CDS 73 - 1011 /gene="1" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_1" /note=Original Glimmer call @bp 73 has strength 13.6; Genemark calls start at 73 /note= /note=SSC: 73-1011 CP: yes SCS: both ST: NA BLAST-Start: [DUF4082 domain-containing protein [Glutamicibacter ardleyensis] ],,NCBI, q1:s1 53.5256% 2.21565E-31 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.911, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[DUF4082 domain-containing protein [Glutamicibacter ardleyensis] ],,WP_188684507,20.8955,2.21565E-31 SIF-HHPRED: SIF-Syn: /note= /note=Orpham, NCBI Blast shows 4 hits with an e value below 10-4, PhagesDB Blast shows no significant alignments below an e value of 10-7, HHPred shows no significant alignments above 90% probability, could possibly be phosphoesterase /note= /note= /note= /note=SSC: 73, 1011 CP: Yes SCS: Both ST: NA /note= /note= /note= /note=BLAST-Start: no significant blast alignments for PhageDB, DUF4082 Glutamicibacter ardleyensis, NCBI, Q1:S1, 43.11%, 2e-31 Gap: 0 92 LO: Yes RBS: Kibler6, Karlin Medium, 2.929, -2.845, Yes F: NKF /note= /note= /note= /note=SIF-BLAST: NKF, no matches with e values below 10-7 for PhagesDB, domain containing protein, NCBI, DUF4082 Glutamicibacter ardleyensis, WP_188684507.1, 43.11%, 2e-31 SIF-HHPred: NKF, no significant alignments with probability above 90% SIF-Syn: NKF, orpham CDS 1032 - 1481 /gene="2" /function="terminase, small subunit" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_2" /note=Original Glimmer call @bp 1032 has strength 15.09; Genemark calls start at 1032 /note= /note=SSC: 1032-1481 CP: yes SCS: both ST: NI BLAST-Start: [terminase small subunit [Arthrobacter phage DrManhattan] ],,NCBI, q1:s1 100.0% 2.06368E-94 GAP: 20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.302, -2.0162541296952132, yes F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Arthrobacter phage DrManhattan] ],,YP_009815344,94.6667,2.06368E-94 SIF-HHPRED: Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97},,,6Z6E_B,54.3624,98.3 SIF-Syn: Upstream gene- NKF (not seen in Adolin) /note= /note=Original Glimmer call @bp 1032 has strength 15.09 /note= /note=SSC: 1032, 1481 /note= /note=CP: yes /note= /note=SCS: Both /note= /note=ST: NI /note= /note=BLAST-Start: Matches DrManhattan gp 1, PhagesDB, Q1:S1, 91.3%, 284, e= 4e-77, Matches DrManhattan gp 1, PECAAN, Q1:S1, 284, e=4e-77 /note= /note=Gap: 20 /note= /note=LO: no /note= /note=RBS: Kibler6, Karlin Medium, 3.322, -2.016, yes /note= /note=F: terminase, small subunit /note= /note=SIF-BLAST: terminase small subunit, NCBI through PECAAN, DrManhattan gp 1, AYN57721.1, 94.67%, e=2.06e-94 SIF-HHPred: Phage terminase small subunit, HHPred through PECAAN, Enterobacteriophage HK97, 6Z6E_B, 54.3%, 98.3 /note= /note=SIF-Syn: Phamerator, NKF upstream gene, downstream gene is terminase large subunit as seen in Adolin CDS 1478 - 3184 /gene="3" /function="terminase, large subunit" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_3" /note=Original Glimmer call @bp 1478 has strength 15.21; Genemark calls start at 1478 /note= /note=SSC: 1478-3184 CP: yes SCS: both ST: NI BLAST-Start: [terminase large subunit [Arthrobacter phage Amyev] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.166, -4.394706008439538, yes F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Arthrobacter phage Amyev] ],,YP_010677705,98.7676,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,93.3099,100.0 SIF-Syn: termiane large subunit, Amyev, upstream gene terminase small subunit downstream gene portal protein /note= /note=SSC: 1479-3184 CP:yes SCS: both ST: NI BLAST-Start: Matches Amyev, gp 2, PhagesDB, Q1S1, 97%, evalue 0, Matches Amyev, NCBI, Q1S1, 100%, evalue 0 Gap: overlap 4 LO:NA RBS: Kibler6/Karlin Medium, 2.177, -4.395, yes F: terminase large subunit SIF-BLAST: terminase small subunit, phagesDB, Amyev, gp 2, 97%, evalue 0, terminase small subunit, NCBI, Amyev, 100%, evalue 0, YP 010677705.1 SIF-HHPred: Terminase large subunit, PDB_mmCIF70_10_Jan, 6Z6D_A, 0.2706, 100% SIF-Syn: termiane large subunit, Amyev, upstream gene terminase small subunit downstream gene portal protein CDS 3217 - 4587 /gene="4" /function="portal protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_4" /note=Original Glimmer call @bp 3217 has strength 14.32; Genemark calls start at 3217 /note= /note=SSC: 3217-4587 CP: yes SCS: both ST: NI BLAST-Start: [portal protein [Arthrobacter phage DrSierra] ],,NCBI, q2:s3 99.7807% 0.0 GAP: 32 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.302, -2.0162541296952132, yes F: portal protein SIF-BLAST: ,,[portal protein [Arthrobacter phage DrSierra] ],,YP_010678328,96.9365,0.0 SIF-HHPRED: Portal protein; Bacteriophage, SPP1, Portal Protein, Head completion proteins, Connector Complex, DNA Channel, VIRAL PROTEIN; 2.7A {Bacillus subtilis},,,7Z4W_D,91.0088,100.0 SIF-Syn: portal protein CDS 4609 - 6660 /gene="5" /function="VIP2-like ADP-ribosyltransferase toxin" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_5" /note=Original Glimmer call @bp 4609 has strength 17.82; Genemark calls start at 4609 /note= /note=SSC: 4609-6660 CP: yes SCS: both ST: SS BLAST-Start: [VIP2-like ADP-ribosyltransferase toxin [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 0.0 GAP: 21 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.911, -2.827683592113848, yes F: VIP2-like ADP-ribosyltransferase toxin SIF-BLAST: ,,[VIP2-like ADP-ribosyltransferase toxin [Arthrobacter phage DrSierra] ],,YP_010678329,96.0469,0.0 SIF-HHPRED: d.166.1.1 (A:265-550) automated matches {Anthrax bacillus (Bacillus anthracis) [TaxId: 1392]} | CLASS: Alpha and beta proteins (a+b), FOLD: ADP-ribosylation, SUPFAM: ADP-ribosylation, FAM: ADP-ribosylating toxins,,,SCOP_d4dv8a1,37.7745,99.7 SIF-Syn: VIP2-like ADP-ribosyltransferase, In same position as phage Tuck_5, upstream gene is portal protein, downstream gene is NKF CDS 6717 - 7076 /gene="6" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_6" /note=Original Glimmer call @bp 6717 has strength 10.12; Genemark calls start at 6717 /note= /note=SSC: 6717-7076 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE18_gp05 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 7.16251E-72 GAP: 56 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.147, -2.9284886490054283, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp05 [Arthrobacter phage DrSierra] ],,YP_010678330,94.958,7.16251E-72 SIF-HHPRED: SIF-Syn: NKF, upstream gene is VIP2-like ADP-ribosyltransferase toxin, downstream gene is scaffolding protein, just like in phage Warda CDS 7194 - 7712 /gene="7" /function="scaffolding protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_7" /note=Original Glimmer call @bp 7194 has strength 14.87; Genemark calls start at 7194 /note= /note=SSC: 7194-7712 CP: yes SCS: both ST: SS BLAST-Start: [scaffolding protein [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 8.27829E-105 GAP: 117 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.066, -3.3503726477288405, yes F: scaffolding protein SIF-BLAST: ,,[scaffolding protein [Arthrobacter phage DrSierra] ],,YP_010678331,94.8864,8.27829E-105 SIF-HHPRED: Scaffold protein; major capsid protein, HK97-like fold, scaffolding protein, procapsid, VIRUS; 3.72A {Staphylococcus phage 80alpha},,,6B0X_b,35.4651,98.3 SIF-Syn: SIF-Syn [Scaffoling protein, DrSierra, downstream major capsid protein] /note= /note=SSC: [7194,7712] CP: Yes SCS: Both ST: SS BLAST-Start: [DrSierra, 6, phagesDB, 1:1, 90%, 1e-87], [DrSierra, NCBI, 1:1, 100%, 8e-105] Gap: 117 LO: Yes RBS: [Kibler 6, Karlin Medium, 3.085, -3.350, yes] F: Scaffolding Protein SIF-BLAST: [Scaffolding protein, phagesDB, DrSierra 6, 90%, 94%, 1e-87] [Scaffolding Protein, NCBI Dr Sierra, YP_010678331.1, 90.91%, 8e-105] SIF-HHPred: [Scaffolding Protein, HHPred, 80alpha, 6B0X_b, 12.9%, 98.3%] CDS 7740 - 8687 /gene="8" /function="major capsid protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_8" /note=Original Glimmer call @bp 7740 has strength 20.17; Genemark calls start at 7740 /note= /note=SSC: 7740-8687 CP: no SCS: both ST: SS BLAST-Start: [major capsid protein [Arthrobacter phage Powerpuff] ],,NCBI, q1:s1 100.0% 0.0 GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.204, -2.5074698667202133, yes F: major capsid protein SIF-BLAST: ,,[major capsid protein [Arthrobacter phage Powerpuff] ],,QGZ17305,98.7302,0.0 SIF-HHPRED: P22_CoatProtein ; P22 coat protein - gene protein 5,,,PF11651.11,91.4286,100.0 SIF-Syn: The gene with the most alignment is Powerpuff 7 which has the function of major capsid protein. The upstream gene is Powerpuff 6 with the function of a scaffolding protein and the downstream gene is Powerpuff 8 with the function of a head-to-tail adaptor. /note= /note=SSC: 7740/8687 CP: yes SCS: both ST: SS BLAST-Start: Powerpuff_7, NCBI Q1 : S1, 97%, 0.0 , significant Gap: 27bp LO: yes RBS: Kibler 6, Karlin Medium, 3.224, –2.507, yes F: major capsid protein SIF-BLAST: major capsid protein, NCBI, Powerpuff_7, QGZ17305.1., 97.46%, 0.0 SIF-HHPred: major capsid protein, PECAAN, Powerpuff_7, Hit 5L35_B, 66.35%, 99.96 SIF-Syn: Major Capsid Protein, Powerpuff_7 CDS 8762 - 9178 /gene="9" /function="head-to-tail adaptor" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_9" /note=Original Glimmer call @bp 8762 has strength 8.98; Genemark calls start at 8762 /note= /note=SSC: 8762-9178 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail adaptor [Arthrobacter phage