CDS 77 - 1702 /gene="1" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_1" /note=Original Glimmer call @bp 77 has strength 6.88; Genemark calls start at 143 /note= /note=SSC: 77-1702 CP: no SCS: both-gl ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 99.8152% 0.0 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.138, -4.387988835334809, no F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage GreenHearts] ],,YP_010049921,89.6104,0.0 SIF-HHPRED: Collar spike protein; Myoviridae, Phage, 6-fold neck region, VIRAL PROTEIN;{Vibrio phage XM1},,,7KJK_I3,23.475,99.1 SIF-Syn: When looking at the Phamerator map in comparison to other AK phages Greenhearts and Albanese there is no known function for gene one. There is also no known or shared function to the right of gene one on gene 2 for Greenhearts and Albanese. /note= /note=Genemarks calls the start at 143, but glimmer calls it at 77. After a blast on NCBI, it is seen that the 77bp start is conserved and represented across other phages genomes so the true start should be placed at 77bp /note= /note= /note= /note=There is NKF due to synteny showing similar phages in the pham have no function for gene 1 and the phagesdb function blast shows low frequency probability for a specific function CDS 1712 - 2563 /gene="2" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_2" /note=Original Glimmer call @bp 1712 has strength 10.62; Genemark calls start at 1712 /note= /note=SSC: 1712-2563 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Salgado] ],,NCBI, q1:s1 100.0% 2.90942E-147 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.138, -4.325675514574479, no F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Salgado] ],,YP_010082638,87.1886,2.90942E-147 SIF-HHPRED: putative baseplate protein; Phage, Lactococcus lactis, receptor binding protein, head domain, VIRAL PROTEIN; 2.3A {unidentified phage},,,2FSD_A,37.4558,96.9 SIF-Syn: When comparing gene two to phages in the same AK pham it was found there was no similarity continued throughout gene two (looking at Greenheart and Albanese). There is NKF upstream from the gene and NKF downstream which leads me to believe that there is NKF on gene two as well. /note= /note=The gene extends longer than the coding potential as seen in the Genemarks, but that is ok and both glimmer and Genemarks agree on the selected start. /note= /note= /note= /note=Salgado was the closest hit for the phagesdb blast but when looking at it in the phamerator there was no connection between each phages second gene. /note= /note= /note= /note=Also looking at the synteny with phages in the same cluster, as well as the low probability of the function found in phagesdb, it can be assumed that there is NKF CDS 2572 - 2748 /gene="3" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_3" /note= /note= /note=SSC: 2572-2748 CP: yes SCS: neither ST: NA BLAST-Start: [hypothetical protein KDI97_gp03 [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 2.94538E-26 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.379, -3.893834241316366, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDI97_gp03 [Arthrobacter phage GreenHearts] ],,YP_010049923,93.1034,2.94538E-26 SIF-HHPRED: SIF-Syn: NKF matches Albanese /note= /note=SSC: 2572-2748 CP: Yes SCS: Neither ST: NA Gap: 8bp LO: yes RBS: Kibler6, Karlin Medium, 2.379, -3.894, yes F: NKF SIF-HHPred: NKF, no matches with probability above 90% /note= /note= /note= /note=Gene inserted, matches Albanese_3 (Pham 2087) CDS 2750 - 3175 /gene="4" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_4" /note=Original Glimmer call @bp 2750 has strength 9.69; Genemark calls start at 2750 /note= /note=SSC: 2750-3175 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein KDJ04_gp04 [Arthrobacter phage Nubia] ],,NCBI, q1:s8 100.0% 2.84075E-98 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.824, -4.9912573797770525, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDJ04_gp04 [Arthrobacter phage Nubia] ],,YP_010050295,95.2703,2.84075E-98 SIF-HHPRED: SIF-Syn: Phamerator showed synteny between the 4th gene on Ak phages Albanese and Nubia. Both 4th genes on the other similar AK phages have NKF /note= /note=Expanded the gene past the called starts by Glimmer and GeneMarks to include the extra coding potential. Was able to do this due to the deletion of gene 3. CDS 3282 - 4673 /gene="5" /function="terminase" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_5" /note=Original Glimmer call @bp 3282 has strength 11.56; Genemark calls start at 3282 /note= /note=SSC: 3282-4673 CP: yes SCS: both ST: NI BLAST-Start: [terminase [Arthrobacter phage Greenhouse] ],,NCBI, q1:s59 100.0% 0.0 GAP: 106 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.442, -6.629016321583214, no F: terminase SIF-BLAST: ,,[terminase [Arthrobacter phage Greenhouse] ],,YP_010049987,88.8676,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,96.1123,100.0 SIF-Syn: Phamerator showed synteny between the 5th gene on similar AK phages Greenhouse and Albanese, and both upstream and downstream genes are similar. Both 5th genes on the similar phages marked the gene as a terminase /note= /note=There is extra coding potential shown in GeneMarks was ignored because the overlap it would have caused would not have viable, so it was ignored CDS 4692 - 6710 /gene="6" /function="portal protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_6" /note=Original Glimmer call @bp 4692 has strength 9.04; Genemark calls start at 4758 /note= /note=SSC: 4692-6710 CP: no SCS: both-gl ST: SS BLAST-Start: [portal protein [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 0.0 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.648, -3.595227487224058, no F: portal protein SIF-BLAST: ,,[portal protein [Arthrobacter phage GreenHearts] ],,YP_010049926,100.0,0.0 SIF-HHPRED: Phage portal protein, HK97 family; /note=Glimmer and Genemarks disagree on the start call, but after looking at the gene predictions glimmers call of 4692 should be used because it covers the missing coding potential seen on the Genemarks graph and it allows for a smaller gap between genes CDS 6730 - 7503 /gene="7" /function="capsid maturation protease" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_7" /note=Original Glimmer call @bp 6730 has strength 9.92; Genemark calls start at 6736 /note= /note=SSC: 6730-7503 CP: no SCS: both-gl ST: SS BLAST-Start: [capsid maturation protease [Arthrobacter phage Albanese]],,NCBI, q1:s1 100.0% 0.0 GAP: 19 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.754, -3.081776789475849, yes F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease [Arthrobacter phage Albanese]],,UYL86734,100.0,0.0 SIF-HHPRED: Peptidase_S78 ; Caudovirus prohead serine protease,,,PF04586.20,64.9805,99.9 SIF-Syn: Phamerator showed synteny between the 7th gene and other AK phages 7th genes likeAlbanese and Greenhouse. Both phages have their 7th gene marked as capsid maturation proteases and the genes upstream and downstream match well /note= /note=Genemarks calls for more coding potential, however it cannot be included due to the LORF causing a large overlap and the resulting sequence not matching up with any known proteins after blasting it accross databases /note= /note= /note= /note=Genemarks and Glimmer disagree on the start call, but Glimmer is chosen because it has better combined Z-score and Final score values than the GeneMarks call CDS 7510 - 8760 /gene="8" /function="major capsid protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_8" /note=Original Glimmer call @bp 7510 has strength 15.92; Genemark calls start at 7510 /note= /note=SSC: 7510-8760 CP: yes SCS: both ST: SS BLAST-Start: [major head protein [Arthrobacter phage Oxynfrius] ],,NCBI, q1:s1 100.0% 0.0 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.302, -4.117648872463813, no F: major capsid protein SIF-BLAST: ,,[major head protein [Arthrobacter phage Oxynfrius] ],,YP_010050360,100.0,0.0 SIF-HHPRED: Major capsid protein; Virus Procapsid particles, VIRUS; 5.2A {Enterobacteria phage HK97},,,3QPR_B,99.7596,100.0 SIF-Syn: Phamerator showed synteny between the 8th gene and other AK phages 8th genes like GreenHearts and Albanese. Both phages have their 8th gene marked as major capsid proteins /note= /note=This gene seems to be highly conserved across most AK phages and the 8th gene usually has an agreed upon function of being a major capsid protein CDS 8762 - 8965 /gene="9" /function="head fiber protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_9" /note=Original Glimmer call @bp 8762 has strength 8.03; Genemark calls start at 8762 /note= /note=SSC: 8762-8965 CP: yes SCS: both ST: SS BLAST-Start: [head fiber protein [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 5.29409E-37 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.115, -4.437015170511684, yes F: head fiber protein SIF-BLAST: ,,[head fiber protein [Arthrobacter phage GreenHearts] ],,YP_010049929,100.0,5.29409E-37 SIF-HHPRED: SIF-Syn: /note= /note=SSC: (8762,8965) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (Albanese 9, PhagesDB, Q1:S1, 2e-29)(Greenhearts 9, NCBI, Q1:S1, 100%, 5e-37) Gap: (1) LO: (yes) RBS: (Kibler 6, Karlin Medium, 2.115, -4.437) F: (NKF) SIF-BLAST: (Head fiber protein, Greenhearts 9, NCBI, MK279854, 100%, 5.29e-37) SIF-HHPred: (NKF, no matches with an e-value lower than 1e-7) SIF-Syn: (NKF, compared to GreenHearts, and flanked by gene 8 and 10 [major capsid protein and NKF]) CDS 9037 - 9231 /gene="10" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_10" /note=Original Glimmer call @bp 9037 has strength 13.06; Genemark calls start at 9037 /note= /note=SSC: 9037-9231 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH59_gp10 [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 9.78221E-37 GAP: 71 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.931, -2.707694805492614, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH59_gp10 [Arthrobacter phage Joann] ],,YP_009602690,100.0,9.78221E-37 SIF-HHPRED: SIF-Syn: /note= /note=SSC: (9037, 9231) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (GreenHearts 10, phagesDB, Q1:S1, 4e-30) (Joann 10, NCBI, Q1:S1, 100%, 1e-36) Gap: (71) LO: (yes) RBS: (Kibler 6, Karlin Medium, 2.931, -2.708, yes) F: (NKF) SIF-BLAST: (NKF, phagesDB, Albanese 10, 100%, 4e-30) (NFK, NCBI, Joann 10, YP_009602690.1, 100%, 1e-36) SIF-HHPred: (NKF, there were no matches with an e-value lower than 1e-7) SIF-Syn (NKF, ) CDS 9244 - 9822 /gene="11" /function="head-to-tail adaptor" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_11" /note=Original Glimmer call @bp 9244 has strength 7.82; Genemark calls start at 9244 /note= /note=SSC: 9244-9822 CP: yes SCS: both ST: NI BLAST-Start: [head-tail adaptor [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 7.70547E-137 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.513, -4.057188185093195, no F: head-to-tail adaptor SIF-BLAST: ,,[head-tail adaptor [Arthrobacter phage GreenHearts] ],,YP_010049931,100.0,7.70547E-137 SIF-HHPRED: Adaptor protein Rcc01688; /note=SSC: (9244, 9822) CP: (yes) SCS: (both) ST: (NI, gene does not have the most annotated start) BLAST-Start: (GreenHearts 11, phagesDB, Q1:S1, 100%, 1e-107) (Greenhearts 11, NCBI, Q1:S1, 100%, 8e-137) Gap: (12) LO: (yes) RBS: (2.513, -4.057, no) F: (head-to-tail adaptor) SIF-BLAST: (Head-to-tail adaptor, GreenHearts 11, phagesDB, 100%, 1e-107) (head-to-tail adaptor, GreenHearts 11, phagesDB, YP_010049931.1, 100% 8e-137) SIF-HHPred: (adaptor protein, PDB_mmCIF70, 6TE9_D, 87.6%,99.9) SIF-Syn: (Head-to-tail adaptor, Korra 11, 10 and 12 are flanking) CDS 9822 - 10160 /gene="12" /function="head-to-tail stopper" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_12" /note=Original Glimmer call @bp 9822 has strength 4.95; Genemark calls start at 9822 /note= /note=SSC: 9822-10160 CP: no SCS: both ST: SS BLAST-Start: [head closure Hc1 [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 6.16534E-78 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.107, -4.4713484557894425, no F: head-to-tail stopper SIF-BLAST: ,,[head closure Hc1 [Arthrobacter phage GreenHearts] ],,YP_010049932,100.0,6.16534E-78 SIF-HHPRED: DUF3599 ; Domain of unknown function (DUF3599),,,PF12206.11,98.2143,99.7 SIF-Syn: /note= /note=SSC: (9822,10160) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (Greenhearts 12, phagesDB, Q1:S1, 99%, 9e-62) (Joann 12, NCBI, 100%, 6.17e-78) Gap: (no gap) LO: (yes) RBS: (Kibler 6, Karlin Medium, 2.107, -4.471, yes) F: (head-to-tail stopper) SIF-Blast: (head-to-tail stopper, NCBI, GreenHearts 12, YP_010049932.1, 100%, 6.17e-78) (head-to-tail stopper, phagesDB, GreenHearts 12, 99%, 9e-62) SIF-HHPred: (NKF, PDB_mmCIF70, 3F3B_A, 93.8%, 99.7%) SIF-Syn: (head-to-tail stopper, flanked by 11 [head-to-tail adaptor], and 13 [NKF], compared to Greenhearts and Korra) CDS 10160 - 10450 /gene="13" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_13" /note=Original Glimmer call @bp 10160 has strength 8.95; Genemark calls start at 10160 /note= /note=SSC: 10160-10450 CP: yes SCS: both ST: SS BLAST-Start: [neck protein [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 5.56572E-61 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.031, -4.551528886052257, no F: hypothetical protein SIF-BLAST: ,,[neck protein [Arthrobacter phage GreenHearts] ],,YP_010049933,100.0,5.56572E-61 SIF-HHPRED: SIF-Syn: /note= /note=SSC: (10160, 10450) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (Greenhearts 13, phagesDB, Q1:S1, 100%, 1e-46) (GreenHearts 13, NCBI, Q1:S1, 100%, 5.56e-61) Gap: (-1) LO: (yes) RBS: (2.031, -4.552, no) F: (NKF) SIF-Blast: (neck protein, NCBI, GreenHearts 13, YP_010049995.1, 100%, 5.57e-61) (NKF, Greenhearts 13, 100%, 1e-46) SIF-HHPred: (NKF, there are no proteins with an e-value lower than 1e-7) SIF-Syn: (NKF, flanked by genes 12 and 14 on Joann which are head-to-tail stopper, and terminator, respectively. Joann does not have a listed function for gene 13) CDS 10452 - 10862 /gene="14" /function="tail terminator" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_14" /note=Original Glimmer call @bp 10452 has strength 7.36; Genemark calls start at 10452 /note= /note=SSC: 10452-10862 CP: yes SCS: both ST: NI BLAST-Start: [tail terminator [Arthrobacter phage Greenhouse] ],,NCBI, q1:s1 100.0% 1.86185E-91 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.86, -2.8742224756987462, yes F: tail terminator SIF-BLAST: ,,[tail terminator [Arthrobacter phage Greenhouse] ],,YP_010049996,100.0,1.86185E-91 SIF-HHPRED: PROPHAGE LAMBDALM01, ANTIGEN B; IMMUNE SYSTEM, SURFACE, PHAGE-RELATED; 2.401A {LISTERIA MONOCYTOGENES},,,4ACV_A,95.5882,99.5 SIF-Syn: /note= /note=SSC: (10452, 10862) CP: (yes) SCS: (both) ST: (NI, gene does not have the most annotated start) Blast-Start: (Greenhouse 14, PhagesDB, Q1:S1, 100%, 3e-72) (Greenhouse 14, NCBI, Q1:S1, 100%, 2e-91) Gap: (1) LO: (yes) RBS: (Kibler 6 Karlin Medium, 2.86, -2.874, yes) F: (tail terminator) SIF-Blast: (tail terminator, Greenhouse 14, PhagesDB, 100%, 3e-72) (tail terminator, Greenhouse 14, NCBI, YP_010049996.1, 100%, 2e-91) Sif-HHPred: (tail-to-head joining protein, PDB_mmCIF70, 5A21_G, 95.6%, 99.49) SIF-Syn: (tail terminator, compared to Greenhouse 14 which has this gene labeled as CDS 10878 - 11786 /gene="15" /function="major tail protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_15" /note=Original Glimmer call @bp 10878 has strength 9.99; Genemark calls start at 10878 /note= /note=SSC: 10878-11786 CP: yes SCS: both ST: NI BLAST-Start: [major tail protein [Arthrobacter phage Nubia] ],,NCBI, q1:s1 100.0% 0.0 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.754, -3.370572328722819, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage Nubia] ],,YP_010050306,100.0,0.0 SIF-HHPRED: SIF-Syn: /note= /note=SSC: (10878, 11786) CP: (yes) SCS: (both) ST: (NI, gene does not have the most annotated start) Blast-Start: (Oxynfrius 15, PhagesDB, Q1:S1, 100%, 1e-171) (Nubia 15, NCBI, Q1:S1, 100%, 0) Gap: (15) LO: (yes) RBS: (Kibler 6 Karlin medium, 2.754, -3.371, yes) F: (major tail protein) SIF-Blast: (Major tail protein, Nubia 15, NCBI, YP_010050306.1, 100%, 0) (Major tail protein, Oxynfrius 15, PhagesDB, 100%, 1e-171) SIF-HHPred: (NKF, there are no proteins with an e-value less than 1e-7) SIF-Syn: (major tail protein, compared to Joann which lists gene 15 as a major tail protein, flanking genes are 14 and 16 which are terminator and tail assembly chaperone respectively) CDS 11870 - 12280 /gene="16" /function="tail assembly chaperone" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_16" /note=Original Glimmer call @bp 11870 has strength 10.69; Genemark calls start at 11870 /note= /note=SSC: 11870-12280 CP: yes SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Arthrobacter phage Greenhouse] ],,NCBI, q1:s1 100.0% 1.33624E-92 GAP: 83 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.026, -2.442961286954254, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage Greenhouse] ],,YP_010049999,100.0,1.33624E-92 SIF-HHPRED: SIF-Syn: /note= /note=SSC: (11870,12280) CP: (yes) SCS: (both) ST: (NI, does not have the most annotated start) Blast-Start: (Greenhouse 16, PhagesDB, Q1:S1, 100% 7e-72) (Greenhouse 16, NCBI, Q1:S1, 100%, 1e-92) Gap: (83) LO: (no, there is a longer possible start, but it overlaps another gene by 193 bp) RBS: (kibler6, karlin medium, 3.026, -2.443, yes) F: (tail assembly chaperone) SIF-Blast: (tail assembly chaperone, Greenhouse 16, PhagesDB, 100%, 7e-72) (tail assembly chaperone, Greenhouse 16, NCBI, YP_010049999.1, 100%, 1e-92) SIF-HHPred: (NKF, no hits below 1e-7) SIF-Syn: (tail assembly chaperone, it was compared to Joann and it is flanked by genes 15 and 17 which are major tail protein and NKF respectively) CDS join(11870. .12280;12280. .12630) /gene="17" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_17" /note=Original Glimmer call @bp 12421 has strength 0.9; Genemark calls start at 12421 /note= /note=SSC: 11870-12630 CP: no SCS: both-cs ST: NI BLAST-Start: [tail assembly chaperone [Arthrobacter phage Joann] ],,NCBI, q10:s128 93.3333% 2.23352E-85 GAP: -58 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.026, -5.213475109731446, no F: hypothetical protein SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage Joann] ],,YP_009602696,49.8024,2.23352E-85 