52628 /note=SSC: 52628-52972 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp90 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 2.06032E-75 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.375, -3.9109350188549152, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp90 [Microbacterium phage Honeyfin] ],,YP_010751471,100.0,2.06032E-75 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 91 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: no /note=Is all of the coding potential captured on GeneMark file: yes, 2nd /note=Is there a 1:1 alignment on blast and with which phage? yes. YP_010751471 /note=Z score = 2.375 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Everything except the ORF seemed to agree /note=FUNCTION: NKF /note=Synteny: yes, Honeyfin /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Honeyfin , Piperis /note=Blast NCBI function match with E value should be 10^-7 or less: YP_010751471 , QCW22649 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None CDS 52969 - 53343 /gene="93" /product="gp93" /function="hypothetical protein" /locus tag="Yeti_93" /note=Original Glimmer call @bp 52969 has strength 8.71; Genemark calls start at 52969 /note=SSC: 52969-53343 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein QDA05_gp91 [Microbacterium phage Honeyfin] ],,NCBI, q1:s1 100.0% 7.90188E-84 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.817, -5.0535707005373816, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDA05_gp91 [Microbacterium phage Honeyfin] ],,YP_010751472,99.1936,7.90188E-84 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 92 /note=Did the start site stay the same or change: same /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? yes /note=Is the ORF chosen the longest ORF: yes /note=Is all of the coding potential captured on GeneMark file: yes, to the second /note=Is there a 1:1 alignment on blast and with which phage? yes. YP_010751472 /note=Z score = 1.817 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=most things seem to agree. ORF needs review /note=FUNCTION: NKF /note=Synteny: 1:1, Honeyfin. /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Honeyfin , Piperis /note=Blast NCBI function match with E value should be 10^-7 or less: YP_010751472 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None