Janeemi]],,NCBI, q1:s1 97.8261% 9.40867E-81 GAP: 74 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.302, -2.0162541296952132, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Arthrobacter phage Janeemi]],,UVK63529,90.2098,9.40867E-81 SIF-HHPRED: Head completion protein gp15; Bacteriophage, SPP1, Portal Protein, Head completion proteins, Connector Complex, DNA Channel, VIRAL PROTEIN; 2.7A {Bacillus subtilis},,,7Z4W_h,78.2609,98.9 SIF-Syn: /note= /note=SSC: 8762, 417 CP: Yes SCS: Both ST: SS /note= /note= /note= /note=BLAST-Start: Tuck, gp9, PhagesDB, Q1:S1, 91%, 3e-65, Janeemi, gp9, NCBI, Q1:S1, 97%, 9e-81 Gap: 74 LO: Yes RBS: Kibler6, Karlin Medium, 3.322, -2.016, Yes F: head-to-tail adaptor /note= /note= /note= /note=SIF-BLAST: head-to-tail adaptor, PhagesDB, Tucker, gp9, 91%, 3e-65, head-to-tail adaptor, NCBI, Janeemi, gp9, UVK63529.1, 97%, 9e-81 /note= /note=SIF-HHPred: head completion protein, PDB_mmCIF70, SPP1, gp15, 7Z4W_h, 71.2%, 98.91% /note= /note=SIF-Syn: head-to-tail adaptor, inferred from Tuck_9, Yang_8, and Warda_8. CDS 9179 - 9289 /gene="10" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_10" /note=Genemark calls start at 9179 /note= /note=SSC: 9179-9289 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein PQE18_gp09 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 5.04027E-15 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.434, -3.8183153089559627, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp09 [Arthrobacter phage DrSierra] ],,YP_010678334,100.0,5.04027E-15 SIF-HHPRED: SIF-Syn: - Upstream gene: head to tail adaptor /note= /note=Original GeneMark call @bp 9179 /note= /note=SSC: 9179, 9289 /note= /note=CP: yes /note= /note=SCS: GeneMark /note= /note=ST: SS /note= /note=BLAST-Start: Matches DrSierra gp 9, NCBI, Q1:S1, 100%, e=5e-15 /note= /note=Gap: 0 /note= /note=LO: yes /note= /note=RBS: Kibler6, Karlin Medium, 2.448, -3.818, yes /note= /note=F: NKF /note= /note=SIF-BLAST: NKF, NCBI, DrSierra gp 9, YP_010678334.1, 100%, e=5.04e-15 SIF-HHPred: NKF, no matches above 90% probability /note= /note=SIF-Syn: Phamerator, upstream is head-to-tail adaptor, downstream is head-to-tail stopper, conserved in Adumb2043 CDS 9289 - 9633 /gene="11" /function="head-to-tail stopper" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_11" /note=Original Glimmer call @bp 9289 has strength 15.13; Genemark calls start at 9289 /note= /note=SSC: 9289-9633 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail stopper [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 2.23393E-70 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.147, -3.1837611541087343, yes F: head-to-tail stopper SIF-BLAST: ,,[head-to-tail stopper [Arthrobacter phage DrSierra] ],,YP_010678335,96.4912,2.23393E-70 SIF-HHPRED: Putative head-tail adaptor; Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Unknown function; NMR {Shigella flexneri},,,2KZ4_A,96.4912,99.7 SIF-Syn: head to tail stopper, Dr. Sierra, downstream gene head to tail adaptor upstream gene tail terminator /note= /note=SSC: 9289-9633 CP: yes SCS: both ST: SS BLAST-Start: Matches DrSierra, gp 10, PhagesDB, Q1S1, 92%, evalue 2e-57, Matches DrSierra, NCBI, Q1S1, 100% , evlaue 2e-70 Gap: overlap 1 LO: N/A RBS: Kibler 6/Karlin Medium, 3.166, -3.184, yes F: head-to-tail stopper SIF-BLAST: heat to tail stopper, phages DB, DrSierra, gp 10, 92%, evalue 2e-57, head closure Hc1, NCBI, DrSierra, 100%, evalue 2e-70 YP_010678335.1 SIF-HHPred: head to tail adaptor, PDB_mmCIF70_10_jan, 2KZ4_A, 0.307, 99.71% SIF-Syn: head to tail stopper, Dr. Sierra, downstream gene head to tail adaptor upstream gene tail terminator CDS 9644 - 9949 /gene="12" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_12" /note=Original Glimmer call @bp 9644 has strength 13.25; Genemark calls start at 9644 /note= /note=SSC: 9644-9949 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE18_gp11 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 99.0099% 4.88735E-57 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.302, -2.4811409279978642, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp11 [Arthrobacter phage DrSierra] ],,YP_010678336,96.0396,4.88735E-57 SIF-HHPRED: SIF-Syn: NKF CDS 9954 - 10370 /gene="13" /function="tail terminator" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_13" /note=Original Glimmer call @bp 9954 has strength 8.53; Genemark calls start at 9954 /note= /note=SSC: 9954-10370 CP: yes SCS: both ST: NI BLAST-Start: [tail terminator [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 1.67414E-71 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.638, -5.411464006628378, no F: tail terminator SIF-BLAST: ,,[tail terminator [Arthrobacter phage DrSierra] ],,YP_010678337,95.6522,1.67414E-71 SIF-HHPRED: TAIL-TO-HEAD JOINING PROTEIN GP17; VIRAL PROTEIN, VIRAL INFECTION, TAILED BACTERIOPHAGE, SIPHOVIRIDAE, SPP1, VIRAL ASSEMBLY, HEAD-TO-TAIL INTERFACE, DNA GATEKEEPER, ALLOSTERIC MECHANISM; 7.2A {BACILLUS PHAGE SPP1},,,5A21_G,96.3768,99.4 SIF-Syn: tail terminator, In same position as Tuck_13, upstream gene is NKF, downstream gene is major tail protein CDS 10387 - 10935 /gene="14" /function="major tail protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_14" /note=Original Glimmer call @bp 10387 has strength 17.5; Genemark calls start at 10387 /note= /note=SSC: 10387-10935 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Arthrobacter phage VResidence]],,NCBI, q1:s1 100.0% 7.03992E-114 GAP: 16 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.302, -2.0162541296952132, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage VResidence]],,UYL87618,94.5055,7.03992E-114 SIF-HHPRED: YSD1_22 major tail protein; Bacteriophage tail, helical assembly, VIRAL PROTEIN; 3.5A {Bacteriophage sp.},,,6XGR_L,92.3077,98.3 SIF-Syn: major tail protein, upstream gene is NKF, downstream gene is tail assembly chaperone, just like in phage Warda CDS 11039 - 11308 /gene="15" /function="tail assembly chaperone" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_15" /note=Original Glimmer call @bp 11039 has strength 20.84; Genemark calls start at 11039 /note= /note=SSC: 11039-11308 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 3.86741E-54 GAP: 103 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.313, -1.993391246735709, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage DrSierra] ],,YP_010678340,97.7528,3.86741E-54 SIF-HHPRED: Phage_TAC_10 ; Phage tail assembly chaperone,,,PF10963.11,78.6517,93.0 SIF-Syn: SIF-Syn: [Tail Assembly Chaperone, DrSierra 13 and 16, upstream is major tail protein, downstream is tail assembly chaperone] /note= /note=SSC: [11039, 11308] CP: Yes SCS: Both ST: SS BLAST-Start: [DrSierra, 14, phagesDB, Q1:S1, 96%, 5e-42] [DrSierra, NCBI, Q1:S1, 97%, 4e-57] Gap: 103 LO: Yes RBS: [Kibler6, Karlin Medium, 3.33, -1.993, Yes] F: Tail Assembly Chaperone SIF-BLAST: [Tail Assembly Chaperone, phages DB, DrSierra 14, 96%, 5e-42] [Tail Assembly Chaperone, NCBI, DrSierra, YP_010678340.1, 97%, 4e-57] SIF-HHPred: [Tail Assembly Chaperone, HHPred, TAC 10, PF10963.11, 6.3%, 93] CDS join(11039. .11308;11308. .11667) /gene="16" /function="tail assembly chaperone" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_16" /note=Original Glimmer call @bp 11344 has strength 10.35; Genemark calls start at 11344 /note= /note=SSC: 11039-11667 CP: no SCS: both-cs ST: SS BLAST-Start: [tail assembly chaperone [Arthrobacter phage DrSierra] ],,NCBI, q55:s88 69.3182% 3.80457E-65 GAP: -172 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.98, -7.684363352293865, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage DrSierra] ],,YP_010678339,53.8462,3.80457E-65 SIF-HHPRED: SIF-Syn: Although on phagesdb and NCBI, DrSierra gene 15 had the most alignments with Wildwest gene 16, on phamerator and on PECAAN pham maps it shows that gene 16 does not have synteny with any other gene in the pham. /note= /note=SSC: 11344/11667 CP: no SCS: both ST: SS BLAST-Start: DrSierra_15, Phagesdb, Q1 : S103, 85%, 2e-57. Gap: 35 LO: no RBS: Kibler 6, Karlin Medium, 1.767, -5.158, no F: tail assembly chaperone SIF-BLAST: tail assembly chaperone, DrSierra_15, YP_010678339.1, 85.05%, 2e-57. SIF-HHPred: tail assembly chaperone, PECAAN, DrSierra_15, Hit 5L35_, 66.35%, 99.96, SIF-Syn: NKF /note= /note=tail assembly chaperone frameshift protein CDS 11664 - 13910 /gene="17" /function="tape measure protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_17" /note=Original Glimmer call @bp 11664 has strength 14.4; Genemark calls start at 11664 /note= /note=SSC: 11664-13910 CP: yes SCS: both ST: NI BLAST-Start: [tape measure protein [Arthrobacter phage Crewmate] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.066, -2.583959800616441, yes F: tape measure protein SIF-BLAST: ,,[tape measure protein [Arthrobacter phage Crewmate] ],,YP_010678268,83.5938,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_CF,11.7647,99.9 SIF-Syn: /note= /note=NI because the most annotated start is not available /note= /note= /note= /note=Evidence to suggest Wildwest_17 being a transmembrane protein /note= /note= /note= /note=SSC: 11664, 13910 CP: yes SCS: Both ST: NI /note= /note= /note= /note=BLAST-Start: Crewmate gp17, PhagesDB, Q1:S1, 73%, 0, Crewmate gp17, NCBI, Q1:S1, 73.51%, 0 Gap: -4 LO: Yes RBS: Kibler6, Karlin Medium, 3.085, -2.584, Yes F: tape measure protein /note= /note= /note= /note=SIF-BLAST: tape measure protein, PhagesDB, Crewmate gp17, 73%, 0, tape measure protein, NCBI, Crewmate