CDS 1 - 255 /gene="1" /product="gp1" /function="hypothetical protein" /locus tag="Yassified_1" /note=Original Glimmer call @bp 1 has strength 11.99; Genemark calls start at 1 /note=SSC: 1-255 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_1 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 7.89997E-56 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.905, -2.9063687850157054, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_1 [Mycobacterium phage ET08] ],,YP_003347684,100.0,7.89997E-56 SIF-HHPRED: SIF-Syn: gene 1 for Zeenon and BeanWater do not call a function. /note=BLAST PhagesDB and NCBI not informative, HHPred, CDD, do not suggest a function. not a transmembrane protein. CDS 252 - 473 /gene="2" /product="gp2" /function="hypothetical protein" /locus tag="Yassified_2" /note=Original Glimmer call @bp 252 has strength 6.81; Genemark calls start at 252 /note=SSC: 252-473 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein ALICE_2 [Mycobacterium phage Alice] ],,NCBI, q1:s1 100.0% 4.59158E-47 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.486, -6.094858505415773, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ALICE_2 [Mycobacterium phage Alice] ],,YP_009216267,100.0,4.59158E-47 SIF-HHPRED: SIF-Syn: /note=NCBI Blast- hypothetical protein; CDD and BLAST PhagesDB are not informative. CDS 477 - 1343 /gene="3" /product="gp3" /function="HNH endonuclease" /locus tag="Yassified_3" /note=Original Glimmer call @bp 477 has strength 13.08; Genemark calls start at 477 /note=SSC: 477-1343 CP: no SCS: both ST: SS BLAST-Start: [HNH endonuclease [Mycobacterium phage BadAgartude]],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.886, -3.711231203526307, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage BadAgartude]],,QAY12988,99.6528,0.0 SIF-HHPRED: SIF-Syn: CDS 1334 - 1594 /gene="4" /product="gp4" /function="hypothetical protein" /locus tag="Yassified_4" /note=Original Glimmer call @bp 1334 has strength 7.92; Genemark calls start at 1373 /note=SSC: 1334-1594 CP: no SCS: both-gl ST: NI BLAST-Start: [gp4 [Mycobacterium phage Cali] ],,NCBI, q4:s1 96.5116% 3.13762E-53 GAP: -10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.314, -4.356694780021467, no F: hypothetical protein SIF-BLAST: ,,[gp4 [Mycobacterium phage Cali] ],,YP_002224481,100.0,3.13762E-53 SIF-HHPRED: SIF-Syn: /note=BLAST PhagesDB and HHpred not informative; NCBI Blast, CDD, PhagesDB indicate unknown function. CDS 1587 - 1766 /gene="5" /product="gp5" /function="hypothetical protein" /locus tag="Yassified_5" /note=Original Glimmer call @bp 1587 has strength 5.68; Genemark calls start at 1587 /note=SSC: 1587-1766 CP: no SCS: both ST: NI BLAST-Start: [gp5 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 9.84251E-36 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.808, -3.0301037898918786, no F: hypothetical protein SIF-BLAST: ,,[gp5 [Mycobacterium phage Cali] ],,YP_002224482,100.0,9.84251E-36 SIF-HHPRED: SIF-Syn: /note=HHpred not informative, E-value too high. BLAST Phages DB, NCBI Blast support unknown function. CDS 1770 - 2210 /gene="6" /product="gp6" /function="HNH endonuclease" /locus tag="Yassified_6" /note=Genemark calls start at 1770 /note=SSC: 1770-2210 CP: no SCS: genemark ST: NI BLAST-Start: [gp6 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 7.2214E-103 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.561, -3.83711508627892, yes F: HNH endonuclease SIF-BLAST: ,,[gp6 [Mycobacterium phage Cali] ],,YP_002224483,100.0,7.2214E-103 SIF-HHPRED: SIF-Syn: /note=HHpred, BLAST PhagesDB support unknown function. NCBI Blast states hypothetical protein. PhagesDB supports HNH Endonuclease. CDS 2222 - 2338 /gene="7" /product="gp7" /function="hypothetical protein" /locus tag="Yassified_7" /note=Original Glimmer call @bp 2222 has strength 11.32; Genemark calls start at 2243 /note=SSC: 2222-2338 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein ET08_6 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 1.46095E-18 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.076, -4.585118207934747, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_6 [Mycobacterium phage ET08] ],,YP_003347689,100.0,1.46095E-18 SIF-HHPRED: SIF-Syn: /note=BLAST PhagesDB supports unknown function CDS 2335 - 2634 /gene="8" /product="gp8" /function="hypothetical protein" /locus tag="Yassified_8" /note=Original Glimmer call @bp 2335 has strength 7.11; Genemark calls start at 2335 /note=SSC: 2335-2634 CP: no SCS: both ST: NI BLAST-Start: [gp8 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 4.98902E-66 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.417, -4.1404541646896895, yes F: hypothetical protein SIF-BLAST: ,,[gp8 [Mycobacterium phage Cali] ],,YP_002224485,100.0,4.98902E-66 SIF-HHPRED: SIF-Syn: CDS 2631 - 2837 /gene="9" /product="gp9" /function="hypothetical protein" /locus tag="Yassified_9" /note=Original Glimmer call @bp 2631 has strength 15.86; Genemark calls start at 2631 /note=SSC: 2631-2837 CP: no SCS: both ST: NI BLAST-Start: [gp12 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.86006E-37 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.561, -3.5660483139923818, yes F: hypothetical protein SIF-BLAST: ,,[gp12 [Mycobacterium phage Bxz1] ],,NP_818088,100.0,1.86006E-37 SIF-HHPRED: SIF-Syn: /note=BLAST PhagesDB supports unknown function. NCBI Blast predicts hypothetical protein. PhagesDB and CDD are not informative. CDS 2923 - 3606 /gene="10" /product="gp10" /function="hypothetical protein" /locus tag="Yassified_10" /note=Original Glimmer call @bp 2923 has strength 7.56; Genemark calls start at 2923 /note=SSC: 2923-3606 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RONAN_10 [Mycobacterium phage Ronan]],,NCBI, q1:s1 100.0% 5.87767E-161 GAP: 85 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.905, -3.2925703904164987, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RONAN_10 [Mycobacterium phage Ronan]],,QKO02102,99.1189,5.87767E-161 SIF-HHPRED: DUF6197 ; Family of unknown function (DUF6197),,,PF19698.2,51.1013,46.2 SIF-Syn: Yassified gene 10 is syntenic with gene 9 in Bean Water. Not informative of function. /note=HHPred not informative (E-value of 160 is too high). BLAST, CDD and Synteny are not informative /note=Not a transmembrane domain. CDS 3644 - 3898 /gene="11" /product="gp11" /function="hypothetical protein" /locus tag="Yassified_11" /note=Original Glimmer call @bp 3644 has strength 12.17; Genemark calls start at 3644 /note=SSC: 3644-3898 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_13 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 3.09416E-55 GAP: 37 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.561, -3.5660483139923818, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_13 [Mycobacterium phage ScottMcG] ],,YP_002224046,100.0,3.09416E-55 SIF-HHPRED: FlbD ; Flagellar and Swarming motility proteins,,,PF06289.14,98.8095,94.5 SIF-Syn: Not informative. /note=HHPred not informative (E-value of 0.92). BLAST, and CDD do not support calling a function. It doesn`t have a transmembrane domain. CDS 3898 - 4110 /gene="12" /product="gp12" /function="hypothetical protein" /locus tag="Yassified_12" /note=Original Glimmer call @bp 3898 has strength 8.03; Genemark calls start at 3898 /note=SSC: 3898-4110 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_14 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 3.5215E-44 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.15, -4.490107201936413, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_14 [Mycobacterium phage ScottMcG] ],,YP_002224047,100.0,3.5215E-44 SIF-HHPRED: DUF3640 ; Protein of unknown function (DUF3640),,,PF12342.11,14.2857,50.4 SIF-Syn: Not informative /note=HHPred not informative (E-value of 24) .Other sources of evidence are not supportive a function being called. It doesn`t have any TMB domains. CDS 4163 - 4537 /gene="13" /product="gp13" /function="hypothetical protein" /locus tag="Yassified_13" /note=Original Glimmer call @bp 4163 has strength 4.9; Genemark calls start at 4163 /note=SSC: 4163-4537 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FGG25_gp78 [Mycobacterium phage KSSJEB] ],,NCBI, q3:s2 85.4839% 4.76618E-67 GAP: 52 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.009, -4.997292723641609, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FGG25_gp78 [Mycobacterium phage KSSJEB] ],,YP_009637516,83.7398,4.76618E-67 SIF-HHPRED: DUF6324 ; Family of unknown function (DUF6324),,,PF19849.2,30.6452,93.2 SIF-Syn: Not informative /note=HHPred not informative (E-value of 0.91), all other sources of evidence do not support calling a function. CDS 4530 - 4718 /gene="14" /product="gp14" /function="hypothetical protein" /locus tag="Yassified_14" /note=Genemark calls start at 4530 /note=SSC: 4530-4718 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein KHO60_gp016 [Mycobacterium phage CharlieB] ],,NCBI, q1:s1 100.0% 7.30066E-36 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.962, -3.1725816037952645, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KHO60_gp016 [Mycobacterium phage CharlieB] ],,YP_010057424,100.0,7.30066E-36 SIF-HHPRED: Ryanodine receptor 1; Ryanodine Receptor Calcium Release Channel, Phosphorylation, Muscle, Skeletal, METAL TRANSPORT; HET: GOL; 1.59A {Oryctolagus cuniculus},,,4ESU_A,85.4839,91.0 SIF-Syn: Not informative. /note=HHPred not informative (E-value of 0.91) /note=No Glimmer Score. GM calls start at 4530. /note=PhagesDB Function Frequency, BLAST and CDD are not informative CDS 4715 - 5224 /gene="15" /product="gp15" /function="hypothetical protein" /locus tag="Yassified_15" /note=Original Glimmer call @bp 4715 has strength 5.39; Genemark calls start at 4715 /note=SSC: 4715-5224 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_14 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 1.28424E-119 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.808, -3.0478325568523097, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_14 [Mycobacterium phage ET08] ],,YP_003347697,100.0,1.28424E-119 SIF-HHPRED: MmcB-like ; DNA repair protein MmcB-like,,,PF06319.15,92.3077,99.9 SIF-Syn: Alice gene 14 is syntenic with Yassified_15 but the HHPred match is not as strong. /note=HHPred is informative (E-value of 9.8 e-21) identifies a Mmc-B like DNA repair protein. /note=Starterator: Start 5 @4715 has the most annotated start sites within this gene family and has 31 MA’s /note=Glimmer score of 5.39, GM and GL both call start site at 4715 /note=PhagesDB Function Frequency: one instance of a similar gene but in a different Phamin and cluster, BR, calling reca-like dna recombinase. CDS 5361 - 5699 /gene="16" /product="gp16" /function="membrane protein" /locus tag="Yassified_16" /note=Original Glimmer call @bp 5361 has strength 6.04; Genemark calls start at 5361 /note=SSC: 5361-5699 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein KHO60_gp019 [Mycobacterium phage CharlieB] ],,NCBI, q1:s1 100.0% 1.0518E-73 GAP: 136 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.905, -2.8454123590742793, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein KHO60_gp019 [Mycobacterium phage CharlieB] ],,YP_010057427,100.0,1.0518E-73 SIF-HHPRED: Stannin; Stannin. Stannin (SNN) is a monotopic membrane protein containing an N-terminal single transmembrane helix that transverses the lipid bilayer, an unstructured linker which includes a conserved CXC metal-binding motif and a putative 14-3-3zeta binding site, and a C-terminal distorted cytoplasmic helix.,,,cd20257,21.4286,76.0 SIF-Syn: Not informative /note=HHPred not informative (E-value of 15) /note=Starterator: Start 22 @5361 has the most annotated start sites within this gene family and has 98 MA’s /note=Glimmer score of 6.04, GM and GL both call start site at 5361 /note=PhagesDB Function Frequency: unavailable. BLAST and CDD do not support calling a function. Has one TMB domain supported by TmHmm and SOSUI. CDS 5751 - 5936 /gene="17" /product="gp17" /function="hypothetical protein" /locus tag="Yassified_17" /note=Original Glimmer call @bp 5751 has strength 14.22; Genemark calls start at 5751 /note=SSC: 5751-5936 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein LINSTU_21 [Mycobacterium phage LinStu] ],,NCBI, q1:s7 100.0% 4.31528E-34 GAP: 51 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein LINSTU_21 [Mycobacterium phage LinStu] ],,YP_009014615,91.0448,4.31528E-34 SIF-HHPRED: IL4I1 protein; nuclear pore complex, inner ring, Nup205, Nup93, Nup188, Nup155, NDC1, Aladin, STRUCTURAL PROTEIN; 4.2A {Xenopus laevis},,,7WKK_h,68.8525,88.7 SIF-Syn: Not informative. /note=Starterator: Start 11 @5751 has the most annotated start sites within this gene family and has 118 MA’s /note=Glimmer score of 14.22, GM and GL both call start site at 5751 /note=HHPred not informative (E-value of 6.3). None of the other sources of evidence offers a strong match to a function. No tmb domain. CDS 6030 - 6314 /gene="18" /product="gp18" /function="hypothetical protein" /locus tag="Yassified_18" /note=Original Glimmer call @bp 6036 has strength 7.74; Genemark calls start at 6078 /note=SSC: 6030-6314 CP: yes SCS: both-cs ST: SS BLAST-Start: [gp22 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 1.05424E-62 GAP: 93 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.43, -6.210473446429151, no F: hypothetical protein SIF-BLAST: ,,[gp22 [Mycobacterium phage Cali] ],,YP_002224499,100.0,1.05424E-62 SIF-HHPRED: DUF5678 ; Family of unknown function (DUF5678),,,PF18929.3,12.766,54.9 SIF-Syn: Not informative /note=Starterator: Start 1 @6030 has the most annotated start sites within this gene family and has 107 MA’s /note=Glimmer score of 7.74, GM calls start site at 6078 and GL calls start site at 6036 /note=None of the sources of evidence supports calling a function. CDS 6311 - 6538 /gene="19" /product="gp19" /function="membrane protein" /locus tag="Yassified_19" /note=Original Glimmer call @bp 6311 has strength 18.98; Genemark calls start at 6311 /note=SSC: 6311-6538 CP: yes SCS: both ST: SS BLAST-Start: [gp23 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 5.51546E-42 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.151, -4.34663776219455, yes F: membrane protein SIF-BLAST: ,,[gp23 [Mycobacterium phage Bxz1] ],,NP_818099,100.0,5.51546E-42 SIF-HHPRED: SIF-Syn: Yassified (19) and Zeenon (24) have the same suggested start. A 53% query. The function of the gene is unknown compared to BeanWater and Zennon. Beanwater Cluster does not align with Yassified because, they both have different starts. 6728 for Beanwater (17) and 6311 for Yassified. /note=HHPRED is not very informative, it suggests an Eisosome Protein function with only 87% probability and a query of 53%, it is not enough to indicate is related to Yassified. /note=NCBI Blast provides enough information to deduce that there is alignment and coverage from other similar genes. For example: SEA_BERT is a hypothetical protein(100% alignment) and WALY_20(98%) is a protein. PhagesBlast suggests no known functions. /note=Thmm, Topcon, and SOSUI show one tmb domain. CDS 6597 - 6740 /gene="20" /product="gp20" /function="hypothetical protein" /locus tag="Yassified_20" /note=Original Glimmer call @bp 6594 has strength 8.09; Genemark calls start at 6597 /note=SSC: 6597-6740 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein LINSTU_24 [Mycobacterium phage LinStu] ],,NCBI, q1:s2 100.0% 2.35816E-25 GAP: 58 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.186, -4.4157344874810125, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein LINSTU_24 [Mycobacterium phage LinStu] ],,YP_009014618,97.9167,2.35816E-25 SIF-HHPRED: SIF-Syn: Zenon 20 has a white background, this could have been an insertion or deletion. It implies that this gene is not very close in familiriaty with Yassfied gene 20. /note=Start codon supported by Glimmer start /note=BLASTNCBI has enough data to support there is a close phage relative with a similar gene (97%coverage,93%identiy with closely related phages, 1:1 alignment with LLRHOOD_21) /note=Starterator supports the suggested start and is manually annotated. /note=HHPRED, low hits(Less than 90%)Low coverage of 50%, query43%. Found no function /note=Phamerator(No nucleotide similarity) /note=Not a tmb based on thmm and topcon. CDS 6743 - 6895 /gene="21" /product="gp21" /function="hypothetical protein" /locus tag="Yassified_21" /note= /note=SSC: 6743-6895 CP: yes SCS: neither ST: NI BLAST-Start: [hypothetical protein KHO60_gp024 [Mycobacterium phage CharlieB] ],,NCBI, q1:s1 100.0% 1.31821E-27 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.905, -2.9063687850157054, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KHO60_gp024 [Mycobacterium phage CharlieB] ],,YP_010057432,100.0,1.31821E-27 SIF-HHPRED: SIF-Syn: /note=no evidence of a function based on BLAST, HHPred, CDD. Not a TMB. CDS 6978 - 7262 /gene="22" /product="gp22" /function="hypothetical protein" /locus tag="Yassified_22" /note=Original Glimmer call @bp 6978 has strength 6.56; Genemark calls start at 6978 /note=SSC: 6978-7262 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_25 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s22 100.0% 1.80909E-57 GAP: 82 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.009, -4.7084971843946395, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_25 [Mycobacterium phage ScottMcG] ],,YP_002224058,81.7391,1.80909E-57 SIF-HHPRED: SIF-Syn: High nucleotide similarity with Zennon, both genes 22 have a purple background. While compared to gene 22 from Beanwater background is white. /note=PhagesDB Frequency(0%) No data /note=BLASTNBCI suggests Hypothetical protein, shows evalue=1e-57, 80% identity, query coverage;100%, more than 10 hits. /note=Glimmer predicted start 6978, start 4: manual annotated once but does not call it. Gene: Yassified_22 Start: 6978, Stop: 7262, Start Num: 4 /note=Candidate Starts for Yassified_22: (1, 6915), (Start: 2 @6963 has 6 MA`s), (3, 6975), (Start: 4 @6978 has 1 MA`s).HHPred does not show valuable matches. CDS 7354 - 7710 /gene="23" /product="gp23" /function="hypothetical protein" /locus tag="Yassified_23" /note=Original Glimmer call @bp 7354 has strength 6.41; Genemark calls start at 7354 /note=SSC: 7354-7710 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_26 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 5.45661E-79 GAP: 91 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.055, -4.900166819979879, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_26 [Mycobacterium phage ScottMcG] ],,YP_002224059,100.0,5.45661E-79 SIF-HHPRED: SIF-Syn: Similarity to Phage Zennon, both have a close E-value /note=BLASTNCBI Evalue:2e-42, Query coverage is 96%, 62% Identity. More than 10 similar hits with even lower data. Closest phage function is a Hypothetical protein. /note=Glimmer predicts the start 7354, start 53. Was the most often called 99%, 157 mannual annotations. Gene: Yassified_23 Start: 7354, Stop: 7710, Start Num: 53 Candidate Starts for Yassified_23:(Start: 53 @7354 has 157 MA`s), (101, 7561), (117, 7657) /note=HHPred-Highest probability is 86%, coverage of 25%, Query of 3.2%, too low to be considered, but it suggests a function of Protein unknown function /note=Not a TMB protein. CDS 7721 - 7828 /gene="24" /product="gp24" /function="hypothetical protein" /locus tag="Yassified_24" /note=Genemark calls start at 7721 /note=SSC: 7721-7828 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_27 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.61588E-16 GAP: 10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.597, -5.509286325636915, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_27 [Mycobacterium phage ScottMcG] ],,YP_002224060,100.0,1.61588E-16 SIF-HHPRED: SIF-Syn: In comparison to Zennon phage, the background is mostly purple but there is small white background touching the corner of gene 24 in Zennon. Both still have a lot of nucleotide similarity. And a close family number. /note=BLASTNCBI-value=1e-16, Query coverage 100%, 100% Identity, this is the second hit option. The first hit option has evalue=7e-16, 100%coverage, 97% identity. /note=Genemark predicted start 7721, start 3, it is the most annotated 153 out of 153. MA called 100% when present. Gene: Yassified_24 Start: 7721, Stop: 7828, Start Num: 3-Candidate Starts for Yassified_24: (1, 7367), (2, 7649), (Start: 3 @7721 has 153 MA`s) . /note=HHpred suggests No function. /note=Not a TMP protein. CDS 7828 - 8028 /gene="25" /product="gp25" /function="hypothetical protein" /locus tag="Yassified_25" /note=Original Glimmer call @bp 7828 has strength 14.29; Genemark calls start at 7828 /note=SSC: 7828-8028 CP: yes SCS: both ST: SS BLAST-Start: [gp28 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 5.71218E-40 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.905, -3.6727816321281046, yes F: hypothetical protein SIF-BLAST: ,,[gp28 [Mycobacterium phage Cali] ],,YP_002224505,100.0,5.71218E-40 SIF-HHPRED: SIF-Syn: not informative. Homologous with same locus are also NKF. /note=BLASTNCBI (Similar to Gp28, evalue=5e-40, Query coverage of 100%, 100% identity, more than 10 similar hits). /note=Glimmer predicted start 7828, start 7. most annotated start site, 158 Mannual Annotations out of 170. Found in 90% of genes in Pham. Gene: Yassified_25 Start: 7828, Stop: 8028, Start Num: 7, Candidate Starts for Yassified_25:(Start: 7 @7828 has 158 MA`s), (12, 7864), (19, 7966), (20, 7990). /note=HHPred does not suggest any function to be considered, Both Blast and Phamerator agree on the same start and Blast has 100% alignment and coverage with a familiar phage that is a hypothetical protein. CDS 8064 - 9002 /gene="26" /product="gp26" /function="membrane protein, Band-7 -like" /locus tag="Yassified_26" /note=Original Glimmer call @bp 8064 has strength 18.21; Genemark calls start at 8058 /note=SSC: 8064-9002 CP: yes SCS: both-gl ST: SS BLAST-Start: [gp31 [Mycobacterium phage Spud] ],,NCBI, q1:s3 100.0% 0.0 GAP: 35 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.918, -5.743069600988506, no F: membrane protein, Band-7 -like SIF-BLAST: ,,[gp31 [Mycobacterium phage Spud] ],,YP_002224285,99.3631,0.0 SIF-HHPRED: Protein HflK; membrane microdomain organization, MEMBRANE PROTEIN; 3.27A {Escherichia coli},,,7VHP_S,82.0513,100.0 SIF-Syn: Beanwater and Yassified Gene 26, both have a purple background, this indicates high nucleotide similarity. Yassified and Zennon gene 26, also has a good nuleotide similarity. (Both backgrounds are purple). /note=BLASTNCBI (Similar to gp31, e value of 0, Query coverage is 100%, 99.3% Identity. More than 10 similar hits) /note=Glimmer predicted start: 8064. MA 18 times. • Found in 174 of 207 ( 84.1% ) of genes in pham Start: 23. Yassified has the most annotated start but it is not called. Gene: Yassified_26 Start: 8064, Stop: 9002, Start Num: 23 Candidate Starts for Yassified_26: (Start: 20 @8058 has 130 MA`s), (Start: 23 @8064 has 19 MA`s) CDS 9006 - 9368 /gene="27" /product="gp27" /function="hypothetical protein" /locus tag="Yassified_27" /note=Original Glimmer call @bp 9006 has strength 8.45; Genemark calls start at 9006 /note=SSC: 9006-9368 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_30 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 2.35662E-83 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.091, -4.473102278738214, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_30 [Mycobacterium phage ScottMcG] ],,YP_002224063,100.0,2.35662E-83 SIF-HHPRED: SIF-Syn: When compared to Zennon, the background is purple-Meaning there is nucleotide similarity. When gene 27 is compared to gene from Beanwater, it shows a white background all around. No similarity at all. Gene 27, falls under the category of "Binding protein" for Zennon, this can support the idea of gene 27 from Yassified being also a protein. /note=BLASTNCBI 1:1 alignment with Scottmcg_30, Linstu_30, FDI20_gp030 and several other phages, also poorer alignment with other phages /note=HHPred suggests unknown function /note=Glimmer predicted start: 9006. start 5 Most Annotated start that calls it, 151 annotations out of 158. Called 94.7% Gene: Yassified_27 Start: 9006, Stop: 9368, Start Num: 5 /note=Candidate Starts for Yassified_27: /note=(Start: 5 @9006 has 151 MA`s), (Start: 7 @9021 has 4 MA`s), (9, 9072), (17, 9210) CDS 9365 - 9496 /gene="28" /product="gp28" /function="helix-turn-helix DNA binding domain" /locus tag="Yassified_28" /note=Original Glimmer call @bp 9365 has strength 14.75; Genemark calls start at 9365 /note=SSC: 9365-9496 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ESSENCE_30 [Mycobacterium phage Essence]],,NCBI, q1:s1 100.0% 5.63759E-22 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -3.3503726477288405, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein SEA_ESSENCE_30 [Mycobacterium phage Essence]],,QAY13748,97.6744,5.63759E-22 SIF-HHPRED: Zn-ribbon_RPB9; C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II. The C-terminal zinc ribbon domain (C-ribbon) of subunit B9 (Zn-ribbon_RPB9) in RNA polymerase (Pol) II is involved in intrinsic transcript cleavage.,,,cd10508,74.4186,95.6 SIF-Syn: There are 6 phages in C1 with the same gene calling the same function. /note=Gene: Yassified_28 Start: 9365, Stop: 9496, Start Num: 2 Candidate Starts for Yassified_28: (1, 9191), (Start: 2 @9365 has 158 MA`s), (3, 9440), (4, 9446), /note=With all the evidence and a z score of 3.058, A high glimmer score of 14.75, so we can conclude that the predicted start site is correctly. /note=It also has the smallest gap and is in the forward strand. /note=Pharm maps also agrees with the same exact start and end codon. /note=Zn-ribbon_RPB9; C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II. The C-terminal zinc ribbon domain (C-ribbon) of subunit B9 (Zn-ribbon_RPB9) in RNA polymerase (Pol) II is involved in intrinsic transcript cleavage. CDS 9570 - 9920 /gene="29" /product="gp29" /function="hypothetical protein" /locus tag="Yassified_29" /note=Original Glimmer call @bp 9570 has strength 15.74; Genemark calls start at 9570 /note=SSC: 9570-9920 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_32 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.92701E-80 GAP: 73 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.886, -4.410201207862326, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_32 [Mycobacterium phage ScottMcG] ],,YP_002224065,100.0,1.92701E-80 SIF-HHPRED: PGDYG ; PGDYG protein,,,PF14083.9,24.1379,99.1 SIF-Syn: not informative /note=Start site 9570 has the longest length and the shortest gap space. /note=The function of this gene is supported by PhagesDB, BLAST, HHpred is an informative E value is very low at {8.1}^{E-10}. /note=The function states that gene 29 has a PGDYG motif. But that is not a function. /note=Phagesdb BLAST states the function is unknown. /note=HHPRED states that the protein is a PGDYG ; PGDYG protein the probability is more than 99.1% and there is a very small E value. CDS 9997 - 10284 /gene="30" /product="gp30" /function="hypothetical protein" /locus tag="Yassified_30" /note=Original Glimmer call @bp 9997 has strength 22.62; Genemark calls start at 9997 /note=SSC: 9997-10284 CP: yes SCS: both ST: SS BLAST-Start: [gp33 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.61783E-63 GAP: 76 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.983, -2.6013996449736907, yes F: hypothetical protein SIF-BLAST: ,,[gp33 [Mycobacterium phage Bxz1] ],,NP_818109,100.0,2.61783E-63 SIF-HHPRED: DUF3622 ; Protein of unknown function (DUF3622),,,PF12286.11,20.0,89.7 SIF-Syn: /note=Glimmer’s start site at 9997 and stop site at 10,284 although on the Host-Trained report there is coding potential but, there is not an actual gene showed marked by a dark solid black line. GenMark and Glimmer also agree with the starting codon. Upon looking on the report it not clear that there is a gene start site at 9997, but rather at 10000 base pairs. Since these starting sites are similar. /note=On Pham Starterator map it states Gene: Yassified_30 Start: 9997, Stop: 10284, Start Num: 6 Candidate Starts for Yassified_30: (1, 9760), (2, 9781), (Start: 6 @9997 has 157 MA`s), (7, 10054), (9, 10186) I can conclude that predicted start site is correct. /note= /note=hhpred- DUF3622 ; Protein of unknown function (DUF3622) 89% probability /note=NCBI BLAST- States it is a Hypothetical Protein /note=TmHmm (Transmembrane prediction)- doesn`t have a tmb motif. CDS 10286 - 10447 /gene="31" /product="gp31" /function="hypothetical protein" /locus tag="Yassified_31" /note=Original Glimmer call @bp 10286 has strength 16.21; Genemark calls start at 10286 /note=SSC: 10286-10447 CP: yes SCS: both ST: SS BLAST-Start: [gp34 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 7.08297E-31 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.049, -4.6236495748204955, yes F: hypothetical protein SIF-BLAST: ,,[gp34 [Mycobacterium phage Bxz1] ],,NP_818110,100.0,7.08297E-31 SIF-HHPRED: SIF-Syn: not informative. /note=: I agree with the Glimmer and gene mark report for the start being 10286. On the host- trained report there are multiple genes coding for 10286 in the direct sequence. /note=Phagesdb BLAST - States the function is unknown. /note=HHPRED- not strong. /note=NCBI BLAST- states that this is a hypothetical protein /note=TmHmm (Transmembrane prediction)- 0 tmb domains. CDS 10447 - 10665 /gene="32" /product="gp32" /function="ribbon-helix-helix DNA binding domain" /locus tag="Yassified_32" /note=Original Glimmer call @bp 10447 has strength 3.51; Genemark