CDS 803 - 1234 /gene="1" /product="gp1" /function="terminase, small subunit" /locus tag="Taquarus-MitchellCC_1" /note=Original Glimmer call @bp 803 has strength 8.77; Genemark calls start at 803 /note=SSC: 803-1234 CP: yes SCS: both ST: SS BLAST-Start: [terminase small subunit [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 3.10966E-100 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.946, -2.66371296573402, yes F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Mycobacterium phage Peaches] ],,YP_003358705,100.0,3.10966E-100 SIF-HHPRED: Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97},,,6Z6E_B,47.5524,98.1 SIF-Syn: Small subunit terminase protein found upstream from small subunit terminase protein as in Clarenza /note=Current Gene Number: 1 /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? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 2.946 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /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: 2e-78 /note=HHPRED Match with > 90% probability: 98.1 /note=Conserved Domain: N/A CDS 1329 - 1643 /gene="2" /product="gp2" /function="minor tail protein" /locus tag="Taquarus-MitchellCC_2" /note=Original Glimmer call @bp 1329 has strength 15.01; Genemark calls start at 1329 /note=SSC: 1329-1643 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_OBAMA12_3 [Mycobacterium phage Obama12] ],,NCBI, q1:s1 100.0% 2.76745E-67 GAP: 94 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.157, -2.6835611257758942, yes F: minor tail protein SIF-BLAST: ,,[hypothetical protein PBI_OBAMA12_3 [Mycobacterium phage Obama12] ],,YP_009007195,100.0,2.76745E-67 SIF-HHPRED: b.1.18.9 (A:15-145) Transglutaminase N-terminal domain {Human (Homo sapiens), tissue isozyme [TaxId: 9606]},,,d2q3za1,58.6538,90.6 SIF-Syn: Minor tail protein found downstream from terminase, small subunit /note=Current Gene Number: 2 /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? 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 /note=Z score = 3.157 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and agrees with starterator. /note= /note=FUNCTION /note=Synteny: NKF /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-54 /note=Blast NCBI function match with E value should be 10^-7 or less: 2.76745e-67 /note=HHPRED Match with > 90% probability: 90.6 /note=Conserved Domain: N/A CDS 1648 - 2721 /gene="3" /product="gp3" /function="minor tail protein" /locus tag="Taquarus-MitchellCC_3" /note=Original Glimmer call @bp 1648 has strength 2.52; Genemark calls start at 1648 /note=SSC: 1648-2721 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_KAMPY_4 [Mycobacterium phage Kampy] ],,NCBI, q1:s1 100.0% 0.0 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.779, -3.0149320667577513, yes F: minor tail protein SIF-BLAST: ,,[hypothetical protein PBI_KAMPY_4 [Mycobacterium phage Kampy] ],,YP_009031864,100.0,0.0 SIF-HHPRED: Collagen alpha-1(I) chain; NATIVE, IN SITU, Molecular envelope, TRIPLE-helical, SUPERMOLECULAR, supramolecular, PACKING STRUCTURE, STRUCTURAL PROTEIN-CONTRACTILE PROTEIN COMPLEX, Collagen, Extracellular; HET: HYP, LYZ; 5.16A {Rattus norvegicus} SCOP: i.25.1.1,,,3HQV_C,0.0,98.5 SIF-Syn: Minor tail protein found upstream from lysin A protein as in Clarenza /note=Current Gene Number: 3 /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? 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 /note=Z score = 2.779 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and agrees with starterator. /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: 98.5 /note=Conserved Domain: No CDS 2725 - 3387 /gene="4" /product="gp4" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_4" /note=Original Glimmer call @bp 2725 has strength 6.63; Genemark calls start at 2725 /note=SSC: 2725-3387 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BURGER_4 [Mycobacterium phage Burger] ],,NCBI, q1:s1 100.0% 8.99792E-144 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.04, -4.513079314654054, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BURGER_4 [Mycobacterium phage Burger] ],,AMW64175,99.5455,8.99792E-144 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 4 /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? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 2.04 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /note= /note=FUNCTION /note=Synteny: No /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-131 /note=Blast NCBI function match with E value should be 10^-7 or less: 8.99792e-144 /note=HHPRED Match with > 90% probability: No /note=Conserved Domain: N/A CDS 3366 - 3758 /gene="5" /product="gp5" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_5" /note=Original Glimmer call @bp 3366 has strength 12.29; Genemark calls start at 3387 /note=SSC: 3366-3758 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein PBI_ABDIEL_6 [Mycobacterium phage Abdiel] ],,NCBI, q1:s1 100.0% 3.30394E-89 GAP: -22 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.253, -3.2592921783815076, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_ABDIEL_6 [Mycobacterium phage Abdiel] ],,APD17269,100.0,3.30394E-89 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 5 /note=Did the start site stay the same or change: It changes /note=Do the Glimmer and Genemark start sites agree? No - called based on Glimmer and starterator. /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 3.253 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /note= /note=FUNCTION /note=Synteny: No /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 5e-75 /note=Blast NCBI function match with E value should be 10^-7 or less: 3.30394e-89 /note=HHPRED Match with > 90% probability: No /note=Conserved Domain: N/A CDS 3787 - 3924 /gene="6" /product="gp6" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_6" /note=Original Glimmer call @bp 3787 has strength 16.88; Genemark calls start at 3787 /note=SSC: 3787-3924 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_7 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 8.5586E-22 GAP: 28 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.253, -2.0162541296952132, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_7 [Mycobacterium phage Peaches] ],,YP_003358710,100.0,8.5586E-22 SIF-HHPRED: Tai4; ANTITOXIN; HET: EDO; 1.55A {Rhizobium radiobacter},,,6IJE_B,75.5556,92.8 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 6 /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? N/A /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; Peaches /note=Z score = 3.253 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it agrees with Glimmer and GeneMark and it has a 1:1 ratio with Peaches. /note= /note=FUNCTION /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2^-18 /note=Blast NCBI function match with E value should be 10^-7 or less: 8.5586^-22 /note=HHPRED Match with > 90% probability: Yes; 92.8 /note=Conserved Domain: N/A /note=Checked CDS 3924 - 5426 /gene="7" /product="gp7" /function="lysin A" /locus tag="Taquarus-MitchellCC_7" /note=Original Glimmer call @bp 3924 has strength 9.16; Genemark calls start at 3924 /note=SSC: 3924-5426 CP: no SCS: both ST: NI BLAST-Start: [lysin A [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.64, -5.437750947756905, no F: lysin A SIF-BLAST: ,,[lysin A [Mycobacterium phage Peaches] ],,YP_003358711,100.0,0.0 SIF-HHPRED: d.2.1.0 (A:) automated matches {Bryum coronatum [TaxId: 216087]},,,d3wh1a_,34.8,99.0 SIF-Syn: Lysin A found upstream from lysin B as in Clarenza /note=NOTE /note=Current Gene Number: 7 /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? N/A /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; Peaches /note=Z score = 1.64 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with GeneMark and Glimmer. /note= /note=FUNCTION /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: Yes; 99% /note=Conserved Domain: No /note=Checked CDS 5423 - 5884 /gene="8" /product="gp8" /function="holin" /locus tag="Taquarus-MitchellCC_8" /note=Original Glimmer call @bp 5423 has strength 11.96; Genemark calls start at 5423 /note=SSC: 5423-5884 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_9 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 1.37823E-99 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.612, -3.3861058366776207, yes F: holin SIF-BLAST: ,,[hypothetical protein PEACHES_9 [Mycobacterium phage Peaches] ],,YP_003358712,100.0,1.37823E-99 SIF-HHPRED: Phage_holin_7_1 ; Mycobacterial 2 TMS Phage Holin (M2 Hol) Family,,,PF16081.8,80.3922,100.0 SIF-Syn: Holin found upstream from terminase large subunit in Clarenza /note=NOTE /note=Current Gene Number: 8 /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? N/A /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; Peaches /note=Z score = 2.612 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with GeneMark and Glimmer. /note= /note=FUNCTION /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2^-81 /note=Blast NCBI function match with E value should be 10^-7 or less: 1.37823^-99 /note=HHPRED Match with > 90% probability: Yes; 100% /note=Conserved Domain: No /note=Checked CDS 5884 - 6864 /gene="9" /product="gp9" /function="lysin B" /locus tag="Taquarus-MitchellCC_9" /note=Original Glimmer call @bp 5884 has strength 13.85; Genemark calls start at 5887 /note=SSC: 5884-6864 CP: yes SCS: both-gl ST: SS BLAST-Start: [lysin B [Mycobacterium phage Arturo] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.022, -4.551528886052257, no F: lysin B SIF-BLAST: ,,[lysin B [Mycobacterium phage Arturo] ],,YP_009638667,100.0,0.0 SIF-HHPRED: Gene 12 protein; alpha/beta sandwich, CELL ADHESION; 2.0A {Mycobacterium phage D29},,,3HC7_A,72.6994,100.0 SIF-Syn: Lysin B found upstream from portal protein in Clarenza /note=NOTE /note=Current Gene Number: 9 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? No - called based on Glimmer /note=What about Starterator? N/A /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; Arturo /note=Z score = 2.022 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with Glimmer. /note= /note=FUNCTION /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: Yes; 100% /note=Conserved Domain: N/A /note=Checked CDS 6887 - 8584 /gene="10" /product="gp10" /function="terminase, large subunit" /locus tag="Taquarus-MitchellCC_10" /note=Original Glimmer call @bp 6887 has strength 14.08; Genemark calls start at 6911 /note=SSC: 6887-8584 CP: yes SCS: both-gl ST: SS BLAST-Start: [terminase [Mycobacterium phage Kampy] ],,NCBI, q1:s1 100.0% 0.0 GAP: 22 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.516, -3.50848394673489, no F: terminase, large subunit SIF-BLAST: ,,[terminase [Mycobacterium phage Kampy] ],,YP_009031871,100.0,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,91.1504,100.0 SIF-Syn: Terminase, large subunit found upstream from capsid