gp17, YP_010678268.1, 73.51%, 0 SIF-HHPred: tape measure protein, PDB_CIF70, gp57, 6V8I_CF, 11.9%, 99.88% SIF-Syn: tape measure protein, upstream is a minor tail protein, downstream is a tail assembley chaperone, inferred from Tuck_17, Phives_17, and Crewmate_17, CDS 13910 - 15367 /gene="18" /function="minor tail protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_18" /note=Original Glimmer call @bp 13910 has strength 16.9; Genemark calls start at 13910 /note= /note=SSC: 13910-15367 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Adolin]],,NCBI, q1:s1 100.0% 3.90028E-157 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.99, -3.2535385006449706, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Adolin]],,QHB36599,71.7622,3.90028E-157 SIF-HHPRED: HYPOTHETICAL PROTEIN 19.1; VIRAL PROTEIN, DISTAL TAIL PROTEIN; 2.95A {BACILLUS PHAGE SPP1},,,2X8K_C,99.7938,99.9 SIF-Syn: - upstream: tape measure protein /note= /note=Original Glimmer call @bp 13910 has strength 16.90 /note= /note=SSC: 13910, 15367 /note= /note=CP: yes /note= /note=SCS: both /note= /note=ST: SS /note= /note=BLAST-Start: Matches Adolin gp 17, NCBI Blast, PhagesDB, Q1:S1, 67%, e=e-145 /note= /note=Gap: overlap of 1 /note= /note=LO: yes, but N/A due to no gap /note= /note=RBS: Kibler6, Karlin Medium, 3.008, -3.254, yes /note= /note=F: minor tail protein /note= /note=SIF-BLAST: minor tail protein, NCBI, Adolin gp 17, QHB36599.1, 58%, e-145 /note= /note=SIF-HHPred: tail protein, HHPred, Bacillus phage, 2X8K_C, 239/252, 99.92 /note= /note=SIF-Syn: upstream gene is tape measure protein, downstream is minor tail protein, this is also seen in Adolin CDS 15358 - 16572 /gene="19" /function="minor tail protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_19" /note=Original Glimmer call @bp 15358 has strength 17.47; Genemark calls start at 15358 /note= /note=SSC: 15358-16572 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 0.0 GAP: -10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.407, -4.465931009266885, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage DrSierra] ],,YP_010678343,95.5446,0.0 SIF-HHPRED: Protein gp18; NP_465809.1, prophage tail protein gp18, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative; HET: MSE, MLY; 1.7A {Listeria monocytogenes EGD-e},,,3GS9_A,99.2574,99.7 SIF-Syn: minor tail protein, Drsierra, upstream gene minor tail protein downstream gene minor tail protein /note= /note=SSC: 15358-16572 CP: Yes SCS: both ST: SS BLAST-Start: Matches DrSierra, gp 18, PhagesDB, Q1S1, 89%, evalue 0. Matches DrSierra, NCBI, Q1S1, 100%, evalue 0 Gap: overlap 10 LO: NA RBS: Kibler 6/Karlin medium, 2.40, -4.466, yes F: minor tail protein SIF-BLAST: minor tail protein, phagesDB, DrSierra, gp 18, 89%, evalue 0, minor tail protein, NCBI, DrSierra, 100%, evalue 0, YP_010678343.1 SIF-HHPred: prophage tail protein, PDB_mmCIF70_10_Jan, 3GS9_A, gp18, 0.2568, 99.74% SIF-Syn: minor tail protein, Drsierra, upstream gene minor tail protein downstream gene minor tail protein CDS 16573 - 17577 /gene="20" /function="minor tail protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_20" /note=Original Glimmer call @bp 16573 has strength 16.29; Genemark calls start at 16573 /note= /note=SSC: 16573-17577 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.969, -2.7863799983944713, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage DrSierra] ],,YP_010678344,90.1198,0.0 SIF-HHPRED: Long tail fiber distal subunit; Bacteriophage, Helical sandwich, Tail fiber, polyglycine, VIRAL PROTEIN; HET: MRD, IMD, MPD; 1.70355818561A {Salmonella phage vB_SenMS16},,,6F45_C,36.8263,98.2 SIF-Syn: DrSierra, upstream minor tail protein, downstream minor tail protein CDS 17574 - 18656 /gene="21" /function="minor tail protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_21" /note=Original Glimmer call @bp 17574 has strength 18.2; Genemark calls start at 17574 /note= /note=SSC: 17574-18656 CP: yes SCS: both ST: SS BLAST-Start: [virion structural protein [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 83.8889% 7.19742E-120 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, yes F: minor tail protein SIF-BLAST: ,,[virion structural protein [Arthrobacter phage DrSierra] ],,YP_010678345,68.0791,7.19742E-120 SIF-HHPRED: Receptor Binding Protein; beta sandwich domain, phage receptor binding protein, Lactococcus lactis pellicle cell wall polyphosphosaccharide, VIRAL PROTEIN; 1.75A {Lactococcus phage 1358},,,4L9B_A,48.8889,99.5 SIF-Syn: minor tail protein, In same position as Tuck_21, upstream is minor tail protein, downstream NKF CDS 18728 - 19186 /gene="22" /function="membrane protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_22" /note=Original Glimmer call @bp 18728 has strength 9.29; Genemark calls start at 18728 /note= /note=SSC: 18728-19186 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage Phives] ],,NCBI, q1:s1 100.0% 9.60435E-71 GAP: 71 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.816, -3.3136498407041004, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Phives] ],,YP_010677657,87.7419,9.60435E-71 SIF-HHPRED: SIF-Syn: NKF, upstream gene is minor tail protein, downstream gene is NKF, just like in phage DrSierra /note= /note=There is conflicting evidence on HHPred, NCBI BLAST, and PhagesDB BLAST, however, the SEA-PHAGES bioinformatics guide says that these types of genes should be evaluated on TMHMM for membrane domains. The TMHMM ran on this gene found that there were membrane domains, so the function has been assigned as a membrane protein, which coincides with the NCBI BLAST results. CDS 19187 - 19603 /gene="23" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_23" /note=Original Glimmer call @bp 19187 has strength 16.39; Genemark calls start at 19187 /note= /note=SSC: 19187-19603 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PQE18_gp22 [Arthrobacter phage DrSierra] ],,NCBI, q3:s2 98.5507% 1.82829E-81 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.434, -4.408140843866914, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp22 [Arthrobacter phage DrSierra] ],,YP_010678347,94.1606,1.82829E-81 SIF-HHPRED: DUF2730 ; Protein of unknown function (DUF2730),,,PF10805.11,78.2609,97.7 SIF-Syn: SIF-Syn: [NKF, upstream is minor tail protein, downstream is deoxynucleoside monophosphate kinase] /note= /note=SSC: [19187, 19603] CP: Yes SCS: Both ST: NI BLAST-Start: [DrSierra, 22, phagesDB, 3:2, 86%, 5e-65] [DrSierra, NCBI, 3:2, 87%, 2e-81] Gap: 0 LO: N/A RBS: [Kibler6, Karlin Medium, 2.448, -4.408, No] F: NKF SIF-BLAST:[NKF, phagesDB, DrSierra 22, 86%, 5e-65] [NKF, NCBI, DrSierra, YP_010678347.1, 87%, 2e-81] SIF-HHPred: [NKF, no matches with a probability above 90%] CDS 19604 - 19855 /gene="24" /function="membrane protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_24" /note=Original Glimmer call @bp 19604 has strength 17.98; Genemark calls start at 19604 /note= /note=SSC: 19604-19855 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQE18_gp23 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 3.80779E-48 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.204, -2.2186743274732437, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein PQE18_gp23 [Arthrobacter phage DrSierra] ],,YP_010678348,98.7952,3.80779E-48 SIF-HHPRED: SIF-Syn: On PECAAN pham maps Wildwest gene 24 has synteny with DrSierra gene 23 however, DrSierra gene 23 has no known function. /note= /note=SSC: 19604/19855 CP: yes SCS: both ST: SS BLAST-Start: DrSierra_23, Phagesdb, Q1 : S1, /note= /note=98%, 4e-40; DrSierra, NCBI, Q1 : S1, 99%, 4e-48 Gap: 0 bp LO: N/A RBS: Kibler 6, Karlin /note= /note=Medium, 3.224, -2.219, yes F: NKF SIF-BLAST: NKF, NCBI, DrSierra, YP_010678348.1, /note= /note=98.80%, 4e-48 SIF-HHPred: Membrane Protein, low e-value PECAAN, PF04531.16, 19.84%, 90.2 SIF- /note= /note=Syn: Not in correct location for Holin CDS 20005 - 20619 /gene="25" /function="deoxynucleoside monophosphate kinase" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_25" /note=Original Glimmer call @bp 19936 has strength 20.08; Genemark calls start at 20005 /note= /note=SSC: 20005-20619 CP: yes SCS: both-gm ST: NI BLAST-Start: [deoxynucleoside monophosphate kinase [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 1.27557E-136 GAP: 149 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.16, -4.4057176022952405, yes F: deoxynucleoside monophosphate kinase SIF-BLAST: ,,[deoxynucleoside monophosphate kinase [Arthrobacter phage DrSierra] ],,YP_010678349,97.0588,1.27557E-136 SIF-HHPRED: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE; TRANSFERASE, PHOSPHOTRANSFERASE; HET: DGP, OCS; 2.0A {Enterobacteria phage T4} SCOP: c.37.1.1,,,1DEK_A,93.1373,99.8 SIF-Syn: /note= /note=Discrepancy between GeneMark and Glimmer on start, decided to select GeneMark`s prediction of 20005 instead of Glimmer`s prediction of 19936 due to better z-score, raw score and final score, NI because the most annotated start is not present on starterator report /note= /note= /note= /note=SSC: 20005, 20619 CP: Yes SCS: Both-GM ST: NI /note= /note= /note= /note=BLAST-Start: DrSierra gp24, PhagesDB, Q24:S1, 93%, e-109, DrSierra gp24, NCBI, Q24:S1, 93.14%, 2e-136 Gap: 149 LO: No RBS: Kibler6, Karlin Medium, 2.172, -4.406, Yes F: deoxynucleoside monophosphate kinase /note= /note= /note= /note=SIF-BLAST: deoxynucleoside monophosphate kinase, PhagesDB, DrSierra gp24, 93%. e-109, deoxynucleoside monophosphate kinase, NCBI, DrSierra gp24, YP_010678349.1, 