calls start at 10447 /note=SSC: 10447-10665 CP: yes SCS: both ST: SS BLAST-Start: [gp35 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 7.20847E-43 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.561, -3.5660483139923818, yes F: ribbon-helix-helix DNA binding domain SIF-BLAST: ,,[gp35 [Mycobacterium phage Cali] ],,YP_002224512,100.0,7.20847E-43 SIF-HHPRED: CdbA; nucleoid ribbon-helix-helix, DNA BINDING PROTEIN; 2.24A {Myxococcus xanthus DK 1622},,,6SBW_A,63.8889,98.6 SIF-Syn: A number of c1 phages with genes in same locus call the same function. /note=Phagesdb BLAST- ribbon-helix-helix DNA binding protein /note=HHPRED- states that this is a nucleoid ribbon-helix-helix, DNA BINDING PROTEIN; /note=NBCI BLAST- hypothetical protein /note= /note=TmHmm (Transmembrane prediction)- 0 tmb domains. /note=gene Mark and Glimmer Start at 10447. On the host-trained report, there is coding potential and genes on the first forward strand that could be for 10447. On the suggested start site. /note=Phagesdb Function Frequency- ribbon-helix-helix DNA binding protein with a 76% frequency. CDS 10665 - 10826 /gene="33" /product="gp33" /function="hypothetical protein" /locus tag="Yassified_33" /note=Original Glimmer call @bp 10665 has strength 7.69; Genemark calls start at 10665 /note=SSC: 10665-10826 CP: yes SCS: both ST: SS BLAST-Start: [gp36 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.06894E-29 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.561, -3.5660483139923818, yes F: hypothetical protein SIF-BLAST: ,,[gp36 [Mycobacterium phage Bxz1] ],,NP_818112,100.0,1.06894E-29 SIF-HHPRED: SIF-Syn: not informative /note=: Glimmer and gene mark agree with a score of 7.69. On pecaan it states that the stop codon is 10,826 and the start codon is 10,665, it gives us the longest ORF and shortest overlap. GenMark and Glimmer also agree with the starting codon. Upon looking on the report, I can agree of this starting point as there is genes present in the second and third forward reading strands. The coding potential is strong with under 100 base pairs. Start site of 10665 has 95 manual annotations as per starrator. When I blast the sequence, I found at least four genes from phages that have the same gene with 100% cover and 100% identity and E value of 5E-77. One of the hits, Charlie has Q1:S11032. Therefore, the alignment doesn’t support the start site chosen. /note=Phagesdb Function Frequency- states that this is a DNA-binding protein. /note=Phagesdb BLAST- states that the function is unknown. /note=HHPRED- states that this is a Coenzyme PQQ synthesis protein D; helix-turn-helix, PQQ with 60% coverage and 93 probability. /note=NCBI BLAST- states that this is a hypothetical protein /note= /note=TmHmm (Transmembrane prediction) is insignificant due to the number being below 2. CDS 10891 - 11139 /gene="34" /product="gp34" /function="hypothetical protein" /locus tag="Yassified_34" /note=Original Glimmer call @bp 10891 has strength 17.46; Genemark calls start at 10891 /note=SSC: 10891-11139 CP: yes SCS: both ST: SS BLAST-Start: [gp37 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.40249E-51 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[gp37 [Mycobacterium phage Bxz1] ],,NP_818113,100.0,2.40249E-51 SIF-HHPRED: SIF-Syn: not informative. /note=On pecaan it states that the stop codon is 11,139 and the start codon is 10,891. gene mark and Glimmer also agree with the starting codon. Upon looking on the report, I can agree of this start point as there is genes present in the third forward reading strands. /note=Phagesdb BLAST- states that the function in unknown. /note=HHPRED- states that this is an Uncharacterized conserved protein; /note=NCBI BLASTS- states that this is a hypothetical protein. /note=TmHmm (Transmembrane prediction) not a tmb protein. CDS 11210 - 11539 /gene="35" /product="gp35" /function="hypothetical protein" /locus tag="Yassified_35" /note=Original Glimmer call @bp 11210 has strength 15.85; Genemark calls start at 11210 /note=SSC: 11210-11539 CP: yes SCS: both ST: SS BLAST-Start: [gp38 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 6.40316E-74 GAP: 70 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[gp38 [Mycobacterium phage Bxz1] ],,NP_818114,100.0,6.40316E-74 SIF-HHPRED: SIF-Syn: not informative /note=GenMark and glimmer share the same start site at 11210, although on the Host-Trained report, there is coding potential and a gene showed marked by a dark solid black line. /note=Phagesdb BLAST- states the function is unknown. /note=HHPRED- 84 probability that the Domain of unknown function (DUF4761). This has a 48% coverage. /note=NBCI BLAST- states that this is a hypothetical protein. /note=TmHmm (Transmembrane prediction) no tmb domain. CDS 11612 - 11866 /gene="36" /product="gp36" /function="hypothetical protein" /locus tag="Yassified_36" /note=Original Glimmer call @bp 11612 has strength 18.64; Genemark calls start at 11612 /note=SSC: 11612-11866 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LIFESAVOR_39 [Mycobacterium phage LifeSavor] ],,NCBI, q1:s1 100.0% 1.29993E-51 GAP: 72 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.216, -2.1924212546750814, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LIFESAVOR_39 [Mycobacterium phage LifeSavor] ],,AVI04643,100.0,1.29993E-51 SIF-HHPRED: a.195.1.1 (A:) Hypothetical protein YpjQ {Bacillus subtilis [TaxId: 1423]} | CLASS: All alpha proteins, FOLD: YutG-like, SUPFAM: YutG-like, FAM: YutG-like,,,SCOP_d1tlqa_,67.8571,83.1 SIF-Syn: not informative /note=Glimmer and gene mark agree at the start site being 11612 and I also agree as I seen a black line representing a gene and coding potential. /note=Phagesdb BLAST- states the function is unknown. /note=HHPRED- states this is a Hypothetical protein with an 83.1 probability. /note=NCBI BLAST- also states this is a Hypothetical protein with 98% identified. /note=TmHmm (Transmembrane prediction), no tmb domains. CDS 11863 - 12033 /gene="37" /product="gp37" /function="hypothetical protein" /locus tag="Yassified_37" /note=Original Glimmer call @bp 11863 has strength 19.98; Genemark calls start at 11863 /note=SSC: 11863-12033 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_38 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.90186E-29 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.785, -5.256359229020349, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_38 [Mycobacterium phage ScottMcG] ],,YP_002224071,100.0,1.90186E-29 SIF-HHPRED: RNA12 ; RNA12 protein,,,PF10443.12,85.7143,88.4 SIF-Syn: Not informative. /note=None of the evidence supports calling a function for this gene. CDS 12112 - 12399 /gene="38" /product="gp38" /function="hypothetical protein" /locus tag="Yassified_38" /note=Original Glimmer call @bp 12112 has strength 11.48; Genemark calls start at 12112 /note=SSC: 12112-12399 CP: yes SCS: both ST: SS BLAST-Start: [gp41 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 4.18317E-64 GAP: 78 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.657, -3.364992052816827, yes F: hypothetical protein SIF-BLAST: ,,[gp41 [Mycobacterium phage Cali] ],,YP_002224518,100.0,4.18317E-64 SIF-HHPRED: DUF2020 ; Domain of unknown function (DUF2020),,,PF09449.13,47.3684,71.1 SIF-Syn: Not informative. /note=None of the sources of evidence support calling a function for this gene. CDS 12489 - 12917 /gene="39" /product="gp39" /function="hypothetical protein" /locus tag="Yassified_39" /note=Original Glimmer call @bp 12489 has strength 14.82; Genemark calls start at 12489 /note=SSC: 12489-12917 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein M182_gp043 [Mycobacterium phage Astraea] ],,NCBI, q1:s13 100.0% 3.65108E-99 GAP: 89 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.227, -2.0895162839948163, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M182_gp043 [Mycobacterium phage Astraea] ],,YP_008061538,92.2078,3.65108E-99 SIF-HHPRED: TcfC ; E-set like domain,,,PF16967.8,45.7746,68.0 SIF-Syn: not informative. /note=A similar gene from a different Pham and cluster has been called a minor tail protein but none of the functional sources of evidence support that call. It doesn`t have a transmembrane domain. CDS 13009 - 13296 /gene="40" /product="gp40" /function="hypothetical protein" /locus tag="Yassified_40" /note=Original Glimmer call @bp 13009 has strength 16.53; Genemark calls start at 13009 /note=SSC: 13009-13296 CP: yes SCS: both ST: SS BLAST-Start: [gp43 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 2.23537E-61 GAP: 91 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[gp43 [Mycobacterium phage Cali] ],,YP_002224520,100.0,2.23537E-61 SIF-HHPRED: b.34.5.0 (B:3-65) automated matches {Escherichia coli [TaxId: 562]} | CLASS: All beta proteins, FOLD: SH3-like barrel, SUPFAM: Translation proteins SH3-like domain, FAM: automated matches,,,SCOP_d3a5zb1,21.0526,73.4 SIF-Syn: not informative. /note=No evidence supporting a function call. No TMB domain. CDS 13293 - 13562 /gene="41" /product="gp41" /function="hypothetical protein" /locus tag="Yassified_41" /note=Original Glimmer call @bp 13293 has strength 16.43; Genemark calls start at 13293 /note=SSC: 13293-13562 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein ET08_38 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 2.23197E-56 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.58, -4.547770211785489, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_38 [Mycobacterium phage ET08] ],,YP_003347721,100.0,2.23197E-56 SIF-HHPRED: d.328.1.1 (A:13-244) Magnesium transport protein CorA, soluble domain {Thermotoga maritima [TaxId: 2336]} | CLASS: Alpha and beta proteins (a+b), FOLD: CorA soluble domain-like, SUPFAM: CorA soluble domain-like, FAM: CorA soluble domain-like,,,SCOP_d2bbha1,89.8876,70.5 SIF-Syn: not informative. /note=No evidence supporting a function call. CDS 13668 - 14033 /gene="42" /product="gp42" /function="hypothetical protein" /locus tag="Yassified_42" /note=Original Glimmer call @bp 13668 has strength 15.28; Genemark calls start at 13668 /note=SSC: 13668-14033 CP: yes SCS: both ST: SS BLAST-Start: [gp45 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 1.78178E-84 GAP: 105 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.801, -5.080915947802713, no F: hypothetical protein SIF-BLAST: ,,[gp45 [Mycobacterium phage Cali] ],,YP_002224522,100.0,1.78178E-84 SIF-HHPRED: DotD; 3-layer(bab) sandwich, MTH1598-like, PROTON TRANSPORT; 2.0A {Legionella pneumophila},,,3ADY_A,55.3719,80.6 SIF-Syn: Not informative /note=no evidence supporting a function call. No TMB domain. CDS 14070 - 14345 /gene="43" /product="gp43" /function="hypothetical protein" /locus tag="Yassified_43" /note=Original Glimmer call @bp 14070 has strength 10.45; Genemark calls start at 14070 /note=SSC: 14070-14345 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein M182_gp047 [Mycobacterium phage Astraea] ],,NCBI, q1:s1 100.0% 1.26443E-59 GAP: 36 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.227, -2.1695583717155773, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M182_gp047 [Mycobacterium phage Astraea] ],,YP_008061542,100.0,1.26443E-59 SIF-HHPRED: ALR0975 PROTEIN; PHYTOCHELATIN SYNTHASE, PCS, ALR0975, ACYL-ENZYME INTERMEDIATE, NOSTOC, GLUTATHIONE METABOLISM, CYSTEINE PROTEASE, TRANSFERASE; HET: 3GC, MSE; 1.4A {ANABAENA SP.} SCOP: d.3.1.14,,,2BU3_A,32.967,37.2 SIF-Syn: not informative. /note=No supportive evidence for a function call. No TMB domains. CDS 14395 - 14691 /gene="44" /product="gp44" /function="helix-turn-helix DNA binding domain" /locus tag="Yassified_44" /note=Original Glimmer call @bp 14464 has strength 4.29; Genemark calls start at 14395 /note=SSC: 14395-14691 CP: yes SCS: both-gm ST: SS BLAST-Start: [HTH DNA binding protein [Mycobacterium phage Astraea] ],,NCBI, q1:s1 100.0% 1.15853E-64 GAP: 49 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.087, -5.787564606701106, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding protein [Mycobacterium phage Astraea] ],,YP_008061543,100.0,1.15853E-64 SIF-HHPRED: SIF-Syn: Lukilu_40 is syntenic with same function, as well as up- and down-stream genes. /note=Called twice in PhagesDB for a C1 phage. Supported by CDD, Evalue = 1.38e-03]cl21459, Helix-turn-helix domains ;A large family of mostly alpha-helical protein domains with a characteristic fold; most members function as sequence-specific DNA binding domains, such as in transcription regulators. This superfamily also includes the winged helix-turn-helix domains. and HHPred (MarR family regulatory protein; Winged helix-turn-helix, DNA binding protein, transcription regulation, multidrug resist Prob: 99.18, E value- 3.4e-10. CDS 14688 - 15200 /gene="45" /product="gp45" /function="immunity repressor" /locus tag="Yassified_45" /note=Genemark calls start at 14676 /note=SSC: 14688-15200 CP: yes SCS: genemark-cs ST: SS BLAST-Start: [immunity repressor [Mycobacterium phage Koguma]],,NCBI, q1:s1 100.0% 2.70085E-122 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.129, -4.39309052803282, no F: immunity repressor SIF-BLAST: ,,[immunity repressor [Mycobacterium phage Koguma]],,ATN90007,100.0,2.70085E-122 SIF-HHPRED: Immunity repressor; Immunity repressor, helix-turn-helix motif, DNA binding protein, GENE REGULATION, GENE REGULATION-DNA complex; HET: MSE; 2.79A {Mycobacterium phage TipsytheTRex},,,7TZ1_A,95.8824,100.0 SIF-Syn: this region of the genome is different from that of Zeenon and Beanwater its closest relatives meaning that this gene is unique compared to Zeenon and BeanWater. Not informative. /note=PhagesDB frequency(72%), PhagesDB BLAST(E=3e -95), NCBI BLAST(95.88% coverage, 100% aligned, 100% identity, E=2.70085e-122) and HHPred support the function (100%Prob, 95.88% coverage, Q6:169, E=1.2e-28). CDS complement (15244 - 15336) /gene="46" /product="gp46" /function="hypothetical protein" /locus tag="Yassified_46" /note=Genemark calls start at 15336 /note=SSC: 15336-15244 CP: yes SCS: genemark ST: SS BLAST-Start: [gp36 [Mycobacterium phage Fruitloop] ],,NCBI, q1:s1 100.0% 2.67399E-10 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.765, -5.220380545373514, no F: hypothetical protein SIF-BLAST: ,,[gp36 [Mycobacterium phage Fruitloop] ],,YP_002241721,100.0,2.67399E-10 SIF-HHPRED: SIF-Syn: this region of the genome is different from that of Zeenon and Beanwater its closest relatives. Not informative. /note=Not known function supported by PhagesDB_BLAST, NCBI BLAST /note=, HHPred is not informative E value is too high. CDS complement (15329 - 15547) /gene="47" /product="gp47" /function="hypothetical protein" /locus tag="Yassified_47" /note=Original Glimmer call @bp 15481 has strength 1.58; Genemark calls start at 15550 /note=SSC: 15547-15329 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein I5H28_gp037 [Mycobacterium phage Donkeykong] ],,NCBI, q1:s2 100.0% 1.45247E-43 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.773, -5.282466758366553, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein I5H28_gp037 [Mycobacterium phage Donkeykong] ],,YP_009956066,98.6301,1.45247E-43 SIF-HHPRED: SIF-Syn: based on the Pham maps there are no similarities between Zeenon and BeanWater meaning that this gene is unique to Yassified. Not informative. /note=Not known function supported by PhagesDB_BLAST, NCBI BLAST, HHPred is not informative E value is too high. Orpham CDS complement (15537 - 15725) /gene="48" /product="gp48" /function="hypothetical protein" /locus tag="Yassified_48" /note=Original Glimmer call @bp 15725 has strength 3.04 /note=SSC: 15725-15537 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein FDI16_gp033 [Mycobacterium phage Shauna1] ],,NCBI, q26:s1 59.6774% 4.3021E-17 GAP: 24 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.016, -4.629584883725491, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI16_gp033 [Mycobacterium phage Shauna1] ],,YP_009608215,100.0,4.3021E-17 SIF-HHPRED: SIF-Syn: based on the Pham maps there are no similarities between Zeenon and BeanWater meaning that this gene is unique to Yassified. Not informative. /note=Not known function supported by PhagesDB_BLAST, NCBI BLAST, HHPred is not informative E value is too high. CDS 15750 - 15989 /gene="49" /product="gp49" /function="hypothetical protein" /locus tag="Yassified_49" /note=Original Glimmer call @bp 15750 has strength 19.14; Genemark calls start at 15750 /note=SSC: 15750-15989 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein AWH68_gp051 [Mycobacterium phage Breeniome] ],,NCBI, q1:s3 100.0% 6.01093E-49 GAP: 24 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.216, -2.17469248771465, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein AWH68_gp051 [Mycobacterium phage Breeniome] ],,YP_009221181,97.5309,6.01093E-49 SIF-HHPRED: SIF-Syn: Even though there is no known function for this gene there are similarities between Zeenon and BeanWater which are Yassified`s closest relatives. /note=Not known function supported by PhagesDB_BLAST, NCBI BLAST, HHPred is not informative E value is too high. not a transmembrane domain. CDS 15991 - 16206 /gene="50" /product="gp50" /function="hypothetical protein" /locus tag="Yassified_50" /note=Original Glimmer call @bp 15991 has strength 14.36; Genemark calls start at 15991 /note=SSC: 15991-16206 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PLEIONE_53 [Mycobacterium phage Pleione] ],,NCBI, q1:s1 100.0% 4.59251E-42 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.741, -3.459652012164126, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PLEIONE_53 [Mycobacterium phage Pleione] ],,YP_009017827,100.0,4.59251E-42 SIF-HHPRED: SIF-Syn: Even though there is no known function for this gene there are similarities between Zeenon and BeanWater which are Yassified`s closest relatives. /note=Not known function supported by PhagesDB_BLAST, NCBI BLAST, HHPred is not informative E value is too high. CDS 16206 - 16532 /gene="51" /product="gp51" /function="hypothetical protein" /locus tag="Yassified_51" /note=Original Glimmer call @bp 16206 has strength 14.12; Genemark calls start at 16206 /note=SSC: 16206-16532 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_50 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.18008E-75 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.905, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_50 [Mycobacterium phage ScottMcG] ],,YP_002224083,100.0,1.18008E-75 SIF-HHPRED: SIF-Syn: With no function for this gene, there is a similar gene in Zeenon but not BeanWater which are the closest relatives to Yassified. The gene that is similar to Yassified`s gene 52 is Zeenon`s gene 54. /note=Not known function supported by PhagesDB_BLAST, NCBI BLAST, HHPred is not informative E value is too high. No tmb domain. CDS 16705 - 16935 /gene="52" /product="gp52" /function="hypothetical protein" /locus tag="Yassified_52" /note=Original Glimmer call @bp 16705 has strength 16.87; Genemark calls start at 16705 /note=SSC: 16705-16935 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_52 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 3.05939E-48 GAP: 172 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.983, -2.6013996449736907, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_52 [Mycobacterium phage ScottMcG] ],,YP_002224085,100.0,3.05939E-48 SIF-HHPRED: SIF-Syn: With no function for this gene, there is a similar gene in Zeenon and BeanWater. Yassified and BeanWater have a similar gene between gene 53 in Yassified and gene 47 in BeanWater. The gene that is similar to Yassified`s gene 53 is Zeenon`s gene 56. Zeenon and BeanWater are the 2 closest relatives to Yassified. /note=Not known function supported by PhagesDB_BLAST, NCBI BLAST, HHPred is not informative E value is too high. No tmb domain. CDS 16939 - 17313 /gene="53" /product="gp53" /function="hypothetical protein" /locus tag="Yassified_53" /note=Original Glimmer call @bp 16939 has strength 15.56; Genemark calls start at 16939 /note=SSC: 16939-17313 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_53 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.41722E-85 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.794070146961553, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_53 [Mycobacterium phage ScottMcG] ],,YP_002224086,100.0,1.41722E-85 SIF-HHPRED: SIF-Syn: With no function for this gene, there is a similar gene in Zeenon and BeanWater. The genes that are similar to Yassifed and BeanWater are gene 54 in Yassified and gene 48 in BeanWater. The genes that are similar to Yassified and Zeenon are genes 54 in Yassified and gene 57 in Zeenon. /note=Not known function supported by PhagesDB_BLAST, NCBI BLAST, HHPred is not informative E value is too high. No tmb domain. CDS 17343 - 17645 /gene="54" /product="gp54" /function="helix-turn-helix DNA binding domain" /locus tag="Yassified_54" /note=Original Glimmer call @bp 17343 has strength 16.67; Genemark calls start at 17343 /note=SSC: 17343-17645 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Mycobacterium phage Janiyra]],,NCBI, q1:s1 100.0% 3.05251E-64 GAP: 29 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.442961286954254, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Mycobacterium phage Janiyra]],,QOC58945,100.0,3.05251E-64 SIF-HHPRED: SIF-Syn: Backyarding_53 is a HTH binding domain protein and up and downstream genes are also similar to Yassified. /note=It has been. called 56% of the entries for this gene in phagesDB. Supported by BLAST PhagesDB and NCBI. HHPred matches are not strong. Phamerator supports the function in a number of C1 phages. CDS 17645 - 17785 /gene="55" /product="gp55" /function="hypothetical protein" /locus tag="Yassified_55" /note=Original Glimmer call @bp 17645 has strength 7.2; Genemark calls start at 17645 /note=SSC: 17645-17785 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_55 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.21376E-25 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.627, -3.4283035164720754, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_55 [Mycobacterium phage ScottMcG] ],,YP_002224088,100.0,1.21376E-25 SIF-HHPRED: SIF-Syn: Genes from Close relative phages with the same locus do not call a function. /note=All the sources of evidence point to a hypothetical protein. Not a transmembrane protein based on tmhmm and topcon. HHPred matches are weak. CDS 17785 - 18036 /gene="56" /product="gp56" /function="hypothetical protein" /locus tag="Yassified_56" /note=Original Glimmer call @bp 17785 has strength 13.5; Genemark calls start at 17785 /note=SSC: 17785-18036 CP: yes SCS: both ST: SS BLAST-Start: [gp58 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.64502E-54 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.084, -4.839586000312467, yes F: hypothetical protein SIF-BLAST: ,,[gp58 [Mycobacterium phage Bxz1] ],,NP_818134,100.0,1.64502E-54 SIF-HHPRED: SIF-Syn: Not informative. Not a transmembrane protein. /note=None of the sources of evidence call for a function. CDS 18033 - 18359 /gene="57" /product="gp57" /function="hypothetical protein" /locus tag="Yassified_57" /note=Original Glimmer call @bp 18033 has strength 11.47; Genemark calls start at 18033 /note=SSC: 18033-18359 CP: yes SCS: both ST: SS BLAST-Start: [gp59 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.82812E-72 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.492, -6.080970649622256, no F: hypothetical protein SIF-BLAST: ,,[gp59 [Mycobacterium phage Bxz1] ],,NP_818135,100.0,1.82812E-72 SIF-HHPRED: SIF-Syn: Not informative. /note=None of the sources of evidence call a function. It is not a transmembrane protein. CDS 18440 - 18727 /gene="58" /product="gp58" /function="hypothetical protein" /locus tag="Yassified_58" /note=Original Glimmer call @bp 18440 has strength 12.39; Genemark calls start at 18440 /note=SSC: 18440-18727 CP: yes SCS: both ST: SS BLAST-Start: [gp57 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 1.36381E-61 GAP: 80 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[gp57 [Mycobacterium phage Cali] ],,YP_002224534,100.0,1.36381E-61 SIF-HHPRED: SIF-Syn: Not informative. /note=No evidence of a function. Not a transmembrane protein. CDS 18818 - 19513 /gene="59" /product="gp59" /function="hypothetical protein" /locus tag="Yassified_59" /note=Original Glimmer call @bp 18818 has strength 15.28; Genemark calls start at 18818 /note=SSC: 18818-19513 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ERNIEJ_60 [Mycobacterium phage ErnieJ] ],,NCBI, q1:s1 100.0% 2.34487E-165 GAP: 90 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -2.583959800616441, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ERNIEJ_60 [Mycobacterium phage ErnieJ] ],,ALF51156,100.0,2.34487E-165 SIF-HHPRED: SIF-Syn: not informative /note=No evidence supporting a function. Not a transmembrane protein. CDS 19513 - 19824 /gene="60" /product="gp60" /function="hypothetical protein" /locus tag="Yassified_60" /note=Original Glimmer call @bp 19513 has strength 13.79; Genemark calls start at 19513 /note=SSC: 19513-19824 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_60 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 8.72035E-69 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.923, -4.966271270034708, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_60 [Mycobacterium phage ScottMcG] ],,YP_002224093,100.0,8.72035E-69 SIF-HHPRED: SIF-Syn: Not informative /note=No evidence supporting a function. Not a transmembrane protein. CDS 19821 - 20027 /gene="61" /product="gp61" /function="helix-turn-helix DNA binding domain" /locus tag="Yassified_61" /note=Original Glimmer call @bp 19821 has strength 15.0; Genemark calls start at 19821 /note=SSC: 19821-20027 CP: yes SCS: both ST: SS BLAST-Start: [gp63 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 3.99011E-41 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.523003374675015, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[gp63 [Mycobacterium phage Bxz1] ],,NP_818139,100.0,3.99011E-41 SIF-HHPRED: Orf20; SaPI, Repressor, STRUCTURAL PROTEIN; HET: SO4; 1.8A {Staphylococcus aureus},,,6H49_A,83.8235,99.0 SIF-Syn: Zennon_65 same locus is also a HTH DNA binding domain protein. Flanking genes are also homologous to those in Yassified. /note=Most often called in phagesDB, supported by BLAST in phagesDB and NCBI, HHPred and CDD. Not a transmembrane protein. CDS 20024 - 20332 /gene="62" /product="gp62" /function="helix-turn-helix DNA binding domain" /locus tag="Yassified_62" /note=Original Glimmer call @bp 20063 has strength 12.88; Genemark calls start at 20024 /note=SSC: 20024-20332 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein M182_gp066 [Mycobacterium phage Astraea] ],,NCBI, q1:s1 100.0% 3.96664E-67 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.676, -5.4858509637772555, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein M182_gp066 [Mycobacterium phage Astraea] ],,YP_008061561,99.0196,3.96664E-67 SIF-HHPRED: a.4.5.28 (A:) automated matches {Yersinia pseudotuberculosis [TaxId: 502800]} | CLASS: All alpha proteins, FOLD: DNA/RNA-binding 3-helical bundle, SUPFAM: `Winged helix` DNA-binding domain, FAM: MarR-like transcriptional regulators,,,SCOP_d4aiha_,95.098,99.5 SIF-Syn: Blackbrain_58 has the same function and flanking genes are also similar to those in Yassified. /note=Most often called in PhagesDB 84% of the times in C1 cluster, Also supported by BLAST in PhagesDB and NCBI. Also supported by HHPred. Is not a transmembrane protein. CDS 20332 - 20667 /gene="63" /product="gp63" /function="hypothetical protein" /locus tag="Yassified_63" /note=Original Glimmer call @bp 20332 has strength 12.55; Genemark calls start at 20332 /note=SSC: 20332-20667 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein M182_gp067 [Mycobacterium phage Astraea] ],,NCBI, q1:s1 100.0% 8.75272E-74 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.077, -5.030063891036238, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M182_gp067 [Mycobacterium phage Astraea] ],,YP_008061562,100.0,8.75272E-74 SIF-HHPRED: eS19; Microsporidia, Ribosome, Intracellular Parasite; HET: MG; 3.4A {Vairimorpha necatrix},,,6RM3_ST0,91.8919,81.3 SIF-Syn: Gene 64 has synteny to Gene 67 in Zeenon and Gene 58 in BeanWater. The function of the gene is unknown. /note=PhagesDB Frequency: (N/A) /note=PhagesDB Blast E - Value: (7e-61) /note=NCBI Blast shows ascension YP_008061562: 100% aligned, 100% coverage, 100% identity, E=8.75e-74 /note=HHpred top hit supports it as intracellular parasite: 81.3% probability, 91.89% coverage, Q7:S40, E=2 /note=No data for transmembrane prediction CDS 21243 - 21473 /gene="64" /product="gp64" /function="hypothetical protein" /locus tag="Yassified_64" /note=Original Glimmer call @bp 21243 has strength 17.36; Genemark calls start at 21243 /note=SSC: 21243-21473 CP: yes SCS: both ST: SS BLAST-Start: [gp65 [Mycobacterium phage Catera] ],,NCBI, q1:s54 100.0% 1.63697E-45 GAP: 575 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.291, -1.953940808934884, yes F: hypothetical protein SIF-BLAST: ,,[gp65 [Mycobacterium phage Catera] ],,YP_656078,58.9147,1.63697E-45 SIF-HHPRED: AhlB; Tripartite pore-forming toxin, TOXIN; 2.33A {Aeromonas hydrophila},,,6GRK_B,90.7895,68.6 SIF-Syn: Gene 65 has synteny to Gene 68 in Zeenon has no synteny to BeanWater. The function of the Gene is unknown. /note=PhagesDB Frequency: N/A /note=PhagesDB Blast E-Value: 7e-37 /note=NCBI Blast shows ascension YP_656078: 58.91% identity, 58.915 aligned, 100% coverage, E=1.6e-45 /note=HHpred top hit presents it as