CDS 1 - 603 /gene="1" /product="gp1" /function="terminase, small subunit" /locus tag="Htur_1" /note=Original Glimmer call @bp 1 has strength 11.52; Genemark calls start at 1 /note=SSC: 1-603 CP: yes SCS: both ST: SS BLAST-Start: [terminase small subunit [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 7.82054E-142 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.711, -3.200406812432904, yes F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Microbacterium phage Rasovi]],,QJD49978,100.0,7.82054E-142 SIF-HHPRED: HTH_58 ; Helix-turn-helix domain,,,PF19575.3,22.5,98.5 SIF-Syn: found upstream of terminase large subunit as in Rasovi /note=Current Gene Number: 1 /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? Yes, Rasovi /note=Z score = 2.711 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION: Terminase Small Subunit /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi, 1e-109 /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi, 7.82054e-142 /note=HHPRED Match with > 90% probability: Helix-turn-helix domain or terminase small subunit /note=Conserved Domain: CDS 600 - 872 /gene="2" /product="gp2" /function="hypothetical protein" /locus tag="Htur_2" /note=Original Glimmer call @bp 600 has strength 10.12; Genemark calls start at 600 /note=SSC: 600-872 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_2 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 1.20246E-58 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.153, -4.9668027763900575, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_2 [Microbacterium phage Rasovi]],,QJD49979,100.0,1.20246E-58 SIF-HHPRED: Heterocyst differentiation control protein; single helix, loop packing around, heterocyst development, heterocyst patterning, TRANSCRIPTION; 2.049A {Nostoc},,,4LH9_A,44.4444,90.6 SIF-Syn: NKF /note=Current Gene Number: 2 /note=Did the start site stay the same or change: Changed to 600 /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, Rasovi /note=Z score = 2.153 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION: NKF /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-46 /note=Blast NCBI function match with E value should be 10^-7 or less: 1.20246e-58 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: CDS 869 - 2281 /gene="3" /product="gp3" /function="terminase, large subunit" /locus tag="Htur_3" /note=Original Glimmer call @bp 869 has strength 11.83; Genemark calls start at 869 /note=SSC: 869-2281 CP: yes SCS: both ST: SS BLAST-Start: [terminase large subunit [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.166, -7.224343665540421, no F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Microbacterium phage Rasovi]],,QJD49980,99.7872,0.0 SIF-HHPRED: Large subunit terminase; large terminase, VIRAL PROTEIN; 2.2A {Deep-sea thermophilic phage D6E},,,5OE8_B,90.8511,100.0 SIF-Syn: found upstream of portal protein as in Rasovi /note=Current Gene Number: 3 /note=Did the start site stay the same or change: Changed to 869 /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, Rasovi /note=Z score = 1.166 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION: terminase large subunit /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0, terminase large subunit /note=Blast NCBI function match with E value should be 10^-7 or less: terminase large subunit /note=HHPRED Match with > 90% probability: 7.40026e-42, terminase large subunit /note=Conserved Domain: CDS 2347 - 4128 /gene="4" /product="gp4" /function="portal protein" /locus tag="Htur_4" /note=Original Glimmer call @bp 2347 has strength 12.82; Genemark calls start at 2347 /note=SSC: 2347-4128 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: 65 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.284, -1.9310779259753799, yes F: portal protein SIF-BLAST: ,,[portal protein [Microbacterium phage Rasovi]],,QJD49981,99.6627,0.0 SIF-HHPRED: Portal protein; Bacteriophage, SPP1, Portal Protein, Head completion proteins, Connector Complex, DNA Channel, VIRAL PROTEIN; 2.7A {Bacillus subtilis},,,7Z4W_B,81.4503,100.0 SIF-Syn: Found downstream of terminase, large subunit as in Rasovi. /note=Current Gene Number: 4 /note=Did the start site stay the same or change: Changed to 2347 /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, Rasovi /note=Z score = 3.284 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=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 4132 - 7062 /gene="5" /product="gp5" /function="VIP2-like ADP-ribosyltransferase toxin" /locus tag="Htur_5" /note=Original Glimmer call @bp 4132 has strength 15.85; Genemark calls start at 4132 /note=SSC: 4132-7062 CP: yes SCS: both ST: SS BLAST-Start: [MuF-like minor capsid & VIP2-like ADP-ribosyltransferase toxin [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.888, -2.7653702713535186, no F: VIP2-like ADP-ribosyltransferase toxin SIF-BLAST: ,,[MuF-like minor capsid & VIP2-like ADP-ribosyltransferase toxin [Microbacterium phage Rasovi]],,QJD49982,99.6926,0.0 SIF-HHPRED: Phage_min_cap2 ; Phage minor capsid protein 2,,,PF06152.15,35.5533,100.0 SIF-Syn: /note=Current Gene Number: 5 /note=Did the start site stay the same or change:Changed to 4132 /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, typher /note=Z score = 2.888 /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 complement (7064 - 7276) /gene="6" /product="gp6" /function="hypothetical protein" /locus tag="Htur_6" /note=Original Glimmer call @bp 7276 has strength 17.52; Genemark calls start at 7276 /note=SSC: 7276-7064 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ZANELLA_6 [Microbacterium phage Zanella] ],,NCBI, q1:s1 100.0% 1.14673E-41 GAP: 31 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.906, -5.186767100221219, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ZANELLA_6 [Microbacterium phage Zanella] ],,QGH80664,100.0,1.14673E-41 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 6 /note=Did the start site stay the same or change: Changed to 7,276. /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? Yes, Rasovi. /note=Z score = 1.906 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi /note=HHPRED Match with > 90% probability: NKF /note=Conserved Domain: CDS complement (7308 - 7646) /gene="7" /product="gp7" /function="hypothetical protein" /locus tag="Htur_7" /note=Original Glimmer call @bp 7646 has strength 10.01; Genemark calls start at 7646 /note=SSC: 7646-7308 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_7 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 5.71613E-75 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.143, -5.243663639127738, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_7 [Microbacterium phage Rasovi]],,QJD49984,100.0,5.71613E-75 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 7 /note=Did the start site stay the same or change: Changed to 7,646 /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? Yes, Rasovi. /note=Z score = 2.143 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi /note=HHPRED Match with > 90% probability: N/A /note=Conserved Domain: CDS complement (7639 - 8010) /gene="8" /product="gp8" /function="hypothetical protein" /locus tag="Htur_8" /note=Original Glimmer call @bp 8010 has strength 12.47; Genemark calls start at 8010 /note=SSC: 8010-7639 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_8 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 2.63302E-83 GAP: 413 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.888, -2.9063687850157054, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_8 [Microbacterium phage Rasovi]],,QJD49985,100.0,2.63302E-83 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 8 /note=Did the start site stay the same or change: Changed to 8,010 /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? Yes, Rasovi. /note=Z score = 2.888 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi, NKF /note=Blast NCBI function match with E value should be 10^-7 or less: NKF /note=HHPRED Match with > 90% probability: n/a /note=Conserved Domain: CDS 8424 - 9035 /gene="9" /product="gp9" /function="hypothetical protein" /locus tag="Htur_9" /note=Original