93.14%, 2e-136 SIF-HHPred: deoxynucleoside monophosphate kinase, PDB_CIF70, 1DEK_A, 92.7%, 99.77% SIF-Syn: deoxynucleoside monophosphate kinase, inferred from Yang_24 and DrSierra_24 CDS 20723 - 21316 /gene="26" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_26" /note=Original Glimmer call @bp 20723 has strength 9.91; Genemark calls start at 20723 /note= /note=SSC: 20723-21316 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE18_gp25 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 1.60939E-126 GAP: 103 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.423, -5.857463951082417, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp25 [Arthrobacter phage DrSierra] ],,YP_010678350,95.9391,1.60939E-126 SIF-HHPRED: SIF-Syn: upstream: deoxynucleoside monophosphate kinase /note= /note=Original Glimmer call @bp 20723 has strength 9.91 /note= /note= /note= /note=SSC: 20723, 21316 /note= /note= /note= /note=CP: yes /note= /note= /note= /note=SCS: Both /note= /note= /note= /note=ST: SS /note= /note= /note= /note=BLAST-Start: Matches DrSierra gp 25, NCBI Blast, PhagesDB, Q1:S1, 91.8%, e=1.6e-126 /note= /note= /note= /note=Gap: 103 /note= /note= /note= /note=LO: yes /note= /note= /note= /note=RBS: Kibler6, Karlin Medium, 1.423, -5.857, yes (N/A bc z score is too low and final score is very neg) /note= /note= /note= /note=F: NKF /note= /note= /note= /note=SIF-BLAST: NKF, matches hypothetical protein 25, DrSierra, NCBI Blast, 96%, 1.6e-126 /note= /note= /note= /note=SIF-HHPred: NKF, no matches with prob above 90% /note= /note= /note= /note=SIF-Syn: upstream gene is deoxynucleoside monophosphate kinase, downstream gene is exonuclease, this is seen in Adolin CDS 21505 - 22341 /gene="27" /function="exonuclease" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_27" /note=Original Glimmer call @bp 21505 has strength 14.53; Genemark calls start at 21556 /note= /note=SSC: 21505-22341 CP: yes SCS: both-gl ST: SS BLAST-Start: [exonuclease [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 0.0 GAP: 188 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.302, -2.606079664606164, yes F: exonuclease SIF-BLAST: ,,[exonuclease [Arthrobacter phage DrSierra] ],,YP_010678351,98.5611,0.0 SIF-HHPRED: Mitochondrial genome maintenance exonuclease 1; human MGME1, DNA complex, DNA exonuclease, DNA BINDING PROTEIN; 2.702A {Homo sapiens},,,5ZYT_C,79.4964,99.8 SIF-Syn: exonuclease, DrSierra upsteam gene deoxynucleoside monophosphate kinase, downstream gene nucleoside deoxyribosyltransferase /note= /note=Glimmer called it at 21505 and GeneMark called the start at 21556. After reviewing all the evidence, went along with the start that Glimmer called because the RBS score at where Glimmer called the gene was the best, the strength of the call was good, and the coding potential covered the gene start that Glimmer called. /note= /note= /note= /note=SSC: 21505-22341 CP: Yes SCS: Both-GL ST: SS BLAST-Start: Matches DrSierra, gp 26, PhagesDB, Q1S1, 98%, evalue e-158, Matches DrSierra, NCBI, Q1S1, 100%, evalue 0 Gap: 188 LO: NO RBS: Kibler6/ Karlin Medium, 3.322, -2.606, yes F: exonuclease SIF-BLAST: exonuclease, PhagesDB, DrSierra, gp 26, 98%, evalue e-158, exonuclease, NCBI, DrSierra, 100%, evalue 0, YP_010678351.1 SIF-HHPred: mitochondrial genome maintenance exonuclease, PDB_mmCIF70_10_Jan, 5ZYT_C, 0.229, 99.76% SIF-Syn: exonuclease, DrSierra upsteam gene deoxynucleoside monophosphate kinase, downstream gene nucleoside deoxyribosyltransferase CDS 22362 - 22703 /gene="28" /function="nucleoside deoxyribosyltransferase" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_28" /note=Original Glimmer call @bp 22362 has strength 9.49; Genemark calls start at 22362 /note= /note=SSC: 22362-22703 CP: yes SCS: both ST: NI BLAST-Start: [nucleoside deoxyribosyltransferase [Arthrobacter phage Powerpuff] ],,NCBI, q1:s9 100.0% 1.40576E-71 GAP: 20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.949, -5.814681024300869, yes F: nucleoside deoxyribosyltransferase SIF-BLAST: ,,[nucleoside deoxyribosyltransferase [Arthrobacter phage Powerpuff] ],,QGZ17325,92.562,1.40576E-71 SIF-HHPRED: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE; active site, alpha/beta protein, biocatalyst, nucleoside, TRANSFERASE; HET: 5MD; 2.4A {Lactobacillus leichmannii} SCOP: c.23.14.1,,,1F8Y_B,83.1858,99.1 SIF-Syn: nucleoside deoxyribosyltransferase, Lizalica, upstream exonuclease, downstream LAGLIDAD endonuclease /note= /note=SSC: 22362 CP: yes SCS: both ST: NI BLAST-Start: Lizalica gp27, PhagesDB, Q1 S9, 97% identity, 7e-61. Lizalica gp27, NCBI, Q1 S9, 100% query cover, 6e-72 Gap: 20bp LO: no RBS: Kibler6, Karlin Medium, Z Score 1.959, Final Score -5.815, yes F: nucleoside deoxyribosyltransferase SIF-BLAST: nucleoside deoxyribosyltransferase, NCBI, Lizalica gp27, YP_010677592.1, 93% alignment, 6e-72 SIF-HHPred: nucleoside deoxyribosyltransferase, PDC_mmCIF70_10_Jan, 1F8Y_B, 27% alignment, 99.01% probability SIF-Syn: nucleoside deoxyribosyltransferase, Lizalica, upstream exonuclease, downstream LAGLIDAD endonuclease CDS 22700 - 23104 /gene="29" /function="LAGLIDADG endonuclease" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_29" /note=Original Glimmer call @bp 22700 has strength 13.66; Genemark calls start at 22700 /note= /note=SSC: 22700-23104 CP: yes SCS: both ST: SS BLAST-Start: [LAGLIDADG endonuclease [Arthrobacter phage Elezi] ],,NCBI, q1:s1 100.0% 3.47227E-89 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.139, -2.4329349954350334, yes F: LAGLIDADG endonuclease SIF-BLAST: ,,[LAGLIDADG endonuclease [Arthrobacter phage Elezi] ],,YP_010678008,99.2537,3.47227E-89 SIF-HHPRED: I-CREI; ENDONUCLEASE, GROUP I MOBILE INTRON, INTRON HOMING, CHLOROPLAST DNA, LAGLIDADG MOTIF; 3.0A {Chlamydomonas reinhardtii} SCOP: d.95.2.1,,,1AF5_A,76.1194,99.6 SIF-Syn: LAGLIDADG endonuclease, In same position as VResidence_29, upstream is nucleoside deoxyribosyltransferase, downstream is recombination directionality factor CDS 23248 - 23961 /gene="30" /function="recombination directionality factor" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_30" /note=Original Glimmer call @bp 23248 has strength 18.18; Genemark calls start at 23248 /note= /note=SSC: 23248-23961 CP: yes SCS: both ST: SS BLAST-Start: [recombination directionality factor [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 9.35436E-169 GAP: 143 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.581, -4.103700314387452, yes F: recombination directionality factor SIF-BLAST: ,,[recombination directionality factor [Arthrobacter phage DrSierra] ],,YP_010678354,98.7342,9.35436E-169 SIF-HHPRED: Gp3-like ; Recombination directionality factor-like,,,PF18897.3,87.7637,100.0 SIF-Syn: recombination directionality factor, upstream gene is LAGLIDADG endonuclease, downstream gene is NKF, just like in phage Tbone CDS 23961 - 24098 /gene="31" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_31" /note=Original Glimmer call @bp 23961 has strength 17.88; Genemark calls start at 23961 /note= /note=SSC: 23961-24098 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein PQE18_gp30 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 2.56941E-15 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.166, -4.455662434380964, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp30 [Arthrobacter phage DrSierra] ],,YP_010678355,91.1111,2.56941E-15 SIF-HHPRED: SIF-Syn: SIF-Syn: [NKF, DrSierra, upstream is recombination directionality factor, downstream is NKF] /note= /note=Original Glimmer call @bp 23961 has strength 17.88 /note= /note=SSC: [23961, 24098] CP: No SCS: Both ST: SS BLAST-Start: [DrSierra, 30, phagesDB, 1:1, 73%, 2*10^-14] [DrSierra, 30, NCBI, 1:1, 73%, 3*10^-15] Gap: Overlap of 1 LO: N/A RBS: [Kibler 6, Karlin Medium, 2.177, -4.456, Yes] F: NKF SIF-BLAST: [NKF, phagesDB, DrSierra_30, 73%, 2*10^-14] [NKF, NCBI, DrSierra, YP_010678355.1, 73%, 3*10^-15] SIF-HHPred: [NFK, no matches with a probability above 90%] CDS 24171 - 24521 /gene="32" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_32" /note=Original Glimmer call @bp 24171 has strength 14.4; Genemark calls start at 24171 /note= /note=SSC: 24171-24521 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQE18_gp31 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 3.9526E-72 GAP: 72 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.066, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp31 [Arthrobacter phage DrSierra] ],,YP_010678356,93.1034,3.9526E-72 SIF-HHPRED: SIF-Syn: On PECAAN pham maps Wildwest gene 32 has synteny with DrSierra gene 31 however, DrSierra gene 31 has no known function. /note= /note=SSC: 24171/24521 CP: no SCS: both ST: SS BLAST-Start: DrSierra, 31, /note= /note=Phagesdb, Q1: S1, 90%, 4e-57; DrSierra, NCBI, Q1:S1, 91%, 4e-72 Gap: 72bp LO: yes /note= /note=RBS: Kibler 6, Karlin Medium , 3.085, -2.443, yes F: NKF SIF-BLAST: NKF, NCBI, /note= /note=DrSierra_31, YP_010678356.1, 90.52%, 4e-72 SIF-HHPred: NKF, no matches with a /note= /note=probability above 90% SIF-Syn: NKF CDS 24524 - 24790 /gene="33" /function="NrdH-like glutaredoxin" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_33" /note=Original Glimmer call @bp 24524 has strength 17.57; Genemark calls start at 24524 /note= /note=SSC: 24524-24790 CP: yes SCS: both ST: NI BLAST-Start: [NrdH-like glutaredoxin [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 5.50438E-58 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.911, -3.4175091270247986, yes