maturation protease /note=NOTE /note=Current Gene Number: 10 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? No - called based on Glimmer /note=What about Starterator? N/A /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; Kampy /note=Z score = 2.516 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with Glimmer /note= /note=FUNCTION /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: Yes; 100% /note=Conserved Domain: No /note=Checked CDS 8581 - 10032 /gene="11" /product="gp11" /function="portal protein" /locus tag="Taquarus-MitchellCC_11" /note=Original Glimmer call @bp 8581 has strength 15.1; Genemark calls start at 8581 /note=SSC: 8581-10032 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.124, -4.477250792015338, no F: portal protein SIF-BLAST: ,,[portal protein [Mycobacterium phage Peaches] ],,YP_003358715,100.0,0.0 SIF-HHPRED: PORTAL PROTEIN; BACTERIOPHAGE SPP1, DNA TRANSLOCATION, MOLECULAR MOTOR, VIRAL PORTAL PROTEIN, VIRAL PROTEIN; HET: CA, HG; 3.4A {BACTERIOPHAGE SPP1},,,2JES_Q,90.8903,100.0 SIF-Syn: Portal protein found upstream from scaffolding protein in Clarenza /note=NOTE /note=Current Gene Number: 11 /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? N/A /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; Peaches /note=Z score = 2.124 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with GeneMark and Glimmer. /note= /note=FUNCTION /note=Synteny: Yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: Yes; 100% /note=Conserved Domain: No /note=Checked CDS 10029 - 10889 /gene="12" /product="gp12" /function="capsid maturation protease" /locus tag="Taquarus-MitchellCC_12" /note=Original Glimmer call @bp 10029 has strength 12.16; Genemark calls start at 10029 /note=SSC: 10029-10889 CP: yes SCS: both ST: SS BLAST-Start: [capsid maturation protease [Mycobacterium phage Nyxis] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.021, -3.3503726477288405, yes F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease [Mycobacterium phage Nyxis] ],,YP_009005852,100.0,0.0 SIF-HHPRED: Phage_min_cap2 ; Phage minor capsid protein 2,,,PF06152.14,57.3427,96.6 SIF-Syn: Found downstream of portal protein as in Clarenza /note=*No notes in this section* CDS 10942 - 11454 /gene="13" /product="gp13" /function="scaffolding protein" /locus tag="Taquarus-MitchellCC_13" /note=Original Glimmer call @bp 10942 has strength 12.93; Genemark calls start at 10942 /note=SSC: 10942-11454 CP: yes SCS: both ST: SS BLAST-Start: [scaffolding protein [Mycobacterium phage BellusTerra] ],,NCBI, q1:s1 100.0% 7.93581E-120 GAP: 52 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.946, -2.9525085049809894, yes F: scaffolding protein SIF-BLAST: ,,[scaffolding protein [Mycobacterium phage BellusTerra] ],,YP_009005572,100.0,7.93581E-120 SIF-HHPRED: DUF4355 ; Domain of unknown function (DUF4355),,,PF14265.9,65.2941,99.2 SIF-Syn: Scaffolding protein found upstream from major capsid protein as in Avle17. /note=NOTE /note=Current Gene Number: 13 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Yes - called based on Glimmer and starterator. /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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, Avle17. /note=Z score = 1.932 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /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 11482 - 12414 /gene="14" /product="gp14" /function="major capsid protein" /locus tag="Taquarus-MitchellCC_14" /note=Original Glimmer call @bp 11482 has strength 19.34; Genemark calls start at 11482 /note=SSC: 11482-12414 CP: yes SCS: both ST: SS BLAST-Start: [major capsid protein [Mycobacterium phage BellusTerra] ],,NCBI, q1:s1 100.0% 0.0 GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.082, -2.66590822473965, yes F: major capsid protein SIF-BLAST: ,,[major capsid protein [Mycobacterium phage BellusTerra] ],,YP_009005573,100.0,0.0 SIF-HHPRED: SIF-Syn: Major capsid protein found downstream from scaffolding protein as in Avle17. /note=NOTE /note=Current Gene Number: 14 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Yes - called based on Glimmer and starterator. /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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, Avle17 /note=Z score = 2.134 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a longer ORF, and agrees with starterator. /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 12481 - 12687 /gene="15" /product="gp15" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_15" /note=Original Glimmer call @bp 12481 has strength 9.55; Genemark calls start at 12481 /note=SSC: 12481-12687 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein CH07_gp16 [Mycobacterium phage BellusTerra] ],,NCBI, q1:s1 100.0% 3.61375E-39 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.62, -3.42909898063754, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein CH07_gp16 [Mycobacterium phage BellusTerra] ],,YP_009005574,100.0,3.61375E-39 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 15 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Yes - called based on Glimmer and starterator. /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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, Avle17 /note=Z score = 2.62 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /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 12691 - 13047 /gene="16" /product="gp16" /function="head-to-tail adaptor" /locus tag="Taquarus-MitchellCC_16" /note=Original Glimmer call @bp 12691 has strength 11.6; Genemark calls start at 12691 /note=SSC: 12691-13047 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail adaptor [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 1.20213E-79 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.868, -2.7653702713535186, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Mycobacterium phage Peaches] ],,YP_003358720,100.0,1.20213E-79 SIF-HHPRED: Phage_Gp19 ; Phage protein Gp19/Gp15/Gp42,,,PF09355.13,83.0508,99.8 SIF-Syn: Head-to-tail adaptor found upstream of head-to-tail stopper as in Avle17. /note=NOTE /note=Current Gene Number: 16 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Yes - called based on Glimmer and starterator. /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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, Avle17 /note=Z score = 2.039 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /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 13044 - 13211 /gene="17" /product="gp17" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_17" /note=Original Glimmer call @bp 13044 has strength 6.83; Genemark calls start at 13044 /note=SSC: 13044-13211 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_18 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 2.03777E-33 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.306, -6.143409454131006, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_18 [Mycobacterium phage Peaches] ],,YP_003358721,100.0,2.03777E-33 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 17 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Yes - called based on Glimmer and starterator. /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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, Avle17 /note=Z score = 1.812 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /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 13208 - 13570 /gene="18" /product="gp18" /function="head-to-tail stopper" /locus tag="Taquarus-MitchellCC_18" /note=Original Glimmer call @bp 13208 has strength 11.65; Genemark calls start at 13208 /note=SSC: 13208-13570 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail stopper [Mycobacterium phage BellusTerra] ],,NCBI, q1:s1 100.0% 3.53512E-84 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.813, -4.9912573797770525, no F: head-to-tail stopper SIF-BLAST: ,,[head-to-tail stopper [Mycobacterium phage BellusTerra] ],,YP_009005577,100.0,3.53512E-84 SIF-HHPRED: DUF3599 ; Domain of unknown function (DUF3599),,,PF12206.11,98.3333,99.5 SIF-Syn: Found upstream from the tail terminator as in Albee /note=NOTE /note=Current Gene Number: 18 /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? _ /note=Is the ORF chosen the longest ORF: ORF was the LORF /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, BellusTarra /note=Z score = 1.813 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. It is the LORF, both the GeneMark and the Glimmer score matched. Z score very close to 1, and the final score is one of the closest to 0. /note= /note=FUNCTION /note=Synteny- yes /note=Phagesdb blast- Head-to-Tail Stopper 6e-67 /note=Blast NCBI function match- Head-to-Tail Stopper /note=HHPRED Match- 99.5% probability /note= /note=Reviewed by tnborn. CDS 13572 - 13964 /gene="19" /product="gp19" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_19" /note=Original Glimmer call @bp 13572 has strength 9.91; Genemark calls start at 13572 /note=SSC: 13572-13964 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_20 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 7.14273E-88 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.575, -3.46411222063, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_20 [Mycobacterium phage Peaches] ],,YP_003358723,100.0,7.14273E-88 SIF-HHPRED: DUF5403 ; Family of unknown function (DUF5403),,,PF17395.5,85.3846,99.9 SIF-Syn: nkf /note=NOTE /note=Current Gene Number: 19 /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? _ /note=Is the ORF chosen the longest ORF: ORF was the LORF /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, peaches /note=Z score = 2.575 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. LORF, GeneMark and Glimmer agree, final score closest to 0. /note= /note=FUNCTION /note=Synteny- /note=Phagesdb blast- function unknown 3e-70 /note=Blast NCBI function match- hypothetical protein /note=HHPRED Match- 99.9% family of unknown function /note= /note=Reviewed by tnborn. CDS 13964 - 14401 /gene="20" /product="gp20" /function="tail terminator" /locus tag="Taquarus-MitchellCC_20" /note=Original Glimmer call @bp 13964 has strength 8.82; Genemark calls start at 13964 /note=SSC: 13964-14401 CP: yes SCS: both ST: SS BLAST-Start: [tail terminator [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 6.69359E-104 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.459, -3.979581593363423, yes F: tail terminator SIF-BLAST: ,,[tail terminator [Mycobacterium phage Peaches] ],,YP_003358724,100.0,6.69359E-104 SIF-HHPRED: TAIL-TO-HEAD JOINING PROTEIN GP17; VIRAL PROTEIN, VIRAL INFECTION, TAILED BACTERIOPHAGE, SIPHOVIRIDAE, SPP1, VIRAL ASSEMBLY, HEAD-TO-TAIL INTERFACE, DNA GATEKEEPER, ALLOSTERIC MECHANISM; 7.2A {BACILLUS PHAGE SPP1},,,5A21_G,91.7241,99.2 SIF-Syn: found downstream from head-to-tail stopper, just like Albee /note=NOTE /note=Current Gene Number: 20 /note=Did the start site stay the same or change: yes /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? _ /note=Is the ORF chosen the longest ORF: ORF is the LORF /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, peaches /note=Z score = 2.459 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Lowest score closest to 0, the z score is better than the rest, has the LORF, both start sites agree. /note= /note=FUNCTION /note=Synteny- yes /note=Phagesdb blast- Tail Terminator, Abdiel /note=Blast NCBI function match- Tail Terminator 6.69359e-104 /note=HHPRED Match- 99% Tail Terminator /note= /note=Reviewed by tnborn. CDS 14391 - 14981 /gene="21" /product="gp21" /function="major tail protein" /locus tag="Taquarus-MitchellCC_21" /note=Original Glimmer call @bp 14391 has strength 14.66; Genemark calls start at 14391 /note=SSC: 14391-14981 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 6.62182E-140 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.253, -2.305049668942183, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Mycobacterium phage Peaches] ],,YP_003358725,100.0,6.62182E-140 SIF-HHPRED: YSD1_22 major tail protein; Bacteriophage tail, helical assembly, VIRAL PROTEIN; 3.5A {Bacteriophage sp.