SIF-HHPRED: SIF-Syn: SIF-Syn: NKF /note= /note=SSC: 12421, 12630 CP: yes SCS: both ST: NI. Most common starterator is not present. BLAST-Start: Albanese gp17, PhagesDB, Q1:S1, 100%, 4e-37. Nubia gp17, NCBI, Q1:S1, 100%, 5.03e-42. Gap:140 LO: no RBS: Kibler6, Karlin Medium, 1.479, -5.721, yes F: NKF SIF-BLAST: tail assembly chaperone, PhagesDB, Albanese gp17, Q1:S1, 100%, 4e-37. Tail assembly chaperone, NCBI, Nubia gp17, Q1:S1, 100%, 5.03e-42 SIF-HHPred: NKF no hit over 90% SIF-Syn: NFK /note= /note=tail assembly chaperone frameshift protein CDS 12636 - 15197 /gene="18" /function="tape measure protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_18" /note=Original Glimmer call @bp 12636 has strength 8.89; Genemark calls start at 12636 /note= /note=SSC: 12636-15197 CP: yes SCS: both ST: SS BLAST-Start: [tail length tape measure protein [Arthrobacter phage Oxynfrius] ],,NCBI, q1:s1 100.0% 0.0 GAP: 5 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.609, -3.9797067239234645, no F: tape measure protein SIF-BLAST: ,,[tail length tape measure protein [Arthrobacter phage Oxynfrius] ],,YP_010050370,100.0,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_CF,15.0059,99.9 SIF-Syn: SIF-Syn: tape measure protein, upstream is tail assembly protein, downstream is minor tail protein, Albanese and Oxynfrius gp17 and gp19 /note= /note=SSC: 12636, 15197 CP: yes SCS: both ST: SS BLAST-Start: Albanese gp18, PhagesDB, Q1:S1, 100%, 0. Oxynfrius gp18, NCBI, Q1:S1, 100%, 0. Gap: 5 LO: no RBS: Kibler6, Karlin Medium, 2.609, -3.980, yes F: tape measure protein SIF-BLAST: tape measure protein, PhagesDB, Albanese gp18, Q1:S1, 100%, 0. Tape measure protein, NCBI, Oxynfrius gp18, Q1:S1, 100%, 0 SIF-HHPred: tape measure protein, PDB, Staphylococcus virus 80alpha gp57, 6V8I_CF, 99.9% CDS 15194 - 16066 /gene="19" /function="minor tail protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_19" /note=Original Glimmer call @bp 15194 has strength 10.87; Genemark calls start at 15194 /note= /note=SSC: 15194-16066 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.71, -5.293288977131869, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Joann] ],,YP_009602699,100.0,0.0 SIF-HHPRED: HYPOTHETICAL PROTEIN 19.1; VIRAL PROTEIN, DISTAL TAIL PROTEIN; 2.95A {BACILLUS PHAGE SPP1},,,2X8K_C,88.2759,100.0 SIF-Syn: SIF-Syn: minor tail protein, upstream is tape measure protein, downstream is minor tail protein, Albanese and Joann gp18 and gp20. /note= /note=SSC: 15194, 16066 CP: yes SCS: both ST: SS BLAST-Start: Albanese gp19, PhagesDB, Q1:S1, 100%, 1e-170. Joann gp19, NCBI, Q1:S1, 100%, 0. Gap: -4 LO: yes RBS: Kibler6, Karlin Medium, 1.71, -5.293, yes F: minor tail protein SIF-BLAST: minor tail protein, PhagesDB, Albanese gp19, Q1:S1, 100%, 1e-170. Minor tail protein, NCBI, Joann gp19, Q1:S1, 100%, 0 SIF-HHPred: distal tail protein, PDB, Bacillus phage SPP1 gp19.1, 2X8K_C, 88.27%, 100% SIF-Syn: minor tail protein, upstream is tape measure protein, downstream is minor tail protein, Albanese and Joann gp18 and gp20. CDS 16057 - 17214 /gene="20" /function="minor tail protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_20" /note=Original Glimmer call @bp 16057 has strength 11.61; Genemark calls start at 16057 /note= /note=SSC: 16057-17214 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 0.0 GAP: -10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.212, -4.308385737595809, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Joann] ],,YP_009602700,100.0,0.0 SIF-HHPRED: Sipho_Gp37 ; Siphovirus ReqiPepy6 Gp37-like protein,,,PF14594.9,93.5065,99.9 SIF-Syn: SIF-Syn: minor tail protein, upstream is minor tail protein, downstream is minor tail protein, Albanese and Joann gp19 and gp21. /note= /note=SSC: 16057, 17214 CP: yes SCS: both ST: SS BLAST-Start: Albanese gp20, PhagesDB, Q1:S1, 100%, 0. Joann gp20, NCBI, Q1:S1, 100%, 0. Gap: -10 LO: yes RBS: Kibler6, Karlin Medium, 2.212, -4.308, yes F: minor tail protein SIF-BLAST: minor tail protein, PhagesDB, Albanese gp20, Q1:S1, 100%, 0. Minor tail protein, NCBI, Joann gp20, Q1:S1, 100%, 0 SIF-HHPred: NKF SIF-Syn: minor tail protein, upstream is minor tail protein, downstream is minor tail protein, Albanese and Joann gp19 and gp21. CDS 17214 - 18239 /gene="21" /function="minor tail protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_21" /note=Original Glimmer call @bp 17214 has strength 11.72; Genemark calls start at 17214 /note= /note=SSC: 17214-18239 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.523, -3.5707972674952195, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Joann] ],,YP_009602701,100.0,0.0 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,36.6569,98.3 SIF-Syn: SIF-Syn: minor tail protein, upstream is minor tail protein, downstream is minor tail protein, Albanese and Joann gp20 and gp22 /note= /note=SSC: 17214, 18239 CP: yes SCS: both ST: SS BLAST-Start: Albanese gp21, PhagesDB, Q1:S1, 100%, 0. Joann gp21, NCBI, Q1:S1, 100%, 0. Gap: -1 LO: yes RBS: Kibler6, Karlin Medium, 2.523, -3.571, yes F: minor tail protein SIF-BLAST: minor tail protein, PhagesDB, Albanese gp21, Q1:S1, 100%, 0. Minor tail protein, NCBI, Joann gp21, Q1:S1, 100%, 0 SIF-HHPred: tail fiber, PDB, Salmonella phage vB_SenM-S16, 6F45, 36.85%, 98.3% SIF-Syn: minor tail protein, upstream is minor tail protein, downstream is minor tail protein, Albanese and Joann gp20 and gp22 CDS 18236 - 19312 /gene="22" /function="minor tail protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_22" /note=Original Glimmer call @bp 18305 has strength 7.88; Genemark calls start at 18236 /note= /note=SSC: 18236-19312 CP: yes SCS: both-gm ST: NI BLAST-Start: [virion structural protein [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.609, -3.9797067239234645, no F: minor tail protein SIF-BLAST: ,,[virion structural protein [Arthrobacter phage Joann] ],,YP_009602702,100.0,0.0 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,48.6034,99.3 SIF-Syn: SIF-Syn: minor tail protein, upstream is minor tail protein, downstream is NKF, Albanese and Joann gp21 and gp23 /note= /note=SSC: 18236, 19312 start changed due to better RBS values and CP CP: yes SCS: GeneMark ST: NI most annotated start but does not call it BLAST-Start: Albanese gp22, PhagesDB, Q1:S24, 99%, 0. Joann gp22, NCBI, Q1:S24, 100%, 0. Gap: -4 LO: yes RBS: Kibler6, Karlin Medium, 2.609, -3.980, yes F: minor tail protein SIF-BLAST: minor tail protein, PhagesDB, Albanese gp22, Q1:S24, 99%, 0. virion structural protein, NCBI, Joann gp22, Q1:S24, 100%, 0 SIF-HHPred: receptor binding protein, PDB, Lactococcus phage 1358, 4L9B, 48.60%, 99.3% SIF-Syn: minor tail protein, upstream is minor tail protein, downstream is NKF, Albanese and Joann gp21 and gp23 CDS 19305 - 19745 /gene="23" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_23" /note=Original Glimmer call @bp 19305 has strength 5.3; Genemark calls start at 19305 /note= /note=SSC: 19305-19745 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 2.52612E-99 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.447, -4.322809268821859, no F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Joann] ],,YP_009602703,100.0,2.52612E-99 SIF-HHPRED: SIF-Syn: SIF-Syn: NKF /note= /note=SSC: 19305, 19745 CP: yes SCS: both ST: SS BLAST-Start: Albanese gp23, PhagesDB, Q1:S1, 100%, 4e-81. Joann gp23, NCBI, Q1:S1, 100%, 2.52612e-99. Gap: -8 LO: no RBS: Kibler6, Karlin Medium, 2.477, -4.323, yes F: NKF SIF-BLAST: NKF, PhagesDB, Albanese gp23, Q1:S1, 100%, 4e-81. minor tail protein, NCBI, Joann gp23, Q1:S1, 100%, 2.52612e-99 SIF-HHPred: NKF no hit over 90% SIF-Syn: NKF CDS 19747 - 20037 /gene="24" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_24" /note=Original Glimmer call @bp 19747 has strength 5.94; Genemark calls start at 19747 /note= /note=SSC: 19747-20037 CP: yes SCS: both ST: SS BLAST-Start: [hol-like chemotaxis [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 5.12016E-63 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.257, -2.0162541296952132, yes F: hypothetical protein SIF-BLAST: ,,[hol-like chemotaxis [Arthrobacter phage Joann] ],,YP_009602704,100.0,5.12016E-63 SIF-HHPRED: DUF2730 ; Protein of unknown function (DUF2730),,,PF10805.11,77.0833,96.3 SIF-Syn: SIF-Syn: NKF /note= /note=SSC: 19747, 20037 CP: yes SCS: both ST: SS BLAST-Start: Albanese gp24, PhagesDB, Q1:S1, 100%, 4e-48. Joann gp24, NCBI, Q1:S1, 100%, 5e-63. Gap: 1 LO: yes RBS: Kibler6, Karlin Medium, 3.257, -2.016, yes F: NKF SIF-BLAST: NKF, PhagesDB, Albanese gp24, Q1:S1, 100%, 4e-48. hol-like chemotaxis, NCBI, Joann gp24, Q1:S1, 100%, 5e-63 SIF-HHPred: NKF SIF-Syn: NKF CDS 20034 - 20870 /gene="25" /function="endolysin" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_25" /note=Original Glimmer call @bp 20034 has strength 12.91; Genemark calls start at 20034 /note= /note=SSC: 20034-20870 CP: yes SCS: both ST: SS BLAST-Start: [amidase [Arthrobacter phage Oxynfrius] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.009, -3.3861813518867647, no F: endolysin SIF-BLAST: ,,[amidase [Arthrobacter phage Oxynfrius] ],,YP_010050377,100.0,0.0 SIF-HHPRED: N-acetylmuramoyl-L-alanine amidase; amidase, zinc binding, cell wall