Glimmer call @bp 8424 has strength 16.06; Genemark calls start at 8424 /note=SSC: 8424-9035 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_9 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 3.47095E-142 GAP: 413 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.55, -5.938885535067504, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_9 [Microbacterium phage Rasovi]],,QJD49986,100.0,3.47095E-142 SIF-HHPRED: Phage_GP20 ; Phage minor structural protein GP20,,,PF06810.15,71.9212,96.5 SIF-Syn: NKF /note=Current Gene Number: 9 /note=Did the start site stay the same or change: Changed to 8,424 /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, Rasovi. /note=Z score = 1.55 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi NKF /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS 9054 - 9911 /gene="10" /product="gp10" /function="major capsid protein" /locus tag="Htur_10" /note=Original Glimmer call @bp 9054 has strength 16.23; Genemark calls start at 9054 /note=SSC: 9054-9911 CP: yes SCS: both ST: SS BLAST-Start: [major capsid protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.391, -3.8137921535956054, no F: major capsid protein SIF-BLAST: ,,[major capsid protein [Microbacterium phage Rasovi]],,QJD49987,100.0,0.0 SIF-HHPRED: The capsid protein(gp 19) of P-SCSP1u; Whole virus, Capsid, cyanophage, T7-like virus, VIRUS;{Prochlorococcus phage P-SCSP1u},,,8I4L_B,95.4386,99.9 SIF-Syn: Found upstream of head-to-tail adaptor as in Rasovi /note=Current Gene Number: 10 /note=Did the start site stay the same or change: Changed to 9054. /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, Rasovi. /note=Z score = 2.391 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi, major capsid protein /note=HHPRED Match with > 90% probability: Major capsid protein /note=Conserved Domain: Major capsid protein CDS 9915 - 10517 /gene="11" /product="gp11" /function="hypothetical protein" /locus tag="Htur_11" /note=Original Glimmer call @bp 9915 has strength 11.16; Genemark calls start at 9915 /note=SSC: 9915-10517 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_11 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 8.44615E-135 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.117, -4.742415228075981, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_11 [Microbacterium phage Rasovi]],,QJD49988,100.0,8.44615E-135 SIF-HHPRED: SIF-Syn: NKF /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 /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, with Rasovi. /note=Z score = 2.117 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Starting site was kept the same. /note= /note=FUNCTION: NKF /note= /note=Synteny: NKF /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Yes, Rasovi and PermaG /note= /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi; 0 /note= /note=HHPRED Match with > 90% probability: No /note= /note=Conserved Domain: No CDS 10585 - 11064 /gene="12" /product="gp12" /function="head-to-tail adaptor" /locus tag="Htur_12" /note=Original Glimmer call @bp 10585 has strength 12.42; Genemark calls start at 10585 /note=SSC: 10585-11064 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail adaptor [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 2.1147E-109 GAP: 67 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.131, -2.3158002311349737, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Microbacterium phage Rasovi]],,QJD49989,100.0,2.1147E-109 SIF-HHPRED: Yqbg; Putative Head-Tail Connector Protein Yqbg from Bacillus subtilis and similar proteins.,,,cd08053,84.2767,99.8 SIF-Syn: Upstream to major tail protein as in Rasovi /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 /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, with Rasovi /note=Z score = 3.131 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=The starting site did not change. /note= /note=FUNCTION: Head to Tail Adaptor Protein /note= /note=Synteny: Yes /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Yes, Ravosi and SBlackberry /note= /note=Blast NCBI function match with E value should be 10^-7 or less: Yes, Rasovi /note= /note=HHPRED Match with > 90% probability: Yes, cd08053; 99.8% /note= /note=Conserved Domain: no CDS 11064 - 11387 /gene="13" /product="gp13" /function="head-to-tail stopper" /locus tag="Htur_13" /note=Original Glimmer call @bp 11064 has strength 8.36; Genemark calls start at 11064 /note=SSC: 11064-11387 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail stopper [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 4.39995E-72 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.911, -4.825272756372522, no F: head-to-tail stopper SIF-BLAST: ,,[head-to-tail stopper [Microbacterium phage Rasovi]],,QJD49990,100.0,4.39995E-72 SIF-HHPRED: Pam3 connector protein; fiber, VIRUS, VIRAL PROTEIN; 3.66A {uncultured cyanophage},,,8HDR_F,97.1963,99.0 SIF-Syn: Upstream to head-to-tail adaptor as in Rasovi /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 /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, with Rasovi /note=Z score = 1.911 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION: head-to-tail stopper /note= /note=Synteny: Up- stream of major tail protein 16 /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Yes, Rasovi and SBlackberry /note= /note=Blast NCBI function match with E value should be 10^-7 or less: Yes, Rasovi and TurboVicky /note= /note=HHPRED Match with > 90% probability: Yes, 8HDR_F; 99%, 6TE9_E; 98.8 /note= /note=Conserved Domain: no CDS 11384 - 11749 /gene="14" /product="gp14" /function="hypothetical protein" /locus tag="Htur_14" /note=Original Glimmer call @bp 11384 has strength 6.94; Genemark calls start at 11384 /note=SSC: 11384-11749 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_14 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 7.50521E-83 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.459, -3.8116689268127657, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_14 [Microbacterium phage Rasovi]],,QJD49991,100.0,7.50521E-83 SIF-HHPRED: DUF5403 ; Family of unknown function (DUF5403),,,PF17395.6,71.0744,97.7 SIF-Syn: NKF /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 /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, with Rasovi /note=Z score = 2.459 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION: NKF /note=Synteny: NKF /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Yes, Rasovi and Cicada /note= /note=Blast NCBI function match with E value should be 10^-7 or less: Yes, Rasovi and Cicada. /note= /note=HHPRED Match with > 90% probability: Yes, PF17395.6; 97.7% /note= /note=Conserved Domain: no CDS 11746 - 12186 /gene="15" /product="gp15" /function="tail terminator" /locus tag="Htur_15" /note=Original Glimmer call @bp 11746 has strength 10.58; Genemark calls start at 11746 /note=SSC: 11746-12186 CP: yes SCS: both ST: SS BLAST-Start: [tail terminator [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 1.11406E-103 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.865, -5.273552388616308, no F: tail terminator SIF-BLAST: ,,[tail terminator [Microbacterium phage Rasovi]],,QJD49992,100.0,1.11406E-103 SIF-HHPRED: Tail terminator protein Rcc01690; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_F,95.2055,99.3 SIF-Syn: Downstream to Major tail protein as in Rasovi /note=Did the start site stay the same or change: /note= /note=Do the Glimmer and Genemark start sites agree? Yes /note= /note=What about Starterator? Yes /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, with Rasovi /note=Z score = 1.865 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=FUNCTION: Tail terminator /note= /note=Synteny: ? /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Yes, Rasovi and SBlackberry /note= /note=Blast NCBI function match with E value should be 10^-7 or less: Yes, Rasovi and SBlackberry /note= /note=HHPRED Match with > 90% probability: Yes, 6TE9_F; 99.3% /note= /note=Conserved Domain: no CDS 12213 - 12713 /gene="16" /product="gp16" /function="major tail protein" /locus tag="Htur_16" /note=Original Glimmer call @bp 12213 has