},,,6XGR_M,90.8163,98.1 SIF-Syn: Found upstream from the tape measure protein, just like Albee /note=NOTE /note=Current Gene Number: 21 /note=Did the start site stay the same or change: stayed /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? _ /note=Is the ORF chosen the longest ORF: ORF is LORF /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, peaches /note=Z score = 3.253 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Even though the z-score is relatively high compared to others, it is the LORF and the start sites agree. The final score is also still the best. /note= /note=FUNCTION /note=Synteny- yes /note=Phagesdb blast- major tail protein 1e-112 /note=Blast NCBI function match- Major tail protein 6.62182e-140 /note=HHPRED Match- 98.1% major tail protein /note= /note=Reviewed by tnborn. CDS 15101 - 15472 /gene="22" /product="gp22" /function="tail assembly chaperone" /locus tag="Taquarus-MitchellCC_22" /note=Original Glimmer call @bp 15101 has strength 14.46; Genemark calls start at 15101 /note=SSC: 15101-15472 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 4.4203E-80 GAP: 119 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.346, -4.395041241556842, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage Peaches] ],,YP_003358727,100.0,4.4203E-80 SIF-HHPRED: GP24_25 ; Mycobacteriophage tail assembly protein,,,PF17388.5,95.1219,100.0 SIF-Syn: found downstream from the major tail protein, just like Albee /note=NOTE /note=Current Gene Number: 22 /note=Did the start site stay the same or change: stayed /note=Do the Glimmer and Genemark start sites agree? yes /note=What about Starterator? _ /note=Is the ORF chosen the longest ORF: ORF is LORF /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, peaches /note=Z score = 2.346 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Best z-score, best final score, same start for GeneMark and Glimmer, LORF. /note= /note=FUNCTION /note=Synteny- yes /note=Phagesdb blast- Tail assembly chaperone 4e-63 /note=Blast NCBI function match- Tail assembly chaperone 4.4203e-80 /note=HHPRED Match- Tail assembly protein 100% /note= /note=Reviewed by tnborn. CDS 15424 - 15969 /gene="23" /product="gp23" /function="tail assembly chaperone" /locus tag="Taquarus-MitchellCC_23" /note=Original Glimmer call @bp 15424 has strength 6.9; Genemark calls start at 15424 /note=SSC: 15424-15969 CP: no SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Mycobacterium phage KFPoly]],,NCBI, q1:s109 100.0% 4.52858E-130 GAP: -49 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.431, -4.738505288392969, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage KFPoly]],,APL99968,62.6298,4.52858E-130 SIF-HHPRED: SIF-Syn: Tail assembly chaperone found upstream from tape measure protein as in Kingmustick0402 /note=Current Gene Number: 23 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Y /note=What about Starterator? N/A /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 = 2.431 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and the longest ORF. /note= /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-101 /note=Blast NCBI function match with E value should be 10^-7 or less: 4.52858e-130 /note=HHPRED Match with > 90% probability: 98.6% /note=Conserved Domain: N/A /note= /note=reviewed CDS 15888 - 18488 /gene="24" /product="gp24" /function="tape measure protein" /locus tag="Taquarus-MitchellCC_24" /note=Original Glimmer call @bp 16029 has strength 13.95; Genemark calls start at 15888 /note=SSC: 15888-18488 CP: yes SCS: both-gm ST: SS BLAST-Start: [tape measure protein [Mycobacterium phage Ruin] ],,NCBI, q1:s1 100.0% 0.0 GAP: -82 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.253, -2.033982896655645, yes F: tape measure protein SIF-BLAST: ,,[tape measure protein [Mycobacterium phage Ruin] ],,AYD87149,99.8845,0.0 SIF-HHPRED: SIF-Syn: Tape measure protein found upstream from minor tail protein as in ICleared /note=Current Gene Number: 24 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? N /note=What about Starterator? N/A /note=Is the ORF chosen the longest ORF: N /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? Y /note=Z score = 2.114 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Not the longest ORF, and Glimmer/Genemark disagreed /note= /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: 99.9% /note=Conserved Domain: N /note= /note=reviewed: /note=make sure you have selected the correct starting gene in the top section CDS 18493 - 19833 /gene="25" /product="gp25" /function="minor tail protein" /locus tag="Taquarus-MitchellCC_25" /note=Original Glimmer call @bp 18493 has strength 7.27; Genemark calls start at 18493 /note=SSC: 18493-19833 CP: yes SCS: both ST: SS BLAST-Start: [tail protein [Mycobacterium phage Nyxis] ],,NCBI, q1:s1 100.0% 0.0 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.343, -3.9531326986493704, no F: minor tail protein SIF-BLAST: ,,[tail protein [Mycobacterium phage Nyxis] ],,YP_009005865,100.0,0.0 SIF-HHPRED: Distal Tail Protein, gp58; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BD,47.7578,99.6 SIF-Syn: Minor tail protein found upstream from minor tail protein as in Annyong /note=Current Gene Number: 25 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Y /note=What about Starterator? N/A /note=Is the ORF chosen the longest ORF: N /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? N /note=Z score = 2.343 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The alignment was not 1:1 and the ORF chosen was not the longest. /note= /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: 99.6% /note=Conserved Domain: N /note= /note=reviewed CDS 19830 - 21608 /gene="26" /product="gp26" /function="minor tail protein" /locus tag="Taquarus-MitchellCC_26" /note=Original Glimmer call @bp 19830 has strength 15.55; Genemark calls start at 19830 /note=SSC: 19830-21608 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.118, -4.349108688274226, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Peaches] ],,YP_003358730,100.0,0.0 SIF-HHPRED: Sipho_Gp37 ; Siphovirus ReqiPepy6 Gp37-like protein,,,PF14594.9,88.0068,99.9 SIF-Syn: Found downstream from tape measure as in Clarenza /note=Current Gene Number: 26 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Y /note=What about Starterator? N/A /note=Is the ORF chosen the longest ORF: N /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? Y /note=Z score = 2.118 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The alignment 1:1 and Glimmer + Genemark agreed /note= /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: 99.9% /note=Conserved Domain: N/A /note= /note=reviewed CDS 21630 - 22076 /gene="27" /product="gp27" /function="minor tail protein" /locus tag="Taquarus-MitchellCC_27" /note=Original Glimmer call @bp 21630 has strength 10.02; Genemark calls start at 21630 /note=SSC: 21630-22076 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PEACHES_28 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 1.85757E-106 GAP: 21 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.153, -4.274735973818826, no F: minor tail protein SIF-BLAST: ,,[hypothetical protein PEACHES_28 [Mycobacterium phage Peaches] ],,YP_003358731,100.0,1.85757E-106 SIF-HHPRED: DUF2744 ; Protein of unknown function (DUF2744),,,PF10910.11,89.8649,100.0 SIF-Syn: Minor tail protein found downstream from tape measure as in Clarenza. /note=Current Gene Number: 27 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Y /note=What about Starterator? N/A /note=Is the ORF chosen the longest ORF: Y /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? Y /note=Z score = 2.153 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The alignment is 1:1 and the ORF chosen is the longest. /note= /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 2e-87 /note=Blast NCBI function match with E value should be 10^-7 or less: 1.85757e-106 /note=HHPRED Match with > 90% probability: 100% /note=Conserved Domain: N /note= /note=reviewed CDS 22085 - 22531 /gene="28" /product="gp28" /function="minor tail protein" /locus tag="Taquarus-MitchellCC_28" /note=Original Glimmer call @bp 22136 has strength 9.99; Genemark calls start at 22124 /note=SSC: 22085-22531 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein PEACHES_29 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 2.18265E-101 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.651, -5.414317774057158, no F: minor tail protein SIF-BLAST: ,,[hypothetical protein PEACHES_29 [Mycobacterium phage Peaches] ],,YP_003358732,100.0,2.18265E-101 SIF-HHPRED: SIF-Syn: Found downstream of minor tail protein as in Albee /note=Staterator data shows strong evidence for start 22085. Lots of MA of this particular start. Makes it a longer gene with very little gap between previous gene. CDS 22521 - 22949 /gene="29" /product="gp29" /function="minor tail protein" /locus tag="Taquarus-MitchellCC_29" /note=Original Glimmer call @bp 22521 has strength 13.27; Genemark calls start at 22521 /note=SSC: 22521-22949 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_30 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 1.87457E-101 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.399, -4.66341334897022, yes F: minor tail protein SIF-BLAST: ,,[hypothetical protein PEACHES_30 [Mycobacterium phage Peaches] ],,YP_003358733,100.0,1.87457E-101 SIF-HHPRED: PspB ; Phage shock protein B,,,PF06667.15,54.9296,93.6 SIF-Syn: Found downstream of minor tail protein as in Albee CDS 22963 - 24819 /gene="30" /product="gp30" /function="minor tail protein" /locus tag="Taquarus-MitchellCC_30" /note=Original Glimmer call @bp 22963 has strength 17.44; Genemark calls start at 22963 /note=SSC: 22963-24819 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Mycobacterium phage Flux] ],,NCBI, q1:s1 100.0% 0.0 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.343, -4.40029072999159, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Flux] ],,AFL47851,100.0,0.0 SIF-HHPRED: b.22.1.1 (A:) 30 kDa adipocyte complement-related protein {Mouse (Mus musculus) [TaxId: 10090]},,,d1c3ha_,20.3883,96.9 SIF-Syn: Found downstream of minor tail protein as in Albee CDS complement (24882 - 25100) /gene="31" /product="gp31" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_31" /note=Original Glimmer call @bp 25088 has strength 9.21; Genemark calls start at 25100 /note=SSC: 25100-24882 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein PBI_ERIS_31 [Mycobacterium phage Eris] ],,NCBI, q1:s15 100.0% 1.53497E-42 GAP: 25 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.239, -4.155204357786937, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_ERIS_31 [Mycobacterium phage Eris] ],,APD17727,83.7209,1.53497E-42 SIF-HHPRED: SIF-Syn: NKF CDS complement (25126 - 26640) /gene="32" /product="gp32" /function="serine integrase" /locus tag="Taquarus-MitchellCC_32" /note=Original Glimmer call @bp 26640 has strength 9.98; Genemark calls start at 26640 /note=SSC: 26640-25126 CP: yes SCS: both ST: SS BLAST-Start: [serine integrase [Mycobacterium phage MeeZee] ],,NCBI, q1:s1 100.0% 0.0 GAP: 78 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.845, -5.751911930358031, no F: serine integrase SIF-BLAST: ,,[serine integrase [Mycobacterium phage MeeZee] ],,AEL19841,100.0,0.0 SIF-HHPRED: INTEGRASE; HYDROLASE, SERINE RECOMBINASE, UNIDIRECTIONAL, SITE-SPECIFIC RECOMBINATION; 2.15A {STREPTOMYCES PHAGE PHIC31},,,4BQQ_A,64.881,100.0 SIF-Syn: Found downstream of minor tail protein as in Albee CDS 26719 - 27138 /gene="33" /product="gp33" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_33" /note=Genemark calls start at 26719 /note=SSC: 26719-27138 CP: yes SCS: genemark ST: NI BLAST-Start: [hypothetical protein MEEZEE_34 [Mycobacterium phage MeeZee] ],,NCBI, q1:s3 100.0% 2.13836E-90 GAP: 78 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.921, -6.9549522782349085, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein MEEZEE_34 [Mycobacterium phage MeeZee] ],,AEL19787,98.5816,2.13836E-90 SIF-HHPRED: DUF2637 ; Protein of unknown function (DUF2637),,,PF10935.11,76.259,99.6 SIF-Syn: NKF CDS complement (27211 - 27408) /gene="34" /product="gp34" /function="deoxycytidylate deaminase" /locus tag="Taquarus-MitchellCC_34" /note=Original Glimmer call @bp 27408 has strength 10.2; Genemark calls start at 27444 /note=SSC: 27408-27211 CP: yes SCS: both-gl ST: SS BLAST-Start: [deoxycytidylate deaminase [Mycobacterium phage OKaNui]],,NCBI, q1:s1 100.0% 4.92235E-41 GAP: 62 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.303, -3.9584221859736637, no F: deoxycytidylate deaminase SIF-BLAST: ,,[deoxycytidylate deaminase [Mycobacterium phage OKaNui]],,QKW95510,100.0,4.92235E-41 SIF-HHPRED: SIF-Syn: Found downstream from serine integrase as in Albee CDS complement (27471 - 27728) /gene="35" /product="gp35" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_35" /note=Genemark calls start at 27728 /note=SSC: 27728-27471 CP: yes SCS: genemark ST: NA BLAST-Start: [hypothetical protein SEA_OKANUI_37 [Mycobacterium phage OKaNui]],,NCBI, q1:s1 100.0% 1.61477E-51 GAP: 233 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.253, -2.033982896655645, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_OKANUI_37 [Mycobacterium phage OKaNui]],,QKW95511,98.8235,1.61477E-51 SIF-HHPRED: SIF-Syn: NKF CDS complement (27962 - 28114) /gene="36" /product="gp36" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_36" /note=Original Glimmer call @bp 28114 has strength 10.0; Genemark calls start at 28114 /note=SSC: 28114-27962 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PIPCRAFT_36 [Mycobacterium phage Pipcraft]],,NCBI, q1:s98 100.0% 5.68056E-27 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.004, -3.005970110175159, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PIPCRAFT_36 [Mycobacterium phage Pipcraft]],,AWN05718,34.0136,5.68056E-27 SIF-HHPRED: Lipid binding protein LpqN; Lipid Binding Protein, (6DDTre)Lauryl-6-Trehaloside; HET: L6T; 1.37A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)},,,6E5F_A,60.0,93.7 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 38 /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? N/A /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 = 3.004 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and Glimmer and GeneMark match. /note= /note=FUNCTION /note=Synteny: no /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Albee /note=Blast NCBI function match with E value should be 10^-7 or less: hypothetical protein /note=HHPRED Match with > 90% probability: Lipid binding protein /note=Conserved Domain: n/a CDS complement (28111 - 28377) /gene="37" /product="gp37" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_37" /note=Original Glimmer call @bp 28377 has strength 6.91; Genemark calls start at 28377 /note=SSC: 28377-28111 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_38 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 1.04182E-56 GAP: 79 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.049, -4.635604911695725, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_38 [Mycobacterium phage Peaches] ],,YP_003358741,100.0,1.04182E-56 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 39 /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? N/A /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 = 2.049 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and Glimmer and GeneMark match. /note= /note=FUNCTION /note=Synteny: no /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Albee /note=Blast NCBI function match with E value should be 10^-7 or less: hypothetical protein /note=HHPRED Match with > 90% probability: n/a /note=Conserved Domain: n/a CDS complement (28457 - 28714) /gene="38" /product="gp38" /function="helix-turn-helix DNA binding domain" /locus tag="Taquarus-MitchellCC_38" /note=Original Glimmer call @bp 28714 has strength 9.34; Genemark calls start at 28714 /note=SSC: 28714-28457 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_OBAMA12_40 [Mycobacterium phage Obama12] ],,NCBI, q1:s1 100.0% 1.05247E-54 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.157, -2.297359520375101, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein PBI_OBAMA12_40 [Mycobacterium phage Obama12] ],,YP_009007232,100.0,1.05247E-54 SIF-HHPRED: a.4.5.63 (A:11-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]},,,d3bp8a1,76.4706,98.9 SIF-Syn: found upstream of DNA polymerase I as in Albee /note=NOTE /note=Current Gene Number: 40 /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? N/A /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 = 3.157 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and Glimmer and GeneMark match. /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Albee /note=Blast NCBI function match with E value should be 10^-7 or less: helix-turn-helix DNA-binding protein /note=HHPRED Match with > 90% probability: Mlc protein N-terminal domain /note=Conserved Domain: no CDS complement (28711 - 29067) /gene="39" /product="gp39" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_39" /note=Original Glimmer call @bp 29067 has strength 12.3; Genemark calls start at 29067 /note=SSC: 29067-28711 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_41 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 3.51529E-80 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.516, -3.5707972674952195, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_41 [Mycobacterium phage Peaches] ],,YP_003358744,100.0,3.51529E-80 SIF-HHPRED: Cep57_CLD_2 ; Centrosome localisation domain of PPC89,,,PF14197.9,42.3729,94.2 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 41 /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? N/A /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 = 2.516 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and Glimmer and GeneMark match. /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Abdiel /note=Blast NCBI function match with E value should be 10^-7 or less: hypothetical protein /note=HHPRED Match with > 90% probability: Cep57_CLD_2 ; Centrosome localisation domain of PPC89 /note=Conserved Domain: no CDS complement (29054 - 29329) /gene="40" /product="gp40" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_40" /note=Original Glimmer call @bp 29329 has strength 12.24; Genemark calls start at 29329 /note=SSC: 29329-29054 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein CH07_gp43 [Mycobacterium phage BellusTerra] ],,NCBI, q1:s1 100.0% 6.09361E-59 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.283, -4.142194467337367, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein CH07_gp43 [Mycobacterium phage BellusTerra] ],,YP_009005601,100.0,6.09361E-59 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /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? N/A /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 = 2.283 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and Glimmer and GeneMark match. /note= /note=FUNCTION /note=Synteny: no /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Abdiel /note=Blast NCBI function match with E value should be 10^-7 or less: hypothetical protein /note=HHPRED Match with > 90% probability: Centrosome localisation domain of PPC89 /note=Conserved Domain: no CDS complement (29326 - 29559) /gene="41" /product="gp41" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_41" /note=Original Glimmer call @bp 29559 has strength 13.11; Genemark calls start at 29559 /note=SSC: 29559-29326 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_NYXIS_43 [Mycobacterium phage Nyxis] ],,NCBI, q1:s1 100.0% 2.57771E-46 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.459, -3.708514821076885, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_NYXIS_43 [Mycobacterium phage Nyxis] ],,YP_009005882,100.0,2.57771E-46 SIF-HHPRED: SIF-Syn: NKF /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? Y /note=What about Starterator? N /note=Is the ORF chosen the longest ORF: Y, there was no overlap /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? Y /note=Z score = 2.459 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it is the longest ORF and both applications agree. /note=Synteny: NKF CDS complement (29556 - 29726) /gene="42" /product="gp42" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_42" /note=Original Glimmer call @bp 29726 has strength 18.11; Genemark calls start at 29726 /note=SSC: 29726-29556 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_44 