degradation, endolysine, hydrolase; HET: PO4, GOL; 1.21A {Clostridium intestinale},,,6SSC_A,43.5252,99.6 SIF-Syn: endolysin downstream of Pham 1160 and upstream of holin /note= /note=SSC: 20034 20870 CP: yes SCS: Glimmer ST: SS BLAST-Start: matches Oxynfrius_25 on PhagesDB q1:s1 100% E-166; matches Oxynfrius gp 25 on NCBI q1:s1 100% 0.0 Gap: -4 LO: NA RBS: Kibler6 Karlin Medium 2.986 -3.386 F: endolysin SIF-BLAST: endolysin NCBI Oxynfrius gp 25 YP_010050377.1 100% 0.0, PhagesDB Oxynfrius_25 100% E-166 SIF-HHPred: endolysin, 43.0% alignment 99.38, probability SIF-Syn: endolysin downstream of Pham 1160 and upstream of holin CDS 20855 - 21370 /gene="26" /function="holin" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_26" /note=Original Glimmer call @bp 20855 has strength 8.23; Genemark calls start at 20867 /note= /note=SSC: 20855-21370 CP: yes SCS: both-gl ST: NA BLAST-Start: [holin [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 2.55478E-117 GAP: -16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.84, -2.916420155493201, yes F: holin SIF-BLAST: ,,[holin [Arthrobacter phage Joann] ],,YP_009602706,100.0,2.55478E-117 SIF-HHPRED: SIF-Syn: holin, upstream of endolysin and downstream of helix-turn-helix DNA-binding protein, like in Canowicakte gp 26 and Immaculata gp 2 /note= /note=SSC: 20855 21370 CP: yes SCS: Both-GL ST: NI BLAST-Start: matches with Joann_26 on PhagesDB q1:s1 98% 2E-93; matches with Joann gp 26 and Oxynfrius gp 26 on NCBI, both q1:s1 99% 3E-117 Gap: -16 LO: NA RBS: Kibler6 Karlin Medium 2.84 -2.916 F: holin SIF-BLAST: holin NCBI Joann_26 YP_009602706 99% 3E-117  SIF-HHPred: NKF, no matches with probability over 90% SIF-Syn: holin, upstream of endolysin and downstream of helix-turn-helix DNA-binding protein, like in Canowicakte gp 26 and Immaculata gp 26 SIF-Mem: 3 from TMHMM 3 from SOSUI CDS 21527 - 21832 /gene="27" /function="helix-turn-helix DNA binding domain" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_27" /note=Original Glimmer call @bp 21527 has strength 9.24; Genemark calls start at 21527 /note= /note=SSC: 21527-21832 CP: yes SCS: both ST: NA BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage Albanese]],,NCBI, q1:s41 100.0% 7.2055E-68 GAP: 156 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.083, -5.094319939317197, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage Albanese]],,UYL86754,71.6312,7.2055E-68 SIF-HHPRED: SIF-Syn: downstream of a holin /note= /note=SSC: 21407 21832 CP: yes SCS: Both-CS ST: NA BLAST-Start: matches with Albanese gene 27 on NCBI q1:s1 99% 3E-100, matches with Albanese_27 on PhagesDB q1:s1 1E-77 Gap: 37 LO: yes RBS: Kibler6 Karlin Medium 2.032 -5.032 F: helix-turn-helix DNA binding domain protein SIF-BLAST: SIF-HHPred: NKF SIF-Syn: downstream of a holin CDS 21807 - 22151 /gene="28" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_28" /note=Original Glimmer call @bp 21909 has strength 3.65; Genemark calls start at 21810 /note= /note=SSC: 21807-22151 CP: yes SCS: both-cs ST: NA BLAST-Start: [hypothetical protein KDI99_gp28 [Arthrobacter phage Greenhouse] ],,NCBI, q2:s1 99.1228% 8.12302E-73 GAP: -26 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.128, -4.99877661786583, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDI99_gp28 [Arthrobacter phage Greenhouse] ],,YP_010050010,97.3451,8.12302E-73 SIF-HHPRED: SIF-Syn: NKF /note= /note=SSC: 21807 22151 CP: yes SCS: neither ST: NA BLAST-Start: aligns with hypothetical protein KDI99_gp28 from Greenhouse on NCBI q2:s1 98% 8E-73, aligns with Albanese_28 on PhagesDB q7:s1 99% 2E-58 Gap: -26 LO: no RBS: Kibler6 Karlin Medium 2.107 -4.698 F: NKF SIF-BLAST: NKF SIF-HHPred: NKF, no hits with a probability above 90% SIF-Syn: NKF CDS 22120 - 23511 /gene="29" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_29" /note=Original Glimmer call @bp 22120 has strength 3.49; Genemark calls start at 22279 /note= /note=SSC: 22120-23511 CP: no SCS: both-gl ST: SS BLAST-Start: [DNA helicase [Arthrobacter phage Albanese]],,NCBI, q1:s1 100.0% 0.0 GAP: -32 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.523, -3.5707972674952195, no F: hypothetical protein SIF-BLAST: ,,[DNA helicase [Arthrobacter phage Albanese]],,UYL86756,100.0,0.0 SIF-HHPRED: SIF-Syn: NKF /note= /note=SSC: 22120 23511 CP: no SCS: Both-GL ST: SS BLAST-Start: matches with Albanese DNA helicase on NCBI q1:s1 99.78% 0.0, matches with Albanese_29 on PhagesDB q1:s1 99% 0.0 Gap: -32 LO: yes RBS: Kibler6 Karlin Medium 2.501 -3.571 F: NKF SIF-BLAST: DNA helicase NCBI Albanese UYL86756 100% 0 SIF-HHPred: NKF SIF-Syn: NKF /note= /note= /note= /note=BLAST results indicate could be DNA helicase but lack of coding potential led to calling NKF; many varied HHPred results with high probability and low e-values decided as inconclusive. CDS 23627 - 24037 /gene="30" /function="helix-turn-helix DNA binding domain" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_30" /note=Original Glimmer call @bp 23627 has strength 6.01; Genemark calls start at 23627 /note= /note=SSC: 23627-24037 CP: yes SCS: both ST: SS BLAST-Start: [HTH DNA binding protein [Arthrobacter phage Huntingdon] ],,NCBI, q1:s1 100.0% 1.75937E-96 GAP: 115 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.138, -4.325675514574479, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding protein [Arthrobacter phage Huntingdon] ],,YP_010050073,100.0,1.75937E-96 SIF-HHPRED: SIF-Syn: AK Arthrobacter phages Joann, Oxynfrius, and Albanese also both have an endolysin followed by a holin, then a helix-turn-helix DNA binding domain protein as the fourth gene downstream of the holin /note= /note=SSC: 23627 24037 CP: yes SCS: Both ST: SS BLAST-Start: matches with Huntingdon gp 30 on NCBI q1:s1 100% 2E-96 matches with RcigaStruga_30 on PhagesDB q1:s1 100% 3E-77 Gap: 115 LO: yes RBS: Kibler6 Karlin Medium 2.116 -4.326 F: helix-turn-helix DNA binding domain protein SIF-BLAST: HTH DNA binding domain protein Albanese gp 30 on NCBI UYL86757.1 SIF-HHPred: NKF SIF-Syn: AK Arthrobacter phages Joann, Oxynfrius, and Albanese also both have an endolysin followed by a holin, then a helix-turn-helix DNA binding domain protein as the fourth gene downstream of the holin /note= /note= /note= /note=high HHPred e-values CDS 24046 - 24651 /gene="31" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_31" /note=Original Glimmer call @bp 24046 has strength 8.99; Genemark calls start at 24046 /note= /note=SSC: 24046-24651 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein KDJ04_gp31 [Arthrobacter phage Nubia] ],,NCBI, q1:s1 100.0% 3.80632E-144 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.138, -4.4057176022952405, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDJ04_gp31 [Arthrobacter phage Nubia] ],,YP_010050322,99.5025,3.80632E-144 SIF-HHPRED: SIF-Syn: /note= /note=SSC: 240046 24651 CP: yes SCS: Both ST: SS BLAST-Start: matches with Oxynfrius_31 on PhagesDB q1:s1 99% E-121 Gap: 8 LO: no RBS: Kibler6 Karlin Medium 2.116 -4.406 F: NKF SIF-BLAST: SIF-HHPred: NKF SIF-Syn: NKF CDS 24665 - 25141 /gene="32" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_32" /note=Original Glimmer call @bp 24665 has strength 5.11; Genemark calls start at 24692 /note= /note=SSC: 24665-25141 CP: no SCS: both-gl ST: NA BLAST-Start: [hypothetical protein KDJ05_gp32 [Arthrobacter phage Oxynfrius] ],,NCBI, q1:s1 100.0% 1.38449E-111 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.161, -2.2364030944336752, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDJ05_gp32 [Arthrobacter phage Oxynfrius] ],,YP_010050384,99.3671,1.38449E-111 SIF-HHPRED: SIF-Syn: NKF /note= /note=SSC: 24665 25141 CP: yes SCS: Both-GL ST: NA BLAST-Start: matches with hypothetical protein KDJ05_gp32 from Oxynfrius on NCBI 100% 1E-111, matches with Oxynfrius_32 on PhagesDB q1:s1 98% 1E-87 Gap: 13 LO: yes RBS: Kibler6 Karlin Medium 3.138 -2.236 F: NKF SIF-BLAST: Oxynfrius gp 32 on NCBI YP_010050384.1 SIF-HHPred: NKF SIF-Syn: NKF /note= /note=low coding potential for first 30 bp CDS 25122 - 25679 /gene="33" /function="RuvC-like resolvase" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_33" /note=Original Glimmer call @bp 25122 has strength 10.62; Genemark calls start at 25134 /note= /note=SSC: 25122-25679 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein KDI97_gp33 [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 2.14957E-134 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.15, -4.826259462263871, no F: RuvC-like resolvase SIF-BLAST: ,,[hypothetical protein KDI97_gp33 [Arthrobacter phage GreenHearts] ],,YP_010049953,100.0,2.14957E-134 SIF-HHPRED: c.55.3.6 (A:) automated matches {Pseudomonas aeruginosa [TaxId: 287]} | CLASS: Alpha and beta proteins (a/b), FOLD: Ribonuclease H-like motif, SUPFAM: Ribonuclease H-like, FAM: RuvC resolvase,,,SCOP_d6lw3a_,82.1622,99.9 SIF-Syn: /note= /note=SSC: 25122, 25679 /note= /note=CP: Yes /note= /note=SCS: Both-GL /note= /note=ST: SS /note= /note=BLAST-Start: /note= /note=GreenHearts, 33, Phagesdb, 1:1, 100%, e^-104] /note= /note=GreenHearts, 33, NCBI, 1:1, 100%, e^-134] /note= /note=Gap: 21 (overlap) /note= /note=LO: NA /note= /note=RBS: [Kibler6, Karlin Medium, 