strength 15.43; Genemark calls start at 12213 /note=SSC: 12213-12713 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 6.39762E-117 GAP: 26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.131, -2.394485424036831, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Microbacterium phage Rasovi]],,QJD49993,100.0,6.39762E-117 SIF-HHPRED: Phage major tail protein, TP901-1 family; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_G,89.1566,99.7 SIF-Syn: Downstream to assembly chaperone as in Rasovi /note=Current Gene Number: 16 /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 (30.5%) /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 /note=Z score = 3.131 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Stayed the same /note= /note=FUNCTION : major tail protein /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi (4e^-95) /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi (3.37576e^-113) /note=HHPRED Match with > 90% probability: Yes (99.7%) /note=Conserved Domain: N/A CDS 12781 - 13233 /gene="17" /product="gp17" /function="tail assembly chaperone" /locus tag="Htur_17" /note=Original Glimmer call @bp 12781 has strength 15.79; Genemark calls start at 12781 /note=SSC: 12781-13233 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 3.6016E-106 GAP: 67 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.391, -3.8137921535956054, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Rasovi]],,QJD49994,100.0,3.6016E-106 SIF-HHPRED: SIF-Syn: Upstream to Major tail protein as in Rasovi /note=Current Gene Number: 17 /note= /note=Did the start site stay the same or change: Yes /note= /note=Do the Glimmer and Genemark start sites agree? Yes /note= /note=What about Starterator? No (39.3%) /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, Rasovi /note=Z score = 2.391 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Stayed the same /note= /note=FUNCTION: Tail assembly chaperone /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi (1e^-81) /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi (3.6016e^-106) /note=HHPRED Match with > 90% probability: N/A /note=Conserved Domain: N/A /note= /note=Slip happens at position 13224 (Reads G again) CDS join(12781..13224,13224..13508) /gene="18" /product="gp18" /function="tail assembly chaperone" /locus tag="Htur_18" /note= /note=SSC: 12781-13508 CP: yes SCS: neither ST: SS BLAST-Start: [tail assembly chaperone [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 2.50515E-177 GAP: -453 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.391, -3.8137921535956054, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Rasovi]],,QJD49995,99.5868,2.50515E-177 SIF-HHPRED: SIF-Syn: Upstream of tape measure as in Rasovi CDS 13514 - 15508 /gene="19" /product="gp19" /function="tape measure protein" /locus tag="Htur_19" /note=Original Glimmer call @bp 13514 has strength 13.01; Genemark calls start at 13514 /note=SSC: 13514-15508 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.536, -3.649482460397077, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Microbacterium phage Rasovi]],,QJD49996,100.0,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BF,12.3494,99.9 SIF-Syn: Upstream to tail assembly chaperone as in Rasovi /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? No /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 /note=Z score = 2.536 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Stay the same /note= /note=FUNCTION: Tape measure protein /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi (0) /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi (0) /note=HHPRED Match with > 90% probability: Yes 99.9% /note=Conserved Domain: N/A CDS 15518 - 16411 /gene="20" /product="gp20" /function="minor tail protein" /locus tag="Htur_20" /note=Original Glimmer call @bp 15518 has strength 14.5; Genemark calls start at 15518 /note=SSC: 15518-16411 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.284, -2.0111200136961407, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Rasovi]],,QJD49997,100.0,0.0 SIF-HHPRED: HYPOTHETICAL PROTEIN 19.1; VIRAL PROTEIN, DISTAL TAIL PROTEIN; 2.95A {BACILLUS PHAGE SPP1},,,2X8K_C,91.2458,99.9 SIF-Syn: Upstream to Tape measure protein as in Rasovi /note=Current Gene Number: 20 /note= /note=Did the start site stay the same or change: Yes /note= /note=Do the Glimmer and Genemark start sites agree? Yes /note= /note=What about Starterator? No /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 /note=Z score = 3.284 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Stayed the same /note= /note=FUNCTION: Minor tail protein /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi (1e^-171) /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi (0) /note=HHPRED Match with > 90% probability: Yes; 99.9% /note=Conserved Domain: N/A CDS 16411 - 18312 /gene="21" /product="gp21" /function="minor tail protein" /locus tag="Htur_21" /note=Original Glimmer call @bp 16411 has strength 13.33; Genemark calls start at 16411 /note=SSC: 16411-18312 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.161, -4.440057856863077, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Rasovi]],,QJD49998,100.0,0.0 SIF-HHPRED: Sipho_Gp37 ; Siphovirus ReqiPepy6 Gp37-like protein,,,PF14594.10,56.5561,99.9 SIF-Syn: Downstream to Minor tail protein as in Rasovi /note=Current Gene Number: 21 /note= /note=Did the start site stay the same or change: Yes /note= /note=Do the Glimmer and Genemark start sites agree? Yes /note= /note=What about Starterator? Yes /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; Rasovi /note=Z score = 2.161 /note= /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Kept at start site /note= /note=FUNCTION /note=Synteny: Minor tail protein /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Rasovi; 0 /note=Blast NCBI function match with E value should be 10^-7 or less: Rasovi; 0 /note=HHPRED Match with > 90% probability: Yes; 99.9% /note=Conserved Domain: No CDS 18318 - 18635 /gene="22" /product="gp22" /function="hypothetical protein" /locus tag="Htur_22" /note=Original Glimmer call @bp 18318 has strength 3.45; Genemark calls start at 18318 /note=SSC: 18318-18635 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_22 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 1.43539E-67 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.778, -3.1379842619144376, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_22 [Microbacterium phage Rasovi]],,QJD49999,100.0,1.43539E-67 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 22 /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, Rasovi /note=Z score = 2.778 /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: /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 18637 - 19368 /gene="23" /product="gp23" /function="minor tail protein" /locus tag="Htur_23" /note=Original Glimmer call @bp 18637 has strength 13.18; Genemark calls start at 18637 /note=SSC: 18637-19368 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 1.8268E-172 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.131, -2.3158002311349737, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Rasovi]],,QJD50000,100.0,1.8268E-172 SIF-HHPRED: Receptor Binding Protein; beta sandwich domain, phage receptor binding protein, Lactococcus lactis pellicle cell wall polyphosphosaccharide, VIRAL PROTEIN; 1.75A {Lactococcus phage 1358},,,4L9B_A,60.9053,99.8 SIF-Syn: Found upstream of minor tail protein as in Rasovi. /note=Current Gene Number: 23 /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, Rasovi /note=Z score = 3.131 /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: /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 19383 - 20204 /gene="24" /product="gp24" /function="minor tail protein" /locus tag="Htur_24" /note=Original Glimmer call @bp 19383 has strength 6.54; Genemark calls start at 19383 /note=SSC: 19383-20204 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.701, -3.810925907842985, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Rasovi]],,QJD50001,100.0,0.0 SIF-HHPRED: DUF859 ; Siphovirus protein of unknown function (DUF859),,,PF05895.16,44.3223,99.5 SIF-Syn: Found downstream of minor tail protein as in Rasovi. /note=Current Gene Number: 24 /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, Rasovi /note=Z score = 2.701 /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: /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 20197 - 20394 /gene="25" /product="gp25" /function="hypothetical protein" /locus tag="Htur_25" /note=Original Glimmer call @bp 20197 has strength 8.32; Genemark calls start at 20197 /note=SSC: 20197-20394 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_25 [Microbacterium phage Rasovi] ],,NCBI, q1:s1 100.0% 8.29424E-41 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.59, -3.4560725221641597, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_25 [Microbacterium phage Rasovi] ],,QJD50002,100.0,8.29424E-41 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 25 /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? /note=Z score = 2.59 /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: /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 20391 - 20669 /gene="26" /product="gp26" /function="hypothetical protein" /locus tag="Htur_26" /note=Original Glimmer call @bp 20391 has strength 10.64; Genemark calls start at 20391 /note=SSC: 20391-20669 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_26 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 1.82336E-59 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.778, -3.9043971090268372, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_26 [Microbacterium phage Rasovi]],,QJD50003,100.0,1.82336E-59 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 26 /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, Rasovi /note=Z score = 2.778 /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: /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 20662 - 21537 /gene="27" /product="gp27" /function="endolysin" /locus tag="Htur_27" /note=Original Glimmer call @bp 20662 has strength 15.69; Genemark calls start at 20662 /note=SSC: 20662-21537 CP: yes SCS: both ST: SS BLAST-Start: [endolysin [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.084, -4.522979412939132, no F: endolysin SIF-BLAST: ,,[endolysin [Microbacterium phage Rasovi]],,QJD50004,98.9691,0.0 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,75.6014,99.8 SIF-Syn: Found upstream of minor tail protein as in Rasovi. /note=Current Gene Number: 27 /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, Rasovi is closest /note=Z score = 2.084 /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: /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 21613 - 22002 /gene="28" /product="gp28" /function="hypothetical protein" /locus tag="Htur_28" /note=Original Glimmer call @bp 21613 has strength 7.14; Genemark calls start at 21628 /note=SSC: 21613-22002 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_28 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 2.59714E-83 GAP: 75 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.148, -4.466674028236667, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_28 [Microbacterium phage Rasovi]],,QJD50005,100.0,2.59714E-83 SIF-HHPRED: XhlA ; Haemolysin XhlA,,,PF10779.13,75.1938,95.1 SIF-Syn: NKF /note=PROBLEM /note=Current Gene Number: 28 /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: 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, Rasovi /note=Z score = 2.148 /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 21999 - 22724 /gene="29" /product="gp29" /function="minor tail protein" /locus tag="Htur_29" /note=Original Glimmer call @bp 21999 has strength 3.64; Genemark calls start at 21999 /note=SSC: 21999-22724 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 1.24093E-165 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.487, -4.915351186182232, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Rasovi]],,QJD50006,99.5851,1.24093E-165 SIF-HHPRED: uS2m; Mitochondria, mitoribosome, alga, RIBOSOME; 4.2A {Chlamydomonas reinhardtii},,,7PKQ_b,49.7925,86.5 SIF-Syn: Found upstream of holin as in Rasovi. /note=Current Gene Number: 29 /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 = 2.487 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Starterator, Glimmer, and GeneMark agree /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 22726 - 23004 /gene="30" /product="gp30" /function="holin" /locus tag="Htur_30" /note=Original Glimmer call @bp 22726 has strength 11.67; Genemark calls start at 22726 /note=SSC: 22726-23004 CP: yes SCS: both ST: SS BLAST-Start: [holin [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 6.80277E-56 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.888, -3.1164791313608173, yes F: holin SIF-BLAST: ,,[holin [Microbacterium phage Rasovi]],,QJD50007,100.0,6.80277E-56 SIF-HHPRED: Phage_r1t_holin ; Putative lactococcus lactis phage r1t holin,,,PF16945.9,82.6087,99.8 SIF-Syn: Found upstream of helix-turn-helix DNA binding domain as in Rasovi. /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? 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 = 2.888 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Glimmer, GeneMark, and Starterator all agree. /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 23108 - 23350 /gene="31" /product="gp31" /function="helix-turn-helix DNA binding domain" /locus tag="Htur_31" /note=Original Glimmer call @bp 23147 has strength 7.69; Genemark calls start at 23108 /note=SSC: 23108-23350 CP: yes SCS: both-gm ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 8.01921E-51 GAP: 103 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.096, -5.342699568601861, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Microbacterium phage Rasovi]],,QJD50008,100.0,8.01921E-51 SIF-HHPRED: a.35.1.2 (C:) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]} | CLASS: All alpha proteins, FOLD: lambda repressor-like DNA-binding domains, SUPFAM: lambda repressor-like DNA-binding domains, FAM: Phage repressors,,,SCOP_d3jxbc_,65.0,98.5 SIF-Syn: Found downstream of holin as in Rasovi. /note=Current Gene Number: 31 /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: 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 = 1.943 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Starterator and Glimmer agree, but not GeneMark. /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 23343 - 23468 /gene="32" /product="gp32" /function="hypothetical protein" /locus tag="Htur_32" /note=Original Glimmer call @bp 23343 has strength 7.09; Genemark calls start at 23343 /note=SSC: 23343-23468 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_32 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 1.09667E-20 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.042, -5.200500400297053, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_32 [Microbacterium phage Rasovi]],,QJD50009,100.0,1.09667E-20 SIF-HHPRED: DUF6479 ; Family of unknown function (DUF6479),,,PF20087.3,46.3415,90.4 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 32 /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; 100% /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; Rasovi /note=Z score =2.042 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Starterator was 100% confident with this start. /note= /note=FUNCTION /note=Synteny: Yes; Rasovi /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-19 /note=Blast NCBI function match with E value should be 10^-7 or less: 1.097e-20 /note=HHPRED Match with > 90% probability: 90.4% /note=Conserved Domain: N/A CDS 23465 - 24892 /gene="33" /product="gp33" /function="DNA helicase" /locus tag="Htur_33" /note=Original Glimmer call @bp 23426 has strength 12.33; Genemark calls start at 23465 /note=SSC: 23465-24892 CP: yes SCS: both-gm ST: SS BLAST-Start: [DNA helicase [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.264, -4.0818432048678375, no F: DNA helicase SIF-BLAST: ,,[DNA helicase [Microbacterium phage Rasovi]],,QJD50010,99.7895,0.0 SIF-HHPRED: Chromatin-remodeling ATPase INO80; Chromatin Remodeler, hexasome, DNA BINDING PROTEIN, DNA BINDING PROTEIN-Hydrolase complex; HET: ADP; 3.41A {Saccharomyces cerevisiae S288C},,,8EUF_Q,97.8947,100.0 SIF-Syn: Found downstream of DNA helicase as in Rasovi. /note=Current Gene Number: 33 /note=Did the start site stay the same or change: change, 23465 /note=Do the Glimmer and Genemark start sites agree? no /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? no data /note=Z score = 2.264 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: no data /note=Blast NCBI function match with E value should be 10^-7 or less: no data /note=HHPRED Match with > 90% probability: no data /note=Conserved Domain: no data CDS 24932 - 25132 /gene="34" /product="gp34" /function="hypothetical protein" /locus tag="Htur_34" /note=Original Glimmer call @bp 24932 has strength 16.99; Genemark calls start at 24932 /note=SSC: 24932-25132 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_RASOVI_34 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 9.313E-38 GAP: 39 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.137, -5.001512434791962, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_34 [Microbacterium phage Rasovi]],,QJD50011,98.4848,9.313E-38 SIF-HHPRED: SIF-Syn: NKF /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? no, 33.3% /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 = 2.137 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2e-33 /note=Blast NCBI function match with E value should be 10^-7 or less: 9.313e-38 /note=HHPRED Match with > 90% probability: no /note=Conserved Domain: no data CDS 25147 - 25710 /gene="35" /product="gp35" /function="hypothetical protein" /locus tag="Htur_35" /note=Original Glimmer call @bp 25147 has strength 8.06; Genemark calls start at 25147 /note=SSC: 25147-25710 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_35 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 7.12913E-134 GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.975, -2.723328252647382, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_35 [Microbacterium phage Rasovi]],,QJD50012,100.0,7.12913E-134 SIF-HHPRED: SIF-Syn: NKF /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, 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, Rasovi /note=Z score = 2.975 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-109 /note=Blast NCBI function match with E value should be 10^-7 or less: 7.13e-134 /note=HHPRED Match with > 90% probability: no /note=Conserved Domain: no data CDS 25707 - 25877 /gene="36" /product="gp36" /function="hypothetical protein" /locus tag="Htur_36" /note=Original Glimmer call @bp 25707 has strength 3.26 /note=SSC: 25707-25877 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_36 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 4.9447E-33 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.865, -4.9224435286090085, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_36 [Microbacterium phage Rasovi]],,QJD50013,100.0,4.9447E-33 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 36 /note=Did the start site stay the same or change: change /note=Do the Glimmer and Genemark start sites agree? not sure /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, but weak /note=Is there a 1:1 alignment on blast and with which phage? yes, Rasovi /note=Z score = 1.865 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 5e-30 /note=Blast NCBI function match with E value should be 10^-7 or less: 4.945e-33 /note=HHPRED Match with > 90% probability: no /note=Conserved Domain: no data CDS 25865 - 26131 /gene="37" /product="gp37" /function="hypothetical protein" /locus tag="Htur_37" /note=Original Glimmer call @bp 25865 has strength 8.48; Genemark calls start at 25865 /note=SSC: 25865-26131 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_RASOVI_37 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 3.48094E-58 GAP: -13 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.548, -7.198484264400552, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_37 [Microbacterium phage Rasovi]],,QJD50014,100.0,3.48094E-58 SIF-HHPRED: SIF-Syn: NKF /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? no, 45.5% /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, Rasovi /note=Z score = 1.548 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2e-47 /note=Blast NCBI function match with E value should be 10^-7 or less: 3.481e-58 /note=HHPRED Match with > 90% probability: no /note=Conserved Domain: no data CDS 26121 - 26474 /gene="38" /product="gp38" /function="hypothetical protein" /locus tag="Htur_38" /note=Original Glimmer call @bp 26121 has strength 11.59; Genemark calls start at 26121 /note=SSC: 26121-26474 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_38 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 5.57489E-79 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.778, -3.0592990690125803, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_38 [Microbacterium phage Rasovi]],,QJD50015,100.0,5.57489E-79 SIF-HHPRED: SIF-Syn: NKF /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, 93.3% /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, Rasovi /note=Z score = 2.778 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 3e-64 /note=Blast NCBI function match with E value should be 10^-7 or less: 5.575e-79 /note=HHPRED Match with > 90% probability: no /note=Conserved Domain: no data CDS 26474 - 26869 /gene="39" /product="gp39" /function="hypothetical protein" /locus tag="Htur_39" /note=Original Glimmer call @bp 26489 has strength 7.72; Genemark calls start at 26474 /note=SSC: 26474-26869 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_RASOVI_39 [Microbacterium phage Rasovi]],,NCBI, q1:s2 100.0% 2.51061E-76 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.668, -4.137199935798589, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_39 [Microbacterium phage Rasovi]],,QJD50016,90.9091,2.51061E-76 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 39 /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? no, 25% /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 = 1.567 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-59 /note=Blast NCBI function match with E value should be 10^-7 or less: 6.288e-72 /note=HHPRED Match with > 90% probability: no /note=Conserved Domain: no data CDS 26856 - 27461 /gene="40" /product="gp40" /function="Holliday junction resolvase" /locus tag="Htur_40" /note=Original Glimmer call @bp 26856 has strength 11.13; Genemark calls start at 26856 /note=SSC: 26856-27461 CP: yes SCS: both ST: SS BLAST-Start: [holliday junction resolvase [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 4.07066E-145 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.642, -3.284949965096066, no F: Holliday junction resolvase SIF-BLAST: ,,[holliday junction resolvase [Microbacterium phage Rasovi]],,QJD50017,99.5025,4.07066E-145 SIF-HHPRED: c.55.3.6 (A:) RuvC resolvase {Escherichia coli [TaxId: 562]} | CLASS: Alpha and beta proteins (a/b), FOLD: Ribonuclease H-like motif, SUPFAM: Ribonuclease H-like, FAM: RuvC resolvase,,,SCOP_d1hjra_,76.1194,99.7 SIF-Syn: Found downstream from DNA helicase as in Rasovi. /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? yes, 92.3% /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 = 2.642 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-119 /note=Blast NCBI function match with E value should be 10^-7 or less: 4.071e-145 /note=HHPRED Match with > 90% probability: yes, 99.7% /note=Conserved Domain: no data CDS 27463 - 27804 /gene="41" /product="gp41" /function="hypothetical protein" /locus tag="Htur_41" /note=Original Glimmer call @bp 27514 has strength 14.5; Genemark calls start at 27463 /note=SSC: 27463-27804 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_RASOVI_41 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 2.84893E-76 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.264, -5.131922069211155, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_41 [Microbacterium phage Rasovi]],,QJD50018,100.0,2.84893E-76 SIF-HHPRED: hypothetical protein PA2021; Pat85, NESG, GFT-NMR, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, UNKNOWN FUNCTION; NMR {Pseudomonas