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 3.54925E-30 GAP: 20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.021, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_44 [Mycobacterium phage Peaches] ],,YP_003358747,100.0,3.54925E-30 SIF-HHPRED: 45L; RNA polymerase, transcription termination, anti-termination, RNAP clamp, phage, transcription initiation, P7, NusA, Xanthomonos oryzae, Xp10, transcription; 3.41A {Xanthomonas oryzae pv. oryzae (strain PXO99A)},,,6J9E_J,92.8571,91.9 SIF-Syn: NKF /note=Current Gene Number: 44 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Y /note=What about Starterator? /note=Is the ORF chosen the longest ORF: N /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? /note=Z score = 3.021 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because both annotation softwares agree. /note=Synteny: NKF CDS complement (29747 - 31573) /gene="43" /product="gp43" /function="DNA polymerase I" /locus tag="Taquarus-MitchellCC_43" /note=Original Glimmer call @bp 31573 has strength 15.57; Genemark calls start at 31573 /note=SSC: 31573-29747 CP: yes SCS: both ST: SS BLAST-Start: [DNA polymerase [Mycobacterium phage Kampy] ],,NCBI, q1:s1 100.0% 0.0 GAP: 7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.361, -4.36385515561809, no F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase [Mycobacterium phage Kampy] ],,YP_009031905,99.8355,0.0 SIF-HHPRED: Prex DNA polymerase; DNA polymerase, TRANSFERASE; HET: SO4; 2.9A {Plasmodium falciparum},,,5DKT_A,97.5329,100.0 SIF-Syn: DNA polymerase I found upstream from helix-turn-helix DNA binding protein as in Kampy. /note=Current Gene Number: 45 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Y /note=What about Starterator? /note=Is the ORF chosen the longest ORF: Y, no overlap /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? Y /note=Z score = 2.361 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, is the longest ORF, and both softwares agree. /note=Synteny: Y /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Albee, e-value: 0 /note=Blast NCBI function match with E value should be 10^-7 or less: Y, e-value: 0 /note=HHPRED Match with > 90% probability: Y /note=Conserved Domain: CDS complement (31581 - 31883) /gene="44" /product="gp44" /function="helix-turn-helix DNA binding domain" /locus tag="Taquarus-MitchellCC_44" /note=Original Glimmer call @bp 31883 has strength 10.3; Genemark calls start at 31883 /note=SSC: 31883-31581 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_46 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 6.50566E-65 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.921, -5.2909565709011765, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein PEACHES_46 [Mycobacterium phage Peaches] ],,YP_003358749,100.0,6.50566E-65 SIF-HHPRED: pRO-2.3; De novo protein, Computational Design, helical bundle; 1.28A {synthetic construct},,,6MSQ_A,34.0,96.0 SIF-Syn: helix-turn-helix DNA binding domain found downstream from DNA polymerase 1 as in Kampy /note=Current Gene Number: 46 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Y /note=What about Starterator? /note=Is the ORF chosen the longest ORF: N /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? Y /note=Z score = -5.291 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it is the longest ORF and both applications agree. /note=Synteny: Y /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Abdiel, e-value: 1e-50 /note=Blast NCBI function match with E value should be 10^-7 or less: Y, e-value: 6.50566e-65 /note=HHPRED Match with > 90% probability: Y /note=Conserved Domain: CDS complement (31883 - 32056) /gene="45" /product="gp45" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_45" /note=Original Glimmer call @bp 32056 has strength 16.02; Genemark calls start at 32056 /note=SSC: 32056-31883 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_47 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 3.15636E-32 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.096, -5.444803624783377, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_47 [Mycobacterium phage Peaches] ],,YP_003358750,100.0,3.15636E-32 SIF-HHPRED: DUF903 ; Bacterial protein of unknown function (DUF903),,,PF06004.15,73.6842,95.6 SIF-Syn: NKF /note=Current Gene Number: 47 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Y /note=What about Starterator? /note=Is the ORF chosen the longest ORF: Y, no overlap /note=Is all of the coding potential captured on GeneMark file: Y /note=Is there a 1:1 alignment on blast and with which phage? N /note=Z score = 2.096 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it is the longest ORF and both annotation softwares agree. /note=Synteny: NKF CDS complement (32065 - 32784) /gene="46" /product="gp46" /function="ThyX-like thymidylate synthase" /locus tag="Taquarus-MitchellCC_46" /note=Original Glimmer call @bp 32784 has strength 15.23; Genemark calls start at 32784 /note=SSC: 32784-32065 CP: yes SCS: both ST: SS BLAST-Start: [ThyX-like thymidylate synthase [Mycobacterium phage BellusTerra] ],,NCBI, q1:s1 100.0% 1.20396E-174 GAP: 67 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.004, -3.005970110175159, yes F: ThyX-like thymidylate synthase SIF-BLAST: ,,[ThyX-like thymidylate synthase [Mycobacterium phage BellusTerra] ],,YP_009005607,100.0,1.20396E-174 SIF-HHPRED: Thymidylate synthase thyX; ThyX, FAD, FdUMP, Flavoprotein, Methyltransferase, Nucleotide biosynthesis, Transferase, Structural Genomics, Seattle Structural Genomics Center for Infectious; HET: FAD, UFP; 1.9A {Mycobacterium tuberculosis},,,3GWC_F,97.908,100.0 SIF-Syn: Found downstream of helix-turn-helix DNA binding domain as in Albee /note=Current Gene Number: 48 /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? /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 = 3.004 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and a long ORF. CDS complement (32852 - 33391) /gene="47" /product="gp47" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_47" /note=Original Glimmer call @bp 33391 has strength 10.0; Genemark calls start at 33391 /note=SSC: 33391-32852 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_49 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 8.05737E-120 GAP: 26 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.728, -3.061661148509975, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_49 [Mycobacterium phage Peaches] ],,YP_003358752,100.0,8.05737E-120 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 49 /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? /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 = 2.728 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment. CDS complement (33418 - 35451) /gene="48" /product="gp48" /function="ribonucleotide reductase" /locus tag="Taquarus-MitchellCC_48" /note=Original Glimmer call @bp 35451 has strength 15.93; Genemark calls start at 35451 /note=SSC: 35451-33418 CP: yes SCS: both ST: SS BLAST-Start: [ribonucleotide reductase [Mycobacterium phage TiroTheta9] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.249, -4.599515895103776, no F: ribonucleotide reductase SIF-BLAST: ,,[ribonucleotide reductase [Mycobacterium phage TiroTheta9] ],,AEM05935,100.0,0.0 SIF-HHPRED: RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE; 10-stranded alpha-beta barrel, central finger loop, OXIDOREDUCTASE; 1.75A {Lactobacillus leichmannii} SCOP: c.7.1.4,,,1L1L_B,99.2614,100.0 SIF-Syn: Ribonucleotide found upstream from metallophosphoesterase in TiroTheta. /note=Current Gene Number: 50 /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? /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 TiroTheta9 /note=Z score = 2.249 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and a longer ORF. /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: no /note=Blast NCBI function match with E value should be 10^-7 or less: no /note=HHPRED Match with > 90% probability: 100% with TiroTheta /note=Conserved Domain: 37.5877 CDS complement (35448 - 36344) /gene="49" /product="gp49" /function="DNA binding protein" /locus tag="Taquarus-MitchellCC_49" /note=Original Glimmer call @bp 36344 has strength 13.81; Genemark calls start at 36332 /note=SSC: 36344-35448 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein PEACHES_51 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.961, -4.679270584912496, no F: DNA binding protein SIF-BLAST: ,,[hypothetical protein PEACHES_51 [Mycobacterium phage Peaches] ],,YP_003358754,100.0,0.0 SIF-HHPRED: GP52 ; Phage gene product 52,,,PF17468.5,19.4631,99.9 SIF-Syn: DNA binding protein is found upstream from DNA primase in Albee. /note=Current Gene Number: 51 /note=Did the start site stay the same or change: it changed /note=Do the Glimmer and Genemark start sites agree? No /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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? 1e-170 /note=Z score = 1.961 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start sites are different and starterator is not provided. /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: Albee with 1e-170 /note=Blast NCBI function match with E value should be 10^-7 or less: no /note=HHPRED Match with > 90% probability: 99% with /note=Conserved Domain: no CDS complement (36348 - 37100) /gene="50" /product="gp50" /function="metallophosphoesterase" /locus tag="Taquarus-MitchellCC_50" /note=Original Glimmer call @bp 37100 has strength 16.1; Genemark calls start at 37115 /note=SSC: 37100-36348 CP: yes SCS: both-gl ST: SS BLAST-Start: [metallophosphoesterase [Mycobacterium phage Obama12] ],,NCBI, q1:s1 100.0% 0.0 GAP: 7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.881, -4.91091738217267, no F: metallophosphoesterase SIF-BLAST: ,,[metallophosphoesterase [Mycobacterium phage Obama12] ],,YP_009007245,100.0,0.0 SIF-HHPRED: d.159.1.7 (A:4-196) Vacuolar protein sorting 29, VPS29 {Cryptosporidium parvum [TaxId: 5807]},,,d2a22a1,99.2,99.8 SIF-Syn: Metallophosphoesterase is found upstream from DNA primase as inTiroTheta9. /note=Current Gene Number: 52 /note=Did the start site stay the same or change: it changed /note=Do the Glimmer and Genemark start sites agree? No /note=What about Starterator? /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 1e-146 with Deano /note=Z score = 1.881 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and longer ORF /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: 1e-146 /note=Blast NCBI function match with E value should be 10^-7 or less: 0 /note=HHPRED Match with > 90% probability: 99.8% /note=Conserved Domain: 9.48718 CDS complement (37108 - 37383) /gene="51" /product="gp51" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_51" /note=Original Glimmer call @bp 37383 has strength 12.91; Genemark calls start at 37383 /note=SSC: 37383-37108 