2.15, -4.826, yes] /note= /note=F: NKF /note= /note=SIF-BLAST: /note= /note=GreenHearts, 33, Phagesdb, 100%, e^-104] /note= /note=GreenHearts, 33, NCBI, 100%, e^-134] /note= /note=GreenHearts, 33, Phagesdb, 1:1, 100%, e^-104] /note= /note=GreenHearts, 33, NCBI, 1:1, 100%, e^-134] /note= /note=SIF-HHPred: [NKF, no matches with a probability above 90%] /note= /note=SIF-Syn: [NKF] CDS 25689 - 25946 /gene="34" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_34" /note=Original Glimmer call @bp 25731 has strength 11.61; Genemark calls start at 25731 /note= /note=SSC: 25689-25946 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein FDH59_gp34 [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 2.46075E-57 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.619, -4.6114151184034835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH59_gp34 [Arthrobacter phage Joann] ],,YP_009602714,100.0,2.46075E-57 SIF-HHPRED: SIF-Syn: NKF /note= /note=SSC: 25689, 25946 /note= /note=CP: Yes /note= /note=SCS: neither /note= /note=ST: SS /note= /note=BLAST-Start: /note= /note=Nubia, 34, phagesdb, 1:15, 100% coverage, e^-36] /note= /note=Nubia, 34, NCBI, 1:15, 100% identity, e^-45] /note= /note=Gap: 9 /note= /note=LO: NA /note= /note=RBS: [Kibler6, Karlin Medium, 2.619, -4.611, no] /note= /note=F: NKF /note= /note=SIF-BLAST: /note= /note=NKF, phagesdb, Nubia_34, 272320, 100%, e^-36)] /note= /note=NKF, NCBI, Nubia_34, YP_010050325.1, 100% e^-45] /note= /note=SIF-HHPred: [NKF, no probability above 90%] /note= /note=SIF-Syn: [NKF, flanking genes: 31-33, 35, referenced phages Albanese, Beethoven, BrotherBLo_Draft, Dino, Gisselle, Huntingdon, Kittykat, lasagna, Moki, OurGirlNessie, Pterodactyl, Sergei, Vallejo, Wawa] CDS 26006 - 26356 /gene="35" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_35" /note=Original Glimmer call @bp 26006 has strength 12.31; Genemark calls start at 26006 /note= /note=SSC: 26006-26356 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein KDJ04_gp35 [Arthrobacter phage Nubia] ],,NCBI, q1:s1 100.0% 2.41903E-79 GAP: 59 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.268, -2.0111200136961407, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDJ04_gp35 [Arthrobacter phage Nubia] ],,YP_010050326,100.0,2.41903E-79 SIF-HHPRED: SIF-Syn: NKF /note= /note=SSC: 26006, 26356 CP: Yes SCS: both /note= /note=ST: SS /note= /note=BLAST-Start: /note= /note=Albanese, 35, Phagesdb, 1:1, 100%, e^-63] /note= /note=Nubia, 35, NCBI, 1:1, 100%, e^-79] /note= /note=Gap: 59 /note= /note=LO: yes /note= /note=RBS: [Kibler6, Karlin Medium, 3.268, -2.011, yes] /note= /note=F: NKF /note= /note=SIF-BLAST: /note= /note=NKF, Phagesdb, Albanese, 35, 100%, e^-63] /note= /note=NKF, NCBI, Nubia, 35, YP_010050326.1, 100%, e^-79] /note= /note=SIF-HHPred: [NKF, no probability above 90%] /note= /note=SIF-Syn: [NKF] CDS 26357 - 26707 /gene="36" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_36" /note=Original Glimmer call @bp 26357 has strength 9.08; Genemark calls start at 26357 /note= /note=SSC: 26357-26707 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein KDI97_gp36 [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 1.96358E-79 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.648, -3.896257482888039, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDI97_gp36 [Arthrobacter phage GreenHearts] ],,YP_010049956,100.0,1.96358E-79 SIF-HHPRED: SIF-Syn: NKF /note= /note=Overall Annotation for Lakshmi_36: /note= /note=SSC: 26357, 26707 /note= /note=CP: yes /note= /note=SCS: Both /note= /note=ST: SS /note= /note=BLAST-Start: /note= /note=Albanese, 36, Phagesdb, 1:1, 100%, e^-63] /note= /note=GreenHearts, 36, NCBI, 1:1, 100%, 2e-79] /note= /note=Gap: 0 /note= /note=LO: yes /note= /note=RBS: [Kibler6, Karlin Medium, 2.648, -3.896, yes] /note= /note=F: NKF /note= /note=SIF-BLAST: [NKF, Phagesdb, Albanese, 36, 100%, 2e^-63] /note= /note=NKF, NCBI, GreenHearts, 36, YP_010049956.1, 100%, 2e^-79] /note= /note=SIF-HHPred: NKF no probability above 90% /note= /note=SIF-Syn: NKF CDS 26717 - 27058 /gene="37" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_37" /note=Original Glimmer call @bp 26738 has strength 4.7; Genemark calls start at 26717 /note= /note=SSC: 26717-27058 CP: no SCS: both-gm ST: NA BLAST-Start: [hypothetical protein KDJ04_gp37 [Arthrobacter phage Nubia] ],,NCBI, q1:s1 100.0% 4.45398E-75 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.138, -4.325675514574479, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDJ04_gp37 [Arthrobacter phage Nubia] ],,YP_010050328,100.0,4.45398E-75 SIF-HHPRED: SIF-Syn: NKF /note= /note=SSC: 26738, 27058 /note= /note=CP: yes /note= /note=SCS: Both-GL /note= /note=ST: NI /note= /note=BLAST-Start: /note= /note=Nubia, 37, Phagesdb, 1:8, 100%, 6e^-53] /note= /note=Nubia, 37, NCBI, 1:8, 100%, 8e^-70] /note= /note=Gap: 30 /note= /note=LO: no /note= /note=RBS: [Kibler6, Karlin Medium, 1.626, -5.490, no] /note= /note=F: NKF /note= /note=SIF-BLAST: /note= /note=NKF, Phagesdb, Nubia, 37, 100%, 6e^-53] /note= /note=NKF, NCBI, Nubia, 37, YP_010050328.1, 100%, 8e^-70] /note= /note=SIF-HHPred: /note= /note=terminal protein, HHPred PECAAN? , PF04468.15, how to calculate alignment? 0.16, 99.3] /note= /note=SIF-Syn: NKF CDS 27055 - 27291 /gene="38" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_38" /note=Original Glimmer call @bp 27088 has strength 11.8; Genemark calls start at 27055 /note= /note=SSC: 27055-27291 CP: no SCS: both-gm ST: SS BLAST-Start: [hypothetical protein KDI99_gp39 [Arthrobacter phage Greenhouse] ],,NCBI, q1:s1 100.0% 6.17032E-49 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.268, -2.0720764396375664, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDI99_gp39 [Arthrobacter phage Greenhouse] ],,YP_010050021,100.0,6.17032E-49 SIF-HHPRED: SIF-Syn: showed synteny with similar phages Albanese_38 and Greenhouse_39 /note= /note=SSC: 27088, 27291 /note= /note=CP: yes /note= /note=SCS: called by both, Glimmer selected most accurate/consistent start bp Both-GL /note= /note=ST: NI /note= /note=BLAST-Start: /note= /note=Albanese, 38, Phagesdb, 1:12, 98% 6e^-31] /note= /note=Greenhouse, 39, NCBI, 1:12, 99%, 5e^-39] /note= /note=Gap: 29 /note= /note=LO: no /note= /note=RBS: [Kibler6, Karlin Medium, 2.17, -4.319, no] /note= /note=F: NKF /note= /note=SIF-BLAST: /note= /note=NKF, Phagesdb, Albanese, 38, 98%, 6e^-31] /note= /note=NKF, NCBI, Greenhouse, 39, 99%, 5e^-39] /note= /note=SIF-HHPred: [NKF, no matches with a probability above 90%] /note= /note=SIF-Syn: Phamerator report shows synteny between Lakshmi_38 and similar phages (greenhouse and albanese), but no function listed for gene 38: NKF CDS 27288 - 27719 /gene="39" /function="membrane protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_39" /note=Original Glimmer call @bp 27447 has strength 9.34; Genemark calls start at 27288 /note= /note=SSC: 27288-27719 CP: yes SCS: both-gm ST: NA BLAST-Start: [membrane protein [Arthrobacter phage Albanese]],,NCBI, q1:s1 100.0% 5.13054E-95 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.026, -2.583959800616441, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Albanese]],,UYL86766,98.6014,5.13054E-95 SIF-HHPRED: SIF-Syn: Shows no synteny with similar phage Oxynfrius at gene 39 because it`s an orpham. /note= /note=SSC: 27288, 27719 /note= /note=CP: yes /note= /note=ST: NA (orpham) /note= /note=BLAST-Start: /note= /note=Oxynfrius, 39, NCBI, 1:54, 99%, 1e^-57] /note= /note=Joann, 39, Phagesdb, 1:54, 98%, 2e^-45] /note= /note=Gap: -4 /note= /note=LO: NA /note= /note=RBS: [Kibler6, Karlin Medium, 3.026, -2.584, yes] /note= /note=F: NKF /note= /note=SIF-BLAST: /note= /note=NKF, NCBI, Oxynfrius, 39, 99%, 1e^-57] /note= /note=NKF, Phagesdb, Joann, 39, 98%, 2e^-45] /note= /note=SIF-HHPred: although there was a hit with a probability of 99.1%, there was no known function: NKF /note= /note=SIF-Syn: [NKF] CDS 27719 - 27994 /gene="40" /function="membrane protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_40" /note=Original Glimmer call @bp 27719 has strength 2.73; Genemark calls start at 27719 /note= /note=SSC: 27719-27994 CP: no SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage Albanese]],,NCBI, q1:s1 100.0% 2.51639E-55 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.886, -2.740768097004632, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Albanese]],,UYL86767,100.0,2.51639E-55 SIF-HHPRED: SIF-Syn: Does not display synteny with closest match Albanese /note= /note=SSC: 27719, 27994 /note= /note=CP: no /note= /note=SCS: Both /note= /note=ST: NI /note= /note=BLAST-Start: /note= /note=Albanese, 40, NCBI, 98%, 1:1, 3e^-55] /note= /note=Albanese, 40, Phagesdb, 1:1, 97%, 2e^-47] /note= /note=Gap: -1 /note= /note=LO: NA /note= /note=RBS: [Kibler6, Karlin Medium, 2.886, -2.741, yes] /note= /note=F: NKF /note= /note=SIF-BLAST: /note= /note=NKF, Albanese, 40, NCBI, 98%, 3e^-55] /note= /note=NKF, Albanese, 40, Phagesdb, 97%, 2e^-47] /note= /note=SIF-HHPred: [NKF, no matches with a probability above 90%] /note= /note=SIF-Syn: phage does not show synteny with albanese CDS 27978 - 28160 /gene="41" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_41" /note=Original