tripartite pore-forming toxin: 68.6% probability, 90.8% coverage, Q4:S108, E=56 /note=No transmembrane predictions CDS 21613 - 21819 /gene="65" /product="gp65" /function="hypothetical protein" /locus tag="Yassified_65" /note=Original Glimmer call @bp 21613 has strength 9.56; Genemark calls start at 21613 /note=SSC: 21613-21819 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein M182_gp070 [Mycobacterium phage Astraea] ],,NCBI, q1:s1 100.0% 1.44875E-39 GAP: 139 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.216, -2.639579286017301, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M182_gp070 [Mycobacterium phage Astraea] ],,YP_008061565,100.0,1.44875E-39 SIF-HHPRED: TrwH protein; type IV secretion system, type 4 secretion system, T4SS, O-layer, core complex, outer membrane complex, inner; 2.6A {Escherichia coli},,,7O3J_d,29.4118,97.6 SIF-Syn: Gene 66 has synteny to Gene 70 in Zeenon and Gene 62 in BeanWater. The function of the Gene is unknown. /note=PhagesDB Frequency: N/A /note=PhagesDB Blast E-Value: 2e-32 /note=NCBI Blast top hit shows ascension YP_008061565: 100% identity, 100% aligned, 100% coverage, E-Value: 1.44875e-39 /note=HHpred top hit presents it as TrwH protein: 97.6% probability, 29.4% coverage, Q1:S1, E=0.0002 /note=No transmembrane predictions CDS 21929 - 23164 /gene="66" /product="gp66" /function="hypothetical protein" /locus tag="Yassified_66" /note=Original Glimmer call @bp 21929 has strength 18.44; Genemark calls start at 21929 /note=SSC: 21929-23164 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYRO_64 [Mycobacterium phage HyRo] ],,NCBI, q1:s1 100.0% 0.0 GAP: 109 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYRO_64 [Mycobacterium phage HyRo] ],,YP_009204629,100.0,0.0 SIF-HHPRED: DUF932 ; Domain of unknown function (DUF932),,,PF06067.14,56.4477,99.7 SIF-Syn: Gene 67 has synteny to Gene 71 in Zeenon and Gene 63 in BeanWater. Functions are unknown. /note=PhagesDB Frequency: N/A /note=PhagesDB Blast E-Value: 0 /note=NCBI Blast shows ascension YP_009204629: 100% identity, 100% aligned, 100% coverage, E-Value: 0 /note=HHpred top hit is presented as DUF932: 99.7% probability, 56.4477% coverage, Q153:S2, E-Value: 2.6e-16 /note=No transmembrane predictions CDS 23236 - 23916 /gene="67" /product="gp67" /function="hypothetical protein" /locus tag="Yassified_67" /note=Original Glimmer call @bp 23236 has strength 12.79; Genemark calls start at 23236 /note=SSC: 23236-23916 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PINKCREEK_62 [Mycobacterium phage Pinkcreek]],,NCBI, q1:s1 96.9027% 7.79476E-155 GAP: 71 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.291, -3.055172195725583, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PINKCREEK_62 [Mycobacterium phage Pinkcreek]],,UEM46128,94.2731,7.79476E-155 SIF-HHPRED: Structure-specific endonuclease subunit slx4; RING finger, Endonuclease, HYDROLASE; HET: GOL; 2.0A {Schizosaccharomyces pombe (strain 972 / ATCC 24843)},,,4ZDT_D,13.7168,37.3 SIF-Syn: Gene 68 has synteny to Gene 72 in Zeenon and Gene 64 in BeanWater. Functions of the genes are unkown. /note=PhagesDB Frequency: N/A /note=PhagesDB Blast E-Value for Yassified_Draft: 1e-134; Pinkcreek: 1e-125, Remaining phages: 1e-124 /note=NCBI Blast ascension shows UEM46128: 92.511% identity, 94.2731% aligned, 96.9027% coverage, E-Value: 7.79476e-155 /note=HHpred top hit presented as endonuclease sub-unit: 37.3% probability, 13.7168% coverage, Q157:S38, E-Value: 97 /note=No transmembrane predictions CDS 23952 - 24227 /gene="68" /product="gp68" /function="membrane protein" /locus tag="Yassified_68" /note=Original Glimmer call @bp 23952 has strength 8.1; Genemark calls start at 23952 /note=SSC: 23952-24227 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein BI081_gp085 [Mycobacterium phage Tonenili] ],,NCBI, q1:s1 100.0% 1.06807E-57 GAP: 35 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -2.970161406017234, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein BI081_gp085 [Mycobacterium phage Tonenili] ],,YP_009287949,100.0,1.06807E-57 SIF-HHPRED: DUF732 ; Protein of unknown function (DUF732),,,PF05305.17,51.6483,68.4 SIF-Syn: Gene 69 has no synteny with Zeenon or BeanWater /note=PhagesDB Frequency: Tape Measure Protein; Frequency 100% from cluster BN. All other sources of evidence do not call a function. /note=PhagesDB Blast E-Value for Yassified_Draft and Tonenili: 3e-45, Remaining phages: 1e-44 /note=NCBI Blast shows ascension for YP_009287949: 100% identity, 100% aligned, 100% coverage, E-Value: 1.06807e-57 /note=HHpred top hits presents DUF732: 68.4% probability, 51.6483% coverage, Q36:S29, E-Value: 41 /note=1 predicted transmembrane supported buy SOSUI too. CDS 24370 - 24732 /gene="69" /product="gp69" /function="hypothetical protein" /locus tag="Yassified_69" /note=Original Glimmer call @bp 24370 has strength 11.26; Genemark calls start at 24370 /note=SSC: 24370-24732 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ALICE_65 [Mycobacterium phage Alice] ],,NCBI, q1:s42 100.0% 4.57179E-82 GAP: 142 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.644, -5.490418349731808, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ALICE_65 [Mycobacterium phage Alice] ],,YP_009216330,74.5342,4.57179E-82 SIF-HHPRED: a.60.15.1 (A:1-74) Hypothetical protein YozE {Bacillus subtilis [TaxId: 1423]} | CLASS: All alpha proteins, FOLD: SAM domain-like, SUPFAM: YozE-like, FAM: YozE-like,,,SCOP_d2fj6a1,10.0,61.8 SIF-Syn: Gene 70 has synteny with Gene 74 in Zeenon and Gene 65 in BeanWater. Functions are unkown. /note=None of the sources of evidence point to a function for this gene. /note=PhagesDB Frequency: N/A /note=PhagesDB Blast E-Value: 6e-66 /note=NCBI Blast hit shows accesion YP_009216330: 74.5342% identity, 74.5342% aligned, 100% coverage, E-Value: 4.57179e-82 /note=HHpred top hits present Bacillus subtilis: 61.8% probability, 10% coverage, Q54:S1, E-Value: 13 /note=No transmembrane predictions CDS 24785 - 25519 /gene="70" /product="gp70" /function="hypothetical protein" /locus tag="Yassified_70" /note=Original Glimmer call @bp 24785 has strength 12.42; Genemark calls start at 24785 /note=SSC: 24785-25519 CP: yes SCS: both ST: SS BLAST-Start: [gp72 [Mycobacterium phage Catera] ],,NCBI, q1:s1 100.0% 3.58126E-179 GAP: 52 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.291, -1.953940808934884, yes F: hypothetical protein SIF-BLAST: ,,[gp72 [Mycobacterium phage Catera] ],,YP_656085,100.0,3.58126E-179 SIF-HHPRED: SIF-Syn: Gene 71 has synteny with Gene 75 in Zeenon and Gene 66 in BeanWater. Functions are unknown. /note=None of the sources of evidence support calling a function for this gene. /note=PhagesDB frequency: N/A /note=PhagesDB Blast E-Value: 1e-148 /note=NCBI Blast shows ascension YP_656085: 100% identity, 100% aligned, 100% coverage, E-Value: 3.58126e-179 /note=HHpred top hit presents DUF3956: 17.3% probability, 8.19672 coverage, Q2:S10, E-Value: 290 /note=No transmembrane predictions CDS 25516 - 25728 /gene="71" /product="gp71" /function="hypothetical protein" /locus tag="Yassified_71" /note=Genemark calls start at 25516 /note=SSC: 25516-25728 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_72 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 4.62267E-42 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.387, -4.902475914772797, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_72 [Mycobacterium phage ScottMcG] ],,YP_002224105,100.0,4.62267E-42 SIF-HHPRED: Hypothetical protein; structural genomics, Structural Genomics Consortium, SGC, UNKNOWN FUNCTION; HET: MSE, MES; 2.3A {Cryptosporidium parvum},,,2PD0_D,94.2857,56.3 SIF-Syn: Gene 72 has synteny with Gene 76 in Zeenon and Gene 67 in BeanWater. Functions are unkown. /note=None of the evidence supports calling a function. /note=PhagesDB frequency: N/A /note=PhagesDB Blast E-Value: 1e-34 /note=NCBI Blast shows ascension YP_002224105: 100% identity, 100% aligned, 100% coverage, E-Value: 4.62267e-42 /note=HHpred top hit presented as Structural Genomics: 56.3% probability, 94.2857% coverage, Q3:S71, E-Value: 37 /note=No transmembrane predictions CDS 25725 - 25823 /gene="72" /product="gp72" /function="hypothetical protein" /locus tag="Yassified_72" /note=Genemark calls start at 25731 /note=SSC: 25725-25823 CP: yes SCS: genemark-cs ST: SS BLAST-Start: [hypothetical protein ALICE_68 [Mycobacterium phage Alice] ],,NCBI, q1:s1 100.0% 3.10263E-14 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.795, -3.824830700482977, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ALICE_68 [Mycobacterium phage Alice] ],,YP_009216333,100.0,3.10263E-14 SIF-HHPRED: Interferon regulatory factor 7; Helix-turn-helix, Gene regulation, DNA BINDING PROTEIN; HET: EDO; 1.3A {Mus musculus} SCOP: a.4.5.0,,,3QU3_B,84.375,44.3 SIF-Syn: There is not close relatives with homologous genes with a function. Phages Zeenon and BeanWater are compared as close relatives. /note=Information collected from HHpred proves the theory of there is no known function with ( hit 3QU3_B) an e-value of 61. This high e-value, PhagesDB, and BLAST support that the function of this gene is NKF. Hits state hypothetical protein. The evidence from TmHmm shows that this gene is not a transmembrane protein. CDS 25879 - 26205 /gene="73" /product="gp73" /function="hypothetical protein" /locus tag="Yassified_73" /note=Original Glimmer call @bp 25879 has strength 13.95; Genemark calls start at 25879 /note=SSC: 25879-26205 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_73 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 9.53505E-74 GAP: 55 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.129, -4.534089041695007, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_73 [Mycobacterium phage ScottMcG] ],,YP_002224106,100.0,9.53505E-74 SIF-HHPRED: HpaP ; Type III secretion protein (HpaP),,,PF09483.13,51.8519,47.4 SIF-Syn: There aren`t close relatives with homologous genes with a function. e.g. Zeenon-BeanWater /note=Top hits do not point to a function, e.g. hypothetical protein. Top hits in the HHpred have a very poor e-value of 220. TmHmm with a number of 0 states that this gene is not a transmembrane protein. There is not enough supporting evidence from HHpred, BLAST, or phamerator for any function call. CDS 26244 - 26954 /gene="74" /product="gp74" /function="hypothetical protein" /locus tag="Yassified_74" /note=Original Glimmer call @bp 26244 has strength 13.04; Genemark calls start at 26244 /note=SSC: 26244-26954 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_74 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 3.63846E-173 GAP: 38 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.138, -2.338663114094478, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_74 [Mycobacterium phage ScottMcG] ],,YP_002224107,100.0,3.63846E-173 SIF-HHPRED: LCB3; SARS-CoV-2, COVID-19, spike glycoprotein, fusion protein, neutralizing antibodies, Structural Genomics, Seattle Structural Genomics Center for Infectious; HET: NAG; 3.1A {Severe acute respiratory syndrome coronavirus 2},,,7JZN_G,27.1186,71.0 SIF-Syn: The close relative phages like Zeenon and BeanWater don`t have homologous genes with a function also. /note=Top phages do not point to a function. e.g. hypothetical protein. The top hits in the HHpred report have a very poor e-value of 51. There is not enough evidence from HHrped, BLAST, or phametor for a function call. TmHmm with a number 0, states that this gene is not a transmembrane protein. CDS 26968 - 27177 /gene="75" /product="gp75" /function="hypothetical protein" /locus tag="Yassified_75" /note=Original Glimmer call @bp 26977 has strength 0.88; Genemark calls start at 26968 /note=SSC: 26968-27177 CP: yes SCS: both-gm ST: NI BLAST-Start: [gp78 [Mycobacterium phage Spud] ],,NCBI, q1:s1 100.0% 1.36837E-43 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.335, -6.139661345734753, no F: hypothetical protein SIF-BLAST: ,,[gp78 [Mycobacterium phage Spud] ],,YP_002224332,100.0,1.36837E-43 SIF-HHPRED: d.17.4.0 (A:1-124) automated matches {Methylobacillus flagellatus [TaxId: 265072]} | CLASS: Alpha and beta proteins (a+b), FOLD: Cystatin-like, SUPFAM: NTF2-like, FAM: automated matches,,,SCOP_d3duka1,34.7826,75.8 SIF-Syn: Close relatives like Zeenon and BeanWater don`t have homologous genes with a function, /note=Top hits do not point to a function. e.g. hypothetical protein. Top hits in the HHpred report supports NKF with a poor e-value of 19. There is no enough supporting evidence from HHpred, BLAST nor phamerator for a function call. TmHmm also states that with a number 0, this gene is not a transmembrane protein. CDS 27215 - 27511 /gene="76" /product="gp76" /function="hypothetical protein" /locus tag="Yassified_76" /note=Original Glimmer call @bp 27215 has strength 4.12; Genemark calls start at 27215 /note=SSC: 27215-27511 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_76 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.46223E-63 GAP: 37 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.302, -2.0720764396375664, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_76 [Mycobacterium phage ScottMcG] ],,YP_002224109,100.0,1.46223E-63 SIF-HHPRED: DUF6116 ; Family of unknown function (DUF6116),,,PF19611.2,42.8571,86.4 SIF-Syn: Close relatives like Zeenon and BeanWater`s homologous genes do not call a function. /note=Top phage hits do not point to a function. e.g. hypothetical protein. Top hits in the HHpred report state a poor e-value of 10. There is not enough supporting evidence form HHpred, BLAST nor phamerator for a function call. Also with a number of 0- TmHmm states that this gene is not a transmembrane protein. CDS 27511 - 27672 /gene="77" /product="gp77" /function="hypothetical protein" /locus tag="Yassified_77" /note=Original Glimmer call @bp 27511 has strength 3.45; Genemark calls start at 27511 /note=SSC: 27511-27672 CP: yes SCS: both ST: SS BLAST-Start: [gp81 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 6.20795E-31 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.838, -3.812150084159046, yes F: hypothetical protein SIF-BLAST: ,,[gp81 [Mycobacterium phage Bxz1] ],,NP_818157,100.0,6.20795E-31 SIF-HHPRED: DUF4637 ; Domain of unknown function (DUF4637),,,PF15470.9,75.4717,89.0 SIF-Syn: Close relative phages like Zeenon and BeanWater homologous genes do not call for a function. /note=Top hits do not point to a function. e.g. hypothetical protein. HHpred hit with a value of 0.73 states that this gene belongs to a domain of unknown function. There is enough evidence from HHpred, BLAST nor phamerator for a function call. With the number of 0- TmHmm states that this gene is not a transmembrane protein. CDS 27653 - 28141 /gene="78" /product="gp78" /function="hypothetical protein" /locus tag="Yassified_78" /note=Original Glimmer call @bp 27653 has strength 13.62; Genemark calls start at 27653 /note=SSC: 27653-28141 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ERNIEJ_78 [Mycobacterium phage ErnieJ] ],,NCBI, q1:s1 100.0% 1.08771E-112 GAP: -20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.737, -3.76872822804853, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ERNIEJ_78 [Mycobacterium phage ErnieJ] ],,ALF51174,100.0,1.08771E-112 SIF-HHPRED: Nuclear pore glycoprotein p62; multiprotein complex, nucleocytoplasmic transport, TRANSPORT PROTEIN; 12.0A {Homo sapiens},,,7R5K_J0,66.0494,85.7 SIF-Syn: Close relatives like Zeenon and BeanWater`s homologous genes do not point to a function. /note=There is not enough supporting evidence from HHpred, BLAST, or phamerator for a function call. Hits do not call for a function with very poor e-values. NCBI BLAST hits support that this gene is not have a known function with hypothetical protein calls. TmHmm with the number 1-- shows that this gene is not a transmembrane protein. CDS 28144 - 29871 /gene="79" /product="gp79" /function="ParB-like nuclease domain" /locus tag="Yassified_79" /note=Original Glimmer call @bp 28144 has strength 8.43; Genemark calls start at 28144 /note=SSC: 28144-29871 CP: yes SCS: both ST: SS BLAST-Start: [ParB-like nuclease domain [Mycobacterium phage Pinkcreek]],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.925, -4.883837968736599, no F: ParB-like nuclease domain SIF-BLAST: ,,[ParB-like nuclease domain [Mycobacterium phage Pinkcreek]],,UEM46138,100.0,0.0 SIF-HHPRED: ParB_N_like_MT; ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain.,,,cd16844,9.56522,96.7 SIF-Syn: Close relatives like Zeenon and BeanWater homologous genes do not point to a function. /note=%100 of these genes Phagesdb( %80 frequency) entries state that this gene is ParB-like nuclease. Phagesdb Blast (e-value=0) with PinkCreek, ChaylaJr, and Janiyra phages supports this function. Also HHpred ( %96.7 probability, 9.56522 alignment, Q:225S:2, e-value of 0.0095) supports this function. With the number of 0 TmHmm states that this gene is not a transmembrane protein. tRNA 29962 - 30045 /gene="80" /product="tRNA-Ser(gct)" /locus tag="YASSIFIED_80" /note=tRNA-Ser(gct) tRNA 30238 - 30313 /gene="81" /product="tRNA-Leu(cag)" /locus tag="YASSIFIED_81" /note=tRNA-Leu(cag) tRNA 30433 - 30507 /gene="82" /product="tRNA-Leu(gag)" /locus tag="YASSIFIED_82" /note=tRNA-Leu(gag) tRNA 30508 - 30581 /gene="83" /product="tRNA-Leu(caa)" /locus tag="YASSIFIED_83" /note=tRNA-Leu(caa) CDS 30651 - 34145 /gene="84" /product="gp84" /function="hypothetical protein" /locus tag="Yassified_84" /note=Original Glimmer call @bp 30651 has strength 11.19; Genemark calls start at 30651 /note=SSC: 30651-34145 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein NAPPY_89 [Mycobacterium phage Nappy] ],,NCBI, q1:s1 100.0% 0.0 GAP: 779 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.983, -2.6814417326944517, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein NAPPY_89 [Mycobacterium phage Nappy] ],,YP_009016547,98.547,0.0 SIF-HHPRED: SIF-Syn: Close relatives like Zeenon and BeanWater do not have homologous genes with a function. /note=There is not enough evidence from HHpred, BLAST or phamerator to call a function. Top hits do not call a function e.g. hypothetical protein (e value 0). TmHmm with a number of 0 show that this gene is not a transmembrane protein. CDS 34157 - 34525 /gene="85" /product="gp85" /function="hypothetical protein" /locus tag="Yassified_85" /note=Original Glimmer call @bp 34157 has strength 4.72; Genemark calls start at 34157 /note=SSC: 34157-34525 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein MOMOMIXON_90 [Mycobacterium phage MoMoMixon] ],,NCBI, q1:s1 100.0% 1.43899E-85 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.246, -4.148052427098672, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein MOMOMIXON_90 [Mycobacterium phage MoMoMixon] ],,YP_009017421,100.0,1.43899E-85 SIF-HHPRED: SIF-Syn: Gene 82 shows synteny to gene 91 in Zeenon and gene 81 in Beanwater. /note=Start site: Glimmer and starterator both suggest the start site 34157. Starterator shows 107 MA`s for this start site. The length is 369, 11 gaps, z-score of 2.246, final score -4.148 and it is the longest ORF. Host Trained GeneMark supports this start site and shows that it covers all coding potential. /note=Phagesdb Function Frequency has no data. /note=Phagesdb Blast shows that there are many phages in the C1 cluster that have unknown functions, sequence length of 122, score of 263, and e-value of 1e-70. /note=HHPRED is uninformative since the top hit has an e-value of 0.5. /note=NCBI Blast shows accession YP_009017421 with 5 included hits, has 100% aligned, 100% coverage and 100% identity, 122 positives, query from 1 to 122 and e-value of 1.43899e-85. Most phages in description are hypothetical proteins. /note=Conserved Domain Database has no data. /note=0 transmembrane proteins. CDS 34529 - 37132 /gene="86" /product="gp86" /function="portal protein" /locus tag="Yassified_86" /note=Original Glimmer call @bp 34529 has strength 13.65; Genemark calls start at 34529 /note=SSC: 34529-37132 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Mycobacterium phage MoMoMixon] ],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.716, -3.160956374632079, no F: portal protein SIF-BLAST: ,,[portal protein [Mycobacterium phage MoMoMixon] ],,YP_009017422,100.0,0.0 SIF-HHPRED: Portal protein; G20C, portal protein, bacteriophage, transport protein; 1.9A {Thermus phage P7426},,,5NGD_D,50.4037,99.9 SIF-Syn: Gene 83 shows synteny to gene 92 in Zeenon which is also defined as Portal protein. /note=Start site: Glimmer and Genemark both suggest 34529 start site. Host-Trained Genemark shows that the gene has coding potential and proves that this start site is the best site since it starts right before the genes coding potential and covers the whole gene. 34529 start site stops at 37132 and has a length of 2604 with 3 gaps, 2.716 z-score, -3.161 final score and is classified as the longest ORF. /note=Phagesdb Function Frequency shows that its a portal protein in the C1 subcluster and frequency of 100%. /note=Phagesdb Blast shows many other phages have a portal protein function with an e-value of 0. /note=HHPRED suggests hit 5NGD_D {Thermus phage P7426} is a portal protein with a probability of 99.9, coverage of 50.4037% and 3.3e-20 e-value. There are many other hits such as that shows high similarity to phages that functions as a portal protein. /note=NCBI Blast suggests accession YP_009017422 (2 other phages: Mycobacterium phage MoMoMixon & McWolfish) has a portal protein function 100% aligned, 100% coverage and 100%identity, 867 positives, query from 1 to 867 with an e-value of 0. /note=No Conserved Domain database or transmembrane predictions. CDS 37239 - 37598 /gene="87" /product="gp87" /function="hypothetical protein" /locus tag="Yassified_87" /note=Original Glimmer call @bp 37377 has strength 2.76; Genemark calls start at 37239 /note=SSC: 37239-37598 CP: yes SCS: both-gm ST: NI BLAST-Start: [gp90 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 8.95108E-80 GAP: 106 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.493, -3.769471247018311, yes F: hypothetical protein SIF-BLAST: ,,[gp90 [Mycobacterium phage Bxz1] ],,NP_818163,100.0,8.95108E-80 SIF-HHPRED: SIF-Syn: There are no homolgous genes which can be compared to this gene based on Phagesdb. /note=Start site: Glimmer suggests start site 37377 and Genemark suggests 37239. The latter provides the longest ORF and shortest gap. In the absence of any other evidence the longest ORF and shortest gap prevails. /note=Phages Function Frequency shows no data. /note=Phagesdb Blast shows similarity to other phages with function unknown all have 119 sequence length, 241 score and 3e-64 e-value. /note=HHPRED shows that top hits have a poor e-value 4.1. Not informative. /note=NCBI Blast accession NP_818163 has many phages with a function of hypothetical protein and 100% identity, 100% aligned, 100% coverage and 119 positives with an e-value of 8.95108e-80. /note=No data for conserved domain database and transmembrane predictions. CDS 37670 - 37825 /gene="88" /product="gp88" /function="hypothetical protein" /locus tag="Yassified_88" /note=Original Glimmer call @bp 37670 has strength 14.37; Genemark calls start at 37670 /note=SSC: 37670-37825 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_89 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.63759E-20 GAP: 71 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.657, -3.284949965096066, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_89 [Mycobacterium phage ScottMcG] ],,YP_002224117,98.0392,1.63759E-20 SIF-HHPRED: DUF6131 ; Family of unknown function (DUF6131),,,PF19626.2,98.0392,99.9 SIF-Syn: Gene 85 shows synteny to gene 94 in Zeenon and gene 84 in Beanwater. Neither of these genes have any recorded functions. /note=Start site: Glimmer and Starterator both suggest 37670 start site. There is 164 MA`s for this site on Starterator. Host-Trained GeneMark shows this start site captures the all the genes coding potential. Start site 37670 has a length of 156, gap of 71, a z-score of 2.657, final score of -3.285 and classifies as the longest ORF. /note=Phagesdb Function Frequency shows no data. /note=Phagesdb Blast shows many other phages have an unknown function, sequence length of 51, score of 101 and e-value of 6e-22 all belonging to C1 cluster. Yassified_Draft is also listed there which is in the reverse strand with a score of 103 and e-value of 1e-22. /note=HHPRED suggests hit PF19626.2 (Family of unknown function (DUF6131) with a probability of 99.9, coverage of 98.0392%, has an e-value of 5.1e-21 and a query from 1 to 51. /note=NCBI blast accession YP_002224117 shows 9 phages with 98.0392% identity, 98.0392 aligned, 100% coverage, 0 gaps, query from 1 to 51, Q1:S1, and an e-value of 1.63759e-20. /note=No conserved domain database, 1 transmembrane prediction. CDS 37889 - 38596 /gene="89" /product="gp89" /function="ThyX-like thymidylate synthase" /locus tag="Yassified_89" /note=Original Glimmer call @bp 37889 has strength 8.39; Genemark calls start at 37889 /note=SSC: 37889-38596 CP: yes SCS: both ST: SS BLAST-Start: [gp91 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 4.08082E-176 GAP: 63 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.233, -4.254107899658224, yes F: ThyX-like thymidylate synthase SIF-BLAST: ,,[gp91 [Mycobacterium phage Bxz1] ],,NP_818164,100.0,4.08082E-176 SIF-HHPRED: Thymidylate synthase ThyX; Tetramer, UMP/dUMP methylase, ThyX homolog, TRANSFERASE; HET: 5BU, FAD; 1.76A {Streptomyces cacaoi subsp. asoensis} SCOP: d.207.1.0,,,4P5A_A,99.5745,100.0 SIF-Syn: Gene 86 shows synteny with Beanwater gene 85 and Zeenon gene 95. /note=Start site: Glimmer and Starterator suggest 37889 is the start site, Starterator has 235 MA`s, 708 length, 63 gap, z-score of 2.233, -4.254 final score and is longest ORF. Host-Trained GeneMark shows the gene has coding potential and the start site covers the entire gene. /note=Phagesdb Function Frequency the function ThyX-like thymidylate synthase with a count of 91 and a frequency of 99% in the C1 cluster. /note=Phagesdb Blast shows many other phages in the C1 cluster that have a ThyX-like thymidylate synthase function, sequence length of 235, score of 481 and e-value of 1e-136. /note=HHPRED suggests hit supports the ThyX-like thymidylate synthase function and the top hit has a /note= probability of 100, coverage of 99.5745%, has an e-value of 6.70003e-41 and a query from 1 to 235. /note=NCBI blast accession NP_818164 has 9 phages that are classified as ThyX-like thymidylate synthase with an 100% identity, 100 aligned, 100% coverage, 0 gaps, 235 positives, query from 1 to 235, Q1:S1, and an e-value of 4.08082e-176. /note=Conserved domain database accession PRK00847 (FAD-dependent thymidylate synthase; Reviewed), /note=has an 35.023% identity, 49.3088% aligned, 98.7234% coverage, 0 gaps, 107 positives, query from 4 to 235 and an e-value of 0. /note=0 transmembrane prediction. CDS 38617 - 38865 /gene="90" /product="gp90" /function="hypothetical protein" /locus tag="Yassified_90" /note=Original Glimmer call @bp 38617 has strength 12.92; Genemark calls start at 38617 /note=SSC: 38617-38865 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BEANWATER_86 [Mycobacterium phage BeanWater] ],,NCBI, q1:s6 100.0% 3.35214E-55 GAP: 20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.424, -3.773970443115436, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BEANWATER_86 [Mycobacterium phage BeanWater] ],,ATN87540,94.2529,3.35214E-55 SIF-HHPRED: SIF-Syn: There are no homolgous genes which can be compared to this gene. /note=Start site: Glimmer and Starterator suggest the start site 38617. Starterator has 148 MA`s for this start site. Start site has a length of 249, 20 gaps, a z-score of 2.424 and a final score of -3.774. It is not the longest ORF. Host-Trained GeneMark shows that this start site covers all the coding potential. /note=Phagesdb Function Frequency has no data indicating that there is no known function. /note=Phagesdb Blast shows many phages in the C1 cluster but have no known function, with a sequence length of 82, score of 175 and e-value of 3e-44. /note=HHPRED is uninformative because the top hit has an e-value of 1.3. /note=NCBI blast accession ATN87540 has 5 phages which has an 94.2529 %identity , 94.2529% aligned, 100% coverage, 0 gaps, 82 positives, query from 1 to 82, Q1:S1, and an e-value of 3.35214e-55. Phages are defined as hypothetical proteins. /note=Conserved Domain Database has not data. /note=0 transmembrane prediction. CDS 38866 - 39417 /gene="91" /product="gp91" /function="RNA ligase" /locus tag="Yassified_91" /note=Original Glimmer call @bp 38866 has strength 16.83; Genemark calls start at 38866 /note=SSC: 38866-39417 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein M180_gp230 [Mycobacterium phage ArcherS7] ],,NCBI, q1:s1 100.0% 1.43189E-132 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.291, -1.953940808934884, yes F: RNA ligase SIF-BLAST: ,,[hypothetical protein M180_gp230 [Mycobacterium phage ArcherS7] ],,YP_008061350,100.0,1.43189E-132 SIF-HHPRED: d.61.1.2 (A:) 2`-5` RNA ligase LigT {Thermus thermophilus [TaxId: 274]} | CLASS: Alpha and beta proteins (a+b), FOLD: LigT-like, SUPFAM: LigT-like, FAM: 2`-5` RNA ligase LigT,,,SCOP_d1iuha_,78.6885,99.6 SIF-Syn: Gene 88 shows synteny with Zeenon gene 97 and Beanwater gene 87. /note=Start site: Glimmer and Starterator suggest 38866 is the start site, Starterator has 134 MA`s, 552 length, 0 gap, z-score of 3.291, -1.954 final score and is longest ORF. Host-Trained GeneMark shows the start site covers all the coding potential from the start of the gene. /note=Phagesdb Function Frequency the function RNA ligase with a count of 74 and a frequency of 99% in the C1 cluster. /note=Phagesdb Blast shows many other phages in the C1 cluster that have a RNA ligase function, sequence length of 183, score of 388 and e-value of 1e-108. /note=HHPRED hits support the function RNA ligase top hit SCOP_d1iuha_ and 1IUH_A has a probability of 99.6, coverage of 78.6885%, has an e-value of 7.7e-14 and a query from 31 to 175. /note=NCBI blast accession YP_008061350 has 9 phages that have an 100% identity, 100% aligned, 100% coverage, 0 gaps, 183 positives, query from 1 to 183, Q1:S1, and an e-value of 1.43189e-132. Most phages show the function RNA Ligase, two are classified as hypothetical protein. /note=Conserved domain database is not informative. /note=0 transmembrane prediction. CDS 39414 - 39857 /gene="92" /product="gp92" /function="HNH endonuclease" /locus tag="Yassified_92" /note=Original Glimmer call @bp 39657 has strength 5.06; Genemark calls start at 39414 /note=SSC: 39414-39857 CP: yes SCS: both-gm ST: NI BLAST-Start: [gp91 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 2.90692E-99 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.502, -3.750998330397795, yes F: HNH endonuclease SIF-BLAST: ,,[gp91 [Mycobacterium phage Cali] ],,YP_002224564,100.0,2.90692E-99 SIF-HHPRED: zf-His_Me_endon ; Zinc-binding loop region of homing endonuclease,,,PF05551.14,62.585,99.7 SIF-Syn: There are no homolgous genes which can be compared to this gene. /note=Start site 39414 has a length of 444, -4 gaps, a z-score of 2.502, a final score of -3.751 and is the longest ORF.This starting site has the best cp which covers the whole gene. This start site is based on GeneMark since glimmer suggested 39657 which has 239 gaps and is not as good. /note=Phagesdb blast: shows that gene 89 is very similar to to other genes such as Ading that has the protein number 96, sequence length of 147, 306 score, 1e-83 value and is found in C1 cluster. 