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein KIY78_gp50 [Mycobacterium phage Cindaradix] ],,NCBI, q1:s16 100.0% 7.52097E-61 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.021, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KIY78_gp50 [Mycobacterium phage Cindaradix] ],,YP_010063305,85.8491,7.52097E-61 SIF-HHPRED: DUF6378 ; Domain of unknown function (DUF6378),,,PF19905.2,86.8132,100.0 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 53 /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? N/A /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 3.021 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /note= /note=FUNCTION /note=Synteny: no /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS complement (37376 - 37486) /gene="52" /product="gp52" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_52" /note=Genemark calls start at 37486 /note=SSC: 37486-37376 CP: yes SCS: genemark ST: NI BLAST-Start: [hypothetical protein TIROTHETA9_54 [Mycobacterium phage TiroTheta9]],,NCBI, q1:s68 100.0% 4.13359E-18 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.955, -3.4105598537121566, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein TIROTHETA9_54 [Mycobacterium phage TiroTheta9]],,AEM05954,34.9515,4.13359E-18 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 54 /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? N/A /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /note=Is all of the coding potential captured on GeneMark file: N/A /note=Is there a 1:1 alignment on blast and with which phage? N/A /note=Z score = 2.955 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because there was no discrepancy of where the phage was to start. /note= /note=FUNCTION /note=Synteny: no /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS complement (37483 - 38142) /gene="53" /product="gp53" /function="DNA primase" /locus tag="Taquarus-MitchellCC_53" /note=Original Glimmer call @bp 38142 has strength 11.71; Genemark calls start at 38031 /note=SSC: 38142-37483 CP: yes SCS: both-gl ST: SS BLAST-Start: [DNA primase [Mycobacterium phage Kampy] ],,NCBI, q1:s1 100.0% 3.65252E-161 GAP: 212 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.1, -2.338663114094478, yes F: DNA primase SIF-BLAST: ,,[DNA primase [Mycobacterium phage Kampy] ],,YP_009031914,100.0,3.65252E-161 SIF-HHPRED: e.13.1.1 (A:) DNA primase DnaG catalytic core {Escherichia coli [TaxId: 562]},,,d1dd9a_,95.4338,99.9 SIF-Syn: Found downstream of metallophosphoesterase as in Albee /note=NOTE /note=Current Gene Number: 55 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? No - called based on Glimmer and starterator. /note=What about Starterator? N/A /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 2.612 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was chosen because it had better stats compared to the other start given. /note= /note=FUNCTION /note=Synteny: no /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: /note=**function most likely is DNA primase since in phamerator gene 55 has many matches to this function. Could be a possibility?** CDS complement (38355 - 38489) /gene="54" /product="gp54" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_54" /note=Original Glimmer call @bp 38489 has strength 23.49; Genemark calls start at 38489 /note=SSC: 38489-38355 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_56 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 4.14839E-22 GAP: 21 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.253, -2.4811409279978642, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_56 [Mycobacterium phage Peaches] ],,YP_003358759,100.0,4.14839E-22 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 56 /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? N/A /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 3.253 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /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 complement (38511 - 38981) /gene="55" /product="gp55" /function="endonuclease VII" /locus tag="Taquarus-MitchellCC_55" /note=Original Glimmer call @bp 38981 has strength 5.88; Genemark calls start at 38981 /note=SSC: 38981-38511 CP: yes SCS: both ST: SS BLAST-Start: [endonuclease VII [Mycobacterium phage Maverick]],,NCBI, q1:s13 100.0% 1.34236E-110 GAP: 63 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.602, -3.389881189012514, no F: endonuclease VII SIF-BLAST: ,,[endonuclease VII [Mycobacterium phage Maverick]],,ALF01116,92.8571,1.34236E-110 SIF-HHPRED: Restriction endonuclease Hpy99I; ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, HPY99I, PSEUDOPALINDROME, HYDROLASE-DNA COMPLEX; HET: 1PE; 1.5A {Helicobacter pylori},,,3GOX_A,81.4103,99.8 SIF-Syn: Found downstream of DNA primase as in Albee /note=NOTE /note=Current Gene Number: 57 /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? N/A /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 2.602 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was the same /note= /note=FUNCTION /note=Synteny: no /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS complement (39045 - 39863) /gene="56" /product="gp56" /function="hydrolase" /locus tag="Taquarus-MitchellCC_56" /note=Original Glimmer call @bp 39863 has strength 13.82; Genemark calls start at 39863 /note=SSC: 39863-39045 CP: no SCS: both ST: SS BLAST-Start: [hydrolase [Mycobacterium phage Jaykayelowell] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.021, -2.523003374675015, yes F: hydrolase SIF-BLAST: ,,[hydrolase [Mycobacterium phage Jaykayelowell] ],,AXQ52834,99.6324,0.0 SIF-HHPRED: c.69.1.0 (A:2-264) automated matches {Pseudomonas aeruginosa, PA01 [TaxId: 208964]},,,d3om8a1,97.7941,100.0 SIF-Syn: Found downstream of metallophosphoesterase as in Albee CDS complement (39866 - 40246) /gene="57" /product="gp57" /function="DprA-like DNA processing chain A" /locus tag="Taquarus-MitchellCC_57" /note=Original Glimmer call @bp 40246 has strength 9.93; Genemark calls start at 40246 /note=SSC: 40246-39866 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_59 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 1.89196E-87 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.942, -5.070883472086901, no F: DprA-like DNA processing chain A SIF-BLAST: ,,[hypothetical protein PEACHES_59 [Mycobacterium phage Peaches] ],,YP_003358762,100.0,1.89196E-87 SIF-HHPRED: c.129.1.1 (A:) Hypothetical protein TM1055 {Thermotoga maritima [TaxId: 2336]},,,d1rcua_,97.619,99.7 SIF-Syn: Found downstream of hydrolase as in Albee CDS complement (40243 - 40467) /gene="58" /product="gp58" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_58" /note=Original Glimmer call @bp 40467 has strength 17.08; Genemark calls start at 40467 /note=SSC: 40467-40243 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_NYXIS_61 [Mycobacterium phage Nyxis] ],,NCBI, q1:s11 100.0% 3.67215E-46 GAP: 57 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.157, -2.156361006712914, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_NYXIS_61 [Mycobacterium phage Nyxis] ],,YP_009005900,88.0952,3.67215E-46 SIF-HHPRED: GP63 ; Gene product 63,,,PF17471.5,93.2432,100.0 SIF-Syn: NKF CDS complement (40525 - 41061) /gene="59" /product="gp59" /function="phosphoribosyl transferase" /locus tag="Taquarus-MitchellCC_59" /note=Original Glimmer call @bp 41061 has strength 16.39; Genemark calls start at 41061 /note=SSC: 41061-40525 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_61 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 4.69032E-128 GAP: 19 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.153, -4.926874829490106, no F: phosphoribosyl transferase SIF-BLAST: ,,[hypothetical protein PEACHES_61 [Mycobacterium phage Peaches] ],,YP_003358764,100.0,4.69032E-128 SIF-HHPRED: c.61.1.1 (A:2-180) Adenine PRTase {Giardia intestinalis [TaxId: 5741]},,,d1l1qa1,73.0337,99.6 SIF-Syn: Found downstream of hydrolase as in Albee CDS complement (41081 - 41887) /gene="60" /product="gp60" /function="DnaB-like dsDNA helicase" /locus tag="Taquarus-MitchellCC_60" /note=Original Glimmer call @bp 41887 has strength 14.12; Genemark calls start at 41887 /note=SSC: 41887-41081 CP: yes SCS: both ST: SS BLAST-Start: [dsDNA helicase [Mycobacterium phage Iracema64] ],,NCBI, q1:s16 100.0% 0.0 GAP: 84 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.129, -4.85287563363746, no F: DnaB-like dsDNA helicase SIF-BLAST: ,,[dsDNA helicase [Mycobacterium phage Iracema64] ],,YP_009190924,94.6996,0.0 SIF-HHPRED: DNAB-Like Replicative Helicase; ATPase, REPLICATION; 3.91A {Bacillus phage SPP1},,,3BGW_E,94.7761,99.9 SIF-Syn: Found downstream of phosphoribosyl transferase as in Albee CDS complement (41972 - 42166) /gene="61" /product="gp61" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_61" /note=Original Glimmer call @bp 42166 has strength 14.59; Genemark calls start at 42172 /note=SSC: 42166-41972 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein PEACHES_64 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 2.38555E-40 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.157, -2.2364030944336752, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_64 [Mycobacterium phage Peaches] ],,YP_003358767,100.0,2.38555E-40 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 63 /note=Did the start site stay the same or change: start sites do not agree /note=Do the Glimmer and Genemark start sites agree? No /note=What about Starterator? No starterator present /note=Is the ORF chosen the longest ORF: No /note=Is all of the coding potential captured on GeneMark file: /note=Is there a 1:1 alignment on blast and with which phage? No 1:1 alignment present /note=Z score = 3.157 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. CDS complement (42163 - 42360) /gene="62" /product="gp62" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_62" /note=Original Glimmer call @bp 42360 has strength 3.43; Genemark calls start at 42360 /note=SSC: 42360-42163 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_65 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 4.01302E-40 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.499, -5.734826123116989, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_65 [Mycobacterium phage Peaches] ],,YP_003358768,100.0,4.01302E-40 SIF-HHPRED: DUF2188 ; Uncharacterized protein conserved in bacteria (DUF2188),,,PF09954.12,75.3846,95.2 SIF-Syn: NKF /note=Current Gene Number: 64 /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? Starterator not present /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 1.499 /note=Detailed reasoning/evidence of why you either changed or kept the auto-annotated start site. The start sites agree, this gene is the LORF, and has a good Z-Score. CDS complement (42370 - 43161) /gene="63" /product="gp63" /function="Cas4 family exonuclease" /locus tag="Taquarus-MitchellCC_63" /note=Original