F: NrdH-like glutaredoxin SIF-BLAST: ,,[NrdH-like glutaredoxin [Arthrobacter phage DrSierra] ],,YP_010678357,98.8636,5.50438E-58 SIF-HHPRED: NrdH-redoxin; NRDH, THIOREDOXIN, GLUTAREDOXIN, REDOX PROTEIN, DOMAIN SWAPPING, ELECTRON TRANSPORT; 2.69A {Corynebacterium ammoniagenes} SCOP: c.47.1.1,,,1R7H_A,82.9545,99.5 SIF-Syn: /note= /note=NI because the most annotated start is not present on the starterator report /note= /note= /note= /note=SSC: 24524, 24790 CP: Yes SCS: Both ST: NI /note= /note= /note= /note=BLAST-Start: DrSierra gp32, PhagesDB, Q1:S1, 98%, 8e-47, DrSierra gp32, NCBI, Q1:S1, 98.86%, 6e-58 Gap: 2 LO: No RBS: Kibler6, Karlin Medium, 2.929, -3.418, Yes F: NrdH-like glutaredoxin /note= /note= /note= /note=SIF-BLAST: NrdH-like glutaredoxin, PhagesDB, DrSierra gp32, 98%, 8e-47, NrdH-like glutaredoxin, NCBI, DrSierra gp32, YP_010678357.1, 98.86%, 6e-58 SIF-HHPred: NrdH-redoxin, PDB_mmCIF70, 1R7H_A, 82.02%, 99.34% SIF-Syn: NrdH-like glutaredoxin, inferred from Yang_33, DrSierra_32, Warda_33 CDS 24787 - 25380 /gene="34" /function="metallophosphoesterase" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_34" /note=Original Glimmer call @bp 24787 has strength 14.08; Genemark calls start at 24787 /note= /note=SSC: 24787-25380 CP: yes SCS: both ST: SS BLAST-Start: [phosphoesterase [Arthrobacter phage Iter]],,NCBI, q1:s1 96.9543% 4.25495E-111 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, yes F: metallophosphoesterase SIF-BLAST: ,,[phosphoesterase [Arthrobacter phage Iter]],,URQ05023,87.8173,4.25495E-111 SIF-HHPRED: Hypothetical protein MJ0936; PHOSPHODIESTERASE, NUCLEASE, Structural Genomics, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics; 2.4A {Methanocaldococcus jannaschii} SCOP: d.159.1.7,,,1S3L_A,84.7716,99.7 SIF-Syn: upstream: NrdH-like glutaredoxin /note= /note=Original Glimmer call @bp 24787 has strength 14.08 /note= /note= /note= /note=SSC: 24787, 25380 /note= /note= /note= /note=CP: yes /note= /note= /note= /note=SCS: both /note= /note= /note= /note=ST: SS /note= /note= /note= /note=BLAST-Start: matches Iter gp 35, NCBI BLAST, PhagesDB, Q1:S1, e=4e-111 /note= /note= /note= /note=Gap: overlap of 4 /note= /note= /note= /note=LO: no /note= /note= /note= /note=RBS: Kibler6, Karlin Medium, 3.085, -2.505, yes /note= /note= /note= /note=F: metallophosphoesterase /note= /note= /note= /note=SIF-BLAST: matches aquifex aeolicus metallophosphatase family, CDD, Aquifex aeolicus, cd07390, 80%, e=1.2e-34 /note= /note= /note= /note=SIF-HHPred: phosphodiesterase, HHPred, Methanocaldococcus jannaschii, 1S3L_A, 70%, 99.83 /note= /note= /note= /note=SIF-Syn: upstream gene is NrdH-like glutaredoxin, downstream gene is holliday junction resolvase, this is also seen in Adolin CDS 25377 - 25820 /gene="35" /function="Holliday junction resolvase" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_35" /note=Original Glimmer call @bp 25377 has strength 9.22; Genemark calls start at 25377 /note= /note=SSC: 25377-25820 CP: yes SCS: both ST: NI BLAST-Start: [holliday junction resolvase [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 2.28338E-94 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.079, -4.556919718793868, no F: Holliday junction resolvase SIF-BLAST: ,,[holliday junction resolvase [Arthrobacter phage DrSierra] ],,YP_010678359,97.2789,2.28338E-94 SIF-HHPRED: Holliday junction resolvase; archeal holliday junction resolvase helicase DNA binding enzyme phage 15-6 thermus thermophilus, RECOMBINATION; HET: MSE, SO4; 2.5A {Thermus thermophilus phage 15-6},,,7BGS_A,77.551,99.6 SIF-Syn: holliday junction resolvase, DrSierra, upstream gene NrdH-like glutaredoxin downstream gene DNA polymerase I /note= /note=SSC: 25377-25820 CP: Yes SCS: Both ST: NI BLAST-Start: Matches Dr.Sierra, gp 34 PhagesDB, Q1S1, 93%, evalue 3e-74, Matches DrSierra, NCBI, Q1S1, 100%, evalue 7e-74 Gap: overlap 4 LO: Yes RBS: Kibler6/ Karlin Medium, 2.581, -4.359, Yes F: holliday junction resolvase SIF-BLAST: holliday junction resolvase, phagesDB, DrSierra, gp 34, 93%, evalue 3e-74, holliday junction resolvase, NCBI, DrSierra, 100%, evalue 2e-94, YP_010678359.1 SIF-HHPred: Holliday junction resolvase, PDB_mmCIF79_10_Jan, 7BGS_A, 0.243, 99.4% SIF-Syn: holliday junction resolvase, DrSierra, upstream gene NrdH-like glutaredoxin downstream gene DNA polymerase I CDS complement (25810 - 25977) /gene="36" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_36" /note=Genemark calls start at 25977 /note= /note=SSC: 25977-25810 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein PQE18_gp35 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 6.97569E-29 GAP: 163 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.066, -2.794070146961553, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp35 [Arthrobacter phage DrSierra] ],,YP_010678360,98.1818,6.97569E-29 SIF-HHPRED: SIF-Syn: NKF /note= /note=Since Glimmer did not call Wildwest_36 and running BLAST on both PhagesDB and NCBI revealed no known protein function for this gene, and there were no matches with a probability above 90% on HHPred, assigning NKF to this gene made the most sense. Additionally, when analyzing synteny with Phamerator, there was no match for Wildwest_36 when compared to other phages in the same cluster. CDS 26141 - 28639 /gene="37" /function="DNA primase/helicase" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_37" /note=Original Glimmer call @bp 26141 has strength 13.97; Genemark calls start at 26141 /note= /note=SSC: 26141-28639 CP: yes SCS: both ST: SS BLAST-Start: [DNA primase/helicase [Arthrobacter phage Amyev] ],,NCBI, q1:s1 100.0% 0.0 GAP: 163 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.066, -2.523003374675015, yes F: DNA primase/helicase SIF-BLAST: ,,[DNA primase/helicase [Arthrobacter phage Amyev] ],,YP_010677740,94.9275,0.0 SIF-HHPRED: Primase D5; DNA helicase, D5_N domain, DUF5906 domain, Pox_D5 domain, SF3 helicase, VIRAL PROTEIN;{Vaccinia virus Copenhagen},,,8APM_B,50.7212,100.0 SIF-Syn: DNA primase/helicase, In same position as VResidence_38, upstream is holliday junction resolvase, downstream is NKF /note= /note=Reasoning behind function choice HARD CALL: Both PhagesDB and NCBI had determined that the top match had NKF. However, further down the list, Amyev_37 had a match with known function of DNA helicase with 90% identities number. Also, the synteny matched extremely close to VResidence_38 and the gene that was in the same position was determined to be DNA helicase. Even though two of the protein matching websites determined NKF, further evidence disproves this to a high degree. CDS 28648 - 28761 /gene="38" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_38" /note=Original Glimmer call @bp 28648 has strength 14.25; Genemark calls start at 28648 /note= /note=SSC: 28648-28761 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein PQE18_gp37 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 7.7472E-16 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.16, -4.4057176022952405, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp37 [Arthrobacter phage DrSierra] ],,YP_010678362,94.5946,7.7472E-16 SIF-HHPRED: g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]} | CLASS: Small proteins, FOLD: Rubredoxin-like, SUPFAM: Rubredoxin-like, FAM: Rubredoxin,,,SCOP_d1yuza2,56.7568,93.4 SIF-Syn: NKF, upstream gene is DNA primase/helicase, downstream gene is NKF, just like in phage VResidence /note= /note=The start called was not the CDS 28746 - 28919 /gene="39" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_39" /note=Original Glimmer call @bp 28746 has strength 15.97; Genemark calls start at 28758 /note= /note=SSC: 28746-28919 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PQE16_gp39 [Arthrobacter phage Reedo] ],,NCBI, q5:s1 92.9825% 1.64469E-23 GAP: -16 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.949, -5.814681024300869, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE16_gp39 [Arthrobacter phage Reedo] ],,YP_010678222,89.2857,1.64469E-23 SIF-HHPRED: SIF-Syn: SIF-Syn: [NKF, Reedo, upstream is NKF, downstream is DNA Polymerase I] /note= /note=SSC: [28746, 28919] CP: No SCS: Glimmer ST: NI BLAST-Start: [Reedo_39, phagesDB, 5:1, 86%, 2e-20][Reedo, NCBI, 5:1, 83%, 2e-23] Gap: LO: RBS: [Kibler6, Karlin Medium, 1.959, -5.815, No] F: NKF SIF-BLAST: [NKF, phagesDB, Reedo_39, 86%, 2e-20] [NKF, NCBI, Reedo, YP_010678222.1, 83%, 2e-23] SIF-HHPred: NKF, no matches with a probability above 90% CDS 29139 - 30983 /gene="40" /function="DNA polymerase I" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_40" /note=Original Glimmer call @bp 29139 has strength 19.79; Genemark calls start at 29139 /note= /note=SSC: 29139-30983 CP: yes SCS: both ST: SS BLAST-Start: [DNA polymerase I [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 0.0 GAP: 219 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.16, -4.387988835334809, no F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Arthrobacter phage DrSierra] ],,YP_010678364,98.2085,0.0 SIF-HHPRED: Apicoplast DNA polymerase; DNA polymerase, exonulease, apicoplast, Plasmodium falciparum, REPLICATION, TRANSFERASE; HET: PEG, EDO; 2.5A {Plasmodium falciparum (isolate 3D7)},,,7SXQ_A,96.9055,100.0 SIF-Syn: On PECAAN pham maps Wildwest gene 40 has synteny with DrSierra gene 39 and DrSierra gene 39 had a function of DNA Polymerase I /note= /note=SSC: 29139/20983 CP: no SCS: both ST: NI BLAST-Start: DrSierra_39, /note= /note=phagesdb, Q1 : S1, 