74458 pham. /note=HHPRED: hit (zf-His_Me_endon ; Zinc-binding loop region of homing endonuclease) has a probability of 99.7, 62.585% coverage, query from 28 to 120 and an e-value of 2.6e-17. /note=NCBI Blast: Similar to 9 phages where four are HNH endonuclease (Nappy, ArcherS7,Quasimodo,Sauce) and the rest which are hypothetical proteins ( Sebata, CharlieB, Ghost, Momo, LRRHood). BLAST has an 100% identity, 100% aligned, 100% coverage, 0 gaps, 147 positives, and an e-value of 2.90692e-99. Q1:S1. Query from 1 to 147. /note=No data for conserved domain database, no transmembrane predictions. CDS 39906 - 43751 /gene="93" /product="gp93" /function="LysM-like peptidoglycan binding protein" /locus tag="Yassified_93" /note=Original Glimmer call @bp 39906 has strength 10.78; Genemark calls start at 39906 /note=SSC: 39906-43751 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BREAD_96 [Mycobacterium phage Bread] ],,NCBI, q1:s1 100.0% 0.0 GAP: 48 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.905, -2.8454123590742793, yes F: LysM-like peptidoglycan binding protein SIF-BLAST: ,,[hypothetical protein SEA_BREAD_96 [Mycobacterium phage Bread] ],,AYD83048,100.0,0.0 SIF-HHPRED: SIF-Syn: , gene 90 is similar in color and size to gene 86 in Beanwater and gene 96 in Zeenon No function is listed /note=Glimmer and Genmark agree with the start site at 339006. Checking the genmark map, there is high coding potential for a protein as the score is around 1.0. Phagesdb BLAST indicates that there is no known function based on similar genes, however, several similar genes code for LysM-like peptidoglycan binding proteins.NCBI BLAST indicates that the closest protein would be Ronan Gene 90 as there is 99.9219% allignment and 100% coverage. The e value is 0.00. CDS 43787 - 47647 /gene="94" /product="gp94" /function="hypothetical protein" /locus tag="Yassified_94" /note=Original Glimmer call @bp 43787 has strength 9.34; Genemark calls start at 43787 /note=SSC: 43787-47647 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_86 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 0.0 GAP: 35 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.138, -2.356391881054909, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_86 [Mycobacterium phage ET08] ],,YP_003347765,100.0,0.0 SIF-HHPRED: SIF-Syn: In Pharmerator, the gene is the same color brown and of similar size to gene 96 in Dandelion, gene 87 in Beanwater and 97 In Zeenon. Function unkown for all. /note=Glimmer and Genmark agree that the start site should be 43787. High coding potential in ORF Does not appear to be a transmembrane protein. Review of HHPred and Blast give no indication of protein function. Not a transmembrane domain. CDS 47678 - 48220 /gene="95" /product="gp95" /function="hypothetical protein" /locus tag="Yassified_95" /note=Original Glimmer call @bp 47678 has strength 14.88; Genemark calls start at 47678 /note=SSC: 47678-48220 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_95 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.8953E-124 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.983, -3.2535385006449706, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_95 [Mycobacterium phage ScottMcG] ],,YP_002224123,100.0,1.8953E-124 SIF-HHPRED: SIF-Syn: No similar genes found in either Zeenon or Beanwater. /note=Glimmer and Genmark agree on the start site 47678. TmHmm does not indicate that this gene codes for a transmembrane protein. Phages DB, Blast, HHPred do not indicate any function. CDS 48224 - 49225 /gene="96" /product="gp96" /function="major capsid protein" /locus tag="Yassified_96" /note=Original Glimmer call @bp 48224 has strength 19.06; Genemark calls start at 48224 /note=SSC: 48224-49225 CP: yes SCS: both ST: SS BLAST-Start: [gp97 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.799, -5.227163949899647, no F: major capsid protein SIF-BLAST: ,,[gp97 [Mycobacterium phage Bxz1] ],,NP_818170,100.0,0.0 SIF-HHPRED: Gp27 major capsid protein; phage G, major capsid protein, decoration protein, capsid, icosahedral, gp26, gp27, VIRUS; 6.1A {Bacillus virus G},,,6WKK_D,87.988,100.0 SIF-Syn: Gene 94 appears in the white triangle region of Pharmarator when compared against Beanwater and Zeenon indicating that this gene is unique when compared against Yassified`s two closest phages. /note=Glimmer and Genmark support 48224 as the start site. Suggested start by Starteraror, and all coding potential is included in the ORF. Longest ORF. HHPred hit supports the coding of major capsid protein. Hit 6B0X_F 99.9% probability and 94.2943% with an evalue 1.1e-21. TmmHmm does not support transmembrane functioin. CDS 49446 - 50387 /gene="97" /product="gp97" /function="Holliday junction resolvase" /locus tag="Yassified_97" /note=Original Glimmer call @bp 49446 has strength 7.4; Genemark calls start at 49413 /note=SSC: 49446-50387 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_DELILAH_100 [Mycobacterium phage Delilah] ],,NCBI, q1:s1 99.6805% 0.0 GAP: 220 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.475, -3.729235625514656, no F: Holliday junction resolvase SIF-BLAST: ,,[hypothetical protein SEA_DELILAH_100 [Mycobacterium phage Delilah] ],,QAY09224,99.6795,0.0 SIF-HHPRED: Phage_endo_I ; Phage endonuclease I,,,PF05367.14,28.4345,99.2 SIF-Syn: gene 95 is similar in size and color to gene 88 in Beanwater and 98 in Zeenon. No function listed /note=Glimmer gives a start site of 49446 and Genmark states 49413. Based on the data in the chart and Host-Trained genemark start site 49413 is the most accurate start site. It has a length of 975, least amount of gaps , a z-score of 1.612, a final score of -6.528 and is classified as the longest ORF. But starterator has most manual annotations for 49446. This start site also captures the most coding potential. Often called in PhagesDB a Holliday junction resolvase, also supported by strong matches in BLAST. HHPred matches to an endonuclease.TmHmm does not support transmembrane protein function. CDS 50425 - 51057 /gene="98" /product="gp98" /function="capsid decoration protein" /locus tag="Yassified_98" /note=Original Glimmer call @bp 50425 has strength 16.52; Genemark calls start at 50425 /note=SSC: 50425-51057 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YUCCA_101 [Mycobacterium phage Yucca] ],,NCBI, q1:s1 100.0% 2.16606E-150 GAP: 37 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.379, -3.867841122493862, yes F: capsid decoration protein SIF-BLAST: ,,[hypothetical protein SEA_YUCCA_101 [Mycobacterium phage Yucca] ],,AOZ62973,100.0,2.16606E-150 SIF-HHPRED: SIF-Syn: Yes, gene 96 is similar in size and color to gene 89 in Beanwater and gene 99 in Zeenon. No function is known /note=Glimmer and genmark scores give a start of 50425. No Starterator report available. Strong match to capsid decoration protein in three other C1 phages. This function has been determined experimentally for Rosebush and Patience. TmHmm does not indicate that this is a transmembrane protein. CDS 51139 - 51678 /gene="99" /product="gp99" /function="head fiber protein" /locus tag="Yassified_99" /note=Original Glimmer call @bp 51139 has strength 8.1; Genemark calls start at 51139 /note=SSC: 51139-51678 CP: yes SCS: both ST: SS BLAST-Start: [gp100 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.18577E-116 GAP: 81 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.149, -2.604595770381943, yes F: head fiber protein SIF-BLAST: ,,[gp100 [Mycobacterium phage Bxz1] ],,NP_818173,100.0,1.18577E-116 SIF-HHPRED: Head fiber protein; supercoiled triple repeating helix-turn-helix, VIRAL PROTEIN; 1.52A {Bacillus phage phi29},,,3QC7_A,76.5363,99.6 SIF-Syn: Capablanca 104 and similar genes in C1 support the function. /note=Glimmer and genemark agree on the start site. Starterator also shows this as the most manually annotated start. PhagesDB, Blast, and HHPred support head fiber protein as the function for this gene. TmHmm does not indicate a transmemebrane protein. CDS 51748 - 51969 /gene="100" /product="gp100" /function="hypothetical protein" /locus tag="Yassified_100" /note=Original Glimmer call @bp 51748 has strength 20.4; Genemark calls start at 51748 /note=SSC: 51748-51969 CP: yes SCS: both ST: SS BLAST-Start: [gp101 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 7.18411E-45 GAP: 69 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[gp101 [Mycobacterium phage Bxz1] ],,NP_818174,100.0,7.18411E-45 SIF-HHPRED: SIF-Syn: Yes, gene 98 is similar in size and color to gene 91 in Beanwater and gene 101 in Zeenon. No known function /note=Glimmer and genemark agree on the start site. DB, Blast, Pharmarator, and HHPED do not indicate function. TmHmm does not indicate transmembrane protein. CDS 51985 - 52149 /gene="101" /product="gp101" /function="hypothetical protein" /locus tag="Yassified_101" /note=Original Glimmer call @bp 51985 has strength 17.26; Genemark calls start at 51985 /note=SSC: 51985-52149 CP: no SCS: both ST: NA BLAST-Start: [gp102 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 7.08532E-29 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.149, -3.16089827114923, yes F: hypothetical protein SIF-BLAST: ,,[gp102 [Mycobacterium phage Bxz1] ],,NP_818175,100.0,7.08532E-29 SIF-HHPRED: SIF-Syn: Yes, gene 99 is similar in size and color to gene 92 in Beanwater and gene 102 in Zeenon /note=Glimmer and genemark agee on the start site. No starterator report available, PhagesDB, Blast, Pharmator and HHPred donot support a function of this gene. TmHmm does not indicate that this is a transmemebrane protein. CDS 52193 - 54079 /gene="102" /product="gp102" /function="hypothetical protein" /locus tag="Yassified_102" /note=Original Glimmer call @bp 52193 has strength 9.4; Genemark calls start at 52193 /note=SSC: 52193-54079 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PLEIONE_108 [Mycobacterium phage Pleione] ],,NCBI, q1:s1 100.0% 0.0 GAP: 43 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.149, -2.905625766045924, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PLEIONE_108 [Mycobacterium phage Pleione] ],,YP_009017877,100.0,0.0 SIF-HHPRED: SIF-Syn: shares synteny with gene 97 in Beanwater and 107 in zeenon. /note=There is high coding potential throughout most of the predicted gene, a big dip at around 52550bp and a few small dips at the start of the predicted gene. At least 10 other phages have a similar gene, with E value = 0, 100% aligned, 100% identity, 100% coverage, Q1:S1. Top phage hits do not point to a known function e.g. hypothetical protein. Starterator was inconclusive. There is no supporting evidence from BLAST HHPred or phamerator for a function call. CDS 54072 - 55373 /gene="103" /product="gp103" /function="hypothetical protein" /locus tag="Yassified_103" /note=Original Glimmer call @bp 54072 has strength 11.64; Genemark calls start at 54072 /note=SSC: 54072-55373 CP: yes SCS: both ST: SS BLAST-Start: [gp102 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.717, -3.221100372932034, yes F: hypothetical protein SIF-BLAST: ,,[gp102 [Mycobacterium phage Cali] ],,YP_002224575,100.0,0.0 SIF-HHPRED: SIF-Syn: there is synteny with gene 108 in zeenon and gene 98 in beanwater /note=Neither the BLAST, PhagesDB, NCBI, nor the HHPred are informative of the function. Based on TmmHm is not a transmembrane protein. Prediction by Glimmer Is supported by BLAST alignment because of Q1:S1.Top hits in HHPred had a very poor e-value E=37. CDS 55373 - 55585 /gene="104" /product="gp104" /function="hypothetical protein" /locus tag="Yassified_104" /note=Original Glimmer call @bp 55373 has strength 14.67; Genemark calls start at 55373 /note=SSC: 55373-55585 CP: yes SCS: both ST: SS BLAST-Start: [gp105 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.43302E-41 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.983, -2.9525085049809894, yes F: hypothetical protein SIF-BLAST: ,,[gp105 [Mycobacterium phage Bxz1] ],,NP_818178,100.0,1.43302E-41 SIF-HHPRED: SIF-Syn: there is synteny with gene 99 in beanwater and gene 109 in zeenon but doesn`t support a function. /note=Neither the BLAST against PhageaDB and NCBI, nor the HHPred are informative as to the function. TmmHMM indicates that this is not a transmemebrane protein. At least 4 other phages have a similar gene, with E value = 1.43302e-41, 100% aligned, 100% identity, 100% coverage.Prediction by Glimmer Is supported by BLAST alignment because of Q1:S1.Top phage hits do not point to a known function e.g. hypothetical protein. Starterator shows there are 158 MA`s supporting 55373 as the start site. CDS 55588 - 55959 /gene="105" /product="gp105" /function="membrane protein" /locus tag="Yassified_105" /note=Original Glimmer call @bp 55588 has strength 15.12; Genemark calls start at 55588 /note=SSC: 55588-55959 CP: yes SCS: both ST: SS BLAST-Start: [gp108 [Mycobacterium phage Spud] ],,NCBI, q1:s1 100.0% 4.41227E-84 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.578, -3.5316035464369326, yes F: membrane protein SIF-BLAST: ,,[gp108 [Mycobacterium phage Spud] ],,YP_002224357,100.0,4.41227E-84 SIF-HHPRED: Iron_permease ; Low affinity iron permease,,,PF04120.15,82.1138,99.9 SIF-Syn: there is synteny with gene 100 in beanwater and gene 110 in zeenon /note=Neither the BLAST against PhageDB and NCBI, HHPredd (possible permease) are infromative of the function. TmmHmm predicts 2 TMH`s. At least 7 other phages have a similar gene, with E value = 4.41227e-84, 100% aligned, 100% identity, 100% coverage, Q1:S1.Top phage hits do not point to a known function e.g. hypothetical protein. Starterator shows 55588 as most likely start site. CDS 55959 - 56189 /gene="106" /product="gp106" /function="hypothetical protein" /locus tag="Yassified_106" /note=Original Glimmer call @bp 55959 has strength 12.18; Genemark calls start at 55959 /note=SSC: 55959-56189 CP: yes SCS: both ST: SS BLAST-Start: [gp107 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 4.78494E-46 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.583959800616441, yes F: hypothetical protein SIF-BLAST: ,,[gp107 [Mycobacterium phage Bxz1] ],,NP_818180,100.0,4.78494E-46 SIF-HHPRED: SIF-Syn: there is synteny with gene 111 from zeenon and gene 101 from beanwater /note=Genemark predicts start site 55959. There is high coding potential near 1.0 throughout the predicted gene. At least 3 other phages have a similar gene, with E value = 4.78494e-46, 100% aligned, 100% identity, 100% coverage. Prediction by Glimmer Is supported by BLAST alignment because of Q1:S1. Top phage hits do not point to a known function e.g. hypothetical protein. Starterator supports 55959 as the start. Top hits in HHPred had a very poor e-value E=140 and phamerator showed there are no close relatives with homologoous genes with a function. No transmebrane domains. CDS 56192 - 56413 /gene="107" /product="gp107" /function="hypothetical protein" /locus tag="Yassified_107" /note=Original Glimmer call @bp 56192 has strength 12.67; Genemark calls start at 56192 /note=SSC: 56192-56413 CP: yes SCS: both ST: SS BLAST-Start: [gp108 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.97352E-44 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.055, -5.200500400297053, yes F: hypothetical protein SIF-BLAST: ,,[gp108 [Mycobacterium phage Bxz1] ],,NP_818181,100.0,1.97352E-44 SIF-HHPRED: SIF-Syn: there is synteny with gene 112 from zeenon and gene 102 from beanwater /note=At least 4 other phages have a similar gene, with E value = 1.97352e-44, 100% aligned, 100% identity, 100% coverage. Prediction by Glimmer Is supported by BLAST alignment because of Q1:S1.Top phage hits do not point to a known function e.g. hypothetical protein . Top hits in HHPred had a very poor e-value E=260. No transmembrane domain. CDS 56676 - 56942 /gene="108" /product="gp108" /function="hypothetical protein" /locus tag="Yassified_108" /note=Original Glimmer call @bp 56691 has strength 12.38; Genemark calls start at 56691 /note=SSC: 56676-56942 CP: yes SCS: both-cs ST: NA BLAST-Start: [gp107 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 1.71068E-56 GAP: 262 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.216, -3.2136105537450197, yes F: hypothetical protein SIF-BLAST: ,,[gp107 [Mycobacterium phage Cali] ],,YP_002224580,100.0,1.71068E-56 SIF-HHPRED: SIF-Syn: there is synteny with gene 113 in zeenon and gene 104 in beanwter /note=Genemark and Glimmer agree with 56691 as the start site but starterator has more MA`s for 56676 and it is the longest ORF with the smallest gap. Prediction by Glimmer Is supported by BLAST alignment because of Q1:S1. Top hits in HHPred had a very poor e-value E=85. No transmembrane domain. CDS 57031 - 57150 /gene="109" /product="gp109" /function="hypothetical protein" /locus tag="Yassified_109" /note=Original Glimmer call @bp 57031 has strength 15.98; Genemark calls start at 57031 /note=SSC: 57031-57150 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_109 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 6.31556E-19 GAP: 88 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.983, -2.6814417326944517, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_109 [Mycobacterium phage ScottMcG] ],,YP_002224137,100.0,6.31556E-19 SIF-HHPRED: SIF-Syn: there is synteny with gene 114 in zeenon /note=Prediction by Glimmer Is supported by BLAST alignment because of Q1:S1. Top phage hits do not point to a known function e.g. hypothetical protein. Starterator shows there are 72 MA`s supporting 57031 as the start site. Top hits in HHPred had a very poor e-value E=20. CDS 57212 - 57706 /gene="110" /product="gp110" /function="hypothetical protein" /locus tag="Yassified_110" /note=Original Glimmer call @bp 57212 has strength 14.88; Genemark calls start at 57212 /note=SSC: 57212-57706 CP: yes SCS: both ST: SS BLAST-Start: [gp111 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.61869E-116 GAP: 61 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -3.3503726477288405, yes F: hypothetical protein SIF-BLAST: ,,[gp111 [Mycobacterium phage Bxz1] ],,NP_818184,100.0,2.61869E-116 SIF-HHPRED: SIF-Syn: there is synteny with gene 115 from zeenon and 106 in beanwater. /note=Prediction by Glimmer Is supported by BLAST alignment because of Q1:S1. Top phage hits do not point to a known function e.g. hypothetical protein. Starterator shows there are 84 MA`s supporting 57212 as the start site.57212 produces an ORF that is 495bp long and has a gap of 61. There is a longer ORF with a smaller gap but both are acceptable.Top hits in HHPred had a very poor e-value E=36.There is no supporting evidence from BLAST HHPred or phamerator for a function call. CDS 57724 - 58629 /gene="111" /product="gp111" /function="hypothetical protein" /locus tag="Yassified_111" /note=Original Glimmer call @bp 57724 has strength 16.06; Genemark calls start at 57724 /note=SSC: 57724-58629 CP: yes SCS: both ST: SS BLAST-Start: [head decoration protein [Mycobacterium phage Lukilu] ],,NCBI, q1:s1 100.0% 0.0 GAP: 17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.63, -4.24928381388937, yes F: hypothetical protein SIF-BLAST: ,,[head decoration protein [Mycobacterium phage Lukilu] ],,YP_009597704,99.3355,0.0 SIF-HHPRED: SIF-Syn: NFK not informative /note=Phagesdb function frequency (100%). On the basis of the HHPred, with a low probability of 68.6% and a high e-value of 79, no function is known for this gene. It has been called once in a C1 phage a capsid decoration protein. CDS 58658 - 59476 /gene="112" /product="gp112" /function="hypothetical protein" /locus tag="Yassified_112" /note=Original Glimmer call @bp 58658 has strength 13.09; Genemark calls start at 58658 /note=SSC: 58658-59476 CP: yes SCS: both ST: SS BLAST-Start: [gp113 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 28 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.151, -4.408951082954879, no F: hypothetical protein SIF-BLAST: ,,[gp113 [Mycobacterium phage Bxz1] ],,NP_818186,100.0,0.0 SIF-HHPRED: SIF-Syn: This portion of the genome is syntenic to BeanWater gene 108 and Zeenon gene 117. /note=PhagesDB frequency has no data, PhagesDB BLAST(E=1e -152), and on the basis of HHPred it supports that this gene function is unknown (91.2% Probability, 9.19% coverage, E= 0.39). NCBI BLAST(100% coverage, 100% aligned, Q1:S1, 100% identity, E=0). Not a membrane protein. CDS 59476 - 60084 /gene="113" /product="gp113" /function="hypothetical protein" /locus tag="Yassified_113" /note=Original Glimmer call @bp 59476 has strength 9.11; Genemark calls start at 59476 /note=SSC: 59476-60084 CP: yes SCS: both ST: SS BLAST-Start: [gp114 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 7.72958E-144 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.227, -2.1695583717155773, yes F: hypothetical protein SIF-BLAST: ,,[gp114 [Mycobacterium phage Bxz1] ],,NP_818187,100.0,7.72958E-144 SIF-HHPRED: Structural polyprotein (PP) p1; IBDV, p4, BIRNAVIRUS, DPC, VP2, PORE FORMATION, viral protein; NMR {N/A},,,2IMU_A,7.92079,2.3 SIF-Syn: This portion of the genome is syntenic to BeanWater gene 109 and Zeenon gene 118. Bean water and Zeenon also have no function listed. /note=PhagesDB frequency has no data, PhagesDB BLAST(E=1e -116), and on the basis of HHPred it supports that this gene function is unknown ( 2.3% Probability, 7.9% coverage, E= 1500). NCBI BLAST(100% coverage, 100% aligned, 100% identity, Q1:S1, E=7.7E-144). Not a transmembrane protein. CDS 60156 - 60782 /gene="114" /product="gp114" /function="hypothetical protein" /locus tag="Yassified_114" /note=Original Glimmer call @bp 60156 has strength 15.55; Genemark calls start at 60156 /note=SSC: 60156-60782 CP: yes SCS: both ST: SS BLAST-Start: [gp115 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 3.5672E-153 GAP: 71 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[gp115 [Mycobacterium phage Bxz1] ],,NP_818188,100.0,3.5672E-153 SIF-HHPRED: LBP_C ; Lacto-N-biose phosphorylase C-terminal domain,,,PF17386.5,14.4231,49.3 SIF-Syn: This portion of the genome is syntenic to BeanWater gene 110 and Zeenon gene 119. Bean water and Zeenon also have no function listed. Not a transmembrane protein. /note=PhagesDB frequency has no data, PhagesDB BLAST(E=1e -120), and on the basis of HHPred it supports that this gene function is unknown ( 49.3% Probability, 14.4% coverage, E= 68). NCBI BLAST(100% coverage, 100% aligned, 100% identity, Q1:S1, E= 3.5E-153) CDS 60801 - 61091 /gene="115" /product="gp115" /function="hypothetical protein" /locus tag="Yassified_115" /note=Original Glimmer call @bp 60801 has strength 13.65; Genemark calls start at 60801 /note=SSC: 60801-61091 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein M181_gp210 [Mycobacterium phage Gizmo] ],,NCBI, q1:s1 100.0% 1.7123E-64 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.905, -3.6727816321281046, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M181_gp210 [Mycobacterium phage Gizmo] ],,YP_008060917,100.0,1.7123E-64 SIF-HHPRED: DUF4810 ; Domain of unknown function (DUF4810),,,PF16068.8,33.3333,32.5 SIF-Syn: This portion of the genome is syntenic to BeanWater gene 111 and Zeenon gene 120. Bean water and Zeenon also have no function listed. /note=PhagesDB frequency has no data, PhagesDB BLAST(E= 2E-51), and on the basis of HHPred it supports that this gene function is unknown ( 32.5% Probability, 33.3% coverage, E= 110). NCBI BLAST(100% coverage, 100% aligned, 100% identity, Q1:S1, E= 1.7E-64). Not a transmembrane protein. CDS 61178 - 62788 /gene="116" /product="gp116" /function="hypothetical protein" /locus tag="Yassified_116" /note=Original Glimmer call @bp 61178 has strength 17.87; Genemark calls start at 61178 /note=SSC: 61178-62788 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_108 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 0.0 GAP: 86 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.161, -4.325675514574479, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_108 [Mycobacterium phage ET08] ],,YP_003347787,100.0,0.0 SIF-HHPRED: COLLAGEN X; COLLAGEN, EXTRACELLULAR MATRIX, CONNECTIVE TISSUE; HET: CPS; 2.0A {HOMO SAPIENS} SCOP: b.22.1.1,,,1GR3_A,26.4925,94.8 SIF-Syn: This portion of the genome is syntenic to BeanWater gene 112 and Zeenon gene 121. Bean water and Zeenon also have no function listed. /note=PhagesDB frequency 100% for minor tail protein, PhagesDB BLAST(E= 0), and on the basis of HHPred it supports that this gene function is unknown (94.8% Probability, 26.4% coverage, E= 1.9). NCBI BLAST(100% coverage, 100% aligned, 99.8% identity, Q1:S1, E=0). Not a transmembrane protein. CDS 62799 - 63302 /gene="117" /product="gp117" /function="acetyltransferase" /locus tag="Yassified_117" /note=Original Glimmer call @bp 62799 has strength 16.1; Genemark calls start at 62799 /note=SSC: 62799-63302 CP: yes SCS: both ST: SS BLAST-Start: [acetyltransferase [Mycobacterium phage I3] ],,NCBI, q1:s1 100.0% 4.644E-119 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.302, -1.9310779259753799, yes F: acetyltransferase SIF-BLAST: ,,[acetyltransferase [Mycobacterium phage I3] ],,YP_010510529,100.0,4.644E-119 SIF-HHPRED: SIF-Syn: This portion of the genome is syntenic to BeanWater gene 113 and Zeenon gene 122. Bean water and Zeenon also have no function listed. /note=Phagesdb function frequency 96% for acetyltransferase. On the basis of the HHPred, with a high probability of 93.7% but a high e-value of 0.72, no function is known for this gene. CDS 63299 - 64288 /gene="118" /product="gp118" /function="hypothetical protein" /locus tag="Yassified_118" /note=Original Glimmer call @bp 63299 has strength 17.48; Genemark calls start at 63311 /note=SSC: 63299-64288 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein ET08_110 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.973, -5.371913467750883, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_110 [Mycobacterium phage ET08] ],,YP_003347789,100.0,0.0 SIF-HHPRED: Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH; cytochrome bc1, cbb3-COX, Complex III, Complex IV, OXIDOREDUCTASE, TRANSLOCASE-Oxidoreductase complex; HET: HEC; 5.2A {Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)},,,6XKW_h,28.2675,82.9 SIF-Syn: This portion of the genome is syntenic to BeanWater gene 114 and Zeenon gene 123. Bean water and Zeenon also have no function listed. /note=PhagesDB frequency has no data, PhagesDB BLAST(E= 0), and on the basis of HHPred it supports that this gene function is unknown ( 82.9% Probability, 28.2% coverage, E= 36). NCBI BLAST(100% coverage, 100% aligned, 100% identity, Q1:S1, E=0). Not a transmembrane protein. CDS 64288 - 64884 /gene="119" /product="gp119" /function="hypothetical protein" /locus tag="Yassified_119" /note=Original Glimmer call @bp 64288 has strength 13.21; Genemark calls start at 64288 /note=SSC: 64288-64884 CP: yes SCS: both ST: SS BLAST-Start: [gp120 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.35333E-146 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.174, -4.36137266396122, no F: hypothetical protein SIF-BLAST: ,,[gp120 [Mycobacterium phage Bxz1] ],,NP_818193,100.0,2.35333E-146 SIF-HHPRED: RNR_III; Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides.,,,cd01675,37.8788,88.6 SIF-Syn: This portion of the genome is syntenic to BeanWater gene 115 and Zeenon gene 124. Bean water and Zeenon also have no function listed. /note=PhagesDB frequency has no data, PhagesDB BLAST(E=1e -120), and on the basis of HHPred it supports that this gene function is unknown ( 88.6% Probability, 37.8% coverage, E= 2.3). NCBI BLAST(100% coverage, 100% aligned, 100% identity, Q1:S1, E= 2.3E-146). Not a transmembrane protein. CDS 64881 - 65681 /gene="120" /product="gp120" /function="hypothetical protein" /locus tag="Yassified_120" /note=Original Glimmer call @bp 64881 has strength 12.86; Genemark calls start at 64881 /note=SSC: 64881-65681 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BEANWATER_116 [Mycobacterium phage BeanWater] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.129, -4.45540384879315, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BEANWATER_116 [Mycobacterium phage BeanWater] ],,ATN87570,100.0,0.0 SIF-HHPRED: SIF-Syn: Gene 112 in BeanWater and gene 121 in Xenon are syntenic with this gene. /note=Function listed in phagesdb as parb-like nuclease protein, but not listed entirely in SEAPHAGES function list. Function not supported by HHPRED.100% frequency in 9 hits from phagesdb with E-value=1e-167. NCBI shows hypothetical protein as function, with 99-100% identity, alignment, and coverage with an E-value=0 for all hits on page 1. not a transmembrane protein. CDS 65678 - 66133 /gene="121" /product="gp121" /function="minor capsid protein" /locus tag="Yassified_121" /note=Original Glimmer call @bp 65678 has strength 13.44; Genemark calls start at 65678 /note=SSC: 65678-66133 CP: yes SCS: both ST: SS BLAST-Start: [gp122 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.18339E-104 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.895, -5.711975353186392, no F: minor capsid protein SIF-BLAST: ,,[gp122 [Mycobacterium phage Bxz1] ],,NP_818195,100.0,1.18339E-104 SIF-HHPRED: Minor_capsid_2 ; Minor capsid protein,,,PF11114.11,88.0795,99.3 SIF-Syn: Gene 112 of BeanWater and 122 of Zeenon are syntenic with gene 119 of Yassified. /note=Only one listed function from Phagesdb, minor capsid protein, supported by HHpred, with a 99% probability with 88% coverage, and an E-value=1.4e-11. Not supported by Phamerator, with no function listed for similar genes in Pham, like BeanWater and Zeenon. CDS 66130 - 66843 /gene="122" /product="gp122" /function="hypothetical protein" /locus tag="Yassified_122" /note=Original Glimmer call @bp 66130 has strength 19.86; Genemark calls start at 66130 /note=SSC: 66130-66843 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_RABINOVISH_124 [Mycobacterium phage Rabinovish] ],,NCBI, q1:s1 100.0% 4.63455E-173 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.227, -2.1518296047551457, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RABINOVISH_124 [Mycobacterium phage Rabinovish] ],,AXN53945,100.0,4.63455E-173 SIF-HHPRED: SIF-Syn: Gene 114 of BeanWater and 123 of Zeenon are syntenic with this gene. /note=99-100% identity, with 100% coverage and alignment for more than 15 genes. E value=4.6E-173 for 100% identical genes. Blast data lists hypothetical protein as function, meaning function is unknown. HHpred shows no apparent function, with hits ranging a poor probability with poor coverage. CDS 66909 - 68654 /gene="123" /product="gp123" /function="tail sheath protein" /locus tag="Yassified_123" /note=Original Glimmer call @bp 66909 has strength 19.58; Genemark calls start at 66909 /note=SSC: 66909-68654 CP: yes SCS: both ST: SS BLAST-Start: [tail sheath protein [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 0.0 GAP: 65 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.784, -3.6716023243868, yes F: tail sheath protein SIF-BLAST: ,,[tail sheath protein [Mycobacterium phage ET08] ],,YP_003347794,100.0,0.0 SIF-HHPRED: Pyocin sheath PA0622; bacteriocin, pyocin, helix, ANTIMICROBIAL PROTEIN; 2.9A {Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)},,,6PYT_N,57.1429,100.0 SIF-Syn: Gene 115 of BeanWater and 124 of Zeenon are syntenic with this gene. /note=Phagesdb supports function, 99% frequency in 92 genes. NCBI Blast shows 100% identity, alignment, and coverage. HHPRED lists different functions with a 100% probability, but less than 60% coverage. GL and GM start site is supported by Starterator. 