Glimmer call @bp 43161 has strength 13.11; Genemark calls start at 43161 /note=SSC: 43161-42370 CP: yes SCS: both ST: SS BLAST-Start: [Cas4 family exonuclease [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.141, -4.379101430921652, no F: Cas4 family exonuclease SIF-BLAST: ,,[Cas4 family exonuclease [Mycobacterium phage Peaches] ],,YP_003358769,100.0,0.0 SIF-HHPRED: Csa1 ; CRISPR-associated exonuclease Csa1,,,PF06023.15,96.1977,99.9 SIF-Syn: Found upstream of immunity repressor as in Albee /note=Current Gene Number: 17 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? No - called based on Glimmer and starterator. /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 1.39 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. CDS complement (43158 - 43580) /gene="64" /product="gp64" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_64" /note=Original Glimmer call @bp 43580 has strength 4.58; Genemark calls start at 43580 /note=SSC: 43580-43158 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FGG45_gp67 [Mycobacterium phage Arturo] ],,NCBI, q1:s1 100.0% 2.49891E-97 GAP: 81 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.594, -5.51667142252997, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FGG45_gp67 [Mycobacterium phage Arturo] ],,YP_009638724,100.0,2.49891E-97 SIF-HHPRED: GP70 ; Gene product 70,,,PF17429.5,34.2857,99.8 SIF-Syn: NKF /note=Current Gene Number: 66 /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? Starterator not present /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 Arturo /note=Z score = 1.594 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. CDS complement (43662 - 44174) /gene="65" /product="gp65" /function="immunity repressor" /locus tag="Taquarus-MitchellCC_65" /note=Original Glimmer call @bp 44174 has strength 9.73; Genemark calls start at 44174 /note=SSC: 44174-43662 CP: yes SCS: both ST: SS BLAST-Start: [immunity repressor [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 2.76123E-121 GAP: 210 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.673, -3.5290106867422555, no F: immunity repressor SIF-BLAST: ,,[immunity repressor [Mycobacterium phage Peaches] ],,YP_003358771,100.0,2.76123E-121 SIF-HHPRED: DUF2774 ; Protein of unknown function (DUF2774),,,PF11242.11,19.4118,98.4 SIF-Syn: Found downstream of Cas4 family exonuclease as in Albee /note=NOTE /note=Current Gene Number: 67 /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? N/A /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 2.673 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /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 complement (44385 - 44513) /gene="66" /product="gp66" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_66" /note=Original Glimmer call @bp 44513 has strength 11.68; Genemark calls start at 44519 /note=SSC: 44513-44385 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_IRACEMA64_71 [Mycobacterium phage Iracema64] ],,NCBI, q1:s37 100.0% 4.52625E-19 GAP: 121 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.224, -4.125189544139167, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_IRACEMA64_71 [Mycobacterium phage Iracema64] ],,YP_009190930,53.8462,4.52625E-19 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 68 /note=Did the start site stay the same or change: Changed /note=Do the Glimmer and Genemark start sites agree? No - called based on Glimmer and starterator. /note=What about Starterator? N/A /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 2.224 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. /note= /note=FUNCTION /note=Synteny: NO /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: /note=Blast NCBI function match with E value should be 10^-7 or less: /note=HHPRED Match with > 90% probability: /note=Conserved Domain: CDS complement (44635 - 44883) /gene="67" /product="gp67" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_67" /note=Original Glimmer call @bp 44883 has strength 6.54; Genemark calls start at 44883 /note=SSC: 44883-44635 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_70 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 3.79062E-53 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.439, -3.75071250087134, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_70 [Mycobacterium phage Peaches] ],,YP_003358773,100.0,3.79062E-53 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 69 /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? N/A /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; Peaches /note=Z score = 2.439 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Glimmer and GeneMark agree. /note=Reviewed by Karli Townsell CDS complement (44880 - 45194) /gene="68" /product="gp68" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_68" /note=Original Glimmer call @bp 45194 has strength 13.18; Genemark calls start at 45194 /note=SSC: 45194-44880 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_71 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 2.78076E-69 GAP: 16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.021, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_71 [Mycobacterium phage Peaches] ],,YP_003358774,100.0,2.78076E-69 SIF-HHPRED: DUF6319 ; Family of unknown function (DUF6319),,,PF19844.2,27.8846,88.8 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 70 /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? N/A /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 = 3.021 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Glimmer and GeneMark agree. /note=Reviewed by Karli Townsell CDS complement (45211 - 45351) /gene="69" /product="gp69" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_69" /note=Original Glimmer call @bp 45351 has strength 1.95 /note=SSC: 45351-45211 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein PEACHES_72 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 1.67262E-23 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.234, -4.104706087827342, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_72 [Mycobacterium phage Peaches] ],,YP_003358775,100.0,1.67262E-23 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 71 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? GeneMark is N/A; start site selected based on Glimmer. /note=What about Starterator? N/A /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; Peaches /note=Z score = 2.234 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. It has a 1:1 alignment, it is the LORF, and Glimmer selected it as the start site. /note=Reviewed by Karli Townsell CDS complement (45351 - 45650) /gene="70" /product="gp70" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_70" /note=Original Glimmer call @bp 45650 has strength 8.87; Genemark calls start at 45650 /note=SSC: 45650-45351 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein CH07_gp76 [Mycobacterium phage BellusTerra] ],,NCBI, q1:s1 100.0% 1.52747E-66 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.868, -2.7653702713535186, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein CH07_gp76 [Mycobacterium phage BellusTerra] ],,YP_009005634,100.0,1.52747E-66 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 72 /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? N/A /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; BellusTerra /note=Z score = 2.868 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because Glimmer and GeneMark agree. /note=Reviewed by Karli Townsell CDS complement (45647 - 45805) /gene="71" /product="gp71" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_71" /note=Original Glimmer call @bp 45805 has strength 10.39; Genemark calls start at 45805 /note=SSC: 45805-45647 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_74 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 2.03616E-30 GAP: 7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.129, -4.85287563363746, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_74 [Mycobacterium phage Peaches] ],,YP_003358777,100.0,2.03616E-30 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 73 /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? N/A /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; BellusTerra /note=Z score = 2.129 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Glimmer and Genemark agree on the start site. /note=Reviewed by Karli Townsell CDS complement (45813 - 45956) /gene="72" /product="gp72" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_72" /note=Original Glimmer call @bp 45956 has strength 7.36; Genemark calls start at 45956 /note=SSC: 45956-45813 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_IRACEMA64_77 [Mycobacterium phage Iracema64] ],,NCBI, q1:s26 100.0% 2.08294E-26 GAP: 210 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.1, -2.2763497933341483, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_IRACEMA64_77 [Mycobacterium phage Iracema64] ],,YP_009190936,65.2778,2.08294E-26 SIF-HHPRED: DUF5814 ; Family of unknown function (DUF5814),,,PF19131.3,19.1489,87.8 SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 74 /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? N/A /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 = 3.1 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. Glimmer and GeneMark agree on the start site. /note=Reviewed by Karli Townsell CDS complement (46167 - 46751) /gene="73" /product="gp73" /function="DNA methyltransferase" /locus tag="Taquarus-MitchellCC_73" /note=Original Glimmer call @bp 46751 has strength 7.98; Genemark calls start at 46751 /note=SSC: 46751-46167 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BURGER_76 [Mycobacterium phage Burger] ],,NCBI, q1:s1 100.0% 3.76437E-137 GAP: -23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.887, -5.186767100221219, no F: DNA methyltransferase SIF-BLAST: ,,[hypothetical protein SEA_BURGER_76 [Mycobacterium phage Burger] ],,AMW64247,100.0,3.76437E-137 SIF-HHPRED: DNA CYTOSINE METHYLTRANSFERASE DNMT2; Human DNA Methyltransferase homologue, TRANSFERASE; HET: CSO, SAH; 1.8A {Homo sapiens} SCOP: c.66.1.26,,,1G55_A,31.4433,96.0 SIF-Syn: Found downstream from immunity repressor as in Albee /note=NOTE /note=Current Gene Number: 74 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? No - called based on Glimmer and starterator. /note=What about Starterator? Y /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 = 1.39 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and agrees with starterator. CDS complement (46729 - 47262) /gene="74" /product="gp74" /function="DNA methyltransferase" /locus tag="Taquarus-MitchellCC_74" /note=Original Glimmer call @bp 47262 has strength 6.41; Genemark calls start at 47262 /note=SSC: 47262-46729 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein PEACHES_77 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 2.17475E-123 