Glimmer call @bp 27978 has strength 5.97 /note= /note=SSC: 27978-28160 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein SEA_ALBANESE_41 [Arthrobacter phage Albanese]],,NCBI, q1:s1 100.0% 3.21358E-35 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.543, -3.6079348339453126, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ALBANESE_41 [Arthrobacter phage Albanese]],,UYL86768,100.0,3.21358E-35 SIF-HHPRED: SIF-Syn: SIF-Syn: NKF - ChewChew, Christian, Dino, Fluke, Huckleberry, Lucy, MeganNoll, PitaDog, Riverdale, Wayne – none matched with 41 of Lakshmi, unknown function /note= /note=SSC: 27978, 28160 /note= /note=CP: no /note= /note=SCS: Glimmer only /note= /note=ST: NI /note= /note=BLAST-Start: Albanese 41, PhagesDB, 1:1, 100%, 1e-28. Albanese 41, NCBI, 1:1, 100%, 3e-35 /note= /note=Gap: 17 overlap /note= /note=LO: YES /note= /note=RBS: Kibler6, Karlin Medium, 2.543, -3.608, yes /note= /note=F: NKF /note= /note=SIF-BLAST: NKF /note= /note=SIF-HHPred: NFK, no matches with a probability above 90% /note= /note=SIF-Syn: NKF - ChewChew, Christian, Dino, Fluke, Huckleberry, Lucy, MeganNoll, PitaDog, Riverdale, Wayne – none matched with 41 of Lakshmi, unknown function /note= /note=For gene 41, gene 40 is downstream and gene 42, a Cas4 family exonuclease, have similarities between other phages. /note= /note=41 match with Dino’s 41, NKF, Fluke 41, NKF, Riverdale 41, NFK. Downstream, Gene 40, no known function, upstream, gene 42, cas4 family exonuclease. CDS 28138 - 29085 /gene="42" /function="exonuclease" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_42" /note=Original Glimmer call @bp 28138 has strength 12.09; Genemark calls start at 28138 /note= /note=SSC: 28138-29085 CP: yes SCS: both ST: SS BLAST-Start: [Cas4 family exonuclease [Arthrobacter phage Albanese]],,NCBI, q1:s1 100.0% 0.0 GAP: -23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.592, -3.504375086072296, no F: exonuclease SIF-BLAST: ,,[Cas4 family exonuclease [Arthrobacter phage Albanese]],,UYL86769,100.0,0.0 SIF-HHPRED: ATP-dependent DNA helicase (UvrD/REP); DNA, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; 3.5A {Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)},,,6PPU_A,92.6984,99.9 SIF-Syn: NKF, no matches with probability above 90% on HHPred but on PECAAN, DNA helicase, PECAAN, name unk, 6PPU_A, 92.6984%, 99.9 /note= /note=The Conserved Domain Database had only 2 results, both with low % identity and coverage, however one had a smaller e-value and was picked overall. /note= /note=SSC: 28138, 29085 /note= /note=CP: Yes /note= /note=SCS: Both /note= /note=ST: SS /note= /note=BLAST-Start: Albanese 42, NCBI, 1:1, 100%, 0.0. Albanese 42, PhagedDB, 1:1, 100%, 0.0 /note= /note=Gap: 23 (overlap) /note= /note=LO: yes /note= /note=RBS: (Kibler6, Karlin Medium, 2.592, -3.504, yes) /note= /note=F: Cas4 family exnuclease /note= /note=SIF-BLAST: Cas4 family nuclease, NCBI, Albanese 42, UYL86769, 100%. Cas4 family exonuclease, PhagesDB, Albanese 42, 100% /note= /note=SIF-HHPred: NKF, no matches with probability above 90% on HHPred but on PECAAN, DNA helicase, PECAAN, name unk, 6PPU_A, 92.6984%, 99.9 /note= /note=SIF-Syn: Cas4 family exonuclease /note= /note=39 ChewChew /note= /note=39 Christian /note= /note=42 Dino /note= /note=42 Fluke /note= /note=39 Huckleberry /note= /note=39 Lucy /note= /note=41 MeganNoll /note= /note=39 PitaDog /note= /note=42 Riverdale /note= /note=41 Wayne /note= /note=For gene 42, downstream is gene 41 with an unknown function and upstream is gene 43 with an unknown function. Gene 42 Lakshmi has many other phages with shared genes (all shown). CDS 29086 - 29319 /gene="43" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_43" /note=Original Glimmer call @bp 29086 has strength 6.28; Genemark calls start at 29086 /note= /note=SSC: 29086-29319 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDH59_gp44 [Arthrobacter phage Joann] ],,NCBI, q1:s10 100.0% 2.10529E-49 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.779, -5.613365555300441, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH59_gp44 [Arthrobacter phage Joann] ],,YP_009602724,89.5349,2.10529E-49 SIF-HHPRED: SIF-Syn: SIF-Syn: Riverdale 43, Fluke 43, Dino 43 match with Lakshmi 43, however for each the function is unknown. Downstream gene 42, Cas4 family exonuclease, upstream gene 44 RecA-like DNA recombinase /note= /note=SSC: 29086, 29319 /note= /note=CP: yes /note= /note=SCS: both /note= /note=ST: SS /note= /note=BLAST-Start: Joann 44, PDB, 1:10, 96%, 4e-40 Joann 44, NCBI, 1:10, 100%, 2e-49 /note= /note=Gap: 0 /note= /note=LO: Yes /note= /note=RBS: Kibler6, Karlin Medium, 1.779, -5.613, yes /note= /note=F: NKF /note= /note=SIF-BLAST: NKF /note= /note=SIF-HHPred: NKF, no matches with a probability above 90% /note= /note=SIF-Syn: Riverdale 43, Fluke 43, Dino 43 match with Lakshmi 43, however for each the function is unknown. Downstream gene 42, Cas4 family exonuclease, upstream gene 44 RecA-like DNA recombinase CDS 29420 - 30472 /gene="44" /function="RecA-like DNA recombinase" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_44" /note=Original Glimmer call @bp 29420 has strength 16.01; Genemark calls start at 29420 /note= /note=SSC: 29420-30472 CP: yes SCS: both ST: SS BLAST-Start: [Sak4-like ssDNA annealing protein [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 0.0 GAP: 100 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.629, -4.113180079823027, no F: RecA-like DNA recombinase SIF-BLAST: ,,[Sak4-like ssDNA annealing protein [Arthrobacter phage Joann] ],,YP_009602725,100.0,0.0 SIF-HHPRED: RecA protein; Recombination, Radioresistance, DNA-repair, ATPase, DNA-binding protein, DNA BINDING PROTEIN; HET: AGS; 2.5A {Deinococcus radiodurans} SCOP: c.37.1.11, d.48.1.1,,,1XP8_A,70.8571,99.8 SIF-Syn: SIF-Syn: RecA-like DNA recombinase, downstream gene 43 unknown function similar to Dino, Riverdale, and Fluke, upstream gene 45, unknown function similar to Dino, Riverdale, Fluke. /note= /note=SSC: 29420, 30472 /note= /note=CP: yes /note= /note=SCS: Both /note= /note=ST: SS /note= /note=BLAST-Start: Joann 45, PDB, 1:1, 100%, 0.0 Joann 45, NCBI, 1:1, 100%, 0.0 /note= /note=Gap: 100 /note= /note=LO: yes /note= /note=RBS: Kibler6, Karlin Medium, 2.629, -4.113, yes /note= /note=F: RecA-like DNA recombinase /note= /note=SIF-BLAST: RecA-like DNA recombinase, Joann 45, PDB, 186040, 100%, 0.0. ssDNA annealing protein Joann 45, NCBI, YP_009602725.1, 100% 0.0 /note= /note=SIF-HHPred: RecA-like DNA recombinase, HHPred, /note= /note=SIF-Syn: RecA-like DNA recombinase, downstream gene 43 unknown function similar to Dino, Riverdale, and Fluke, upstream gene 45, unknown function similar to Dino, Riverdale, Fluke. CDS 30544 - 31056 /gene="45" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_45" /note=Original Glimmer call @bp 30544 has strength 13.27; Genemark calls start at 30544 /note= /note=SSC: 30544-31056 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein KDI97_gp46 [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 2.69643E-123 GAP: 71 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.273, -4.390184094340439, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDI97_gp46 [Arthrobacter phage GreenHearts] ],,YP_010049966,100.0,2.69643E-123 SIF-HHPRED: DUF669 ; Protein of unknown function (DUF669),,,PF05037.16,78.8235,99.7 SIF-Syn: SIF-Syn: Lakshmi 45, NKF, Lakshmi 44, RecA-like DNA recobinase, Lakshmi 46, DNA Primase/polymerase/helicase /note= /note=SSC: 30544, 31056 /note= /note=CP: yes /note= /note=SCS: both /note= /note=ST: SS /note= /note=BLAST-Start: Nubia 45, PDB, 1:1, 100%, 2e-97. GreenHearts 46, NCBI, 1:1, 100%, /note= /note=3e-123 /note= /note=Gap: 71 /note= /note=LO: Yes /note= /note=RBS: Kibler6, Karlin Medium, 2.273,-4.390, yes /note= /note=F: NKF /note= /note=SIF-BLAST: NKF, PDB, Nubia 45, 272332, 100%, 2e-97. NKF, NCBI, Greenhearts 46, YP_010049966.1, 100%, 3e-123 /note= /note=SIF-HHPred: NKF, HHPred, PF05037.16, 78.8235, 99.7 /note= /note=SIF-Syn: Lakshmi 45, NKF, Lakshmi 44, RecA-like DNA recobinase, Lakshmi 46, DNA Primase/polymerase/helicase /note= /note=With gene 45 of Lakshmi being similar to BigMack 42, Christian 42, Dino 45, Fluke 45, GreenHearts 46, MamaPearl 43, Potatoes 44, Riverdale 45, Suppi 44, and Wayne 44, which all have no function, it is concluded that gene 45 Lakshmi has NKF. CDS 31127 - 33757 /gene="46" /function="DNA primase/polymerase/helicase" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_46" /note=Original Glimmer call @bp 31148 has strength 10.2; Genemark calls start at 31589 /note= /note=SSC: 31127-33757 CP: yes SCS: both-cs ST: NI BLAST-Start: [DNA polymerase/primase [Arthrobacter phage Oxynfrius] ],,NCBI, q1:s1 100.0% 0.0 GAP: 70 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.379, -3.8137921535956054, no F: DNA primase/polymerase/helicase SIF-BLAST: ,,[DNA polymerase/primase [Arthrobacter phage Oxynfrius] ],,YP_010050398,99.8858,0.0 SIF-HHPRED: SIF-Syn: SIF-Syn: DNA primase/polymerase/helicase seen from BigMack 43, Christian 43, Dino 46, Fluke 46, MamaPearl 44, Potatoes 45, Riverdale 46, Suppi 45,Wayne 45 /note= /note=SSC: 31127, 33,757 /note= /note=CP: yes /note= /note=SCS: Both - neither /note= /note=ST: NI /note= /note=BLAST-Start: Oxynfrius 46, PDB, 1:8, 99%, 0.0. Oxynfrius 46, NCBI, 1:8, 100% 0.0 – on PDB and NCBI its Lakshmi 47 /note= /note=Gap: 70 /note= /note=LO: yes /note= /note=RBS: Kibler6, Karlin Medium, 2.379, -3.814, yes /note= /note=F: dna primase/polymersase/helicase /note= /note=SIF-BLAST: DNA primase/polymerase/helicase, PDB, Oxynfrius 46, 280604. DNA polymerase/primase, NCBI, Oxyngfrius 46, YP_010050398.1 /note= /note=SIF-HHPred: Active Helicase, HHPred, 5DGK_A, 60.2992, 100 /note= /note=SIF-Syn: DNA primase/polymerase/helicase seen from BigMack 43, Christian 43, Dino 46, Fluke 46, MamaPearl 44, Potatoes 45, Riverdale 46, Suppi 45,Wayne 45 /note= /note=Gene 45, NKF, Gene 47, NKF CDS 34135 - 34368 /gene="47" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_47" /note=Original Glimmer call @bp 34135 has strength 7.32; Genemark calls start at 34135 /note= /note=SSC: 34135-34368 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDH59_gp48 [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 1.21021E-49 GAP: 377 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.182, -2.7645180226256008, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH59_gp48 [Arthrobacter phage Joann] ],,YP_009602728,100.0,1.21021E-49 SIF-HHPRED: SIF-Syn: SIF-Syn: (NKF, (according to GreenHearts, Joann, Oxynfrius- upstream; DNA primase/ ploymerase/ helicase downstream; DNA polymerase 1) /note= /note=SSC: 34135/34368 /note= /note=CP: yes /note= /note=SCS: both /note= /note=ST: NI-Most common start is not in the sequence /note= /note=BLAST-Start: (Oxynfrius, 47, phagesdb, Q1:S1, 100%, 1e-39, ) /note= /note=Joann, 48, NCBI, Q1:S1, 100%, 1e-49) /note= /note=Gap: 377 /note= /note=LO: no /note= /note=RBS: Kibler6, Karlin Medium, 14, 1.876, -5.488, no /note= /note=SIF-BLAST:(NKF, NCBI, Joann, 48, YP_009602, 100%, 1e-49) /note= /note=NFK, phagesdb, Oxynfrius, 47, 1e-39) /note= /note=SIF_HHPred (NKF, no matches with probability above 90%) CDS 34368 - 36476 /gene="48" /function="DNA polymerase I" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_48" /note=Original Glimmer call @bp 34368 has strength 14.57; Genemark calls start at 34377 /note= /note=SSC: 34368-36476 CP: yes SCS: both-gl ST: NI BLAST-Start: [DNA polymerase I [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.503, -3.630723714250106, no F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Arthrobacter phage GreenHearts] ],,YP_010049969,99.7151,0.0 SIF-HHPRED: Apicoplast DNA polymerase; DNA polymerase, exonulease, apicoplast, Plasmodium falciparum, REPLICATION, TRANSFERASE; HET: PEG, EDO; 2.5A {Plasmodium falciparum (isolate 3D7)},,,7SXQ_A,99.0028,100.0 SIF-Syn: SIF-Syn: DNA polymerase 1, downstream: synthase upstream: NKF, greenhearts, oxynfrius, Albanese /note= /note=SSC: 34368/36476 /note= /note=CCS: no /note= /note=SCS: glimmer /note= /note=overlap: 1 /note= /note=LO: no /note= /note=BLAST START: (GreenHearts, 49, phagesdb, Q1:S1, 99%, 0) /note= /note=GreenHearts, NCBI, Q1:S1, 99.2878%, 0) /note= /note=SIF-BLAST: (DNA Polymerase, GreenHearts, NCBI, YP_010049969, 99.7151, 100,0) /note= /note=DNA Polymerase 1,GreenHearts, phagesdb,99,0) /note= /note=SIF-HHPred: (DNA Polymerase, PDB, Plasmodium falciparum, 7SXQ, 99.0028, 100) CDS 36542 - 37675 /gene="49" /function="adenylosuccinate synthetase PurA-like" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_49" /note=Original Glimmer call @bp 36542 has strength 14.83; Genemark calls start at 36554 /note= /note=SSC: 36542-37675 CP: yes SCS: both-gl ST: SS BLAST-Start: [PurA-like adenylosuccinate synthetase [Arthrobacter phage Albanese]],,NCBI, q1:s1 100.0% 0.0 GAP: 65 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.73, -3.1513923047253267, no F: adenylosuccinate synthetase PurA-like SIF-BLAST: ,,[PurA-like adenylosuccinate synthetase [Arthrobacter phage Albanese]],,UYL86776,100.0,0.0 SIF-HHPRED: c.37.1.10 (A:) Adenylosuccinate synthetase, PurA {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]} | 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_d1p9ba_,98.939,100.0 SIF-Syn: SIF-SYN: (adenylosuccinate synthetase PurA, upstream:DNA polymerase, downstream: NKF, Albanese 49) /note= /note=GENE 51 phages db /note= /note= /note= /note=SSC:36542/ 37675 /note= /note=CP: yes /note= /note=SCS: glimmer /note= /note=ST: SS /note= /note=BLAST-Start: (Albanese, 49, phagesdb, Q1:S1, 100%, 0) /note= /note=Albanese, 49. NCBI, Q1:S1, 100%, 0) /note= /note=Gap: 65 /note= /note=LO: yes /note= /note=RBS: (Kibler6, Karlin Medium, 2,73, -3.151, yes) /note= /note=SIF-BLAST: (PurA-like adenylosuccinate synthetase, phagesdb, Albanese, 0) /note= /note=PurA-like adenylosuccinate synthetase, NCBI, Albanese, UYL86776.1,0) /note= /note=SIF-HHPred: Adenylosuccinate synthetase, PurA, PDB, Plasmodium falciparum, SCOP_d1p9ba_, 98.939, 100) CDS 37679 - 38389 /gene="50" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_50" /note=Original Glimmer call @bp 37679 has strength 11.19; Genemark calls start at 37775 /note= /note=SSC: 37679-38389 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein KDJ04_gp50 [Arthrobacter phage Nubia] ],,NCBI, q34:s3 86.017% 1.00819E-128 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.369, -6.094669753659028, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDJ04_gp50 [Arthrobacter phage Nubia] ],,YP_010050341,96.0976,1.00819E-128 SIF-HHPRED: SIF-Syn: SIF-Syn: phage used to compare: Nubia, NKF, upstream: adenylosuccinate synthetase PurA-like) /note= /note=GENE 52 on phagesdb /note= /note= /note= /note=SSC: 37679/38389 /note= /note=CP: yes /note= /note=SCS: glimmer /note= /note=ST: NI /note= /note=Blast-Start: (Nubia, 50, phagesdb, Q34:S3, 96%, e-111) /note= /note=Nubia, 50, NCBI, Q34:S3, 86%, 1e-128) /note= /note=Gap:108 /note= /note=LO: yes /note= /note=RBS: (Kibler6, Karlin Medium, 1.031, -7.198) /note= /note=SIF-BLAST: (NKF, phagesdb, Nubia, 50, 96%, e-111) /note= /note=hypothetical protein -NKF, NCBI, Nubia, 50,YP_010050341.1, 96.06%, 1e-128) /note= /note=SIF-HHPred: NKF CDS 38389 - 38610 /gene="51" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_51" /note=Original Glimmer call @bp 38389 has strength 11.12; Genemark calls start at 38389 /note= /note=SSC: 38389-38610 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein KDI97_gp52 [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 1.46815E-45 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.645, -5.72145296840978, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDI97_gp52 [Arthrobacter phage GreenHearts] ],,YP_010049972,100.0,1.46815E-45 SIF-HHPRED: SIF-Syn: SIF-SYN: (NKF, downstream: deoxyundine triphosphatase) phage: greenhearts /note= /note=GENE 53 /note= /note=SSC:38389/38610 /note= /note=CP:yes SCS:both /note= /note=ST:SS /note= /note=BLAST-Start: (GreenHearts, 52, phagesdb, Q1:S1, 100%, 8e-36) /note= /note=GreenHearts, 52,NCBI, 100, 1e-45) /note= /note=Gap: -1 /note= /note=LO: yup /note= /note=RBS: (Kibler6, Karlin Medium, 1.645, -5.721, yes) /note= /note= /note= /note=SIF-BLAST: (GreenHearts, 52, phagesdb, NKF, 100%, 8e-36) /note= /note=GreenHearts, 52, NCBI, NKF, 100%, YP_010049972.1, 1e-45) /note= /note= /note= /note=SIF-HHPred:NKF CDS 38607 - 39518 /gene="52" /function="deoxyuridine triphosphatase" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_52" /note=Original Glimmer call @bp 38607 has strength 12.1; Genemark calls start at 38607 /note= /note=SSC: 38607-39518 CP: yes SCS: both ST: SS BLAST-Start: [dCTP deaminase [Arthrobacter phage Greenhouse] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.781, -3.6146798363680817, yes F: deoxyuridine triphosphatase SIF-BLAST: ,,[dCTP deaminase [Arthrobacter phage Greenhouse] ],,YP_010050035,99.3399,0.0 SIF-HHPRED: Deoxyuridine 5`-triphosphate nucleotidohydrolase; trimer, beta barrel, apo structure, dUTP pyrophosphatase, Saccharomyces cerevisiae, molecular replacement, Hydrolase, Nucleotide metabolism, Phosphoprotein; HET: NA, EDO, PEG, CL, SO4; 2.0A {Saccharomyces cerevisiae} SCOP: b.85.4.0,,,3HHQ_J,49.1749,100.0 SIF-Syn: SIF-SYN: deoxyuridine triphosphatase, both upstream and downstream: NKF /note= /note=GENE 54 ON PHAGESDB /note= /note= /note= /note=SSC: 38607/39518 /note= /note=CP: yes /note= /note=SCS: both /note= /note=ST: SS /note= /note=BLAST-START: (GreenHouse, 53, phagesdb, Q1:S1, 99%, e-173) /note= /note=GreenHouse, 53, NCBI, Q1:S1, 100%, 0) /note= /note=LO: no /note= /note=RBS: Kibler6, Karlin Median, 2.781, -3.615) /note= /note=SIF-BLAST: (deoxyuridine triphosphatase, phagesdb, GreenHouse, 53, 99%,e-173) /note= /note=dCTP deaminase, NCBI, GreenHouse, 100%, YP_010050035.1, 0) /note= /note=SIF-HHPred: Deoxyuridine 5`-triphosphate nucleotidohydrolase, PDB, Saccharomyces cerevisiae, 3HHQ_J, 99.96%, ) CDS complement (39570 - 39827) /gene="53" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_53" /note=Original Glimmer call @bp 39827 has strength 16.6; Genemark calls start at 39827 /note= /note=SSC: 39827-39570 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein KDJ05_gp53 [Arthrobacter phage Oxynfrius] ],,NCBI, q1:s1 100.0% 5.22474E-55 GAP: 121 