1:1 alignment with 10+ hits. CDS 68689 - 69156 /gene="124" /product="gp124" /function="hypothetical protein" /locus tag="Yassified_124" /note=Original Glimmer call @bp 68689 has strength 15.88; Genemark calls start at 68689 /note=SSC: 68689-69156 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_124 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 7.36185E-109 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.302, -2.838489286749966, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_124 [Mycobacterium phage ScottMcG] ],,YP_002224152,100.0,7.36185E-109 SIF-HHPRED: SIF-Syn: Genes 116 in BeanWater and 125 in Xenon show sytenic properties for gene 122 in Yassified. /note=Start site 3 from starterator, found in 173 of 185 (93.5%) of genes in Pham. CP high throughout whole gene and potential present in reading frames. 99-100% identity, 100% alignment and coverage with more than 15 genes.,E-value-7.36e-109 for 100% identity genes. No function listed in Phagesdb, HHpred shows 88% probability with 92% coverage that there is no function. Phagesdb BLAST shows E-value=4-85 for an unknown function. CDS 69159 - 69992 /gene="125" /product="gp125" /function="hypothetical protein" /locus tag="Yassified_125" /note=Original Glimmer call @bp 69159 has strength 6.18; Genemark calls start at 69159 /note=SSC: 69159-69992 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BEANWATER_121 [Mycobacterium phage BeanWater] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.077, -4.582905859694018, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BEANWATER_121 [Mycobacterium phage BeanWater] ],,ATN87575,100.0,0.0 SIF-HHPRED: SIF-Syn: Gene 117 of BeanWater and 126 of Zeenon are syntenic with this gene. /note=Coding Potential high at start of gene, dip at around 69250 bp and 69700 bp. Major dip showing a low coding potential of less than 0.5 at around 69800 bp. Start site supported by GL, GM, and Starterator. No function listed in Phagesdb, HHpred shows very low coverage for a function listed as finger protein 1. Hypothetical protein has 100% alignment, coverage, and identity in 3 closely related genes, BeanWater, Koguma, and Shelob. All have E-value=1e-172. Not a transmembrane protein. CDS 70005 - 70532 /gene="126" /product="gp126" /function="tail assembly chaperone" /locus tag="Yassified_126" /note=Original Glimmer call @bp 70005 has strength 14.61; Genemark calls start at 69993 /note=SSC: 70005-70532 CP: yes SCS: both-gl ST: SS BLAST-Start: [tail assembly chaperone [Mycobacterium phage Gizmo] ],,NCBI, q1:s5 100.0% 4.93064E-124 GAP: 12 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.759, -3.899580331731527, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage Gizmo] ],,YP_008060930,97.7654,4.93064E-124 SIF-HHPRED: Phage_TAC_13 ; Phage tail assembly chaperone, TAC,,,PF16459.8,60.5714,96.9 SIF-Syn: Gene 118 of BeanWater and 127 of Zeenon are syntenic with this gene. /note=Start site used is GL start and Starterator supports this, with 116 MA`s. Phagesdb lists function as tail assembly chaperone with 100% frequency, Blast E-value= 6e-96. HHpred supports the given function with 96-97% probability with around 60% coverage, E-value= 9.7e-3. 10+ hits in NCBI support the function with 97-100% alignment and identity with 100% coverage with very low E-values. CDS join(70005..70520,70520..70903) /gene="127" /product="gp127" /function="tail assembly chaperone" /locus tag="Yassified_127" /note= /note=SSC: 70005-70903 CP: yes SCS: neither ST: NI BLAST-Start: [tail assembly chaperone [Mycobacterium phage Gizmo] ],,NCBI, q1:s5 100.0% 0.0 GAP: -528 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.759, -3.899580331731527, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage Gizmo] ],,YP_008060929,98.6799,0.0 SIF-HHPRED: Phage_TAC_13 ; Phage tail assembly chaperone, TAC,,,PF16459.8,35.4515,96.8 SIF-Syn: Zeenon has the tail assembly chaperon in the same location. The downstream gene is also the tape measure /note=This is the fusion tail assembly protein for genes original 124 and 125. The translation frame shift occurs at base 70520 of gene 24 on frame 3 and it continues reading on frame 2 all the way to the original stop site for gene 125 70903. CDS 70903 - 73161 /gene="128" /product="gp128" /function="tape measure protein" /locus tag="Yassified_128" /note=Original Glimmer call @bp 70903 has strength 14.19; Genemark calls start at 70903 /note=SSC: 70903-73161 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Mycobacterium phage InterFolia] ],,NCBI, q1:s4 100.0% 0.0 GAP: -2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.63, -3.482870966776971, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Mycobacterium phage InterFolia] ],,AVR77638,99.6026,0.0 SIF-HHPRED: SIF-Syn: Gene 124 of BeanWater and 133 of Zeenon are syntenic with this gene. Supported from Pham Maps in PECAAN, not supported in Phamerator because gene 126 is numbered differently ,it is gene 131 in Yassified. Regardless, there is strong nucleotide similarity between the genes. /note=Strong coding potential at 1.0 throughout gene with very small dips in coding potential. Start site is supported by GM,GL, and Starterator. Function listed by Phagesdb is tape measure protein with 100% frequency in 85 hits, E-value=0 for all hits. HHpred lists different function for its hits, with 70% probability for one hit, but 12% coverage. NCBI supports function, with 99-100% identity, alignment, and coverage fro all hits with an E-value=0 for all hits as well. Phamerator shows syntenic genes in BeanWater and Zeenon have same function. CDS 73161 - 73844 /gene="129" /product="gp129" /function="minor tail protein" /locus tag="Yassified_129" /note=Original Glimmer call @bp 73161 has strength 16.27; Genemark calls start at 73161 /note=SSC: 73161-73844 CP: yes SCS: both ST: SS BLAST-Start: [gp130 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.02984E-165 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.493, -3.6907860541164537, no F: minor tail protein SIF-BLAST: ,,[gp130 [Mycobacterium phage Bxz1] ],,NP_818203,99.5595,2.02984E-165 SIF-HHPRED: SIF-Syn: No synteny with BeanWater nor Zeenon. /note=Phagesdb BLAST supports the function of this gene with a low e-value at 1e-130. /note=Phagesdb Function Frequency supports the function of this gene in pham 477 with a frequency of 100%. /note=NCBI BLAST supports the function of this gene with a identity at 99.6% an alignment at 99.6%, a coverage at 100%, query from 1 to 227, and a low e-value at 2.03e-165. /note=HHPRED does not support a function with a low e-value. Not a transmembrane protein. CDS 73860 - 74030 /gene="130" /product="gp130" /function="hypothetical protein" /locus tag="Yassified_130" /note=Original Glimmer call @bp 73860 has strength 11.94; Genemark calls start at 73860 /note=SSC: 73860-74030 CP: yes SCS: both ST: SS BLAST-Start: [gp131 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 9.91253E-33 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.052, -3.3633184689272606, yes F: hypothetical protein SIF-BLAST: ,,[gp131 [Mycobacterium phage Bxz1] ],,NP_818204,100.0,9.91253E-33 SIF-HHPRED: SIF-Syn: No synteny with Zeenon nor BeanWater. /note=Phagesdb Frequency Function does not have data available. /note=Phagesdb BLAST does not support a known function. /note=HHPred does not support a supportable function due to high e-values. (Top hit e-value=8.3) /note=NCBI BLAST supports the function of this gene with a identity at 100% an alignment at 100%, a coverage at 100%, query from 1 to 56 and a low e-value at 9.91e-33. CDS 74034 - 74624 /gene="131" /product="gp131" /function="hypothetical protein" /locus tag="Yassified_131" /note=Original Glimmer call @bp 74034 has strength 11.17; Genemark calls start at 74034 /note=SSC: 74034-74624 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PINKCREEK_126 [Mycobacterium phage Pinkcreek]],,NCBI, q1:s1 100.0% 1.27154E-141 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.611, -5.62127637145861, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PINKCREEK_126 [Mycobacterium phage Pinkcreek]],,UEM46186,100.0,1.27154E-141 SIF-HHPRED: SIF-Syn: No synteny with BeanWater nor Zeenon. /note=Phagesdb Function Frequency supports the function of this gene in pham 428 with a frequency of 100%. /note=Phagesdb BLAST does not support a known function. /note=HHPred does not suggest a supportive function due to high e-values. (Top hit e-value=81) /note=NCBI BLAST supports this function with an identity at 99.5%, an alignment at 100%, query from 1 to 196, and a coverage at 100%. /note=Not a transmembrane domain. CDS 74624 - 77470 /gene="132" /product="gp132" /function="minor tail protein" /locus tag="Yassified_132" /note=Original Glimmer call @bp 74624 has strength 13.63; Genemark calls start at 74624 /note=SSC: 74624-77470 CP: yes SCS: both ST: SS BLAST-Start: [gp133 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.377, -3.935403931688939, no F: minor tail protein SIF-BLAST: ,,[gp133 [Mycobacterium phage Bxz1] ],,NP_818206,100.0,0.0 SIF-HHPRED: SIF-Syn: Slight synteny with BeanWater, overlapping gene 128 of BeanWater more than half. /note=Phagesdb Function Frequency supports this function in Pham 421 at 100% frequency. /note=Phagesdb BLAST support this function with multiple hits with e-value of 0. /note=HHPred does not support this function due to poor coverage of 10% of the gene. /note=NCBI BLAST supports this function with an identity at 100%, an alignment at 100%, a coverage at 100%, query from 1 to 948, and low e-value at 0. CDS 77470 - 78936 /gene="133" /product="gp133" /function="minor tail protein" /locus tag="Yassified_133" /note=Original Glimmer call @bp 77470 has strength 12.11; Genemark calls start at 77470 /note=SSC: 77470-78936 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ALICE_130 [Mycobacterium phage Alice] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.052, -4.6353190821692705, no F: minor tail protein SIF-BLAST: ,,[hypothetical protein ALICE_130 [Mycobacterium phage Alice] ],,YP_009216390,100.0,0.0 SIF-HHPRED: SIF-Syn: Synteny with Delylah_140 and also its up and downstream genes. /note=Phagesdb Function Frequency BLAST PhagesDB support minor tail protein in four instances in Pham 519 for a C1 phage /note=HHPred does not support function with low e-value. (Top hit e-value=670) /note=NCBI BLAST doesn`t support a function with an identity at 100%, an alignment at 100%, a coverage at 100% query from 1 to 488, and a low e-value at 0. CDS 78936 - 79691 /gene="134" /product="gp134" /function="minor tail protein" /locus tag="Yassified_134" /note=Original Glimmer call @bp 78936 has strength 8.02; Genemark calls start at 78936 /note=SSC: 78936-79691 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_126 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 2.96984E-161 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.166, -4.455662434380964, no F: minor tail protein SIF-BLAST: ,,[hypothetical protein ET08_126 [Mycobacterium phage ET08] ],,YP_003347805,100.0,2.96984E-161 SIF-HHPRED: SIF-Syn: No synteny with BeanWater nor Zeenon /note=Phagesdb Function Frequency supports the function of this gene in Pham 75373 with a frequency of 100% /note=Phagesdb BLAST supports the function with a low e-value of 1e-147. /note=HHPred does not suggest a supportive function due to high e-values. (Top hit e-value=50) /note=NCBI BLAST supports the function with an identity at 100%, an alignment at 100%, a coverage at 100% , query from 1 to 251, and a low e-value at 3.0e-166. CDS 79726 - 80142 /gene="135" /product="gp135" /function="baseplate wedge protein" /locus tag="Yassified_135" /note=Original Glimmer call @bp 79726 has strength 12.14; Genemark calls start at 79726 /note=SSC: 79726-80142 CP: yes SCS: both ST: SS BLAST-Start: [baseplate wedge protein [Mycobacterium phage Phabba] ],,NCBI, q1:s1 99.2754% 3.1355E-55 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.149, -2.3335289980954053, yes F: baseplate wedge protein SIF-BLAST: ,,[baseplate wedge protein [Mycobacterium phage Phabba] ],,YP_010056838,76.4286,3.1355E-55 SIF-HHPRED: Baseplate wedge protein gp25; contractile sheath, baseplate, wedge, sheath polymerization, viral protein; HET: MSE; 2.47A {Enterobacteria phage T4},,,5IW9_B,99.2754,99.6 SIF-Syn: Synteny with EasyJones_143 and I3_145 and with up and downstream genes as well. /note=Phagesdb Function Frequency supports the function of this gene in pham 417 with a frequency of 99%. /note=Phagesdb BLAST supports the function of this gene with protein number 144, protein number 133, and protein number 142 all having a low e-value at 9e-72. /note=HHPRED supports the function of this gene with a single hit having a 99.6% probability, a coverage at 99.3%, query from 1 to 138, and e-value of 3.3e-13. /note=NCBI BLAST supports the function with a 61.4% identity, 76,4% alignment, 99.3% coverage, query from 1 to 137, and a low e-value of 3.14e-55. CDS 80153 - 81892 /gene="136" /product="gp136" /function="baseplate J protein" /locus tag="Yassified_136" /note=Original Glimmer call @bp 80153 has strength 19.19; Genemark calls start at 80153 /note=SSC: 80153-81892 CP: yes SCS: both ST: SS BLAST-Start: [gp137 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.302, -1.9310779259753799, yes F: baseplate J protein SIF-BLAST: ,,[gp137 [Mycobacterium phage Bxz1] ],,NP_818210,100.0,0.0 SIF-HHPRED: Baseplate_J ; Baseplate J-like protein,,,PF04865.17,78.2383,99.9 SIF-Syn: Synteny with Alice_133. /note=Phagesdb Function Frequency supports the function of this gene in pham 414 with a frequency of 58% /note=Phagesdb BLAST supports the function of this gene with protein number 133, protein number 136, and protein number 139 all having a low e-value of 0. /note=HHPRED supports the function of this gene with 99.9% probability, 78.2% coverage, query from 62 to 515, and e-value of 2.9e-25. /note=NCBI BLAST supports the function with multiple phases with 100% alignment, 100% coverage, 100% identity, query from 1 to 579, and e-value of 0. CDS 81895 - 82230 /gene="137" /product="gp137" /function="hypothetical protein" /locus tag="Yassified_137" /note=Original Glimmer call @bp 81895 has strength 10.03; Genemark calls start at 81895 /note=SSC: 81895-82230 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein KHO65_gp177 [Mycobacterium phage Sauce] ],,NCBI, q1:s1 100.0% 6.72529E-74 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.688, -4.048329621256372, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KHO65_gp177 [Mycobacterium phage Sauce] ],,YP_010058695,100.0,6.72529E-74 SIF-HHPRED: SIF-Syn: There is no strong evidence based on syteny for an HNH Endonuclease /note=Even though Phagesdb Function Frequency supports the function of this gene in pham 539 with a frequency of 67% there is no other evidence source supporting it. Phamerator doesn`t support the function HNH Endonuclease. /note=Phagesdb BLAST does not support a known function /note=HHPRED does not support a known function /note=NCBI BLAST supports the function with multiple phases with 100% alignment, 100% coverage, 100% identity, query from 1 to 111 and e-value of 6.73e-74 CDS 82227 - 82373 /gene="138" /product="gp138" /function="hypothetical protein" /locus tag="Yassified_138" /note=Original Glimmer call @bp 82227 has strength 9.58; Genemark calls start at 82227 /note=SSC: 82227-82373 CP: yes SCS: both ST: SS BLAST-Start: [gp140 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 7.00339E-26 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.528, -5.795782549058414, no F: hypothetical protein SIF-BLAST: ,,[gp140 [Mycobacterium phage Bxz1] ],,NP_818213,100.0,7.00339E-26 SIF-HHPRED: SIF-Syn: Not informative. /note=None of the evidence supports calling it a function. Not a transmembrane domain. CDS 82370 - 82513 /gene="139" /product="gp139" /function="hypothetical protein" /locus tag="Yassified_139" /note=Original Glimmer call @bp 82370 has strength 20.19; Genemark calls start at 82370 /note=SSC: 82370-82513 CP: yes SCS: both ST: SS BLAST-Start: [gp141 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 4.40942E-22 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.291, -2.0949393225970705, yes F: hypothetical protein SIF-BLAST: ,,[gp141 [Mycobacterium phage Bxz1] ],,NP_818214,100.0,4.40942E-22 SIF-HHPRED: SIF-Syn: Not informative. /note=None of the evidence supports calling a function. It doesn`t have a transmembrane domain. CDS 82515 - 83870 /gene="140" /product="gp140" /function="minor tail protein" /locus tag="Yassified_140" /note=Original Glimmer call @bp 82515 has strength 18.09; Genemark calls start at 82515 /note=SSC: 82515-83870 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_140 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 0.0 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.796, -5.443606692405957, no F: minor tail protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_140 [Mycobacterium phage ScottMcG] ],,YP_002224168,100.0,0.0 SIF-HHPRED: SIF-Syn: Basquiat_141 is syntenic. Flanking genes are also similar. /note=Supported by BLAST in NCBI and PhagesDB. Not supported by CDD. HHpred has a match with a base plate protein. Supported by 53 instances in PhagesDB for C1 phages. CDS 83882 - 87685 /gene="141" /product="gp141" /function="minor tail protein" /locus tag="Yassified_141" /note=Original Glimmer call @bp 83891 has strength 15.57; Genemark calls start at 83882 /note=SSC: 83882-87685 CP: yes SCS: both-gm ST: SS BLAST-Start: [minor tail protein [Mycobacterium phage Blackbrain]],,NCBI, q1:s1 100.0% 0.0 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.291, -2.782170923661845, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Blackbrain]],,QDF16385,99.9211,0.0 SIF-HHPRED: Endo-1,4-beta-xylanase C; Binding Site, Carbohydrates, Enzyme Stability, Substrate Specificity, Endo-1, 4-beta-xylanase, Xylan-binding domain, Thermophilic enzymes, Thermostabilizing Domains, sugar; HET: GOL, CA; 2.43A {Paenibacillus barcinonensis},,,4XUP_F,28.8871,98.7 SIF-Syn: Basquiat_142 is syntenic as well as the up and downstream genes. /note=Supported by BLAST in NCBI and PhagesDB. It has been called 91 times in PhagesDB with 100% frequency. HHPred matches to a and CDD do not support it. CDS complement (87739 - 88065) /gene="142" /product="gp142" /function="hypothetical protein" /locus tag="Yassified_142" /note=Original Glimmer call @bp 88065 has strength 13.01; Genemark calls start at 88065 /note=SSC: 88065-87739 CP: yes SCS: both ST: SS BLAST-Start: [gp145 [Mycobacterium phage Spud] ],,NCBI, q1:s1 100.0% 1.92531E-73 GAP: 38 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.63, -3.4219145408355454, yes F: hypothetical protein SIF-BLAST: ,,[gp145 [Mycobacterium phage Spud] ],,YP_002224394,100.0,1.92531E-73 SIF-HHPRED: SIF-Syn: Not informative /note=None of the evidence supports calling a function. Doesn`t have a transmembrane domain. CDS complement (88104 - 88430) /gene="143" /product="gp143" /function="hypothetical protein" /locus tag="Yassified_143" /note=Original Glimmer call @bp 88430 has strength 13.64; Genemark calls start at 88430 /note=SSC: 88430-88104 CP: yes SCS: both ST: SS BLAST-Start: [gp142 [Mycobacterium phage Rizal] ],,NCBI, q1:s13 100.0% 8.85967E-71 GAP: 176 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.216, -2.1123791669543204, yes F: hypothetical protein SIF-BLAST: ,,[gp142 [Mycobacterium phage Rizal] ],,YP_002224835,90.0,8.85967E-71 SIF-HHPRED: SIF-Syn: Not informative. /note=None of the evidence supports calling a function. Not a transmembrane domain. CDS 88607 - 89080 /gene="144" /product="gp144" /function="hypothetical protein" /locus tag="Yassified_144" /note=Original Glimmer call @bp 88607 has strength 17.01; Genemark calls start at 88607 /note=SSC: 88607-89080 CP: yes SCS: both ST: SS BLAST-Start: [gp146 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 6.10912E-108 GAP: 176 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.216, -2.253377680616507, yes F: hypothetical protein SIF-BLAST: ,,[gp146 [Mycobacterium phage Bxz1] ],,NP_818219,100.0,6.10912E-108 SIF-HHPRED: SIF-Syn: Not informative. /note=None of the evidence supports calling a function. Not a transmembrane domain. CDS 89249 - 89392 /gene="145" /product="gp145" /function="hypothetical protein" /locus tag="Yassified_145" /note=Original Glimmer call @bp 89249 has strength 18.4; Genemark calls start at 89249 /note=SSC: 89249-89392 CP: yes SCS: both ST: SS BLAST-Start: [gp147 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 5.55757E-24 GAP: 168 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.216, -2.1123791669543204, yes F: hypothetical protein SIF-BLAST: ,,[gp147 [Mycobacterium phage Bxz1] ],,NP_818220,100.0,5.55757E-24 SIF-HHPRED: SIF-Syn: Not informative. /note=No evidence supporting calling a function including BLAST, CDD and HHPred. CDS 89392 - 89718 /gene="146" /product="gp146" /function="hypothetical protein" /locus tag="Yassified_146" /note=Original Glimmer call @bp 89392 has strength 14.12; Genemark calls start at 89392 /note=SSC: 89392-89718 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_146 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 2.57714E-71 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_146 [Mycobacterium phage ScottMcG] ],,YP_002224174,100.0,2.57714E-71 SIF-HHPRED: SIF-Syn: Not informative. /note=No evidence supporting calling a function. Not a transmembrane protein. CDS 89783 - 90028 /gene="147" /product="gp147" /function="hypothetical protein" /locus tag="Yassified_147" /note=Original Glimmer call @bp 89783 has strength 14.65; Genemark calls start at 89783 /note=SSC: 89783-90028 CP: yes SCS: both ST: SS BLAST-Start: [gp147 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 1.3348E-48 GAP: 64 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[gp147 [Mycobacterium phage Cali] ],,YP_002224620,100.0,1.3348E-48 SIF-HHPRED: DUF3921 ; Protein of unknown function (DUF3921),,,PF13060.9,29.6296,47.2 SIF-Syn: PECAAN Yassified Gene 145 is syntenic to PECAAN Gene 138 on BeanWater, which also calls for a hypothetical protein. /note=Both Glimmer and GeneMark Agree @89783. Strong Glimmer Score of 14.65 for Start Site. 158 MA`s @89783 on Starterator. /note= /note=No data available in Phagesdb Function Frequency. PhagesDB Blast provides multiple hits of "function unknown" from the C1 cluster including BeanWater, with favorable e-values of 2e-37. Best result on HHPred is for an unknown protein with a probability of 47.2. Best hit on NCBI Blast is the hypothetical protein with an % identity of 100% and favorable e-value of 1.3e-48. CDS 90021 - 90251 /gene="148" /product="gp148" /function="Hypothetical Protein" /locus tag="Yassified_148" /note=Original Glimmer call @bp 90021 has strength 2.85; Genemark calls start at 90021 /note=SSC: 90021-90251 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_148 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 6.15427E-49 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.272, -4.620091156089588, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_148 [Mycobacterium phage ScottMcG] ],,YP_002224176,100.0,6.15427E-49 SIF-HHPRED: DUF1995 ; Domain of unknown function (DUF1995),,,PF09353.13,39.4737,72.1 SIF-Syn: PECAAN Yassified Gene 146 is syntenic to PECAAN Gene 139 on BeanWater, which also calls for a hypothetical protein. /note=Both Glimmer and GeneMark Agree on Start Site 90021. Weak Glimmer Score of 2.85 for Start Site. However, there are 151 MA`s @90021on Starterator. /note= /note=No data available in Phagesdb Function Frequency. PhagesDB Blast provides multiple hits of "function unknown" from the C1 cluster including BeanWater, with favorable e-values of 2e-44. Best result on HHPred is for an unknown protein with a probability of 72.1. Best hit on NCBI Blast is the hypothetical protein with an % identity of 100% and favorable e-value of 6.1e-49. tRNA 90443 - 90517 /gene="149" /product="tRNA-Pro(tgg)" /locus tag="YASSIFIED_149" /note=tRNA-Pro(tgg) tRNA 90532 - 90602 /gene="150" /product="tRNA-Trp(cca)" /locus tag="YASSIFIED_150" /note=tRNA-Trp(cca) tRNA 90604 - 90685 /gene="151" /product="tRNA-Tyr(gta)" /locus tag="YASSIFIED_151" /note=tRNA-Tyr(gta) CDS 90768 - 91049 /gene="152" /product="gp152" /function="Hypothetical Protein" /locus tag="Yassified_152" /note=Original Glimmer call @bp 90768 has strength 7.3; Genemark calls start at 90768 /note=SSC: 90768-91049 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_152 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 5.85775E-61 GAP: 516 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.138, -2.2763497933341483, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_152 [Mycobacterium phage ScottMcG] ],,YP_002224177,100.0,5.85775E-61 SIF-HHPRED: SIF-Syn: PECAAN Yassified Gene 147 is syntenic to PECAAN Gene 140 on BeanWater, which also calls for a hypothetical protein. /note=Both Glimmer and GeneMark Agree on Start Site 90768. Weak Glimmer Score of 7.3 for Start Site. However, there are 155 MA`s @90768 on Starterator. /note= /note=No data available in Phagesdb Function Frequency. PhagesDB Blast provides multiple hits of "function unknown" from the C1 cluster including BeanWater, with favorable e-values of 2e-44. Best hit on NCBI Blast is the hypothetical protein with an % identity of 100% and favorable e-value of 6.1e-49. HHPred provides very weak evidence. CDS 91114 - 91488 /gene="153" /product="gp153" /function="peptidyl tRNA hydrolase" /locus tag="Yassified_153" /note=Original Glimmer call @bp 91114 