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.266, -4.943889544421484, no F: DNA methyltransferase SIF-BLAST: ,,[hypothetical protein PEACHES_77 [Mycobacterium phage Peaches] ],,YP_003358780,100.0,2.17475E-123 SIF-HHPRED: c.66.1.26 (A:) automated matches {Haemophilus aegyptius [TaxId: 197575]},,,d3ubta_,96.6102,100.0 SIF-Syn: Found downstream from the immunity repressor as in Albee. /note=NOTE /note=Current Gene Number: 76 /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? starterator not present /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 = 2.266 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because the start sites agreed and there was a good z-score. /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: yes /note=Blast NCBI function match with E value should be 10^-7 or less: yes /note=HHPRED Match with > 90% probability: 100 /note=Conserved Domain: A4 CDS complement (47259 - 47429) /gene="75" /product="gp75" /function="DNA methyltransferase" /locus tag="Taquarus-MitchellCC_75" /note=Original Glimmer call @bp 47429 has strength 14.6; Genemark calls start at 47429 /note=SSC: 47429-47259 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_78 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 9.7671E-32 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.373, -4.3372389842445, no F: DNA methyltransferase SIF-BLAST: ,,[hypothetical protein PEACHES_78 [Mycobacterium phage Peaches] ],,YP_003358781,100.0,9.7671E-32 SIF-HHPRED: SIF-Syn: DNA methylase is found upstream from DNA methylase in Annyong. /note=NOTE /note=Current Gene Number: 17 /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? no starterator present /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 = 2.373 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because the two presented start sites agree, there is genemark files, and a good z-score. /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: no /note=Blast NCBI function match with E value should be 10^-7 or less: no /note=HHPRED Match with > 90% probability: no /note=Conserved Domain: A4 CDS complement (47432 - 47905) /gene="76" /product="gp76" /function="SprT-like protease" /locus tag="Taquarus-MitchellCC_76" /note=Original Glimmer call @bp 47905 has strength 8.92; Genemark calls start at 47905 /note=SSC: 47905-47432 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_79 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 9.47108E-114 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.506, -4.631219452820914, yes F: SprT-like protease SIF-BLAST: ,,[hypothetical protein PEACHES_79 [Mycobacterium phage Peaches] ],,YP_003358782,100.0,9.47108E-114 SIF-HHPRED: SprT-like domain-containing protein Spartan; DPC repair protease, DNA BINDING PROTEIN; HET: ADP, MLZ, FLC; 1.5A {Homo sapiens},,,6MDW_A,87.8981,99.8 SIF-Syn: SprT-like protease is found downstream from DNA Methylase in Annoying. /note=NOTE /note=Current Gene Number: 78 /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? no starterator /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 with Burger /note=Z score = 2.506 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and the two starts agree with each other. /note= /note=FUNCTION /note=Synteny: yes /note=Phagesdb blast- For any potential functional match, the E value should be 10^-7 or less: yes /note=Blast NCBI function match with E value should be 10^-7 or less: yes /note=HHPRED Match with > 90% probability: 99.8 /note=Conserved Domain: A4 CDS complement (47902 - 48048) /gene="77" /product="gp77" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_77" /note=Original Glimmer call @bp 48048 has strength 5.22; Genemark calls start at 48048 /note=SSC: 48048-47902 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_80 [Mycobacterium phage Peaches] ],,NCBI, q1:s10 100.0% 1.01489E-25 GAP: 23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.673, -3.8300406824062367, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_80 [Mycobacterium phage Peaches] ],,YP_003358783,84.2105,1.01489E-25 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 79 /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? starterator is not present /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 with commander /note=Z score = 2.673 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and the start sites agree. CDS complement (48072 - 48425) /gene="78" /product="gp78" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_78" /note=Original Glimmer call @bp 48425 has strength 12.32; Genemark calls start at 48425 /note=SSC: 48425-48072 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_81 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 4.84513E-80 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.516, -4.16062280240617, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_81 [Mycobacterium phage Peaches] ],,YP_003358784,100.0,4.84513E-80 SIF-HHPRED: SIF-Syn: NKF /note=NOTE /note=Current Gene Number: 80 /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? no starterator present /note=Is the ORF chosen the longest ORF: Yes that makes sense without too much overlap /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 peaches /note=Z score = 2.156 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and the two starts agree. CDS complement (48422 - 48598) /gene="79" /product="gp79" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_79" /note=Original Glimmer call @bp 48598 has strength 13.62; Genemark calls start at 48598 /note=SSC: 48598-48422 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_82 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 3.33995E-34 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.868, -2.827683592113848, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_82 [Mycobacterium phage Peaches] ],,YP_003358785,100.0,3.33995E-34 SIF-HHPRED: DUF5419 ; Family of unknown function (DUF5419),,,PF17441.5,84.4828,99.9 SIF-Syn: NKF /note=Current Gene Number: 81 /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? Y /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 = 2.868 /note=Detailed reasoning/evidence of why you either changed or kept the auto-annotated start site. The start site was kept because Glimmer and GeneMark agree, longer ORF, 1:1 ratio. CDS complement (48600 - 48812) /gene="80" /product="gp80" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_80" /note=Original Glimmer call @bp 48812 has strength 14.97; Genemark calls start at 48812 /note=SSC: 48812-48600 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_83 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 1.02604E-40 GAP: 91 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.516, -3.588526034455651, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_83 [Mycobacterium phage Peaches] ],,YP_003358786,100.0,1.02604E-40 SIF-HHPRED: DUF6440 ; Family of unknown function (DUF6440),,,PF20037.2,27.1429,87.3 SIF-Syn: NKF /note=Current Gene Number: 82 /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? Y /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 = 2.516 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment, longer ORF, and Glimmer and GeneMark agree. CDS complement (48904 - 49110) /gene="81" /product="gp81" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_81" /note=Original Glimmer call @bp 49110 has strength 12.07; Genemark calls start at 49110 /note=SSC: 49110-48904 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PEACHES_84 [Mycobacterium phage Peaches] ],,NCBI, q1:s1 100.0% 1.09136E-39 GAP: 22 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.622, -3.812150084159046, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PEACHES_84 [Mycobacterium phage Peaches] ],,YP_003358787,100.0,1.09136E-39 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 83 /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? 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 /note=Z score = 2.622 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and Glimmer and GeneMark agree. CDS complement (49133 - 50011) /gene="82" /product="gp82" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_82" /note=Original Glimmer call @bp 50011 has strength 10.98; Genemark calls start at 50011 /note=SSC: 50011-49133 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_EROS_88 [Mycobacterium phage Eros]],,NCBI, q1:s1 100.0% 0.0 GAP: 28 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.671, -3.708850054194189, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_EROS_88 [Mycobacterium phage Eros]],,QAY07397,99.6575,0.0 SIF-HHPRED: GP88 ; Gene product 88,,,PF17338.5,75.6849,100.0 SIF-Syn: NKF /note=Current Gene Number: 84 /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? Y /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 /note=Z score = 2.671 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and Glimmer and GeneMark agree. CDS complement (50040 - 50159) /gene="83" /product="gp83" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_83" /note=Original Glimmer call @bp 50159 has strength 9.93; Genemark calls start at 50159 /note=SSC: 50159-50040 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_NYXIS_87 [Mycobacterium phage Nyxis] ],,NCBI, q1:s1 100.0% 8.51794E-19 GAP: 710 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.188, -2.1695583717155773, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_NYXIS_87 [Mycobacterium phage Nyxis] ],,YP_009005926,100.0,8.51794E-19 SIF-HHPRED: TUDOR_SGF29_rpt1; first TUDOR domain found in SAGA-associated factor 29 (SGF29) and similar proteins.,,,cd20393,79.4872,88.4 SIF-Syn: NKF /note=Current Gene Number: 85 /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? Y /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 = 3.188 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and Glimmer and GeneMark agree. CDS complement (50870 - 51040) /gene="84" /product="gp84" /function="hypothetical protein" /locus tag="Taquarus-MitchellCC_84" /note=Original Glimmer call @bp 51040 has strength 0.33 /note=SSC: 51040-50870 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein KIY69_gp92 [Mycobacterium phage Cerulean] ],,NCBI, q1:s1 100.0% 1.20346E-31 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.966, -4.749088834314575, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KIY69_gp92 [Mycobacterium phage Cerulean] ],,YP_010062565,100.0,1.20346E-31 SIF-HHPRED: SIF-Syn: NKF /note=Current Gene Number: 86 /note=Did the start site stay the same or change: It stayed the same /note=Do the Glimmer and Genemark start sites agree? Not data for GeneMark /note=What about Starterator? Y /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 /note=Z score = 1.966 /note=Detailed reasoning / evidence of why you either changed or kept the auto-annotated start site. The start site was kept because it has a 1:1 alignment and Glimmer and GeneMark agree.