aeruginosa} SCOP: b.55.2.1,,,1YWY_A,58.4071,87.8 SIF-Syn: NKF /note=Current Gene Number: 41 /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? no, 67.7% /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 = 2.975 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note= /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-49 /note=Blast NCBI function match with E value should be 10^-7 or less: 2.669e-62 /note=HHPRED Match with > 90% probability: no /note=Conserved Domain: no data CDS 27804 - 27980 /gene="42" /product="gp42" /function="hypothetical protein" /locus tag="Htur_42" /note=Original Glimmer call @bp 27804 has strength 7.48; Genemark calls start at 27804 /note=SSC: 27804-27980 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_42 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 7.02679E-34 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.243, -4.125189544139167, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_42 [Microbacterium phage Rasovi]],,QJD50019,98.2759,7.02679E-34 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 42 /note=Did the start site stay the same or change: it stayed 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 /note=Z score = 2.243 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Everything agreed. /note= /note=FUNCTION: NKF /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 27973 - 28986 /gene="43" /product="gp43" /function="exonuclease" /locus tag="Htur_43" /note=Original Glimmer call @bp 27973 has strength 16.89; Genemark calls start at 27973 /note=SSC: 27973-28986 CP: yes SCS: both ST: SS BLAST-Start: [exonuclease [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.041, -2.5052746077145835, yes F: exonuclease SIF-BLAST: ,,[exonuclease [Microbacterium phage Rasovi]],,QJD50020,99.7033,0.0 SIF-HHPRED: ATP-dependent DNA helicase (UvrD/REP); DNA, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; 3.5A {Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)},,,6PPU_A,86.9436,99.9 SIF-Syn: In same place as exonuclease as in Rasovi. /note=Current Gene Number: 43 /note=Did the start site stay the same or change: it stayed 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 /note=Z score = 3.041 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. starterator had it at a 94% start with 12/276 manual annotations. which agreed with glimmer and genemark. /note= /note=FUNCTION: exonuclease /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 28989 - 29546 /gene="44" /product="gp44" /function="hypothetical protein" /locus tag="Htur_44" /note=Original Glimmer call @bp 28989 has strength 15.72; Genemark calls start at 28989 /note=SSC: 28989-29546 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_44 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 5.68734E-132 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.019, -4.597144958218091, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_44 [Microbacterium phage Rasovi]],,QJD50021,100.0,5.68734E-132 SIF-HHPRED: A118 serine integrase; site-specific recombination, coiled-coil, RECOMBINATION; 2.541A {Listeria innocua},,,5UDO_D,63.2432,93.3 SIF-Syn: NKF /note=Current Gene Number: 44 /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 /note=Z score = 2.019 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. everything agreed. /note= /note=FUNCTION: NKF /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 29546 - 29836 /gene="45" /product="gp45" /function="hypothetical protein" /locus tag="Htur_45" /note=Original Glimmer call @bp 29546 has strength 9.49; Genemark calls start at 29546 /note=SSC: 29546-29836 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_45 [Microbacterium phage Rasovi]],,NCBI, q1:s2 100.0% 1.63662E-63 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.334, -4.586591534678451, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_45 [Microbacterium phage Rasovi]],,QJD50022,97.9381,1.63662E-63 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 45 /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? Rasovi /note=Z score = 2.334 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. All starts were the same and everything agreed. /note= /note=FUNCTION: NKF /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 29833 - 30033 /gene="46" /product="gp46" /function="hypothetical protein" /locus tag="Htur_46" /note=Original Glimmer call @bp 29833 has strength 5.67; Genemark calls start at 29827 /note=SSC: 29833-30033 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_46 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 3.5658E-39 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.413, -3.908839699049252, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_46 [Microbacterium phage Rasovi]],,QJD50023,98.4848,3.5658E-39 SIF-HHPRED: Cell wall surface anchor protein; Adhesins, cell adhesion; 1.89A {Streptococcus agalactiae},,,4Z1P_A,92.4242,96.3 SIF-Syn: NKF /note=PROBLEM /note=Current Gene Number: 46 /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? 7.7% Do not have the most annotated /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 Phage Rasovi /note=Z score = 2.413 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Nothing agrees. next to gap that might be gene. /note= /note=FUNCTION: NKF /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 30030 - 30491 /gene="47" /product="gp47" /function="hypothetical protein" /locus tag="Htur_47" /note= /note=SSC: 30030-30491 CP: yes SCS: neither ST: NI BLAST-Start: [hypothetical protein SEA_RASOVI_47 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 8.02409E-105 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.414, -5.874376955301545, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_47 [Microbacterium phage Rasovi]],,QJD50039,97.3856,8.02409E-105 SIF-HHPRED: SIF-Syn: NKF CDS 30379 - 31446 /gene="48" /product="gp48" /function="RecA-like DNA recombinase" /locus tag="Htur_48" /note=Original Glimmer call @bp 30379 has strength 16.48; Genemark calls start at 30373 /note=SSC: 30379-31446 CP: yes SCS: both-gl ST: SS BLAST-Start: [RecA-like DNA recombinase [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: -113 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.138, -4.34663776219455, no F: RecA-like DNA recombinase SIF-BLAST: ,,[RecA-like DNA recombinase [Microbacterium phage Rasovi]],,QJD50024,99.1549,0.0 SIF-HHPRED: AAA_24 ; AAA domain,,,PF13479.10,61.9718,99.7 SIF-Syn: Found downstream of exonuclease as in Rasovi. /note=PROBLEM /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? No /note=What about Starterator? 12.8% Do not have the most annotated 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? Yes, Rasovi /note=Z score = 2.138 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=most things seemed to agree. next to gap that might be gene. /note= /note=FUNCTION: reca-like dna recombinase /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: tRNA 31468 - 31530 /gene="49" /product="tRNA-Pro(tgg)" /locus tag="HTUR_49" /note=tRNA-Pro(tgg) CDS 31557 - 31808 /gene="50" /product="gp50" /function="hypothetical protein" /locus tag="Htur_50" /note= /note=SSC: 31557-31808 CP: yes SCS: neither ST: NI BLAST-Start: [hypothetical protein SEA_RASOVI_50 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 4.90584E-52 GAP: 110 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.558, -5.632912100754952, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_50 [Microbacterium phage Rasovi]],,QJD50040,100.0,4.90584E-52 SIF-HHPRED: SIF-Syn: NKF CDS 32095 - 32640 /gene="51" /product="gp51" /function="hypothetical protein" /locus tag="Htur_51" /note=Original Glimmer call @bp 32095 has strength 14.98; Genemark calls start at 32095 /note=SSC: 32095-32640 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_51 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 5.02248E-129 GAP: 286 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.138, -4.426679849915311, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_51 [Microbacterium phage Rasovi]],,QJD50025,99.4475,5.02248E-129 SIF-HHPRED: DUF669 ; Protein of unknown function (DUF669),,,PF05037.17,75.6906,99.6 SIF-Syn: NKF /note=Current Gene Number: 48 /note=Did the start site stay the same or change: Stayed the same /note=Do the Glimmer and Genemark start sites agree? Yes /note=What about Starterator? 