has strength 8.29; Genemark calls start at 91114 /note=SSC: 91114-91488 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_153 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.68936E-85 GAP: 64 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.953, -4.843798539558957, no F: peptidyl tRNA hydrolase SIF-BLAST: ,,[hypothetical protein SCOTTMCG_153 [Mycobacterium phage ScottMcG] ],,YP_002224178,100.0,1.68936E-85 SIF-HHPRED: Peptidyl-tRNA hydrolase; alpha-beta, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Cytoplasm, Hydrolase; 1.8A {Archaeoglobus fulgidus} SCOP: c.131.1.1,,,3ERJ_B,87.9032,99.9 SIF-Syn: PECAAN Yassified Gene 148 is syntenic to PECAAN Gene 141 on BeanWater, which also calls for a peptidyl-tna hydrolase protein. /note=Both Glimmer and GeneMark Agree on Start Site 91114. Relatively Weak Glimmer Score of 8.29 for Start Site. However, there are 161 MA`s @91114 on Starterator. /note= /note=Phagesdb Function Frequency has peptidyl trna hydrolase with a 99% frequency and 86 counts. PhagesDB Blast provides multiple hits of "function unknown" from the C1 cluster including BeanWater, with favorable e-values of 2e-44. Best result on HHPred is for an unknown protein with a probability of 72.1. Best hit on NCBI Blast is the hypothetical protein with an % identity of 100% and favorable e-value of 6.1e-49. tRNA 91738 - 91810 /gene="154" /product="tRNA-Stop(cta)" /locus tag="YASSIFIED_154" /note=tRNA-Stop(cta) tRNA 91960 - 92034 /gene="155" /product="tRNA-Met(cat)" /locus tag="YASSIFIED_155" /note=tRNA-Met(cat) tRNA 92248 - 92319 /gene="156" /product="tRNA-Cys(gca)" /locus tag="YASSIFIED_156" /note=tRNA-Cys(gca) tRNA 92387 - 92458 /gene="157" /product="tRNA-Glu(ctc)" /locus tag="YASSIFIED_157" /note=tRNA-Glu(ctc) tRNA 92513 - 92586 /gene="158" /product="tRNA-His(gtg)" /locus tag="YASSIFIED_158" /note=tRNA-His(gtg) tRNA 92744 - 92817 /gene="159" /product="tRNA-Ala(tgc)" /locus tag="YASSIFIED_159" /note=tRNA-Ala(tgc) tRNA 93007 - 93079 /gene="160" /product="tRNA-Phe(gaa)" /locus tag="YASSIFIED_160" /note=tRNA-Phe(gaa) tRNA 93085 - 93158 /gene="161" /product="tRNA-Val(cac)" /locus tag="YASSIFIED_161" /note=tRNA-Val(cac) tRNA 93277 - 93349 /gene="162" /product="tRNA-Lys(ctt)" /locus tag="YASSIFIED_162" /note=tRNA-Lys(ctt) tRNA 93354 - 93430 /gene="163" /product="tRNA-Glu(ttc)" /locus tag="YASSIFIED_163" /note=tRNA-Glu(ttc) tRNA 93510 - 93582 /gene="164" /product="tRNA-Gly(tcc)" /locus tag="YASSIFIED_164" /note=tRNA-Gly(tcc) tRNA 93664 - 93738 /gene="165" /product="tRNA-Thr(cgt)" /locus tag="YASSIFIED_165" /note=tRNA-Thr(cgt) tRNA 93739 - 93811 /gene="166" /product="tRNA-Thr(tgt)" /locus tag="YASSIFIED_166" /note=tRNA-Thr(tgt) CDS 93839 - 94213 /gene="167" /product="gp167" /function="HNH endonuclease" /locus tag="Yassified_167" /note=Original Glimmer call @bp 93839 has strength 3.82; Genemark calls start at 93839 /note=SSC: 93839-94213 CP: yes SCS: both ST: SS BLAST-Start: [Endo VII [Mycobacterium phage ArcherS7] ],,NCBI, q1:s1 100.0% 2.98141E-86 GAP: 2350 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.633, -6.261894655997472, no F: HNH endonuclease SIF-BLAST: ,,[Endo VII [Mycobacterium phage ArcherS7] ],,YP_008061413,100.0,2.98141E-86 SIF-HHPRED: HNH endonuclease; Thermophilic bacteriophage, HNH Endonuclease, DNA nicking, HYDROLASE; 1.52A {Geobacillus virus E2},,,5H0M_A,58.0645,97.7 SIF-Syn: PECAAN Yassified Gene 150 is syntenic to Gene 172 of Zeenon from the Phams Database, which also calls for a HNH endonuclease /note=Both Glimmer and GeneMark Agree on Start Site 93839. Weak Glimmer Score of 3.82 for Start Site. However, there are 7 MA`s @91114 on Starterator, supporting this start site. /note= /note=Phagesdb Function Frequency calls an hnh endonuclease in the C1 cluster with a 87% frequency and 67 counts. PhagesDB Blast provides multiple hits of "HNH endonuclease" from the C1 cluster, with favorable e-values of 1e-72. Best result on HHPred is for an hnh endonuclease with a probability of 97.7. Best hit on NCBI Blast is the hnh endonuclease protein with an % identity of 100% a somewhat weak e-value of 8.3e-5. tRNA 94219 - 94291 /gene="168" /product="tRNA-Thr(ggt)" /locus tag="YASSIFIED_168" /note=tRNA-Thr(ggt) CDS 94361 - 95437 /gene="169" /product="gp169" /function="minor tail protein" /locus tag="Yassified_169" /note=Original Glimmer call @bp 94361 has strength 12.45; Genemark calls start at 94361 /note=SSC: 94361-95437 CP: yes SCS: both ST: SS BLAST-Start: [gp169 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 147 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.726, -3.139452255336754, yes F: minor tail protein SIF-BLAST: ,,[gp169 [Mycobacterium phage Bxz1] ],,NP_818228,99.7207,0.0 SIF-HHPRED: SIF-Syn: Synteny analysis provides poor results as Gene 151 in Yassified corresponds to Gene 143 in Beanwater, which calls for a d-ala-d-ala carboxypeptidase, minor tail protein. There isn`t enough evidence to conclude this gene in Yassified isn`t a minor tail protein. /note=Both Glimmer and GeneMark Agree @94361. Strong Glimmer Score of 12.45 for Start Site. 158 MA`s @94361 on Starterator. /note= /note=Phagesdb Function Frequency calls for aa minor tail protein based on a count of 84 and frequency of 98% in the C1 subcluster. PhagesDB Blast provides multiple hits of "minor tail protein" from the C1 cluster including BeanWater, with favorable e-values of 0. However, HHPred and the Conserved Domain Database do not support this function since they do not call for the minor tail protein at all. Best hit on NCBI Blast is the minor tail protein with an % identity of 99.7% and favorable e-value of 0. CDS 95445 - 95603 /gene="170" /product="gp170" /function="hypothetical protein" /locus tag="Yassified_170" /note=Original Glimmer call @bp 95445 has strength 6.33; Genemark calls start at 95445 /note=SSC: 95445-95603 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_161 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 5.48305E-27 GAP: 7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.298, -4.691784380744663, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_161 [Mycobacterium phage ET08] ],,YP_003347823,100.0,5.48305E-27 SIF-HHPRED: SIF-Syn: PECAAN Yassified Gene 151 is syntenic to PECAAN Gene 144 on BeanWater, which also calls for a hypothetical protein. /note=Both Glimmer and GeneMark Agree @95445. Relatively Weak Glimmer Score of 14.65 for Start Site. However, there are 150 MA`s @95445 on Starterator. /note= /note=Very weak evidence in Phagesdb Function Frequency, which calls for a minor tail protein but there is only a count of 1. PhagesDB Blast provides multiple hits of "function unknown" from the C1 cluster with favorable e-values of 2e-26. HHPred doesn`t provide any evidence. Best hit on NCBI Blast is the hypothetical protein with an % identity of 100% and favorable e-value of 5.4e-27. tRNA 96036 - 96111 /gene="171" /product="tRNA-Gly(gcc)" /locus tag="YASSIFIED_171" /note=tRNA-Gly(gcc) tRNA 96125 - 96197 /gene="172" /product="tRNA-Asp(gtc)" /locus tag="YASSIFIED_172" /note=tRNA-Asp(gtc) tRNA 96257 - 96329 /gene="173" /product="tRNA-Met(cat)" /locus tag="YASSIFIED_173" /note=tRNA-Met(cat) tRNA 96335 - 96409 /gene="174" /product="tRNA-Ile(gat)" /locus tag="YASSIFIED_174" /note=tRNA-Ile(gat) tRNA 96503 - 96575 /gene="175" /product="tRNA-Arg(acg)" /locus tag="YASSIFIED_175" /note=tRNA-Arg(acg) tRNA 96618 - 96690 /gene="176" /product="tRNA-Val(gac)" /locus tag="YASSIFIED_176" /note=tRNA-Val(gac) tRNA 96784 - 96853 /gene="177" /product="tRNA-Gly(tcc)" /locus tag="YASSIFIED_177" /note=tRNA-Gly(tcc) tRNA 96864 - 96937 /gene="178" /product="tRNA-Arg(cct)" /locus tag="YASSIFIED_178" /note=tRNA-Arg(cct) tmRNA 96951 - 97385 /gene="179" /locus tag="YASSIFIED_179" /note= tRNA 97478 - 97553 /gene="180" /product="tRNA-Gln(ttg)" /locus tag="YASSIFIED_180" /note=tRNA-Gln(ttg) tRNA 97557 - 97632 /gene="181" /product="tRNA-Arg(tct)" /locus tag="YASSIFIED_181" /note=tRNA-Arg(tct) tRNA 97634 - 97706 /gene="182" /product="tRNA-Lys(ttt)" /locus tag="YASSIFIED_182" /note=tRNA-Lys(ttt) CDS complement (97721 - 98197) /gene="183" /product="gp183" /function="Hypothetical Protein" /locus tag="Yassified_183" /note=Original Glimmer call @bp 98197 has strength 11.86; Genemark calls start at 98197 /note=SSC: 98197-97721 CP: yes SCS: both ST: SS BLAST-Start: [gp178 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.69121E-111 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.794, -3.077027835973012, yes F: Hypothetical Protein SIF-BLAST: ,,[gp178 [Mycobacterium phage Bxz1] ],,NP_818229,100.0,2.69121E-111 SIF-HHPRED: SIF-Syn: PECAAN Yassified Gene 153 is syntenic to PECAAN Gene 145 on BeanWater, which also a reverse gene that calls for a hypothetical protein. /note=Both Glimmer and GeneMark Agree @98197. Strong Glimmer Score of 11.86 for Start Site. 158 MA`s @98197 on Starterator. /note= /note=No evidence on Phagesdb Function Frequency, which calls a dna binding protein with a count of 1. PhagesDB Blast provides multiple hits of "function unknown" from the C1 cluster, with favorable e-values of 2e-90. HHPred doesn`t provide any evidence. Best hit on NCBI Blast is the hypothetical protein with an % identity of 100% and favorable e-value of 2.6e-111. CDS complement (98197 - 100059) /gene="184" /product="gp184" /function="DNA helicase" /locus tag="Yassified_184" /note=Original Glimmer call @bp 100059 has strength 19.31; Genemark calls start at 100059 /note=SSC: 100059-98197 CP: yes SCS: both ST: SS BLAST-Start: [gp184 [Mycobacterium phage Spud] ],,NCBI, q1:s1 100.0% 0.0 GAP: 115 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.421, -6.530842035202567, no F: DNA helicase SIF-BLAST: ,,[gp184 [Mycobacterium phage Spud] ],,YP_002224405,100.0,0.0 SIF-HHPRED: Chromatin-remodeling ATPase INO80; Chromatin, Remodeller, Nucleosome, DNA Binding, Histones, DNA repair, ATPase, Helicase, Sliding, Complex, DNA BINDING PROTEIN; HET: ADP;{Homo sapiens},,,6HTS_G,78.2258,100.0 SIF-Syn: Zeenon_190 is syntenic same function. /note=The start site is 100059 which is predicted by both glimmer start and geneMark start. The length of the suggested start site is 1863 and the smallest gaps 115. It is a DNA helicase function. Phagesdb BLAST evidence suggests Dandelion with DNA helicase function. HHPRED suggests 6HST_G with 100 probability, 78.2258% coverage, and e-value of 0. NCBI BLAST is YP_002224405 with 100% identity, 100% aligned, 100% coverage and 620 positives. Conserved Domain Database: pfam00271 with 42.7273% aligned and 17.9032% coverage, 47 positive and an e-value of 1.96835e-12. /note=Transmembrane prediction: 0 CDS 100175 - 100477 /gene="185" /product="gp185" /function="hypothetical protein" /locus tag="Yassified_185" /note=Original Glimmer call @bp 100175 has strength 15.69; Genemark calls start at 100175 /note=SSC: 100175-100477 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FUDGETART_184 [Mycobacterium phage FudgeTart] ],,NCBI, q1:s1 100.0% 5.28536E-64 GAP: 115 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FUDGETART_184 [Mycobacterium phage FudgeTart] ],,AYD83625,100.0,5.28536E-64 SIF-HHPRED: KfrA_N ; Plasmid replication region DNA-binding N-term,,,PF11740.11,44.0,78.8 SIF-Syn: not informative. /note=The start site is 100175 which is predicted by both glimmer start and geneMark start. The length of the suggested start site is 303 and the smallest gaps - 50 . It is a NKF. Phagesdb BLAST evidence suggests FudgeTart with NKF. HHPRED suggests PF11740.11 with 78.8 probability, 44% coverage, and e-value of 24. NCBI BLAST is AYD83625 with 100 identity, 100 aligned, 100 coverage and 100 positives. Conserved Domain Database: no data found . /note=Transmembrane prediction: 0 CDS 100628 - 100885 /gene="186" /product="gp186" /function="hypothetical protein" /locus tag="Yassified_186" /note= /note=SSC: 100628-100885 CP: no SCS: neither ST: NI BLAST-Start: GAP: 150 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.47, -6.303967205231885, no F: hypothetical protein SIF-BLAST: SIF-HHPRED: SIF-Syn: not informative. /note=This ORF has a very weak coding capacity according to Genemark, but it is in the middle of a large gap between 155 and 157. No evidence of a function. CDS 100910 - 101335 /gene="187" /product="gp187" /function="hypothetical protein" /locus tag="Yassified_187" /note=Original Glimmer call @bp 100910 has strength 6.81; Genemark calls start at 100910 /note=SSC: 100910-101335 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FUDGETART_185 [Mycobacterium phage FudgeTart]],,NCBI, q1:s1 100.0% 3.52854E-98 GAP: 24 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.362, -4.556208905684731, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FUDGETART_185 [Mycobacterium phage FudgeTart]],,AYD83626,99.2908,3.52854E-98 SIF-HHPRED: Flagellar motor switch protein FliM; Flagellar motor protein, MOTOR PROTEIN; 1.44A {Vibrio alginolyticus},,,7DMA_B,17.0213,70.9 SIF-Syn: not informative. /note=The start site is 100910 which is predicted by both glimmer start and geneMark start. The length of the suggested start site is 426 and the smallest gaps 432. It is a NKF. Phagesdb BLAST evidence suggests Yassified Draft with unknown function. HHPRED suggests 7DMA_B with 70.9 probability, 17.0213 coverage, and e-value of 23. NCBI BLAST is AYD83626 with 99.2908 identity, 52.38 aligned, 93.61 coverage and 66 positives. Conserved Domain Database: no data found /note=Transmembrane prediction: 0 CDS 101385 - 101591 /gene="188" /product="gp188" /function="hypothetical protein" /locus tag="Yassified_188" /note=Original Glimmer call @bp 101385 has strength 11.74; Genemark calls start at 101385 /note=SSC: 101385-101591 CP: yes SCS: both ST: SS BLAST-Start: [gp182 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.69829E-40 GAP: 49 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.551, -4.4158953075094765, yes F: hypothetical protein SIF-BLAST: ,,[gp182 [Mycobacterium phage Bxz1] ],,NP_818233,100.0,2.69829E-40 SIF-HHPRED: SusD superfamily protein; YP_001299712.1, SusD superfamily protein, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2; HET: SO4, MSE, GOL; 1.13A {Bacteroides vulgatus ATCC 8482},,,3JQ0_A,51.4706,57.7 SIF-Syn: not informative. /note=The start site is 101385 which is predicted by both glimmer start and geneMark start. The length of the suggested start site is 207 and the smallest gaps 49. It is a NKF. Phagesdb BLAST evidence suggests Grungle with function unknown. HHPRED suggests 3JQ0_A with 57.7 probability, 51.4706 coverage, and e-value of 84. NCBI BLAST is NP_818233 with 100 identity, 100 aligned, 100 coverage and 68 positives. Conserved Domain Database: no data found. /note=Transmembrane prediction: 0 CDS 101591 - 101767 /gene="189" /product="gp189" /function="hypothetical protein" /locus tag="Yassified_189" /note=Original Glimmer call @bp 101591 has strength 14.27; Genemark calls start at 101591 /note=SSC: 101591-101767 CP: no SCS: both ST: SS BLAST-Start: [gp183 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 5.31404E-31 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.151, -4.487636275856737, yes F: hypothetical protein SIF-BLAST: ,,[gp183 [Mycobacterium phage Bxz1] ],,NP_818234,100.0,5.31404E-31 SIF-HHPRED: TraC ; TraC-like protein,,,PF07820.15,94.8276,66.0 SIF-Syn: /note=The start site is 101591 which is predicted by both glimmer start and geneMark start. The length of the suggested start site is 177 and the smallest gaps -266 and is a TRUE LORF . There is no function. Phagesdb BLAST evidence suggests Guwapp with unknown function. HHPRED PF07820.15 suggests with 66 probability, 94.8276 coverage, and e-value of 20. NCBI BLAST is NP_818234 with 100 identity, 100 aligned, 100 coverage and 58 positives. Conserved Domain Database: no data /note=Transmembrane prediction: 0 CDS 101764 - 101856 /gene="190" /product="gp190" /function="hypothetical protein" /locus tag="Yassified_190" /note=Genemark calls start at 101764 /note=SSC: 101764-101856 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein M182_gp157 [Mycobacterium phage Astraea] ],,NCBI, q1:s1 100.0% 4.76693E-13 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.258, -4.122392812353492, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M182_gp157 [Mycobacterium phage Astraea] ],,YP_008061653,100.0,4.76693E-13 SIF-HHPRED: SIF-Syn: not informative. /note=The start site is the one suggested by Starterator 101764 and also predicted only by geneMark start. The length of the ORF is 93 with a -4 overlap. None of the evidence for function gives a strong match. /note=Transmembrane prediction: 0 CDS 101847 - 102107 /gene="191" /product="gp191" /function="hypothetical protein" /locus tag="Yassified_191" /note=Original Glimmer call @bp 101847 has strength 21.44; Genemark calls start at 101853 /note=SSC: 101847-102107 CP: yes SCS: both-gl ST: SS BLAST-Start: [gp187 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 4.21561E-54 GAP: -10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.746, -3.178158543477495, yes F: hypothetical protein SIF-BLAST: ,,[gp187 [Mycobacterium phage Cali] ],,YP_002224631,100.0,4.21561E-54 SIF-HHPRED: uncharacterized protein; Structural Genomics, PSI-Biology, Northeast Structural Genomics Consortium, NESG, PROPEN_03304, Unknown function; 2.9A {Proteus penneri},,,3RD4_A,36.0465,46.0 SIF-Syn: not informative. /note=The start site is 101847 which is predicted by glimmer start and supported by starterator. The length of the suggested start site is 261 and the smallest gaps 79 . It is a unknown function. Phagesdb BLAST evidence suggests Astraea with unknown function. HHPRED suggests 3RD4_A with 46 probability, 36.0465 coverage, and e-value of 63. NCBI BLAST is YP_002224631 with 100 identity, 100 aligned, 100 coverage and 86 positives. Conserved Domain Database: no data . /note=Transmembrane prediction: 0 CDS 102219 - 102980 /gene="192" /product="gp192" /function="hypothetical protein" /locus tag="Yassified_192" /note=Original Glimmer call @bp 102219 has strength 20.17; Genemark calls start at 102219 /note=SSC: 102219-102980 CP: yes SCS: both ST: SS BLAST-Start: [gp188 [Mycobacterium phage Cali] ],,NCBI, q1:s19 100.0% 0.0 GAP: 111 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[gp188 [Mycobacterium phage Cali] ],,YP_002224632,93.3579,0.0 SIF-HHPRED: SIF-Syn: Not informative. /note=It is a unknown function. Phagesdb BLAST evidence suggests Breeniome with DNA unknown function. HHPRED suggests PF11333.11 with 85.5 probability, 8.85609 coverage, and e-value of 2.5. No strong evidence for a function /note=Transmembrane prediction: 0 CDS 102984 - 103631 /gene="193" /product="gp193" /function="hypothetical protein" /locus tag="Yassified_193" /note=Original Glimmer call @bp 102984 has strength 12.23; Genemark calls start at 102984 /note=SSC: 102984-103631 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_183 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 2.70605E-155 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_183 [Mycobacterium phage ET08] ],,YP_003347833,100.0,2.70605E-155 SIF-HHPRED: DUF5053 ; Domain of unknown function (DUF5053),,,PF16476.8,33.4884,97.5 SIF-Syn: not informative. /note=The start site is 102984 which is predicted by both glimmer start and geneMark start and supported by Starterator. The length of the suggested start site is 648 and the smallest gaps 3 . It is a unknown function. Phagesdb BLAST evidence suggests ArcherS7 unknown function. HHPRED suggests PF16476.8 with 97.5 probability, 33.4884 coverage, and e-value of 0.00068 . NCBI BLAST is YP_003347833 with 100 identity, 100 aligned, 100 coverage and 215 positives. Conserved Domain Database: no data /note=Transmembrane prediction: 0 CDS 103628 - 104152 /gene="194" /product="gp194" /function="hypothetical protein" /locus tag="Yassified_194" /note=Original Glimmer call @bp 103634 has strength 7.5; Genemark calls start at 103628 /note=SSC: 103628-104152 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein ET08_184 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 3.73967E-125 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.998, -4.749088834314575, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_184 [Mycobacterium phage ET08] ],,YP_003347834,100.0,3.73967E-125 SIF-HHPRED: SIF-Syn: Does not inform a function. /note=no evidence supporting calling it a function. No transmembrane domains. CDS 104149 - 104838 /gene="195" /product="gp195" /function="thymidylate kinase" /locus tag="Yassified_195" /note=Original Glimmer call @bp 104149 has strength 13.58; Genemark calls start at 104149 /note=SSC: 104149-104838 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_185 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 1.9052E-164 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.578, -3.5316035464369326, yes F: thymidylate kinase SIF-BLAST: ,,[hypothetical protein ET08_185 [Mycobacterium phage ET08] ],,YP_003347835,100.0,1.9052E-164 SIF-HHPRED: c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]} | CLASS: Alpha and beta proteins (a/b), FOLD: P-loop containing nucleoside triphosphate hydrolases, SUPFAM: P-loop containing nucleoside triphosphate hydrolases, FAM: Nucleotide and nucleoside kinases,,,SCOP_d1nn5a_,97.3799,99.8 SIF-Syn: Zeenon_200. Similar up and downstream genes. /note=PhagesDB fuction is listed as thymidylate kinase in 66 instances. PhagesDB supports function with 100% frequency. NCBI Blast shows 100% identity, alignment, and coverage. CDS 104810 - 105853 /gene="196" /product="gp196" /function="aminotransferase" /locus tag="Yassified_196" /note=Original Glimmer call @bp 104810 has strength 11.03; Genemark calls start at 104810 /note=SSC: 104810-105853 CP: yes SCS: both ST: SS BLAST-Start: [aminotransferase [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 0.0 GAP: -29 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.298, -4.947056885847969, no F: aminotransferase SIF-BLAST: ,,[aminotransferase [Mycobacterium phage ET08] ],,YP_003347836,100.0,0.0 SIF-HHPRED: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; transaminase PLP Complex Fragment, transferase-transferase inhibitor complex; HET: EPE, EDO, PLP, 3VR; 1.35A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)} SCOP: c.67.1.0,,,4WYD_A,89.6254,100.0 SIF-Syn: Zeenon_201 is syntenic and with same function call. Up and downstream genes are also similar. /note=Function listed in phagesdb as aminotransferase 88 times with a frequency of 98%. Function is supported by HHPRED. Phages Blast supports the function with e-value of 0. The NCBI has 100% of identity, aligned, coverage with e-value of 0. CDS 105897 - 106340 /gene="197" /product="gp197" /function="hypothetical protein" /locus tag="Yassified_197" /note=Original Glimmer call @bp 105897 has strength 13.81; Genemark calls start at 105936 /note=SSC: 105897-106340 CP: yes SCS: both-gl ST: NA BLAST-Start: [hypothetical protein M180_gp152 [Mycobacterium phage ArcherS7] ],,NCBI, q1:s1 100.0% 1.56061E-105 GAP: 43 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.905, -3.8666016581442175, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M180_gp152 [Mycobacterium phage ArcherS7] ],,YP_008061428,100.0,1.56061E-105 SIF-HHPRED: DUF2642 ; Protein of unknown function (DUF2642),,,PF10842.11,44.898,96.2 SIF-Syn: /note=Function listed in phagesdb as RNA binding protein only 3 instances Function is not supported by HHPRED, BLAST, and CDD. It doesn`t have a transmembrane domain. CDS 106407 - 106793 /gene="198" /product="gp198" /function="hypothetical protein" /locus tag="Yassified_198" /note=Original Glimmer call @bp 106407 has strength 14.29; Genemark calls start at 106407 /note=SSC: 106407-106793 CP: yes SCS: both ST: SS BLAST-Start: [gp190 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 9.46738E-90 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.216, -2.4634880269616195, yes F: hypothetical protein SIF-BLAST: ,,[gp190 [Mycobacterium phage Bxz1] ],,NP_818241,100.0,9.46738E-90 SIF-HHPRED: HLD_clamp_pol_III_delta; helical lid domain of DNA polymerase III subunits delta. DNA polymerase III subunit delta is part of the DNA polymerase III holoenzyme.,,,cd18138,39.0625,86.2 SIF-Syn: Not informative. /note=No evidence supporting a function call. No TMB domains. CDS 106793 - 107167 /gene="199" /product="gp199" /function="hypothetical protein" /locus tag="Yassified_199" /note=Original Glimmer call @bp 106934 has strength 9.7; Genemark calls start at 106793 /note=SSC: 106793-107167 CP: yes SCS: both-gm ST: NA BLAST-Start: [hypothetical protein ET08_189 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 5.99052E-87 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.312, -6.188708875567495, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_189 [Mycobacterium phage ET08] ],,YP_003347839,100.0,5.99052E-87 SIF-HHPRED: SIF-Syn: Not informative. /note=No function call instances in PhagesDB and no other evidence source calling a function. Not a TMB domain. CDS 107164 - 107946 /gene="200" /product="gp200" /function="DnaC-like helicase loader" /locus tag="Yassified_200" /note=Original Glimmer call @bp 107164 has strength 15.3; Genemark calls start at 107164 /note=SSC: 107164-107946 CP: yes SCS: both ST: SS BLAST-Start: [putative DnaC [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.49, -5.73456940637445, no F: DnaC-like helicase loader SIF-BLAST: ,,[putative DnaC [Mycobacterium phage ScottMcG] ],,YP_002224194,100.0,0.0 SIF-HHPRED: Primosomal protein DnaI; primase, helicase loader, DnaB, DnaG, DnaI, DNA replication, REPLICATION; HET: MSE; 6.1A {Geobacillus stearothermophilus},,,4M4W_K,93.0769,100.0 SIF-Syn: /note=Function listed in phagesdb as dnac-like helicase loader 91 times with a frequency of 99%. Function is supported by HHPRED. Phages Blast supports the function with e-value of 1e-153. The NCBI has 100% of identity, aligned, coverage. CDS 107948 - 109204 /gene="201" /product="gp201" /function="DnaB-like dsDNA helicase" /locus tag="Yassified_201" /note=Original Glimmer call @bp 107939 has strength 17.49; Genemark calls start at 107948 /note=SSC: 107948-109204 CP: yes SCS: both-gm ST: SS BLAST-Start: [gp193 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.993, -6.918086385167798, no F: DnaB-like dsDNA helicase SIF-BLAST: ,,[gp193 [Mycobacterium phage Bxz1] ],,NP_818244,100.0,0.0 SIF-HHPRED: SIF-Syn: Colt_195 is syntenic and has the same function call. /note=Function listed in phagesdb as DnaB-like dsDNA helicase 84 times with a frequency of 97%. Function is supported by HHPRED. Phages Blast supports the function with e-value of 0. The NCBI has 100% of identity, aligned, coverage. No TMB domain. CDS 109201 - 109407 /gene="202" /product="gp202" /function="hypothetical protein" /locus tag="Yassified_202" /note=Original Glimmer call @bp 109201 has strength 15.5; Genemark calls start at 109201 /note=SSC: 109201-109407 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_197 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.24532E-41 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.895, -4.963787326180191, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_197 [Mycobacterium phage ScottMcG] ],,YP_002224196,100.0,1.24532E-41 SIF-HHPRED: AVR-Pia protein; UNKNOWN FUNCTION; NMR {Magnaporthe oryzae},,,2MYW_A,60.2941,23.6 SIF-Syn: Beanwater_196 /note=Function is not listed so is a not known function. Function is not supported by HHPRED or BLAST or CDD, Is not a TMB domain. CDS 109404 - 110477 /gene="203" /product="gp203" /function="DNA primase" /locus tag="Yassified_203" /note=Original Glimmer call @bp 109404 has strength 8.63; Genemark calls start at 109404 /note=SSC: 109404-110477 CP: yes SCS: both ST: SS BLAST-Start: [DNA primase [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.146, -5.40694046485655, no F: DNA primase SIF-BLAST: ,,[DNA primase [Mycobacterium phage ScottMcG] ],,YP_002224197,100.0,0.0 SIF-HHPRED: DNA primase; Zinc Ribbon, TOPRIM, RNA POLYMERASE, DNA REPLICATION, TRANSFERASE; 2.0A {Aquifex aeolicus},,,2AU3_A,96.9188,100.0 SIF-Syn: When taking into account trna genes, gene 172 in yassfied becomes gene 203 in phamerator. BeanWater has similar gene 197 that has same length with purple region showing high nucleotide similarity. BeanWater calls the function DNA primase for gene 197. Zeenon gene 207 also has purple background and shows synteny with gene 172. DNA primase as called function in syntenic genes. /note=Strong evidence for DNA primase function from PhagesDB(90 times), Blast, and HHpred. GeneMark and Glimmer called the same start site: 109404. Best overlap for this start. Q1:S1 alignment with 100% alignment for ScottMcG and many other bacteriophages. 