96%, 0.0; DrSierra , NCBI, Q1:S1, 97%, 0.0 Gap: 219bp LO: no /note= /note=RBS: N/A F: DNA Polymerase I SIF-BLAST: DNA Polymerase I, NCBI, DrSierra, /note= /note=YP_010678364.1, 96.58%, 0.0 SIF-HHPred: DNA Polymerase, PECAAN, 7SXQ_A, /note= /note=28%, 100 SIF-Syn: DNA Polymerase I, DrSierra_39 CDS 30980 - 31282 /gene="41" /function="DNA ligase" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_41" /note=Original Glimmer call @bp 30980 has strength 15.43; Genemark calls start at 30980 /note= /note=SSC: 30980-31282 CP: yes SCS: both ST: NI BLAST-Start: [DNA ligase [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 8.10972E-62 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.545, -5.745379707039719, yes F: DNA ligase SIF-BLAST: ,,[DNA ligase [Arthrobacter phage DrSierra] ],,YP_010678365,95.0,8.10972E-62 SIF-HHPRED: DNA ligase A; Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, LIGASE; HET: NAD, MPD; 2.05A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)} SCOP: d.142.2.0,,,7K72_A,88.0,99.3 SIF-Syn: /note= /note=NI because the most annotated start is not present on the starterator report /note= /note= /note= /note=SSC: 30980, 31282 CP: Yes SCS: Both ST: NI /note= /note=BLAST-Start: DrSierra gp40, PhagesDB, Q1:S1, 94%, 8e-50, DrSierra gp40, NCBI, Q1:S1, 94%, 8e-62 Gap: -4 LO: Yes RBS: Kibler6, Karlin Medium, 1.552, -5.745, Yes F: DNA ligase /note= /note= /note= /note=SIF-BLAST: DNA ligase, DrSierra gp40, 94%, 8e-50, DNA ligase, DrSierra gp40, YP_010678365.1, 94%, 8e-62 SIF-HHPred: DNA ligase, PDB_mmCIF70, 7K72_A, 60.40%, 99.24% SIF-Syn: DNA ligase. two genes upstream is a DNA binding protein, two genes downsteam is DNA polymerase I inferred from the phages Warda and Yang. CDS 31279 - 31584 /gene="42" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_42" /note=Original Glimmer call @bp 31279 has strength 10.84; Genemark calls start at 31279 /note= /note=SSC: 31279-31584 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PQD82_gp46 [Arthrobacter phage Phives] ],,NCBI, q1:s1 100.0% 1.62154E-48 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.816, -2.9625409806968013, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQD82_gp46 [Arthrobacter phage Phives] ],,YP_010677680,86.2745,1.62154E-48 SIF-HHPRED: SIF-Syn: upstream: DNA ligase /note= /note=Original Glimmer call @bp 31279 has strength 10.84 /note= /note= /note= /note=SSC: 31279, 31584 /note= /note= /note= /note=CP: yes /note= /note= /note= /note=SCS: Both /note= /note= /note= /note=ST: NI /note= /note= /note= /note=BLAST-Start: matches hypothetical protein gp46, NCBI Blast, Phives gp 46, 100%, Q1:S1, 2e-48 /note= /note= /note= /note=Gap: overlap of 4 /note= /note= /note= /note=LO: true /note= /note= /note= /note=RBS: Kibler6, Karlin Medium, 2.816, -2.963, yes /note= /note= /note= /note=F: NKF /note= /note= /note= /note=SIF-BLAST: matches hypothetical protein gp46, NCBI Blast, Phives gp46, 79%, YP_010677680.1, e=2e-48 /note= /note= /note= /note=SIF-HHPred: NKF, no matches above 90% /note= /note= /note= /note=SIF-Syn: upstream is DNA ligase, downstream is DNA binding protein, this is also seen in Adolin CDS 31833 - 32639 /gene="43" /function="DNA binding protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_43" /note=Original Glimmer call @bp 31833 has strength 22.59; Genemark calls start at 31833 /note= /note=SSC: 31833-32639 CP: yes SCS: both ST: SS BLAST-Start: [DNA binding protein [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 0.0 GAP: 248 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.066, -3.095100142625534, yes F: DNA binding protein SIF-BLAST: ,,[DNA binding protein [Arthrobacter phage DrSierra] ],,YP_010678367,98.8806,0.0 SIF-HHPRED: RNA polymerase sigma factor SigB; DNA-dependent RNA polymerase, alternative sigma, TRANSCRIPTION; 3.84A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)},,,7PP4_f,96.2687,100.0 SIF-Syn: DNA binding protein, Dr.Sierra, upstream gene DNA ligase downstream gene heliz turn helix DNA binding protein /note= /note=SSC: 31833-32639 CP: yes SCS: both ST: SS BLAST-Start: Matches DrSierra, gp 42, phagesDB, Q1S1, 98%, evalue e-146, Matches DrSierra, NCBI, Q1S1, 100%, evalue 0 Gap: 248 LO: NO RBS: Kilber6/Karlin Medium, 3.085, -3.095, yes F: Dna binding protein SIF-BLAST: DNA binding protein, phages DB, DrSierra, gp 42, 98%, evalue e-146, dna binding proetin, NCBI, DrSierra, 100%, evalue 0, YP_010678367.1 SIF-HHPred: RNA polymerase sigma factor SigB, PCB_mmCIF70_10_jan, 7PP4_f, 0.3098, 100% SIF-Syn: DNA binding protein, Dr.Sierra, upstream gene DNA ligase downstream gene heliz turn helix DNA binding protein CDS 32679 - 33392 /gene="44" /function="G-I-Y Y-I-G endonuclease" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_44" /note=Original Glimmer call @bp 32679 has strength 13.51; Genemark calls start at 32679 /note= /note=SSC: 32679-33392 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE10_gp45 [Arthrobacter phage Tbone] ],,NCBI, q1:s1 100.0% 1.41203E-114 GAP: 39 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.797, -5.143229268563043, no F: G-I-Y Y-I-G endonuclease SIF-BLAST: ,,[hypothetical protein PQE10_gp45 [Arthrobacter phage Tbone] ],,YP_010677816,91.1392,1.41203E-114 SIF-HHPRED: ENDONUCLEASE II; GIY-YIG, NUCLEASE, HYDROLASE; HET: MSE, PEG; 1.9A {ENTEROBACTERIA PHAGE T4},,,2WSH_C,35.865,98.9 SIF-Syn: Upstream DNA binding protein, downstream helix-turn-helix DNA binding protein /note= /note=PhagesDB BLAST reports unknown function for this gene at the highest match: Tbone_45, 83% identity, E-value 1e-115. The third hit on PhagesDB was a G-I-Y Y-I-G endonuclease: Amyev_45, 64% identity, E-value 3e-39. NCBI BLAST reports the function of this gene as endonuclease (Tbone_45) with 91% alignment and an E-value of 1e-114. However, HHPred`s first hit was DNA binding protein with 99.19% probability (but this was for a bacteria with E-value 1e-9) and the third hit was endonuclease with 98.84% (this was for a bacteriophage with E-value 3e-8, which is on the border of being insignificant). Lastly, Phamerator reported that flanking genes for Wildwest_44, whose corresponding gene codes for a G-I-Y Y-I-G endonuclease, are Amyev_44 (DNA binding domain protein) and Amyev_46 (helix-turn-helix DNA binding domain protein). CDS 33392 - 33811 /gene="45" /function="helix-turn-helix DNA binding domain" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_45" /note=Original Glimmer call @bp 33392 has strength 16.11; Genemark calls start at 33392 /note= /note=SSC: 33392-33811 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA-binding protein [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 3.82727E-84 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA-binding protein [Arthrobacter phage DrSierra] ],,YP_010678368,96.3768,3.82727E-84 SIF-HHPRED: Putative uncharacterized protein; DNA BINDING PROTEIN; NMR {Hyperthermus butylicus},,,2LVS_A,58.9928,98.8 SIF-Syn: helix-turn-helix DNA binding domain protein, In same position as Warda_46, upstream is DNA binding protein, upstream is SprT-like protease /note= /note=The suggested start was at 33392, another possible start was at 32825. The suggested start was most called and the other possible start resulted in too large of an overlap, so the suggested start was kept despite half of the gene protein not being sequenced. CDS 33860 - 34456 /gene="46" /function="SprT-like protease" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_46" /note=Original Glimmer call @bp 33860 has strength 17.24; Genemark calls start at 33860 /note= /note=SSC: 33860-34456 CP: yes SCS: both ST: SS BLAST-Start: [SprT-like protease [Arthrobacter phage Janeemi]],,NCBI, q1:s1 100.0% 1.09764E-140 GAP: 48 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.969, -2.707694805492614, yes F: SprT-like protease SIF-BLAST: ,,[SprT-like protease [Arthrobacter phage Janeemi]],,UVK63569,98.9899,1.09764E-140 SIF-HHPRED: SprT-like domain-containing protein Spartan; DPC repair protease, DNA BINDING PROTEIN; HET: ADP, MLZ, FLC; 1.5A {Homo sapiens},,,6MDW_A,50.5051,99.6 SIF-Syn: SprT-like protease, upstream gene is helix-turn-helix DNA binding domain protein, downstream gene is NKF, just like in phage Warda CDS 34578 - 34766 /gene="47" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_47" /note=Original Glimmer call @bp 34578 has strength 22.9; Genemark calls start at 34578 /note= /note=SSC: 34578-34766 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein PQE12_gp45 [Arthrobacter phage Adumb2043] ],,NCBI, q1:s1 100.0% 1.03959E-28 GAP: 121 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.969, -2.707694805492614, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE12_gp45 [Arthrobacter phage Adumb2043] ],,YP_010677955,95.1613,1.03959E-28 SIF-HHPRED: SIF-Syn: SIF-Syn: [NKF, Adumb2043_45, upstream is SprT-like protease, downstream is NKF] /note= /note=SSC: [34578, 34766] CP: No SCS: Both ST: SS BLAST-Start: [Adumb2043, 45, phagesDB, 1:1, 90%, 5e-23] [Adumb2043, NCBI, 1:1, 90%, 1e-28] Gap: 121 LO: Yes RBS: [Kibler6, Karlin Medium, 2.987, -2.708, Yes] F: NKF SIF-BLAST: [NKF, phagesDB, Adumb2043_45, 90%, 5e-23] [NKF, NCBI, Adumb2043, YP_010677955.1, 90%, 1e-28] SIF-HHPred: [NKF, no matches with a probability above 90%] CDS 34842 - 35186 /gene="48" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_48" /note=Original Glimmer call @bp 34842 has strength 19.23; Genemark calls start at 34842 /note= /note=SSC: 34842-35186 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ITER_48 [Arthrobacter phage Iter]],,NCBI, q1:s1 100.0% 6.62624E-74 GAP: 75 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ITER_48 [Arthrobacter phage Iter]],,URQ05036,97.3684,6.62624E-74 SIF-HHPRED: SIF-Syn: On PECAAN pham maps Wildwest gene 48 has synteny with Iter gene 48 but Iter gene 48 had no known function. /note= /note=SSC: 24842/35186 CP: yes SCS: both ST: SS BLAST-Start: Iter_48, /note= /note=phagesdb, Q1 : S1, 97%, 8e-60; Iter_48, NCBI, Q1: S1, 97%, 7e-74 Gap: 75bp LO: yes /note= /note=RBS: Kibler 6, Karlin Medium, 3.085, -2.505, yes F: NKF SIF-BLAST: NKF, NCBI, /note= /note=Iter_48, URQ05036.1, 97.37%, 7e-74 SIF-HHPred: NKF, no matches with a probability /note= /note=above 90% SIF-Syn: NKF CDS 35283 - 36758 /gene="49" /function="serine integrase" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_49" /note=Original Glimmer call @bp 35274 has strength 17.08; Genemark calls start at 35274 /note= /note=SSC: 35283-36758 CP: yes SCS: both-cs ST: NI BLAST-Start: [serine integrase [Arthrobacter phage Tuck]],,NCBI, q1:s4 100.0% 0.0 GAP: 96 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.719, -6.069698296538124, yes F: serine integrase SIF-BLAST: ,,[serine integrase [Arthrobacter phage Tuck]],,WAB10827,94.5344,0.0 SIF-HHPRED: INTEGRASE; HYDROLASE, SERINE RECOMBINASE, UNIDIRECTIONAL, SITE-SPECIFIC RECOMBINATION; 2.15A {STREPTOMYCES PHAGE PHIC31},,,4BQQ_B,65.1731,100.0 SIF-Syn: /note= /note=NI because the most annotated start in not in the starterator report, changed start from 35274 to 35283 due to better z-score, raw score, and final score /note= /note= /note= /note=SSC: 35283, 36758 CP: Yes SCS: Both-CS ST: NI /note= /note= /note= /note=BLAST-Start: Tuck gp53, PhagesDB, Q1:S1, 88%, 0, Tuck gp53, NCBI, Q1:S1, 88.66%, 0 Gap: 96 LO: No RBS: Kibler6, Karlin Medium, 1.728, -6.070, Yes F: serine integrase /note= /note= /note= /note=SIF-BLAST: serine integrase PhagesDB, Tuck gp53, 88%, 0, serine integrase NCBI, Tuck gp53, WAB10827.1, 88.66%, 0 SIF-HHPred: serine integrase, PDB_mmCIF70, 4BQQ_B, 60.77%, 100% SIF-Syn: serine integrase, inferred from Yang_49 and Wards_50 CDS 37020 - 37292 /gene="50" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_50" /note=Original Glimmer call @bp 37020 has strength 15.64; Genemark calls start at 37020 /note= /note=SSC: 37020-37292 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JANEEMI_53 [Arthrobacter phage Janeemi]],,NCBI, q1:s1 100.0% 6.29862E-51 GAP: 261 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_JANEEMI_53 [Arthrobacter phage Janeemi]],,UVK63573,94.4444,6.29862E-51 SIF-HHPRED: SIF-Syn: upstream: serine integrase /note= /note=Original Glimmer call @bp 37020 has strength 15.64 /note= /note= /note= /note=SSC: 37020, 37292 /note= /note= /note= /note=CP: yes /note= /note= /note= /note=SCS: both /note= /note= /note= /note=ST: SS /note= /note= /note= /note=BLAST-Start: matches hypothetical proten 53, NCBI BLAST, PhagesDB, Q1:S1, 100%, 92.22%, 6e-51 /note= /note= /note= /note=Gap: 261 /note= /note= /note= /note=LO: yes /note= /note= /note= /note=RBS: Kibler6, Karlin Medium, 3.066, -2.505, yes /note= /note= /note= /note=F: NKF /note= /note= /note= /note=SIF-BLAST: NKF, matches hypothetical protein 53, Janeemi gene 53, UVK63753.1, 92.22%, 6.3e-51 /note= /note= /note= /note=SIF-HHPred: NKF, no matches above 90% prob /note= /note= /note= /note=SIF-Syn: upstream gene is serine integrase, downstream gene is NKF, also seen in Adolin CDS 37289 - 37513 /gene="51" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_51" /note=Original Glimmer call @bp 37289 has strength 18.92; Genemark calls start at 37289 /note= /note=SSC: 37289-37513 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE18_gp50 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 2.09124E-40 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.302, -2.0949393225970705, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp50 [Arthrobacter phage DrSierra] ],,YP_010678375,95.9459,2.09124E-40 SIF-HHPRED: SIF-Syn: NKF /note= /note=On HHPred, it hits phage 3HFO_B with probability of 96.67%. The function was /note= /note= /note= /note= /note=SSC: 37289-37513 CP: yes SCS: both ST: SS BLAST-Start: Matches DrSierra, gp 50, PhagesDB Q1S1, 89%, 7e-32, Matches DrSierra, NCBI, Q1S1, 100%, evalue, 2e-40 Gap: overlap 4 LO: NA RBS: Kibler6/ Karlin Medium, 3.322, -2.095, yes F: NKF SIF-BLAST: NKF SIF-HHPred: NKF SIF-Syn: NKF CDS 37812 - 38249 /gene="52" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_52" /note=Original Glimmer call @bp 37812 has strength 17.64; Genemark calls start at 37812 /note= /note=SSC: 37812-38249 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage Lizalica] ],,NCBI, q5:s6 95.1724% 1.30246E-49 GAP: 298 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.969, -2.7863799983944713, yes F: hypothetical protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Lizalica] ],,YP_010677618,70.3448,1.30246E-49 SIF-HHPRED: SIF-Syn: NKF on Phamerator /note= /note=PhagesDB BLAST and HHPred all showed no known function (HHPred especially, with only one hit that had 8.28% probability and the function was a photosystem complex). NCBI BLAST`s first hit was a membrane protein function, but the rest of the hits were unknown function. Running Phamerator revealed that the corresponding gene on Lizalica had no known function and the flanking genes also had no known function. CDS 38260 - 38493 /gene="53" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_53" /note=Original Glimmer call @bp 38260 has strength 14.8; Genemark calls start at 38260 /note= /note=SSC: 38260-38493 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein PQE18_gp54 [Arthrobacter phage DrSierra] ],,NCBI, q19:s1 76.6234% 9.78499E-26 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.313, -1.9310779259753799, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp54 [Arthrobacter phage DrSierra] ],,YP_010678379,91.5254,9.78499E-26 SIF-HHPRED: SIF-Syn: NKF, In same position as YesChef_55, upstream is NKF, downstream is NKF CDS 38561 - 40003 /gene="54" /function="endolysin" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_54" /note=Original Glimmer call @bp 38561 has strength 14.14; Genemark calls start at 38657 /note= /note=SSC: 38561-40003 CP: yes SCS: both-gl ST: SS BLAST-Start: [endolysin [Arthrobacter phage Adolin]],,NCBI, q1:s1 100.0% 0.0 GAP: 67 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.302, -2.033982896655645, yes F: endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Adolin]],,QHB36642,90.3885,0.0 SIF-HHPRED: N-acetylmuramoyl-L-alanine amidase; amidase, zinc binding, cell wall degradation, endolysine, hydrolase; HET: PO4, GOL; 1.21A {Clostridium intestinale},,,6SSC_A,26.25,99.5 SIF-Syn: No matching flanking genes were found among the other phages in cluster AZ. /note= /note=The Glimmer start seemed to be better than the Genemark start because there was coding potential for the base pairs covered by the Glimmer start, the Glimmer start was the suggested start on Starterator, and the Glimmer start was the longest open reading frame. CDS 40123 - 40464 /gene="55" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_55" /note=Original Glimmer call @bp 40123 has strength 14.3; Genemark calls start at 40123 /note= /note=SSC: 40123-40464 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JANEEMI_59 [Arthrobacter phage Janeemi]],,NCBI, q1:s1 100.0% 6.69574E-51 GAP: 119 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_JANEEMI_59 [Arthrobacter phage Janeemi]],,UVK63579,87.6106,6.69574E-51 SIF-HHPRED: SIF-Syn: SIF-Syn: [Janeemi, 59, upstream and downstream are NKF] /note= /note=SSC: [40123, 40464] CP: Yes SCS: Both ST: SS BLAST-Start: [Janeemi, 59, phagesDB, 1:1, 82%, 1e-49] [Janeemi, NCBI, 1:1, 82%, 7e-51] Gap: 119 LO: Yes RBS: [Kibler6, Karlin Medium, -2.505, 3.085, Yes] F: NKF SIF-BLAST: [NKF, phagesDB, Janeemi_59, 82%, 1e-49] [NKF, NCBI, Janeemi, UVK63579.1, 82%, 7e-51] SIF-HHPred: NKF, no matches with a probability above 90% CDS 40552 - 40737 /gene="56" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_56" /note=Original Glimmer call @bp 40552 has strength 20.17; Genemark calls start at 40552 /note= /note=SSC: 40552-40737 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ITER_61 [Arthrobacter phage Iter]],,NCBI, q1:s1 93.4426% 4.62324E-26 GAP: 87 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.969, -2.7863799983944713, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ITER_61 [Arthrobacter phage Iter]],,URQ05049,88.1356,4.62324E-26 SIF-HHPRED: SIF-Syn: On PECAAN pham maps Wildwest gene 56 has synteny with Iter gene 61 but Iter gene 61 had no known function. /note= /note=SSC: 40552/40737 CP: yes SCS: both ST: SS BLAST-Start: Tallboi_56, /note= /note=phagesdb, Q1 : S1, 87%, 1e-27; Iter_61, NCBI, Q1: S1, 88% Gap: 97bp LO: yes RBS: /note= /note=Kibler 6, Karlin Medium, 2.987, -2.786, yes F: NKF SIF-BLAST: NKF, NCBI, /note= /note=Iter_61, URQ05049.1, 87.72%, 5e-26 SIF-HHPred: NKF, no matches with a probability /note= /note=above 90% SIF-Syn: NKF CDS 40861 - 41223 /gene="57" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_57" /note=Original Glimmer call @bp 40861 has strength 20.2; Genemark calls start at 40861 /note= /note=SSC: 40861-41223 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE18_gp58 [Arthrobacter phage DrSierra] ],,NCBI, q1:s25 95.0% 9.74637E-59 GAP: 123 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.969, -2.707694805492614, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp58 [Arthrobacter phage DrSierra] ],,YP_010678383,73.0496,9.74637E-59 SIF-HHPRED: SIF-Syn: /note= /note=NKF, no HHPred results above 90% probability, might be lysin A /note= /note= /note= /note=SSC: 40861, 41223 CP: Yes SCS: Both ST:SS /note= /note= /note= /note=BLAST-Start: DrSierra gp58, PhagesDB, Q1:S25, 87%, 2e-53, DrSierra gp58, NCBI, Q1:25, 87.72%, 1e-58 Gap: 123 LO: Yes RBS: Kibler6, Karlin Medium, 2.987, -2.708, Yes F: NKF /note= /note= /note= /note=SIF-BLAST: NKF, PhagesDB, DrSierra gp58, 87%, 2e-53, NKF, NCBI, DrSierra gp53, YP_010678383.1, SIF-HHPred: NKF, no matches with probability above 90% SIF-Syn: NKF CDS 41296 - 41607 /gene="58" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_58" /note=Original Glimmer call @bp 41296 has strength 16.49; Genemark calls start at 41296 /note= /note=SSC: 41296-41607 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQD88_gp62 [Arthrobacter phage Amyev] ],,NCBI, q1:s1 100.0% 1.93738E-63 GAP: 72 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQD88_gp62 [Arthrobacter phage Amyev] ],,YP_010677765,95.1923,1.93738E-63 SIF-HHPRED: SIF-Syn: both upstream and downstream genes have no function, this is conserved in Adolin /note= /note=Original Glimmer call @bp 41296 has strength 16.49 /note= /note= /note= /note=SSC: 41296, 41607 /note= /note= /note= /note=CP: yes /note= /note= /note= /note=SCS: both /note= /note= /note= /note=ST: SS /note= /note= /note= /note=BLAST-Start: matches gp61 of Adumb2043, NCBI Blast, PhagesDB, Q1:S1, 92%, 3e-63 /note= /note= /note= /note=Gap: 72 /note= /note= /note= /note=LO: no /note= /note= /note= /note=RBS: Kibler6, Karlin Medium, 3.066, -2.505, yes /note= /note= /note= /note=F: NKF /note= /note= /note= /note=SIF-BLAST: phosphoenolpyruvate carboxykinase, PLN02597, CDD, 79%, e=1.81e-03 /note= /note= /note= /note=SIF-HHPred: matches NADH-dehydrogenase like complex, but e-value is too high to be sig, N/A /note= /note= /note= /note=SIF-Syn: upstream and downstream genes have no function, this is also seen in Adolin CDS 41597 - 41956 /gene="59" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_59" /note=Original Glimmer call @bp 41597 has strength 16.56; Genemark calls start at 41597 /note= /note=SSC: 41597-41956 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PQE18_gp60 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 1.02915E-71 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp60 [Arthrobacter phage DrSierra] ],,YP_010678385,95.7627,1.02915E-71 SIF-HHPRED: SIF-Syn: NKF /note= /note=SSC: 41597-41956 CP: yes SCS:both ST: NI BLAST-Start: Matches DrSierra, gp 60, PhagesDB, Q4S3, 92%, evalue 5e-59, Matches DrSierra, NCBI, Q1S1, 100%, evalue 1e-71 Gap: overlap 11 LO: NA RBS: Kibler6/ Karlin Meidum, 3.085, -2.505, yes F: NKF SIF-BLAST: NKF SIF-HHPred: NKF, No matches with probability above 90% SIF-Syn: NKF CDS 41956 - 42234 /gene="60" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_60" /note=Original Glimmer call @bp 41956 has strength 9.12; Genemark calls start at 41956 /note= /note=SSC: 41956-42234 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_JANEEMI_63 [Arthrobacter phage Janeemi]],,NCBI, q1:s1 100.0% 1.03576E-53 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.631, -4.255672789525901, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_JANEEMI_63 [Arthrobacter phage Janeemi]],,UVK63583,97.8261,1.03576E-53 SIF-HHPRED: SIF-Syn: NKF /note= /note=Wildwest_60 did not have the “Most Annotated” start, and running BLAST on PhagesDB and NCBI showed that all of the top hits had unknown function. On HHPred, there was only one hit which had a function of inner kinetochore subunit with 31.59% probability, which is not enough to be significant. When comparing Wildwest_60 to Janeemi on Phamerator, the corresponding gene had no known function and the flanking genes also had no known function. CDS 42225 - 42398 /gene="61" /function="membrane protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_61" /note=Original Glimmer call @bp 42225 has strength 14.45; Genemark calls start at 42240 /note= /note=SSC: 42225-42398 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_POWERPUFF_66 [Arthrobacter phage Powerpuff] ],,NCBI, q1:s1 100.0% 2.04328E-25 GAP: -10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.407, -4.164901013602904, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_POWERPUFF_66 [Arthrobacter phage Powerpuff] ],,QGZ17364,93.1034,2.04328E-25 SIF-HHPRED: SIF-Syn: NKF, In same position as Janeemi_64, upstream is NKF, downstream is NKF. Endolysin was annotated on gene 54. /note= /note=Protein had one transmembrane protein. HHPred also referenced a membrane protein as well. However, PhagesDB, NCBI, and Phamerator had yielded no concrete predictions for this protein. The function is decided to be NKF, but there could be some possibility for a membrane protein. Checked on Tmhmm-Deep. CDS 42391 - 42561 /gene="62" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_62" /note=Original Glimmer call @bp 42391 has strength 12.11; Genemark calls start at 42391 /note= /note=SSC: 42391-42561 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE13_gp64 [Arthrobacter phage Elezi] ],,NCBI, q1:s1 94.6429% 1.62134E-20 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE13_gp64 [Arthrobacter phage Elezi] ],,YP_010678042,84.9057,1.62134E-20 SIF-HHPRED: SIF-Syn: NKF, upstream gene is NKF, downstream gene is NKF, just like in phage VResidence CDS 42554 - 42691 /gene="63" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_63" /note=Original Glimmer call @bp 42554 has strength 19.15; Genemark calls start at 42554 /note= /note=SSC: 42554-42691 CP: yes SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage Janeemi]],,NCBI, q1:s1 100.0% 3.17774E-12 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.066, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Janeemi]],,UVK63586,95.5556,3.17774E-12 SIF-HHPRED: SIF-Syn: SIF-Syn: [NKF, Janeemi_66, upstream is NKF, downstream is HNH endonuclease] /note= /note=SSC: [42554, 42691] CP: Yes SCS: Both ST: NI BLAST-Start: [Janeemi, 66, phagesDB, 1:1, 84%, 4e-16] [Janeemi, NCBI, 1:1, 84%, 3e-12] Gap: Overlap of 8 LO: N/A RBS: [Kibler6, Karlin Medium, 3.085, -2.505, Yes] F: NKF SIF-BLAST: [NKF, phagesDB, Janeemi_66, 84%, 4e-16] [NKF, NCBI, Janeemi, UVK63586.1, 84%, 3e-12] SIF-HHPred: NKF, no matches with a probability above 90% CDS 42676 - 42942 /gene="64" /function="HNH endonuclease" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_64" /note=Original Glimmer call @bp 42676 has strength 5.86; Genemark calls start at 42676 /note= /note=SSC: 42676-42942 CP: no SCS: both ST: NI BLAST-Start: [HNH endonuclease [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 2.63442E-52 GAP: -16 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.497, -3.9764835383098616, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage DrSierra] ],,YP_010678390,97.7273,2.63442E-52 SIF-HHPRED: Restriction endonuclease Hpy99I; ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, HPY99I, PSEUDOPALINDROME, HYDROLASE-DNA COMPLEX; HET: 1PE; 1.5A {Helicobacter pylori},,,3GOX_A,55.6818,95.3 SIF-Syn: On PECAAN pham maps Wildwest gene 64 has synteny with DrSierra gene 65 and DrSierra gene 65 had a function of HNH endonuclease /note= /note=SSC: 42676/42942 CP: no SCS: both ST: NI BLAST-Start: DrSierra_65, /note= /note=phagesdb, Q1 : S1, 95%, 5e-46; DrSierra, NCBI, Q1: S1, 97%, 3e-52 Overlap: 14bp LO: n/a /note= /note=RBS: Kibler 6, Karlin Medium, 0.585, -7.661, no F: HNH endonuclease SIF-BLAST: /note= /note=HNH endonuclease, NCBI, DrSierra, YP_010678390.1., 95.45%, 3e-52 SIF-HHPred: /note= /note=HNH endonuclease, PECAAN, 3GOX_A, 15.75%, 95.3 SIF-Syn: HNH endonuclease, /note= /note=DrSierra_65 CDS 43282 - 43584 /gene="65" /function="HNH endonuclease" /product="Hypothetical Protein" /locus tag="SEA_WILDWEST_65" /note=Original Glimmer call @bp 43282 has strength 3.72 /note= /note=SSC: 43282-43584 CP: yes SCS: glimmer ST: SS BLAST-Start: [HNH endonuclease [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 99.0% 3.9605E-55 GAP: 339 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.147, -2.338663114094478, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage DrSierra] ],,YP_010678391,97.0,3.9605E-55 SIF-HHPRED: SIF-Syn: upstream gene has NKF, and no further downstream genes are seen in either Wildwest or Adolin, which shows synteny in regards to this gene /note= /note=Original Glimmer call @bp 43282 has strength 3.72 ** not called by GeneMark /note= /note= /note= /note=SSC: 43282, 43584 /note= /note= /note= /note=CP: no, genemark does not call this gene at any start codon /note= /note= /note= /note=SCS: Glimmer /note= /note= /note= /note=ST: SS /note= /note= /note= /note=BLAST-Start: matches DrSierra gp 67, Q1:S1, 99% query, 96%, e=4e-55 /note= /note= /note= /note=Gap: 339 /note= /note= /note= /note=LO: yes /note= /note= /note= /note=RBS: Kibler6, Karlin Medium, 3.147, -2.339, yes /note= /note= /note= /note=F: HNH endonuclease /note= /note= /note= /note=SIF-BLAST: HNH nuclease, cd00085, CDD, 41%, 1.42e-05 /note= /note= /note= /note=SIF-HHPred: HNH endonuclease, Geobacillus virus E2, 66%, 5H0M_A, 97.33%, e=0.00078, however e-value is very high (0.0016) /note= /note= /note= /note=SIF-Syn: upstream gene has no function, no downstream genes, correlates to HNH endonuclease (gene 71) in Adolin as well BASE COUNT 7956 a 16419 c 12774 g 6504 t ORIGIN