99.1% Call this the most annotated 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? Yes, with Rasovi /note=Z score = 2.87 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Everything Agreed. /note= /note=FUNCTION: NKF /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 32726 - 35431 /gene="52" /product="gp52" /function="DNA primase/polymerase" /locus tag="Htur_52" /note=Original Glimmer call @bp 32726 has strength 9.74; Genemark calls start at 32726 /note=SSC: 32726-35431 CP: yes SCS: both ST: NI BLAST-Start: [DNA primase/polymerase [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: 85 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.563, -4.279791573443133, no F: DNA primase/polymerase SIF-BLAST: ,,[DNA primase/polymerase [Microbacterium phage Rasovi]],,QJD50026,99.778,0.0 SIF-HHPRED: DNA primase; Helicase, DNA binding, AMPPNP, REPLICATION; HET: ANP; 3.1A {Staphylococcus aureus},,,7OM0_D,39.7336,99.9 SIF-Syn: Found down stream of RecA-like DNA recombinase as found in Rasovi /note=Current Gene Number: 49 /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? 100% Say Most annotated /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? /note=Z score = 2.563 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. everything agreed. /note= /note=FUNCTION: DNA primase/polymerase /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 complement (35556 - 35861) /gene="53" /product="gp53" /function="hypothetical protein" /locus tag="Htur_53" /note=Original Glimmer call @bp 35819 has strength 15.04; Genemark calls start at 35861 /note=SSC: 35861-35556 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_53 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 2.13196E-68 GAP: 415 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.894, -5.513395795770837, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_53 [Microbacterium phage Rasovi]],,QJD50027,100.0,2.13196E-68 SIF-HHPRED: SIF-Syn: NKF /note=PROBLEM /note=Current Gene Number: 50 /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? 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 = 1.894 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=In the starterator file, this gene is in only two genes, Rasovi and Htur. The start site as in Rasovi was chosen. /note= /note=FUNCTION: NKF /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 36277 - 38571 /gene="54" /product="gp54" /function="DNA polymerase I" /locus tag="Htur_54" /note=Original Glimmer call @bp 36277 has strength 14.03; Genemark calls start at 36292 /note=SSC: 36277-38571 CP: yes SCS: both-gl ST: SS BLAST-Start: [DNA polymerase I [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: 415 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.12, -2.356391881054909, yes F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Microbacterium phage Rasovi]],,QJD50028,99.8691,0.0 SIF-HHPRED: DNA polymerase theta; DNA polymerase, protein-DNA complex, DNA repair, TRANSFERASE; HET: DDG, DG3; 2.26A {Homo sapiens},,,7ZUS_BBB,76.8325,100.0 SIF-Syn: found same place as dna polymerase i as in Rasovi. /note=Current Gene Number: 51 /note=Did the start site stay the same or change: stay /note=Do the Glimmer and Genemark start sites agree? no /note=What about Starterator? yes, with 36277 /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, Rasovi /note=Z score = 3.12 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. starterator had most annotated and most manual start. genemark file had all potential captured. /note= /note=FUNCTION: dna polymerase i /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 38564 - 38860 /gene="55" /product="gp55" /function="hypothetical protein" /locus tag="Htur_55" /note=Original Glimmer call @bp 38564 has strength 0.58; Genemark calls start at 38564 /note=SSC: 38564-38860 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOU56_gp53 [Microbacterium phage Goodman] ],,NCBI, q1:s1 100.0% 1.55189E-64 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.659, -5.437750947756905, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOU56_gp53 [Microbacterium phage Goodman] ],,YP_009815957,100.0,1.55189E-64 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 52 /note=Did the start site stay the same or change: Stayed 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_009815957, QGH80708 /note=Z score = 1.659 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Has the longest ORF, all start sites agree, all coding potential captured GM. /note= /note=FUNCTION: /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Goodman, Johann /note=Blast NCBI function match with E value should be 10^-7 or less: YP_009815957, QGH80708 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None CDS 38985 - 40205 /gene="56" /product="gp56" /function="adenylosuccinate synthetase PurA-like" /locus tag="Htur_56" /note=Original Glimmer call @bp 38985 has strength 17.32; Genemark calls start at 38985 /note=SSC: 38985-40205 CP: yes SCS: both ST: SS BLAST-Start: [PurA-like adenylosuccinate synthetase [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 0.0 GAP: 124 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.12, -2.338663114094478, yes F: adenylosuccinate synthetase PurA-like SIF-BLAST: ,,[PurA-like adenylosuccinate synthetase [Microbacterium phage Rasovi]],,QJD50030,100.0,0.0 SIF-HHPRED: c.37.1.10 (A:) automated matches {Legionella pneumophila [TaxId: 446]} | CLASS: Alpha and beta proteins (a/b), FOLD: P-loop containing nucleoside triphosphate hydrolases, SUPFAM: P-loop containing nucleoside triphosphate hydrolases, FAM: Nitrogenase iron protein-like,,,SCOP_d6c25a_,93.1034,100.0 SIF-Syn: Found downstream of DNA polymerase I as in Rasovi /note=Current Gene Number: 53 /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? Y /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, QJD50030 /note=Z score = 3.12 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Stayed the same because all start sites agree. Most annotated. /note= /note=FUNCTION /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi , Typher /note=Blast NCBI function match with E value should be 10^-7 or less: QJD50030 , URM86961 /note=HHPRED Match with > 90% probability: SCOP_d6c25a_ , SCOP_d1p9ba_ /note=Conserved Domain: PRK04293 , smart00788 CDS 40207 - 40743 /gene="57" /product="gp57" /function="hypothetical protein" /locus tag="Htur_57" /note=Original Glimmer call @bp 40207 has strength 12.27; Genemark calls start at 40207 /note=SSC: 40207-40743 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_57 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 5.69708E-127 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.459, -4.021779273157878, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_57 [Microbacterium phage Rasovi]],,QJD50031,100.0,5.69708E-127 SIF-HHPRED: DUF6378 ; Domain of unknown function (DUF6378),,,PF19905.3,53.9326,94.1 SIF-Syn: NKF /note=Current Gene Number: 54 /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? Yes, QJD50031 /note=Z score = 2.459 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Stayed the same, all start sites agree, all coding potential on GM file. The start number is called 100% of the time when present. /note= /note=FUNCTION: /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi , PermaG /note=Blast NCBI function match with E value should be 10^-7 or less: QJD50031 , YP_009815959 /note=HHPRED Match with > 90% probability: PF19905.3 /note=Conserved Domain: None CDS 40740 - 40877 /gene="58" /product="gp58" /function="hypothetical protein" /locus tag="Htur_58" /note=Original Glimmer call @bp 40740 has strength 5.02; Genemark calls start at 40740 /note=SSC: 40740-40877 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_58 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 2.64067E-23 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.784, -5.443606692405957, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_58 [Microbacterium phage Rasovi]],,QJD50032,100.0,2.64067E-23 SIF-HHPRED: Multi_ubiq ; Multiubiquitin,,,PF14452.10,48.8889,89.8 SIF-Syn: NKF /note=**Problem: Two different subclusters of pham, start num6 is called 100% when present, but is found in a different subcluster. Start num7 is found in subject EJ but only called 66.7% when present.