109404 has 162 MA`s in Starterator. CDS 110481 - 110720 /gene="204" /product="gp204" /function="hypothetical protein" /locus tag="Yassified_204" /note=Original Glimmer call @bp 110481 has strength 8.58; Genemark calls start at 110481 /note=SSC: 110481-110720 CP: yes SCS: both ST: SS BLAST-Start: [gp196 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.60253E-49 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.62, -4.01551542808139, yes F: hypothetical protein SIF-BLAST: ,,[gp196 [Mycobacterium phage Bxz1] ],,NP_818247,100.0,1.60253E-49 SIF-HHPRED: DUF5446 ; Family of unknown function (DUF5446),,,PF17522.5,48.1013,69.5 SIF-Syn: When comparing to BeanWater and Zeenon gene 173 is similar to genes in both these phages indicated by purple background. No function called for this gene in both similar phages from C1 group. /note=Start supported by glimmer and genemark. Best gap possible. Contains all GM coding capacity. No function supported by PhagesDB, Blast, or HHpred. In one instance in a C1 phage is called a DNA primase/polymerase, but all other evidence is not supportive of that call. CDS 110683 - 111471 /gene="205" /product="gp205" /function="chaperonin, DnaJ-like" /locus tag="Yassified_205" /note=Original Glimmer call @bp 110683 has strength 10.59; Genemark calls start at 110941 /note=SSC: 110683-111471 CP: yes SCS: both-gl ST: SS BLAST-Start: [DnaJ domain protein [Mycobacterium phage Gizmo] ],,NCBI, q1:s1 100.0% 0.0 GAP: -38 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.648, -5.465638252962307, no F: chaperonin, DnaJ-like SIF-BLAST: ,,[DnaJ domain protein [Mycobacterium phage Gizmo] ],,YP_008060979,100.0,0.0 SIF-HHPRED: Co-chaperone protein HscB, mitochondrial precursor; Co-chaperone protein HscB, Structural Genomics Medical Relevance, Protein Structure Initiative, PSI-2, Center for Eukaryotic Structural Genomics; HET: MSE; 3.0A {Homo sapiens},,,3BVO_A,46.5649,99.2 SIF-Syn: Gene 174 in yassified has strong nucleotide similarity to BeanWater gene 199 indicated by purple background. The same is true for Zeenon gene 209. Both BeanWater and Zeenon call the function DnaJ-like chaperonin in there similar gene to yassified 174. /note=Genemark and Glimmer disagree on start. Glimmer start has all GM coding potential. Glimmer start also has more MA`s. Function is supported by HHpred, Blast, and Phamerator. Low coverage on HHpred hit. e-value of zero for NCBI blast hits. 93 instances in PhagesDB in C1 phages. No TMB domain. CDS 111578 - 112528 /gene="206" /product="gp206" /function="SSB protein" /locus tag="Yassified_206" /note=Original Glimmer call @bp 111578 has strength 12.75; Genemark calls start at 111578 /note=SSC: 111578-112528 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ZEENON_210 [Mycobacterium phage Zeenon] ],,NCBI, q1:s1 100.0% 0.0 GAP: 106 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.064, -4.6716733337618095, no F: SSB protein SIF-BLAST: ,,[hypothetical protein SEA_ZEENON_210 [Mycobacterium phage Zeenon] ],,AKY02470,99.6835,0.0 SIF-HHPRED: gp32 single stranded DNA binding protein; Zn2+ binding subdomain, 5-stranded beta-sheet, OB fold, single-stranded DNA binding, DNA BINDING PROTEIN; 2.0A {Enterobacteria phage RB69} SCOP: b.40.4.7,,,2A1K_B,57.2785,99.6 SIF-Syn: Gene 175 in yassified has strong nucleotide similarity to BeanWater gene 200 indicated by purple background. The same is true for Zeenon gene 210. Both BeanWater and Zeenon call the no function. /note=Start site called by GM and glimmer cause huge gap. Start 111557 might be better option as it makes smaller gap and has more MA`s however is not supported by GM or glimmer. Function is supported by HHpred but, only partially by Blast. Can be hypothetical protein. CDS 112716 - 116111 /gene="207" /product="gp207" /function="DnaE-like DNA polymerase III (alpha)" /locus tag="Yassified_207" /note=Original Glimmer call @bp 112716 has strength 20.51; Genemark calls start at 112716 /note=SSC: 112716-116111 CP: yes SCS: both ST: SS BLAST-Start: [DNA pol III alpha [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 0.0 GAP: 187 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -2.970161406017234, yes F: DnaE-like DNA polymerase III (alpha) SIF-BLAST: ,,[DNA pol III alpha [Mycobacterium phage ScottMcG] ],,YP_002224201,100.0,0.0 SIF-HHPRED: DNA POLYMERASE III ALPHA; TRANSFERASE, DNA REPLICATION, DNA POLYMERASE III ALPHA, DNA POLYMERASE III BETA, DNA POLYMERASE III EPSILON; 7.3A {ESCHERICHIA COLI K-12},,,5FKW_A,99.7347,100.0 SIF-Syn: Gene 176 in yassified has strong nucleotide similarity to BeanWater gene 201 indicated by purple background. The same is true for Zeenon gene 211. Both BeanWater and Zeenon call the function DnaE-like DNA polymerase III in there similar gene to yassified 176. /note=Blast results show very high match with many genes with the same function : DnaE-like DNA polymerase III (alpha). Mycobacterium phage ScottMcG and several other phages show have similar gene with 99%-100% coverage, identity, and alignment. The e-value is zero for these hits. Q1:S1 alignment with 100% for strong hits like ScottMcG, Spud, and others. Auto Annotated Start causes a gap of 187 bases which is not ideal at all. Other start sites that cause fewer gaps are available but where not supported by genemark or glimmer. Start: 112623 has 43 MA`s while start site 112716 has 96 MA`s. Start 112716 is called by genemark and gllimmer. Start 112623 causes a much smaller gap however but is not supported. CDS 116263 - 116514 /gene="208" /product="gp208" /function="RF-1 peptide chain release factor" /locus tag="Yassified_208" /note=Original Glimmer call @bp 116263 has strength 15.31; Genemark calls start at 116263 /note=SSC: 116263-116514 CP: yes SCS: both ST: SS BLAST-Start: [RF-1 peptide chain release factor [Mycobacterium phage Sauce] ],,NCBI, q1:s1 100.0% 3.97556E-53 GAP: 151 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.475, -3.729235625514656, no F: RF-1 peptide chain release factor SIF-BLAST: ,,[RF-1 peptide chain release factor [Mycobacterium phage Sauce] ],,YP_010058734,100.0,3.97556E-53 SIF-HHPRED: Peptide chain release factor H; PrfH, damaged ribosome, ribotoxin, RIBOSOME; HET: UR3, 5MU, MA6, 3TD, 2MA, 5MC, A3P, MG, 0TD, G7M, 4OC, OMC, OMU, 1MG, PSU, OMG, 6MZ, 2MG;{Escherichia coli},,,7SA4_8,85.5422,99.3 SIF-Syn: Gene 177 in yassified has strong nucleotide similarity to BeanWater gene 202 indicated by purple background. The same is true for Zeenon gene 212. Both BeanWater and Zeenon call the function RF-1 peptide chain release factor in there similar gene to yassified 177. /note=Gap of 151 bases for selected start. Other starts with less gap exist but are not supported. Violation exists as gap is very large however other start sites have no other supporting data. The function chosen is supported by phamerator when comparing syntenic genes. The function is supported by HHPred and Blast. Sea Phages official function list has RecA-like DNA recombinase. CDS 116511 - 117599 /gene="209" /product="gp209" /function="RecA-like DNA recombinase" /locus tag="Yassified_209" /note=Original Glimmer call @bp 116481 has strength 19.62; Genemark calls start at 116511 /note=SSC: 116511-117599 CP: yes SCS: both-gm ST: SS BLAST-Start: [UvsX-like recombinase [Mycobacterium phage I3] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.708, -3.1779018267349564, no F: RecA-like DNA recombinase SIF-BLAST: ,,[UvsX-like recombinase [Mycobacterium phage I3] ],,YP_010510596,100.0,0.0 SIF-HHPRED: Protein recA; Alpha and beta proteins (a/b, a+b), ATP-binding, Cytoplasm, DNA damage, DNA recombination, DNA repair, DNA-binding, Nucleotide-binding; 1.95A {Thermotoga maritima},,,3HR8_A,96.4088,100.0 SIF-Syn: Gene 178 in yassified has strong nucleotide similarity to BeanWater gene 203 indicated by purple background. The same is true for Zeenon gene 213. Both BeanWater and Zeenon call the function RecA-like DNA recombinase in there similar gene to yassified 178. /note=Start site supported differ between glimmer and genemark. Genemark start causes best gap possible and contains all GM coding capacity. Start site supportted by Starterator. Function supported by PhagesDB, Blast, and HHpred. Glimmer start had less MA`s. CDS 117599 - 117979 /gene="210" /product="gp210" /function="Holliday junction resolvase" /locus tag="Yassified_210" /note=Original Glimmer call @bp 117599 has strength 16.79; Genemark calls start at 117599 /note=SSC: 117599-117979 CP: yes SCS: both ST: SS BLAST-Start: [gp202 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 5.64281E-88 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.637, -3.4076099559729456, yes F: Holliday junction resolvase SIF-BLAST: ,,[gp202 [Mycobacterium phage Bxz1] ],,NP_818253,100.0,5.64281E-88 SIF-HHPRED: HOLLIDAY-JUNCTION RESOLVASE; HYDROLASE, ENZYME, HOMOLOGOUS RECOMBINATION, HOLLIDAY JUNCTION RESOLVING ENZYME, NUCLEASE, ARCHAEA, THERMOPHILE; HET: SO4, EDO; 1.8A {SULFOLOBUS SOLFATARICUS} SCOP: c.52.1.18,,,1OB8_A,84.127,99.4 SIF-Syn: Gene 179 in yassified has strong nucleotide similarity to BeanWater gene 204 indicated by purple background. The same is true for Zeenon gene 214. BeanWater called the function holliday junction resolvase in there similar gene to yassified 179. Zeenon calls no function. /note=Mycobacterium phage Bxz1 and 9 other phages have similar gene with 100% coverage, identity, and alignment. The e-value is 5.64281e-88 for these hits. The function chosen is partially supported by phamerator when comparing syntenic genes. The function is supported by HHPred and Blast supports hypothetical protein more. Sea Phages official function list has Holliday junction resolvase. Start site is best one possible with no principles broken. CDS 117976 - 118131 /gene="211" /product="gp211" /function="hypothetical protein" /locus tag="Yassified_211" /note=Original Glimmer call @bp 117976 has strength 8.79; Genemark calls start at 117976 /note=SSC: 117976-118131 CP: yes SCS: both ST: SS BLAST-Start: [gp203 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 4.01039E-30 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.63, -3.482870966776971, yes F: hypothetical protein SIF-BLAST: ,,[gp203 [Mycobacterium phage Bxz1] ],,NP_818254,100.0,4.01039E-30 SIF-HHPRED: Uncharacterized protein; Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function; HET: MSE, SO4; 2.2A {Arthrobacter sp.},,,3BL4_A,29.4118,55.4 SIF-Syn: When comparing to BeanWater and Zeenon gene 180 is similar to genes in both these phages indicated by purple background. No function called for this gene in both similar phages from the same pham groups. /note=Top hits among other phages in blast show hypothetical protein as function. No function was supported from any data so the implied function is NKF or Hypothetical protein. Low percentage HHpred results and start site causes best overlap possible, supported by gl and GM. No TMD domains. CDS 118124 - 119896 /gene="212" /product="gp212" /function="HNH endonuclease" /locus tag="Yassified_212" /note=Original Glimmer call @bp 118124 has strength 9.86; Genemark calls start at 118124 /note=SSC: 118124-119896 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Mycobacterium phage Sauce] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.668, -3.4030855957987485, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage Sauce] ],,YP_010058738,99.8305,0.0 SIF-HHPRED: V-type ATP synthase alpha chain; intein, protein splicing, endonuclease, HYDROLASE; 1.56A {Thermococcus litoralis},,,7QSS_A,45.5932,99.7 SIF-Syn: Zeenon_216 has similar locus with similar genes up and downstream from it as Yassified. /note=100% of the entries for this gene in PhagesDB has been called an HNH Endonuclease. PhagesDB blast also supports this function for this gene. HHPred also supports an endonuclease as the function for this gene. All evidence including genemark, glimmer, starterator, BLAST, gap/overlap and ORF length support 118124. last has an E value of 0 and over 99% in alignment, coverage, and identity. PhagesDB has a frequency of 100% and a count of 83. HHpred shows multiplie hits with 95% probabilty and a low E value. So HNH endonuclease is well supported CDS 119896 - 120351 /gene="213" /product="gp213" /function="RusA-like resolvase (endonuclease)" /locus tag="Yassified_213" /note=Original Glimmer call @bp 119896 has strength 10.3; Genemark calls start at 119896 /note=SSC: 119896-120351 CP: yes SCS: both ST: SS BLAST-Start: [gp208 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 1.1523E-106 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.483, -3.790975366313636, no F: RusA-like resolvase (endonuclease) SIF-BLAST: ,,[gp208 [Mycobacterium phage Cali] ],,YP_002224652,100.0,1.1523E-106 SIF-HHPRED: RusA ; Endodeoxyribonuclease RusA,,,PF05866.14,89.404,99.9 SIF-Syn: Gene shared in similar locus to Zeenon_216 and beanwater. Zeenon_216 and beanwater supports RusA-like resolvase /note=All evidence including genemark, glimmer, starterator, BLAST, gap/overlap and ORF length support 119896. Blast has an E value of 1.1523e-106 and 100% in alignment, coverage, and identity . PhagesDB has a frequency of 98% and a count of 89 . HHpred shows multiple hits with 99% probability and a low E value. So Rusa-like resolvase is well supported. CDS 120335 - 121054 /gene="214" /product="gp214" /function="hypothetical protein" /locus tag="Yassified_214" /note=Original Glimmer call @bp 120335 has strength 8.05; Genemark calls start at 120335 /note=SSC: 120335-121054 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein M180_gp135 [Mycobacterium phage ArcherS7] ],,NCBI, q1:s1 100.0% 3.75446E-175 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.976, -5.367638368103365, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M180_gp135 [Mycobacterium phage ArcherS7] ],,YP_008061445,100.0,3.75446E-175 SIF-HHPRED: VOC_like; uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.,,,cd07238,16.318,42.7 SIF-Syn: Gene shared in similar locus to Zeenon_216 and beanwater. Zeenon_216 and beanwater also have no function listed /note=All evidence including genemark, glimmer, starterator, BLAST, gap/overlap and ORF length support 120335. There is no supporting evidence from BLAST HHPRed nor phamerator for a function call. CDS 121035 - 121904 /gene="215" /product="gp215" /function="DNA binding protein" /locus tag="Yassified_215" /note=Original Glimmer call @bp 121035 has strength 7.28; Genemark calls start at 121101 /note=SSC: 121035-121904 CP: yes SCS: both-gl ST: SS BLAST-Start: [gp207 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 0.0 GAP: -20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.794, -3.1379842619144376, no F: DNA binding protein SIF-BLAST: ,,[gp207 [Mycobacterium phage Bxz1] ],,NP_818258,100.0,0.0 SIF-HHPRED: ECF RNA polymerase sigma factor SigL; Mycobacterium tuberculosis, RNA polymerase, ECF sigma factor, TRANSFERASE, TRANSFERASE-DNA-RNA complex; 3.3A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)},,,6DVC_F,22.1453,99.1 SIF-Syn: Gene shared in similar locus to Zeenon_216 and beanwater. Zeenon_216 and beanwater also have no function listed /note=Genemark and Glimmer provide different answers, but staterator and ORF length supports the Glimmer prediction of 121035. PhagesDB shows that although there is a 100% frequency, there is only a count of 1. HHpred has a probability of 99.1, and a small E value, but also only has 1 hit. This means there is only 1 other phage that can support DNA binding protein. There is a large amount of putative NKF genes for 184, with only 1 hit to support it`s function, despite having low E values and high probability CDS 121956 - 122270 /gene="216" /product="gp216" /function="hypothetical protein" /locus tag="Yassified_216" /note=Original Glimmer call @bp 121956 has strength 3.31; Genemark calls start at 121956 /note=SSC: 121956-122270 CP: yes SCS: both ST: SS BLAST-Start: [gp208 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 5.01968E-69 GAP: 51 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.998, -4.731360067354143, no F: hypothetical protein SIF-BLAST: ,,[gp208 [Mycobacterium phage Bxz1] ],,NP_818259,100.0,5.01968E-69 SIF-HHPRED: DUF6374 ; Family of unknown function (DUF6374),,,PF19901.2,28.8462,51.3 SIF-Syn: Gene shared in similar locus to Zeenon_216 and beanwater. Zeenon_216 and beanwater also have no function listed /note=All evidence including genemark, glimmer, starterator, BLAST, gap/overlap and ORF length support 121956. there is no supporting evidence from BLAST HHPRed nor phamerator for a function call. no TMB domains. CDS 122274 - 123071 /gene="217" /product="gp217" /function="hypothetical protein" /locus tag="Yassified_217" /note=Original Glimmer call @bp 122274 has strength 14.64; Genemark calls start at 122274 /note=SSC: 122274-123071 CP: yes SCS: both ST: SS BLAST-Start: [gp212 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.138, -2.627458653341447, yes F: hypothetical protein SIF-BLAST: ,,[gp212 [Mycobacterium phage Cali] ],,YP_002224656,100.0,0.0 SIF-HHPRED: Phage_Mu_Gp27 ; Bacteriophage Mu, Gp27,,,PF11985.11,17.3585,97.9 SIF-Syn: Gene shared in similar locus to Zeenon_216 and beanwater. Zeenon_216 and beanwater also have no function listed /note=All evidence including genemark, glimmer, starterator, BLAST, gap/overlap and ORF length support 122274 PhagesDB shows that although there is a 100% frequency, there is only a count of 1. HHpred has a probability of 99.1, and a small E value, but also only has 1 hit. This means there is only 1 other phage that can support DNA binding protein. There is a large amount of putative NKF genes for 186, with only 1 hit to support it`s function, despite having low E values and high probability CDS 123068 - 124093 /gene="218" /product="gp218" /function="hydrolase" /locus tag="Yassified_218" /note=Original Glimmer call @bp 123068 has strength 9.86; Genemark calls start at 123077 /note=SSC: 123068-124093 CP: yes SCS: both-gl ST: SS BLAST-Start: [gp210 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.355, -6.018071631562228, no F: hydrolase SIF-BLAST: ,,[gp210 [Mycobacterium phage Bxz1] ],,NP_818261,100.0,0.0 SIF-HHPRED: Putative hydrolase; 5-bladed beta-propeller, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, HYDROLASE; HET: GOL, MSE; 2.8A {Bacteroides ovatus},,,4HBS_A,82.9912,100.0 SIF-Syn: Gene shared in similar locus to Zeenon_216 and beanwater. Zeenon_216 and beanwater also have no function listed. EasyJones_223 is syntenic to Yassified_186 and is called a hydrolase. /note=Genemark and glimmer are not in agreeance, but longest ORF with shortest gap is supported by glimmer, meaning the most likely start site is 123068. Blast has an E value of 0 and 100% in alignment, coverage, and identity. Phages shows 2 hits, one for Hydrolase, and the other for glycoside hydrolase, so although it shows a frequency of 50% for both, this can be rationed that it is 100% for hydrolase. HHPred shows similar results, with 1 hit for each, with 100% probability, and low E values. This is strong evidence to support hydrolase as a function. Although there are only 2 hits to suggest a function, they both provide low E values and high probability for Blast, phagesDB, and HHPred CDS 124146 - 125168 /gene="219" /product="gp219" /function="hypothetical protein" /locus tag="Yassified_219" /note=Original Glimmer call @bp 124146 has strength 17.18; Genemark calls start at 124146 /note=SSC: 124146-125168 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein OLP41_gp132 [Mycobacterium phage I3] ],,NCBI, q1:s1 100.0% 0.0 GAP: 52 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.161, -4.325675514574479, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein OLP41_gp132 [Mycobacterium phage I3] ],,YP_010510606,100.0,0.0 SIF-HHPRED: DUF932 ; Domain of unknown function (DUF932),,,PF06067.14,60.0,99.8 SIF-Syn: Gene shared in similar locus to Zeenon_216 and beanwater. Zeenon_216 and beanwater also have no function listed (beanwater has insertion of gene in-between it`s 213-215, its proxy to 188-189) /note=All evidence including genemark, glimmer, starterator, BLAST, gap/overlap and ORF length support 124146. There is no supporting evidence from BLAST HHPRed nor phamerator for a function call. No TMB domain. CDS 125165 - 125401 /gene="220" /product="gp220" /function="hypothetical protein" /locus tag="Yassified_220" /note=Original Glimmer call @bp 125165 has strength 6.61; Genemark calls start at 125165 /note=SSC: 125165-125401 CP: yes SCS: both ST: SS BLAST-Start: [gp215 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 4.47488E-49 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.857, -4.964641208403463, no F: hypothetical protein SIF-BLAST: ,,[gp215 [Mycobacterium phage Cali] ],,YP_002224659,100.0,4.47488E-49 SIF-HHPRED: HTH-type transcriptional regulator mcbR; GNTR FAMILY, TRANSCRIPTIONAL REGULATOR, Biofilm formation, TRANSCRIPTION; HET: MSE; 2.099A {Escherichia coli UMEA 3718-1},,,4P9F_B,67.9487,80.2 SIF-Syn: Gene shared in similar locus to Zeenon_216 and beanwater. Zeenon_216 and beanwater also have no function listed /note=Genemark, glimmer, starterator, BLAST, and ORF length support 118124. There is no supporting evidence from BLAST HHPRed nor phamerator for a function call. No TMB domain. tRNA 125524 - 125598 /gene="221" /product="tRNA-Gln(ctg)" /locus tag="YASSIFIED_221" /note=tRNA-Gln(ctg) tRNA 125605 - 125680 /gene="222" /product="tRNA-Asn(gtt)" /locus tag="YASSIFIED_222" /note=tRNA-Asn(gtt) CDS 125755 - 126213 /gene="223" /product="gp223" /function="hypothetical protein" /locus tag="Yassified_223" /note=Original Glimmer call @bp 125755 has strength 17.65; Genemark calls start at 125755 /note=SSC: 125755-126213 CP: yes SCS: both ST: SS BLAST-Start: [gp214 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.31251E-108 GAP: 353 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.983, -2.7423981586358774, yes F: hypothetical protein SIF-BLAST: ,,[gp214 [Mycobacterium phage Bxz1] ],,NP_818264,100.0,2.31251E-108 SIF-HHPRED: Clr5 ; Clr5 domain,,,PF14420.9,28.9474,67.6 SIF-Syn: Not informative. /note=No evidence supporting a functional call. No TMB domain. CDS 126210 - 126653 /gene="224" /product="gp224" /function="hypothetical protein" /locus tag="Yassified_224" /note=Original Glimmer call @bp 126210 has strength 10.53; Genemark calls start at 126210 /note=SSC: 126210-126653 CP: yes SCS: both ST: SS BLAST-Start: [gp215 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 7.74995E-105 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.578, -3.5316035464369326, yes F: hypothetical protein SIF-BLAST: ,,[gp215 [Mycobacterium phage Bxz1] ],,NP_818265,100.0,7.74995E-105 SIF-HHPRED: NosL ; NosL,,,PF05573.15,71.4286,85.4 SIF-Syn: Not informative. /note=No functional call in PhagesDB, BLAST matches are hypothetical proteins. No conserved domain matches in CDD or HHPred. No TMB. CDS 126653 - 126922 /gene="225" /product="gp225" /function="hypothetical protein" /locus tag="Yassified_225" /note=Original Glimmer call @bp 126653 has strength 6.5; Genemark calls start at 126653 /note=SSC: 126653-126922 CP: yes SCS: both ST: SS BLAST-Start: [gp220 [Mycobacterium phage Cali] ],,NCBI, q1:s2 100.0% 3.20061E-59 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.551, -4.0338999058337315, no F: hypothetical protein SIF-BLAST: ,,[gp220 [Mycobacterium phage Cali] ],,YP_002224662,98.8889,3.20061E-59 SIF-HHPRED: Double-stranded RNA-specific editase Adar; dsRBD, dsRBM, editing, HYDROLASE; NMR {Drosophila melanogaster} SCOP: d.50.1.0,,,2LJH_A,16.8539,45.8 SIF-Syn: not informative /note=No evidence supporting a functional call. Matches to functional databases are poor. NoTMB domains. CDS 126940 - 127314 /gene="226" /product="gp226" /function="hypothetical protein" /locus tag="Yassified_226" /note=Original Glimmer call @bp 126979 has strength 5.49; Genemark calls start at 126979 /note=SSC: 126940-127314 CP: yes SCS: both-cs ST: NA BLAST-Start: [hypothetical protein LINSTU_227 [Mycobacterium phage LinStu] ],,NCBI, q1:s9 100.0% 1.74249E-87 GAP: 17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.815, -4.002697610340739, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein LINSTU_227 [Mycobacterium phage LinStu] ],,YP_009014785,93.9394,1.74249E-87 SIF-HHPRED: SIF-Syn: Not informative /note=Although Genemark, Glimmer and Starterator support 126979 as start site, we chose 126940 based on the Genemark report the shortest gap and longest ORF. The start coding is also ATG. /note=No evidence supporting a functional call. CDS 127393 - 127746 /gene="227" /product="gp227" /function="membrane protein" /locus tag="Yassified_227" /note=Original Glimmer call @bp 127393 has strength 4.57; Genemark calls start at 127393 /note=SSC: 127393-127746 CP: yes SCS: both ST: SS BLAST-Start: [gp218 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 5.19299E-78 GAP: 78 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.196, -4.6033671133628555, no F: membrane protein SIF-BLAST: ,,[gp218 [Mycobacterium phage Bxz1] ],,NP_818268,100.0,5.19299E-78 SIF-HHPRED: SIF-Syn: Not informative /note=Has 2 TMBS according to TmHmm and topcons. CDS 127697 - 128017 /gene="228" /product="gp228" /function="hypothetical protein" /locus tag="Yassified_228" /note=Original Glimmer call @bp 127697 has strength 7.31; Genemark calls start at 127796 /note=SSC: 127697-128017 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein M182_gp122 [Mycobacterium phage Astraea] ],,NCBI, q1:s1 100.0% 4.32355E-69 GAP: -50 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.843, -5.056409918993686, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M182_gp122 [Mycobacterium phage Astraea] ],,YP_008061688,100.0,4.32355E-69 SIF-HHPRED: SIF-Syn: not informative. /note=No evidence supporting a functional call. No TMB domains. tRNA 128205 - 128268 /gene="229" /product="tRNA-Ser(cga)" /locus tag="YASSIFIED_229" /note=tRNA-Ser(cga) CDS 128298 - 128471 /gene="230" /product="gp230" /function="hypothetical protein" /locus tag="Yassified_230" /note= /note=SSC: 128298-128471 CP: yes SCS: neither ST: NI BLAST-Start: [hypothetical protein M181_gp125 [Mycobacterium phage Gizmo] ],,NCBI, q1:s1 100.0% 1.83653E-32 GAP: 280 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.952, -5.86583354674825, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M181_gp125 [Mycobacterium phage Gizmo] ],,YP_008061002,100.0,1.83653E-32 SIF-HHPRED: antibody m43.149 heavy chain; Malaria, CSP, Junction region, antibody, m43.149, IMMUNE SYSTEM; 1.75A {Mus musculus},,,7RD4_A,15.7895,56.7 SIF-Syn: not informative. /note=Added this gene based on Genemark Report. Autoannotation called for a gene on the reverse strand overlapping with this ORF on the reverse. Both had poor CP. We are inclined to delete the gene on the reverse and add this one on the forward strand filling the gap. CDS 128502 - 130160 /gene="231" /product="gp231" /function="Ro-like RNA binding protein" /locus tag="Yassified_231" /note=Original Glimmer call @bp 128502 has strength 15.51; Genemark calls start at 128502 /note=SSC: 128502-130160 CP: yes SCS: both ST: SS BLAST-Start: [Ro protein [Mycobacterium phage Breeniome] ],,NCBI, q1:s1 100.0% 0.0 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.808, -3.0478325568523097, yes F: Ro-like RNA binding protein SIF-BLAST: ,,[Ro protein [Mycobacterium phage Breeniome] ],,YP_009221330,100.0,0.0 SIF-HHPRED: 60-kDa SS-A/Ro ribonucleoprotein; HEAT repeat von Willebrand Factor A Rossmann fold MIDAS motif`, RNA BINDING PROTEIN; 1.95A {Xenopus laevis} SCOP: c.62.1.5, a.118.25.1,,,1YVR_A,98.0072,100.0 SIF-Syn: Zeenon_233 is syntenic with the same function call. /note=PhagesDN has 94 incidences of this function being called at 100%. BLAST, HHPred, and CDD support the function call. No TMB domains. CDS 130521 - 130844 /gene="232" /product="gp232" /function="hypothetical protein" /locus tag="Yassified_232" /note=Original Glimmer call @bp 130521 has strength 10.59; Genemark calls start at 130521 /note=SSC: 130521-130844 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PINKCREEK_216 [Mycobacterium phage Pinkcreek]],,NCBI, q1:s1 100.0% 2.32339E-70 GAP: 360 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.551, -3.5707972674952195, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PINKCREEK_216 [Mycobacterium phage Pinkcreek]],,UEM46251,100.0,2.32339E-70 SIF-HHPRED: DUF3509 ; Protein of unknown function (DUF3509),,,PF12021.11,26.1682,75.1 SIF-Syn: According to PECAAN Pham maps, gene 199 of Yassified is syntenic to Zeenon gene 234, and BeanWater gene 227, its closest relative. /note=There is no data in PhagesDB frequency, PhagesDB BLAST(E=9e -56), NCBI BLAST(100% coverage, 100% aligned, 99.06% identity, E=2.32339e-70) and HHPred support the function (75.1%Prob, 26.16% coverage, Q49:13, E=5.2). No TMB domain. CDS 130873 - 131112 /gene="233" /product="gp233" /function="hypothetical protein" /locus tag="Yassified_233" /note=Original Glimmer call @bp 130873 has strength 11.04; Genemark calls start at 130873 /note=SSC: 130873-131112 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein M181_gp122 [Mycobacterium phage Gizmo] ],,NCBI, q1:s14 100.0% 4.02485E-51 GAP: 28 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -2.970161406017234, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M181_gp122 [Mycobacterium phage Gizmo] ],,YP_008061005,85.8696,4.02485E-51 SIF-HHPRED: DUF5678 ; Family of unknown function (DUF5678),,,PF18929.3,46.8354,87.3 SIF-Syn: According to PECAAN Pham maps, gene 200 of Yassified is syntenic to Zeenon gene 235, and BeanWater gene 228, its closest relative. /note=PhagesDB frequency(0%), PhagesDB BLAST(E=3e -95), NCBI BLAST(100% coverage, 85.86% aligned, 85.86% identity, E=6e-41) and HHPred support the function (100%Prob, 95.88% coverage, Q6:169, E=4.02485e-51). No TMB domain. CDS 131159 - 131626 /gene="234" /product="gp234" /function="hypothetical protein" /locus tag="Yassified_234" /note=Original Glimmer call @bp 131159 has strength 11.15; Genemark calls start at 131159 /note=SSC: 131159-131626 CP: yes SCS: both ST: SS BLAST-Start: [gp227 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 2.37352E-106 GAP: 46 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.962, -2.707694805492614, yes F: hypothetical protein SIF-BLAST: ,,[gp227 [Mycobacterium phage Cali] ],,YP_002224669,100.0,2.37352E-106 SIF-HHPRED: Lethal (2) giant discs 1, isoform B; ESCRT, ENDOCYTOSIS, PROTEIN BINDING; HET: MSE; 1.101A {Drosophila melanogaster},,,5VNY_A,38.0645,80.0 SIF-Syn: This genome region is syntenic to gene 236 of Zeenon and gene 229 of Beanwater its closest relatives on Pham Maps. /note=PhagesDB frequency has no data, PhagesDB BLAST(E=4e -84), NCBI BLAST(100% coverage, 100% aligned,100% identity, E=2.26518e-106) and HHPreg supports it as a binding protein (80% probability, 38.06% coverage, Q12:2, E= 27). No match in CDD. No TMB domains. CDS 131626 - 132018 /gene="235" /product="gp235" /function="hypothetical protein" /locus tag="Yassified_235" /note=Original Glimmer call @bp 131626 has strength 7.95; Genemark calls start at 131626 /note=SSC: 131626-132018 CP: yes SCS: both ST: SS BLAST-Start: [gp224 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.38136E-91 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.058, -3.3503726477288405, yes F: hypothetical protein SIF-BLAST: ,,[gp224 [Mycobacterium phage Bxz1] ],,NP_818274,100.0,1.38136E-91 SIF-HHPRED: SIF-Syn: Not informative. This region of the genome is syntenic to zeenon gene 237 and BeanWater gene 230 its closest relatives. It is not informative. /note=None of the evidence calls for a function. PhagesDB frequency has no data, PhagesDB BLAST(E=1e -73), NCBI BLAST(100% coverage, 100% aligned, 100% identity, E=1.38136e-91) and HHPred supports it as a phosphohydrolase (67.6% Prob, 21.54% coverage, Q62:S5, E= 14). CDS 132018 - 132224 /gene="236" /product="gp236" /function="hypothetical protein" /locus tag="Yassified_236" /note=Original Glimmer call @bp 132018 has strength 14.45; Genemark calls start at 132018 /note=SSC: 132018-132224 CP: no SCS: both ST: SS BLAST-Start: [gp225 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.46905E-41 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.397, -3.9718914447963414, yes F: hypothetical protein SIF-BLAST: ,,[gp225 [Mycobacterium phage Bxz1] ],,NP_818275,100.0,2.46905E-41 SIF-HHPRED: DUF6307 ; Family of unknown function (DUF6307),,,PF19826.2,48.5294,91.9 SIF-Syn: This portion of the genome is syntenic to BeanWater gene 231 and Zeenon gene 238. Not informative. /note=None of the evidence calls for a function. PhagesDB frequency has no data, PhagesDB BLAST(E=1e -34), NCBI BLAST(100% coverage, 100% aligned, 100% identity, E=2.35498e-41) and HHPred supports its unknown function (91.9% Prob, 48.53% coverage, Q10:S7, E= 0.81). No TMB domain. CDS 132221 - 132352 /gene="237" /product="gp237" /function="hypothetical protein" /locus tag="Yassified_237" /note=Original Glimmer call @bp 132221 has strength 7.24; Genemark calls start at 132221 /note=SSC: 132221-132352 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein DRAZDYS_236 [Mycobacterium phage Drazdys] ],,NCBI, q1:s5 100.0% 2.44032E-24 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.752, -5.183665924498821, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein DRAZDYS_236 [Mycobacterium phage Drazdys] ],,AEK07037,91.4894,2.44032E-24 SIF-HHPRED: Putative uncharacterized protein VPA1370; ACTIN, ACTIN-BINDING PROTEIN, CROSSLINKING, NUCLEATOR, PROTEIN-PROTEIN INTERACTION, ATP-binding, Cytoskeleton, Methylation, Muscle protein, Nucleotide-binding, Phosphoprotein, CONTRACTILE PROTEIN; HET: HIC, ATP; 2.89A {Oryctolagus cuniculus},,,3M1F_V,32.5581,84.8 SIF-Syn: This part of the genome is synthetic to gene 232 of BeanWater and 239 of Zeenon its closest relatives. Not informative. /note=PhagesDB frequency has no data, PhagesDB BLAST(E=3e -21), NCBI BLAST(100% coverage, 91.5% aligned, 91.5% identity, E=2.44032e-24), and HHPred supports its unknown function (84.8% Prob, 32.5% coverage, Q18:S1, E= 1.6). No conserved domain in CDD. No TMB domains. CDS 132404 - 133132 /gene="238" /product="gp238" /function="glycosyltransferase" /locus tag="Yassified_238" /note=Original Glimmer call @bp 132404 has strength 12.82; Genemark calls start at 132404 /note=SSC: 132404-133132 CP: yes SCS: both ST: SS BLAST-Start: [glycosyltransferase [Mycobacterium phage ET08] ],,NCBI, q1:s6 100.0% 0.0 GAP: 51 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.285, -4.1462986041499, no F: glycosyltransferase SIF-BLAST: ,,[glycosyltransferase [Mycobacterium phage ET08] ],,YP_003347875,97.9757,0.0 SIF-HHPRED: CESA_NdvC_like; NdvC_like proteins in this family are putative bacterial beta-(1,6)-glucosyltransferase.,,,cd06435,92.9752,99.9 SIF-Syn: Syntenic to gene 241 of Zeenon and gene 233 of BeanWater. /note=PhagesDB supports this function with 100% frequency on 93 counts, PhagesDB BLAST(E=1e -151), NCBI BLAST(100% coverage, 97.97% aligned, 97.97% identity, E=0.0), and HHPred supports its function (99.9% Prob, 92.97% coverage, Q6:S1, E= 8.3e-22). CDS 133222 - 133893 /gene="239" /product="gp239" /function="glycosyltransferase" /locus tag="Yassified_239" /note=Original Glimmer call @bp 133222 has strength 15.65; Genemark calls start at 133222 /note=SSC: 133222-133893 CP: yes SCS: both ST: SS BLAST-Start: [galactosyl transferase [Mycobacterium phage Breeniome] ],,NCBI, q1:s1 100.0% 7.09121E-164 GAP: 89 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.716, -3.3019548882942655, yes F: glycosyltransferase SIF-BLAST: ,,[galactosyl transferase [Mycobacterium phage Breeniome] ],,YP_009221340,99.5516,7.09121E-164 SIF-HHPRED: CESA_like_2; CESA_like_2 is a member of the cellulose synthase superfamily. The cellulose synthase (CESA) superfamily includes a wide variety of glycosyltransferase family 2 enzymes that share the common characteristic of catalyzing the elongation of polysaccharide chains.,,,cd06427,96.4126,99.9 SIF-Syn: Syntenic to gene 235 of BeanWater and gene 143 of Zeenon. /note=PhagesDB supports this function with 100% frequency on 83 counts, PhagesDB BLAST(E=1e -132), NCBI BLAST(100% coverage, 95.55% aligned, 99.55% identity, E=7.09121e-164), and HHPred supports its function (99.9% Prob, 96.41% coverage, Q1:S3, E=4.7e-21). CDS 133883 - 134590 /gene="240" /product="gp240" /function="glycosyltransferase" /locus tag="Yassified_240" /note=Original Glimmer call @bp 133883 has strength 13.46; Genemark calls start at 133916 /note=SSC: 133883-134590 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_235 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 5.18278E-171 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.508, -4.698795016966896, yes F: glycosyltransferase SIF-BLAST: ,,[hypothetical protein SCOTTMCG_235 [Mycobacterium phage ScottMcG] ],,YP_002224232,98.7395,5.18278E-171 SIF-HHPRED: Glycosyltransferase; SSGCID, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, TRANSFERASE; HET: CIT, EDO, GOL; 1.95A {Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)},,,6P61_D,85.1064,99.9 SIF-Syn: Syntenic to gene 236 of BeanWater and gene 244 of Zeenon /note=PhagesDB supports this function with 92% frequency on 82 counts, PhagesDB BLAST(E=1e -139), NCBI BLAST(100% coverage, 98.7% aligned, 98.7% identity, E=5.18278e-171), and HHPred supports its function (99.5% Prob, 85.1% coverage, Q3:S8, E=9.6e-22). CDD doesn`t find a conserved domain. CDS 134587 - 134889 /gene="241" /product="gp241" /function="PnuC-like Nicotinamide riboside transporter" /locus tag="Yassified_241" /note=Original Glimmer call @bp 134587 has strength 5.85; Genemark calls start at 134587 /note=SSC: 134587-134889 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_230 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 2.46991E-65 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.13, -4.4713484557894425, no F: PnuC-like Nicotinamide riboside transporter SIF-BLAST: ,,[hypothetical protein ET08_230 [Mycobacterium phage ET08] ],,YP_003347878,100.0,2.46991E-65 SIF-HHPRED: NMN_transporter ; Nicotinamide mononucleotide transporter,,,PF04973.15,68.0,99.5 SIF-Syn: Syntenic to gene 237 of BeanWater and gene 245 of Zeenon. /note=PhagesDB supports this function with 93% frequency on 55 counts, PhagesDB BLAST(E=2e -58), NCBI BLAST(100% coverage, 100% aligned, 100% identity, E=2.46991e-65), and HHPred supports its function (99.5% Prob, 68% coverage, Q4:S1, E=1.7e-12). CDS 134886 - 135548 /gene="242" /product="gp242" /function="glycosyltransferase" /locus tag="Yassified_242" /note=Original Glimmer call @bp 134886 has strength 14.74; Genemark calls start at 134886 /note=SSC: 134886-135548 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_231 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 2.43371E-160 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.905, -2.9063687850157054, yes F: glycosyltransferase SIF-BLAST: ,,[hypothetical protein ET08_231 [Mycobacterium phage ET08] ],,YP_003347879,100.0,2.43371E-160 SIF-HHPRED: Envelope protein H3; H3, vaccinia virus, poxvirus, glycosyl transferase, VIRAL PROTEIN; HET: PG0, PDO, MOH, GOL, EDO; 1.9A {Vaccinia virus (strain Western Reserve)},,,5EJ0_A,61.3636,99.7 SIF-Syn: Zeenon has a similar locus to similar genes upstream and downstream /note=100% of the entries for this gene in PhagesDB have been called glycosyltransferase. PhagesDB and HHpred, and NCBI Blast all agree on the function of the gene. CDS 135612 - 139067 /gene="243" /product="gp243" /function="hypothetical protein" /locus tag="Yassified_243" /note=Original Glimmer call @bp 135612 has strength 15.25; Genemark calls start at 135612 /note=SSC: 135612-139067 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LOLAVINCA_242 [Mycobacterium phage LolaVinca]],,NCBI, q1:s1 100.0% 0.0 GAP: 63 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.138, -2.2763497933341483, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LOLAVINCA_242 [Mycobacterium phage LolaVinca]],,QED11403,99.9131,0.0 SIF-HHPRED: DotF; Dot/Icm, Secretion, T4SS, TRANSLOCASE; 4.6A {Legionella pneumophila},,,7MUS_XF,15.8123,61.7 SIF-Syn: Relatives are present however, gene function is not specified. Not informative. /note=Similar to LolaVinca w/99.931% alignment identity,100% coverage and /note=10+ similar hits. Top phage do not point to a function i.e hypothetical protein. No TMB domain. /note=None of the evidence supports a function call. CDS 139067 - 140461 /gene="244" /product="gp244" /function="hypothetical protein" /locus tag="Yassified_244" /note=Original Glimmer call @bp 139067 has strength 13.36; Genemark calls start at 139067 /note=SSC: 139067-140461 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BADAGARTUDE_241 [Mycobacterium phage BadAgartude] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.052, -4.6353190821692705, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BADAGARTUDE_241 [Mycobacterium phage BadAgartude] ],,QAY13192,100.0,0.0 SIF-HHPRED: LEVANASE; HYDROLASE, LEVAN; HET: FRU; 1.65A {BACILLUS SUBTILIS},,,4B1L_A,42.4569,75.7 SIF-Syn: Not informative. /note=None of the evidence call for a function. Similar to BADAGARTUDE w/100% alignment /note=identity,100% coverage and 10+ similar hits. At least 10+ other genes have an E-Value of 0 /note= /note=Top phage do not point to a function i.e hypothetical protein. No conserved domains. No TMB domain. CDS 140472 - 141242 /gene="245" /product="gp245" /function="hypothetical protein" /locus tag="Yassified_245" /note=Original Glimmer call @bp 140472 has strength 17.99; Genemark calls start at 140472 /note=SSC: 140472-141242 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_240 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.149, -2.253486910374644, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_240 [Mycobacterium phage ScottMcG] ],,YP_002224237,99.6094,0.0 SIF-HHPRED: SIF-Syn: Not informative. Syntenic genes are present however, gene function is not specified. /note=No evidence for a function call. /note=Similar to SCOTTMCG_240 w/99.6% alignment identity,100% coverage and 10+ similar hits. /note= /note=Top phage do not point to a function i.e hypothetical protein. no TMB domains. CDS 141255 - 142010 /gene="246" /product="gp246" /function="hypothetical protein" /locus tag="Yassified_246" /note=Original Glimmer call @bp 141255 has strength 16.99; Genemark calls start at 141255 /note=SSC: 141255-142010 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_235 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 4.88356E-180 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.138, -2.2763497933341483, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_235 [Mycobacterium phage ET08] ],,YP_003347883,100.0,4.88356E-180 SIF-HHPRED: b.108.1.0 (A:604-756) automated matches {Enterobacteria phage [TaxId: 948870]} | CLASS: All beta proteins, FOLD: Triple-stranded beta-helix, SUPFAM: Phage fibre proteins, FAM: automated matches,,,SCOP_d4hiza2,14.741,5.1 SIF-Syn: Syntenic genes present however, gene function is not specified /note=No evidence for a function call. /note=Similar to ET08-235w/100% alignmentidentity,100% coverage and 10+ similar hits. /note=Top phage do not point to a function i.e hypothetical protein. No TMB domain. CDS 142078 - 143508 /gene="247" /product="gp247" /function="lysin A" /locus tag="Yassified_247" /note=Original Glimmer call @bp 142078 has strength 11.29; Genemark calls start at 142078 /note=SSC: 142078-143508 CP: yes SCS: both ST: SS BLAST-Start: [lysin A [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 0.0 GAP: 67 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.962, -3.7466128715229834, no F: lysin A SIF-BLAST: ,,[lysin A [Mycobacterium phage ET08] ],,YP_003347884,100.0,0.0 SIF-HHPRED: N-acetylmuramoyl-L-alanine amidase; amidase, zinc binding, cell wall degradation, endolysine, hydrolase; HET: PO4, GOL; 1.21A {Clostridium intestinale},,,6SSC_A,35.7143,99.5 SIF-Syn: Zeenon_251 is syntenic with the same function call. flanking genes in Zeenon are also syntenic. /note=Similar to ET08, LinStu,HyRo,Alice,Sebata w/100% alignment identity,100% coverage and 10+ similar hits. At least 10+ other genes have an E-Value of 0 /note=HHPred calls a Amidase function with an excellent E-Value of 5.9e-13 and a probability score of 99.5% CDS 143505 - 143915 /gene="248" /product="gp248" /function="holin" /locus tag="Yassified_248" /note=Original Glimmer call @bp 143505 has strength 18.36; Genemark calls start at 143505 /note=SSC: 143505-143915 CP: yes SCS: both ST: SS BLAST-Start: [gp237 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 1.37502E-87 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.983, -2.7423981586358774, yes F: holin SIF-BLAST: ,,[gp237 [Mycobacterium phage Bxz1] ],,NP_818287,99.2647,1.37502E-87 SIF-HHPRED: Phage_holin_7_1 ; Mycobacterial 2 TMS Phage Holin (M2 Hol) Family,,,PF16081.8,97.0588,100.0 SIF-Syn: Zeenon_252 and flanking genes are syntenic supporting holin as a function. /note=All evidence points to same function call, holin. Two TMB domains predicted by TmHmm, and topcon. CDS 143912 - 144940 /gene="249" /product="gp249" /function="lysin B" /locus tag="Yassified_249" /note=Original Glimmer call @bp 143912 has strength 14.13; Genemark calls start at 143912 /note=SSC: 143912-144940 CP: yes SCS: both ST: SS BLAST-Start: [gp242 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.491, -6.561440757437232, no F: lysin B SIF-BLAST: ,,[gp242 [Mycobacterium phage Cali] ],,YP_002224684,100.0,0.0 SIF-HHPRED: ACETYL XYLAN ESTERASE; HYDROLASE, ESTERASE, XYLAN DEGRADATION; HET: PCA, NAG; 1.9A {TRICHODERMA REESEI} SCOP: c.69.1.30,,,1QOZ_A,50.2924,99.9 SIF-Syn: Zeenon_253 /note=90 instances of a function called all for lysingB in PhagesDB. Similar to Cali,ET08,Alice,Stubbyw/100% alignment identity,100% coverage and 10+ similar hits. /note=At least 10+ other genes have an E-Value of 0. Top phage hits call Lysin B. CDS 144943 - 147966 /gene="250" /product="gp250" /function="terminase" /locus tag="Yassified_250" /note=Original Glimmer call @bp 144943 has strength 11.65; Genemark calls start at 144943 /note=SSC: 144943-147966 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_ZYGOTAIGA_250 [Mycobacterium phage ZygoTaiga] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.598, -3.4080892535965868, no F: terminase SIF-BLAST: ,,[hypothetical protein PBI_ZYGOTAIGA_250 [Mycobacterium phage ZygoTaiga] ],,AIX12898,100.0,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,24.429,99.9 SIF-Syn: Relatives are present however, gene function is not specified /note=All evidence support function call for a terminase. 81 instances in PhagesDB. Similar to ZygoTaiga, FrayBell,and Nidhogg w/100% alignment /note=identity,100% coverage and 10+ similar hits. CDS 148039 - 148167 /gene="251" /product="gp251" /function="membrane protein" /locus tag="Yassified_251" /note=Original Glimmer call @bp 148039 has strength 14.9; Genemark calls start at 148039 /note=SSC: 148039-148167 CP: yes SCS: both ST: SS BLAST-Start: [gp240 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.96885E-21 GAP: 72 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.394, -3.9166971242758706, yes F: membrane protein SIF-BLAST: ,,[gp240 [Mycobacterium phage Bxz1] ],,NP_818290,100.0,2.96885E-21 SIF-HHPRED: SIF-Syn: Not informative. /note=no data in Phagesdb function frequency. Phagesdb blast E=9e -19, function unknown, NCBI BLAST(100% coverage, 100% aligned, 100% identity, E=2.96885e-21 Q1:S1) function unknown. HHPred (85.3%Prob, 95.23% coverage, Q2:S29, E=11) function unknown, E-value too high to support. TmHmm, topcons and SOSUI supports presence of a transmembrane region. CDS 148164 - 148481 /gene="252" /product="gp252" /function="hypothetical protein" /locus tag="Yassified_252" /note=Original Glimmer call @bp 148188 has strength 13.11; Genemark calls start at 148188 /note=SSC: 148164-148481 CP: yes SCS: both-cs ST: SS BLAST-Start: [gp241 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 4.30719E-70 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.562, -7.682388013302671, no F: hypothetical protein SIF-BLAST: ,,[gp241 [Mycobacterium phage Bxz1] ],,NP_818291,100.0,4.30719E-70 SIF-HHPRED: SIF-Syn: This genome region is syntenic to gene 256 of Zeenon and gene 248 of Beanwater its closest relatives on Phamerator. /note=no data in Phagesdb function frequency. Phagesdb blast E=1e -54, function unknown, NCBI BLAST(100% coverage, 100% aligned, 100% identity, E=4.30719e-70 Q1:S1) function unknown. HHPred (76.3%Prob, 19.04% coverage, Q53:S41, E=10) function unknown, E-value too high to support CDS 148478 - 148723 /gene="253" /product="gp253" /function="hypothetical protein" /locus tag="Yassified_253" /note=Original Glimmer call @bp 148478 has strength 13.25; Genemark calls start at 148478 /note=SSC: 148478-148723 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein M182_gp094 [Mycobacterium phage Astraea] ],,NCBI, q1:s1 100.0% 1.32498E-50 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.156, -5.243579400788688, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein M182_gp094 [Mycobacterium phage Astraea] ],,YP_008061716,100.0,1.32498E-50 SIF-HHPRED: SIF-Syn: This genome region is syntenic to gene 257 of Zeenon and gene 249 of Beanwater its closest relatives on Phamerator. /note=Phagesdb function frequency has no data. phagesdb blast (E=6e-41). NCBI BLAST(100% coverage, 100% aligned,100% identity, E=1.32498e-50 Q1:S1) function unknown. HHPred (79.2%Prob, 65.43% coverage, Q4:S9, E=24) function effector associated domain 9, E-value too high to support. CDS 148720 - 148941 /gene="254" /product="gp254" /function="hypothetical protein" /locus tag="Yassified_254" /note=Original Glimmer call @bp 148720 has strength 10.75; Genemark calls start at 148720 /note=SSC: 148720-148941 CP: no SCS: both ST: SS BLAST-Start: [gp247 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 1.07423E-45 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.811, -3.0425830684175623, yes F: hypothetical protein SIF-BLAST: ,,[gp247 [Mycobacterium phage Cali] ],,YP_002224689,100.0,1.07423E-45 SIF-HHPRED: SIF-Syn: This genome region is syntenic to gene 258 of Zeenon and gene 250 of Beanwater its closest relatives on Phamerator. Very informative. /note=no data in Phagesdb function frequency. Phagesdb blast E=2e -36, function unknown, NCBI BLAST(100% coverage, 100% aligned, 100% identity, E=1.07423e-45 Q1:S1) function unknown. HHPred (53.1%Prob, 31.50% coverage, Q40:S21, E=87) capsid assembly scaffolding, E-value too high to support CDS 148972 - 149493 /gene="255" /product="gp255" /function="polynucleotide kinase" /locus tag="Yassified_255" /note=Original Glimmer call @bp 148972 has strength 18.85; Genemark calls start at 148972 /note=SSC: 148972-149493 CP: no SCS: both ST: SS BLAST-Start: [polynucleotide kinase [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 6.80991E-123 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.811, -3.3136498407041004, yes F: polynucleotide kinase SIF-BLAST: ,,[polynucleotide kinase [Mycobacterium phage ET08] ],,YP_003347892,100.0,6.80991E-123 SIF-HHPRED: HAD_PNKP-C; C-terminal phosphatase domain of T4 polynucleotide kinase/phosphatase (PNKP) and related phosphatases.,,,cd07502,84.9711,99.8 SIF-Syn: This genome region is syntenic to gene 259 of Zeenon and gene 251 of Beanwater its closest relatives on Phamerator. /note=99% frequency in Phagesdb function. Phagesdb blast E=5e -97, polynucleotide kinase, NCBI BLAST(100% coverage, 100% aligned, 100% identity, E=6.80991e-123 Q1:S1) polynucleotide kinase. HHPred (99.8%Prob, 84.97% coverage, Q7:S1, E=1.9e -18) polynucleotide kinase. CDS 149554 - 149790 /gene="256" /product="gp256" /function="hypothetical protein" /locus tag="Yassified_256" /note=Original Glimmer call @bp 149554 has strength 10.97; Genemark calls start at 149575 /note=SSC: 149554-149790 CP: yes SCS: both-gl ST: SS BLAST-Start: [gp245 [Mycobacterium phage Bxz1] ],,NCBI, q1:s1 100.0% 2.84116E-50 GAP: 60 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.578, -3.5925599723783583, yes F: hypothetical protein SIF-BLAST: ,,[gp245 [Mycobacterium phage Bxz1] ],,NP_818295,100.0,2.84116E-50 SIF-HHPRED: SIF-Syn: This genome region is syntenic to gene 260 of Zeenon and gene 252 of Beanwater its closest relatives on Phamerator. /note=no data in Phagesdb function frequency. Phagesdb blast E=5e -41, function unknown, NCBI BLAST(100% coverage, 100% aligned, 98.71% identity, E=2.84116e-50 Q1:S1) function unknown. HHPred (53.1%Prob, 14.10% coverage, Q42:S16, E=17) function unknown, E-value too high to support CDS 149790 - 150233 /gene="257" /product="gp257" /function="hypothetical protein" /locus tag="Yassified_257" /note=Original Glimmer call @bp 149790 has strength 5.17; Genemark calls start at 149790 /note=SSC: 149790-150233 CP: yes SCS: both ST: SS BLAST-Start: [gp252 [Mycobacterium phage Spud] ],,NCBI, q1:s1 100.0% 6.88562E-104 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.983, -3.2535385006449706, yes F: hypothetical protein SIF-BLAST: ,,[gp252 [Mycobacterium phage Spud] ],,YP_002224471,100.0,6.88562E-104 SIF-HHPRED: SIF-Syn: This genome region is syntenic to gene 261 of Zeenon and gene 253 of Beanwater its closest relatives on Phamerator. /note=no data in Phagesdb function frequency. Phagesdb blast E=2e -85, function unknown, NCBI BLAST(100% coverage, 100% aligned, 100% identity, E=6.88562e-104 Q1:S1) function unknown. HHPred (75.4%Prob, 10.20% coverage, Q7:S2, E=7.5) N-terminal subdomain of transcriptional regulator MraZ, E-value too high to support CDS 150230 - 151297 /gene="258" /product="gp258" /function="serine/threonine kinase" /locus tag="Yassified_258" /note=Original Glimmer call @bp 150230 has strength 13.52; Genemark calls start at 150230 /note=SSC: 150230-151297 CP: yes SCS: both ST: SS BLAST-Start: [serine/threonine kinase [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.759, -3.7234890726758456, yes F: serine/threonine kinase SIF-BLAST: ,,[serine/threonine kinase [Mycobacterium phage ET08] ],,YP_003347895,100.0,0.0 SIF-HHPRED: Serine/threonine-protein kinase PknA; PknA, kinase, drug target, Mtb, TRANSFERASE; 2.03A {Mycobacterium tuberculosis},,,4OW8_A,72.3944,100.0 SIF-Syn: This genome region is syntenic to gene 262 of Zeenon and gene 254 of Beanwater its closest relatives on Phamerator. /note=PhagesDB frequency(99%), PhagesDB BLAST(E=0), NCBI BLAST(100% coverage, 100% aligned, 100% identity, E=0 Q1:S1) and HHPred support the function (100%Prob, 72.39% coverage, Q83:S6, E=6.4E-35) CDS 151339 - 153120 /gene="259" /product="gp259" /function="HNH endonuclease" /locus tag="Yassified_259" /note=Original Glimmer call @bp 151339 has strength 15.58; Genemark calls start at 151339 /note=SSC: 151339-153120 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Mycobacterium phage CharlieB] ],,NCBI, q1:s1 100.0% 0.0 GAP: 41 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.291, -1.953940808934884, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage CharlieB] ],,YP_010057635,99.6627,0.0 SIF-HHPRED: Endonuclease PI-PkoII; hydrolase; HET: SO4, GOL, MSE; 2.5A {Thermococcus kodakarensis},,,2CW8_A,24.1147,99.1 SIF-Syn: no synteny with its closest releatives of Zeenon and Beanwater /note=100% hnh endonuclease Phagesdb function frequency. Phagesdb blast E=0, function unknown, NCBI BLAST(100% coverage, 99.66% aligned, 99.66% identity, E=0 Q1:S1) function unknown. HHPred (99.1%Prob, 24.11% coverage, Q298:S365, E=4.3e-8) Endonuclease PI-PkoII; hydrolase, coverage and alignment not good enough to support. not enough support to declare function CDS 153117 - 153383 /gene="260" /product="gp260" /function="hypothetical protein" /locus tag="Yassified_260" /note=Original Glimmer call @bp 153117 has strength 10.34; Genemark calls start at 153117 /note=SSC: 153117-153383 CP: yes SCS: both ST: SS BLAST-Start: [gp253 [Mycobacterium phage Cali] ],,NCBI, q1:s1 100.0% 2.876E-57 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.158, -4.98464302562818, no F: hypothetical protein SIF-BLAST: ,,[gp253 [Mycobacterium phage Cali] ],,YP_002224695,100.0,2.876E-57 SIF-HHPRED: SIF-Syn: Not informative /note=no evidence supporting a function call. Not a transmembrane protein. CDS 153380 - 154708 /gene="261" /product="gp261" /function="adenylosuccinate synthetase PurA-like" /locus tag="Yassified_261" /note=Original Glimmer call @bp 153380 has strength 15.77; Genemark calls start at 153380 /note=SSC: 153380-154708 CP: yes SCS: both ST: SS BLAST-Start: [PurA-like adenylosuccinate synthetase [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.146, -4.497860114175419, no F: adenylosuccinate synthetase PurA-like SIF-BLAST: ,,[PurA-like adenylosuccinate synthetase [Mycobacterium phage ScottMcG] ],,YP_002224252,100.0,0.0 SIF-HHPRED: c.37.1.10 (A:) automated matches {Legionella pneumophila [TaxId: 446]} | CLASS: Alpha and beta proteins (a/b), FOLD: P-loop containing nucleoside triphosphate hydrolases, SUPFAM: P-loop containing nucleoside triphosphate hydrolases, FAM: Nitrogenase iron protein-like,,,SCOP_d6c25a_,98.6425,100.0 SIF-Syn: Ading ,Aditam, Pinkcreek all have an ortholog gene in the same location. /note=Evidence from PhagesDB most frequent function call, BLAST from NCBI and PhagesDB, HHPred and CDD, all support this function call. CDS 154708 - 154794 /gene="262" /product="gp262" /function="membrane protein" /locus tag="Yassified_262" /note= /note=SSC: 154708-154794 CP: yes SCS: neither ST: NI BLAST-Start: [hypothetical protein M181_gp091 [Mycobacterium phage Gizmo] ],,NCBI, q1:s1 100.0% 6.8674E-8 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -3.3503726477288405, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein M181_gp091 [Mycobacterium phage Gizmo] ],,YP_008061036,100.0,6.8674E-8 SIF-HHPRED: SIF-Syn: Several C1 phages have an orrtholog in the same position. /note=One transmembrane domain supported by Tmhmm, topcon and SOSUI. CDS 154791 - 155027 /gene="263" /product="gp263" /function="hypothetical protein" /locus tag="Yassified_263" /note=Original Glimmer call @bp 154791 has strength 12.52; Genemark calls start at 154791 /note=SSC: 154791-155027 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ET08_251 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 1.0315E-45 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.776, -5.2756940258553, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_251 [Mycobacterium phage ET08] ],,YP_003347899,100.0,1.0315E-45 SIF-HHPRED: SIF-Syn: not informative. /note=No evidence supporting a function call for this gene. Not a transmembrane protein. CDS 155024 - 155185 /gene="264" /product="gp264" /function="hypothetical protein" /locus tag="Yassified_264" /note=Original Glimmer call @bp 155024 has strength 6.16; Genemark calls start at 155024 /note=SSC: 155024-155185 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SCOTTMCG_257 [Mycobacterium phage ScottMcG] ],,NCBI, q1:s1 100.0% 1.87211E-29 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.895, -4.963787326180191, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SCOTTMCG_257 [Mycobacterium phage ScottMcG] ],,YP_002224254,100.0,1.87211E-29 SIF-HHPRED: SIF-Syn: not informative. /note=No evidence supporting calling a function. Not a transmembrane protein. CDS join(155280. .155851;1. .4) /gene="265" /product="gp265" /function="hypothetical protein" /locus tag="Yassified_265" /note=Original Glimmer call @bp 155280 has strength 11.74 /note=SSC: 155280-4 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein ET08_253 [Mycobacterium phage ET08] ],,NCBI, q1:s1 100.0% 1.44077E-139 GAP: 94 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.551, -4.609715333525589, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ET08_253 [Mycobacterium phage ET08] ],,YP_003347683,99.4764,1.44077E-139 SIF-HHPRED: SIF-Syn: This gene is also found in a number of C1 phages wtihout a function call. /note=This gene wraps the chromosome from the end to the beginning. No evidence supporting a function call, and not a transmembrane protein