** /note=Current Gene Number: 55 /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: No /note=Is there a 1:1 alignment on blast and with which phage? Yes, QJD50032 /note=Z score = 1.784 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Called majority of the time, start sites agree. /note= /note=FUNCTION: /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi , YuuY /note=Blast NCBI function match with E value should be 10^-7 or less: QJD50032 , QFP95390 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None CDS 40874 - 41116 /gene="59" /product="gp59" /function="hypothetical protein" /locus tag="Htur_59" /note=Original Glimmer call @bp 40874 has strength 14.33; Genemark calls start at 40874 /note=SSC: 40874-41116 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_59 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 2.89648E-47 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.198, -2.17469248771465, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_59 [Microbacterium phage Rasovi]],,QJD50033,98.75,2.89648E-47 SIF-HHPRED: DUF6354 ; Family of unknown function (DUF6354),,,PF19881.3,97.5,97.3 SIF-Syn: NKF /note=Current Gene Number: 56 /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? No /note=Z score = 3.198 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. All start sites agree, start is called 100% of the time when present. All coding potential in GM. /note= /note=FUNCTION: /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi , SBlackberry /note=Blast NCBI function match with E value should be 10^-7 or less: QJD50033 , UAW08799 /note=HHPRED Match with > 90% probability: PF19881.3 /note=Conserved Domain: None CDS 41116 - 41325 /gene="60" /product="gp60" /function="hypothetical protein" /locus tag="Htur_60" /note=Original Glimmer call @bp 41137 has strength 15.09; Genemark calls start at 41116 /note=SSC: 41116-41325 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_60 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 4.59945E-39 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.117, -4.4713484557894425, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_60 [Microbacterium phage Rasovi]],,QJD50034,98.5507,4.59945E-39 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 57 /note=Did the start site stay the same or change: Stay the asme /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: Yes /note=Is there a 1:1 alignment on blast and with which phage? No /note=Z score = 1.613 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Stayed the same, Htur was the only phage that did not call the most annotated start, all other non-draft phages called this start. /note= /note=FUNCTION: /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi, Milani /note=Blast NCBI function match with E value should be 10^-7 or less: QJD50034 , WKW85447 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None CDS 41312 - 41770 /gene="61" /product="gp61" /function="Deoxyuridine triphosphatase" /locus tag="Htur_61" /note=Original Glimmer call @bp 41312 has strength 9.75; Genemark calls start at 41312 /note=SSC: 41312-41770 CP: yes SCS: both ST: SS BLAST-Start: [deoxyuridine triphosphatase [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 4.58531E-105 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.632, -3.95820260462814, yes F: Deoxyuridine triphosphatase SIF-BLAST: ,,[deoxyuridine triphosphatase [Microbacterium phage Rasovi]],,QJD50035,100.0,4.58531E-105 SIF-HHPRED: DUTPase; jelly-roll, hydrolase; HET: DUP; 2.1A {Staphylococcus phage 11} SCOP: b.85.4.0,,,4GV8_B,92.7632,99.9 SIF-Syn: Found downstream of PurA-like adenylosuccinate sythetase as in Rasovi /note=Current Gene Number: 58 /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? Yes, QJD50035 /note=Z score = 2.632 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Stayed the same, the start is called 100% of the time when present. /note= /note=FUNCTION: /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi, Goodman /note=Blast NCBI function match with E value should be 10^-7 or less: QJD50035, YP_009815963 /note=HHPRED Match with > 90% probability: 4GV8_B , 3MDX_A /note=Conserved Domain: TIGR00576 , COG0756 CDS 41745 - 41996 /gene="62" /product="gp62" /function="hypothetical protein" /locus tag="Htur_62" /note=Original Glimmer call @bp 41859 has strength 2.71 /note=SSC: 41745-41996 CP: yes SCS: glimmer-cs ST: NI BLAST-Start: [hypothetical protein SEA_RASOVI_62 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 3.04191E-50 GAP: -26 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.632, -3.3861058366776207, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_62 [Microbacterium phage Rasovi]],,QJD50036,100.0,3.04191E-50 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 59 /note=Did the start site stay the same or change: Changed /note=Do the Glimmer and Genemark start sites agree? No Genemark start noted /note=What about Starterator? With glimmer /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 = 2.632 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. /note=Changed to match Rasovi for the time being (no synteny currently) /note= /note=FUNCTION: /note=Synteny: No /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi, Jera_Draft /note=Blast NCBI function match with E value should be 10^-7 or less: QJD50036, UVK60391 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None CDS 41993 - 42229 /gene="63" /product="gp63" /function="hypothetical protein" /locus tag="Htur_63" /note=Original Glimmer call @bp 42023 has strength 5.33; Genemark calls start at 42023 /note=SSC: 41993-42229 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_63 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 7.94695E-49 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.38, -4.188334187302651, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_63 [Microbacterium phage Rasovi]],,QJD50037,100.0,7.94695E-49 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 60 /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? 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? N/A /note=Z score = 2.38 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Changed, there was only 3 M.A`s for the auto-annotated start but 6 for the start site that it was changed to. The auto-annotated start site of 5 found in 90% of genes in the pham but is only called 44.4% of the time when present; start site 4 found in 100% of genes in pham and is called 60% of the time when present. /note= /note=FUNCTION: /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi, Cicada /note=Blast NCBI function match with E value should be 10^-7 or less: None /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None CDS complement (42278 - 42748) /gene="64" /product="gp64" /function="hypothetical protein" /locus tag="Htur_64" /note=Original Glimmer call @bp 42748 has strength 13.27; Genemark calls start at 42748 /note=SSC: 42748-42278 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RASOVI_64 [Microbacterium phage Rasovi]],,NCBI, q1:s1 100.0% 2.99999E-111 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.9, -2.8030814177649614, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RASOVI_64 [Microbacterium phage Rasovi]],,QJD50038,100.0,2.99999E-111 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 61 /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, QJD50038 /note=Z score = 2.9 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Kept, LORF, start sites agree, all coding potential on GM. /note= /note=FUNCTION: /note=Synteny: /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Rasovi , PermaG /note=Blast NCBI function match with E value should be 10^-7 or less: QJD50038 , QWY83850 /note=HHPRED Match with > 90% probability: None /note=Conserved Domain: None