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.268, -1.9310779259753799, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDJ05_gp53 [Arthrobacter phage Oxynfrius] ],,YP_010050405,100.0,5.22474E-55 SIF-HHPRED: SIF-Syn: SIF-SYN: NKF, phages used to compare: NUBIA, OXYNFRIUS: upstream: deoxyuridine triphosphatase) /note= /note=GENE: 55 on phagesdb /note= /note= /note= /note=SSC: 39570/39827 /note= /note=CP: yes /note= /note=SCS: both /note= /note=ST: SS /note= /note=BLAST-START: (Oxynfrius, 53, phagesdb, Q1:S1, 100%, 1e-44) /note= /note=Oxynfrius, 53, NCBI, Q1:S1, 100%, 5e-55) /note= /note=Gap: 121 /note= /note=LO: yes /note= /note=RBS: (Kiblre6, Karlin Medium, 3.268, -1.931, yes) /note= /note=SIF-BLAST: (NKF, Oxynfrius, 53, phagesdb, 100%, 1e-44) /note= /note=NKF, Oxynfrius, 53, NCBI, 100%, YP_010050405.1, 5e-55) /note= /note=SIF-HHPred: NKF CDS complement (39949 - 40182) /gene="54" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_54" /note=Original Glimmer call @bp 40182 has strength 12.58; Genemark calls start at 40182 /note= /note=SSC: 40182-39949 CP: yes SCS: both ST: SS BLAST-Start: [HTH DNA binding domain protein [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 4.09592E-49 GAP: 124 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.268, -1.9310779259753799, yes F: hypothetical protein SIF-BLAST: ,,[HTH DNA binding domain protein [Arthrobacter phage GreenHearts] ],,YP_010049975,100.0,4.09592E-49 SIF-HHPRED: DUF2774 ; Protein of unknown function (DUF2774),,,PF11242.11,40.2597,97.7 SIF-Syn: SIF-SYN: phages used go compare: GreenHouse and GreenHearts /note= /note=SSC: 39949 / 40182 /note= /note=CP: yes /note= /note=SCS: both /note= /note=ST: SS /note= /note=BLAST-START: (GreenHouse, 56, phagesdb, Q1:S1, 100%, 8e-39) /note= /note=GreenHearts, NCBI, Q1:S1, 98.70%,4e-49) /note= /note=GAP: 124 /note= /note=LO: yes /note= /note=RBS: (Kibler6, Karlin Medium, 3.268, -1.931, yes) /note= /note=SIF-BLAST: (NKF, phagesdb, GreenHouse, 56, 100%, 8e-39) /note= /note=DNA binding domain protein, NCBI, GreenHearts, 98.70%, YP_010049975.1, 4e-49) /note= /note=SIF-HHPred: NKF, ,DUF2774, PF11242.11, 40.2597, 97.7%) CDS complement (40307 - 40894) /gene="55" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_55" /note=Original Glimmer call @bp 40894 has strength 12.66; Genemark calls start at 40909 /note= /note=SSC: 40894-40307 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein KDI99_gp56 [Arthrobacter phage Greenhouse] ],,NCBI, q4:s19 98.4615% 5.93814E-133 GAP: 163 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.026, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDI99_gp56 [Arthrobacter phage Greenhouse] ],,YP_010050038,89.5238,5.93814E-133 SIF-HHPRED: SIF-Syn: NKF, upstream/downstream /note= /note=SSC: [40894, 40307] CP: [No] SCS: [GeneMark-CS] ST: [SS] BLAST-Start: [Nubia_55, Phagesdb, Q1:S1, 91%, 1e-97] Gap: [163 bp] LO: [no] RBS: [Kibler6, KarlinMedium, -2.443, 3.026, yes] F: [NKF] SIF-BLAST: [NKF, NCBI, Nubia_55, YP_010050346, 91.79%, 1e-111] [NKF, Phagesdb, Nubia_55, 91%, 1e-97] SIF-HHPred: [NKF, no matches with a probability above 90%] SIF-Syn: [NKF, upstream/downstream] /note= /note=3rd start matches glimmer Q:1 S:1 with Albanese CDS complement (41058 - 41603) /gene="56" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_56" /note=Original Glimmer call @bp 41603 has strength 12.51; Genemark calls start at 41603 /note= /note=SSC: 41603-41058 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein KDJ04_gp56 [Arthrobacter phage Nubia] ],,NCBI, q1:s1 100.0% 6.51535E-129 GAP: 103 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.026, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDJ04_gp56 [Arthrobacter phage Nubia] ],,YP_010050347,100.0,6.51535E-129 SIF-HHPRED: TUBR; TRANSCRIPTION, TUBULIN, FTSZ, SEGREGATION, PARTITION; HET: MSE; 3.5A {BACILLUS MEGATERIUM},,,4ASN_B,53.5912,97.1 SIF-Syn: NKF, upstream/downstream /note= /note=SSC: [41603, 41058] CP: [Yes] SCS: [Both] ST: [SS] BLAST-Start: [Nubia_56, Phagesdb, Q1:S1, 100%, 3e-99] Gap: [103 bp] LO: [Yes] RBS: [Kibler6, KarlinMedium, 3.026, -2.443, yes] F: [NFK] SIF-BLAST: [NKF, NCBI, Nubia_56, YP_010050347, 100%, 7e-129] [NKF, Phagesdb, Nubia_56, 100%, 3e-99] SIF-HHPred: [NKF, e-value too high] SIF-Syn: [NKF, upstream/downstream] CDS complement (41707 - 42060) /gene="57" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_57" /note=Original Glimmer call @bp 42060 has strength 5.37; Genemark calls start at 42060 /note= /note=SSC: 42060-41707 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein FDH59_gp58 [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 1.25509E-81 GAP: 288 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.268, -2.0720764396375664, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDH59_gp58 [Arthrobacter phage Joann] ],,YP_009602738,100.0,1.25509E-81 SIF-HHPRED: SIF-Syn: NKF, upstream/downstream /note= /note=SSC: [42060, 41707] CP: [Yes] SCS: [Both] ST: [SS] BLAST-Start: [Oxynfrius_57, Phagesdb, Q1:S1, 100%, 2e-64] Gap: [270 bp] LO: [Yes] RBS: [Kibler6, KarlinMedium, 3.268, -2.072, yes] F: [NKF] SIF-BLAST: [NKF, NCBI, Joann_58, YP_009602738, 100%, 1e-81] [NKF, Phagesdb, Oxynfrius_57, 100%, 2e-64] SIF-HHPred: [NKF, no probability above 90%] SIF-Syn: [NKF, upstream/downstream] CDS 42349 - 42543 /gene="58" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_58" /note=Original Glimmer call @bp 42349 has strength 4.97; Genemark calls start at 42331 /note= /note=SSC: 42349-42543 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein KDI97_gp59 [Arthrobacter phage GreenHearts] ],,NCBI, q1:s7 100.0% 1.16521E-36 GAP: 288 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.655, -3.2921018957843318, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDI97_gp59 [Arthrobacter phage GreenHearts] ],,YP_010049979,91.4286,1.16521E-36 SIF-HHPRED: SIF-Syn: NFK, upstream/downstream /note= /note=SSC: [42349, 42543] CP: [No] SCS: [GeneMark] ST: [NI] BLAST-Start: [Greenhouse_59, Phagesdb, Q1:S1, 98%, 7e-29] Gap: [288 bp] LO: [No] RBS: [Kibler6, KarlinMedium, 2.655, -3.292, yes] F: [NFK] SIF-BLAST: [NFK, NCBI, Greenhouse_59, YP_010050041, 98.44%, 1e-36] [NFK, Phagesdb, Greenhouse_59, 98%, 7e-29] SIF-HHPred: [NFK, no probability above 90%] SIF-Syn: [NFK, upstream/downstream] CDS 42540 - 43304 /gene="59" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_59" /note=Original Glimmer call @bp 42540 has strength 9.54; Genemark calls start at 42540 /note= /note=SSC: 42540-43304 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein KDI97_gp60 [Arthrobacter phage GreenHearts] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.421, -5.985256925638024, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDI97_gp60 [Arthrobacter phage GreenHearts] ],,YP_010049980,100.0,0.0 SIF-HHPRED: SIF-Syn: NKF, upstream/downstream /note= /note=SSC: [42540, 43304] CP: [Yes] SCS: [Both] ST: [NI] BLAST-Start: [Greenhearts_60, PhagesDB, Q1:S1, 100%, e-149] Overlap: [4 bp] LO: [Yes] RBS: [Kibler6, KarlinMedium, 1.421, -5.985, no] F: [NKF] SIF-BLAST: [NKF, NCBI, Greenhearts_60, YP_010049980, 100%, 0] [NKF, PhagesDB, Greenhearts_60, 100%, e-149] SIF-HHPred: [NKF, no probability over 90%] SIF-Syn: [NKF, upstream/downstream] CDS 43353 - 43520 /gene="60" /function="hypothetical protein" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_60" /note=Original Glimmer call @bp 43353 has strength 6.72; Genemark calls start at 43347 /note= /note=SSC: 43353-43520 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein KDJ04_gp60 [Arthrobacter phage Nubia] ],,NCBI, q1:s1 100.0% 1.40498E-22 GAP: 48 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.105, -2.417348306996335, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KDJ04_gp60 [Arthrobacter phage Nubia] ],,YP_010050351,85.7143,1.40498E-22 SIF-HHPRED: SIF-Syn: NKF, upstream/downstream /note= /note=SSC: [43353, 43520] CP: [Yes] SCS: [Glimmer] ST: [NI] BLAST-Start: [Nubia_60, PhagesDB, Q1:S1, 81%, 2e-19] Gap: [48 bp] LO: [No] RBS: [Kibler6, Karlin Medium, 3.105, -2.417, yes] F: [NKF] SIF-BLAST: [NKF, NCBI, Nubia_60, YP_010050351, 85%, 1e-22] [NKF, PhagesDB, Nubia_60, 81%, 2e-19] SIF-HHPred: [NKF, no probability over 90%] SIF-Syn: [NKF, upstream/downstream] CDS 43678 - 43938 /gene="61" /function="HNH endonuclease" /product="Hypothetical Protein" /locus tag="SEA_LAKSHMI_61" /note=Original Glimmer call @bp 43678 has strength 7.88; Genemark calls start at 43678 /note= /note=SSC: 43678-43938 CP: no SCS: both ST: NI BLAST-Start: [HNH endonuclease [Arthrobacter phage Joann] ],,NCBI, q1:s1 100.0% 2.26511E-57 GAP: 157 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.85, -2.956683020935497, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage Joann] ],,YP_009602743,100.0,2.26511E-57 SIF-HHPRED: HNH endonuclease; Thermophilic bacteriophage, HNH Endonuclease, DNA nicking, HYDROLASE; 1.52A {Geobacillus virus E2},,,5H0M_A,72.093,98.0 SIF-Syn: HNH endonuclease, Oxynfrius_62 /note= /note=SSC: [43678, 43938] CP: [Yes] SCS: [Both] ST: [SS] BLAST-Start: [Oxynfrius_62, PhagesDB, Q1:S1, 100%, 5e-49] Gap: [157 bp] LO: [Yes] RBS: [Kibler6, KarlinMedium, 2.85, -2.957, yes] F: [HNH endonuclease] SIF-BLAST: [HNH endonuclease, NCBI, Oxynfrius_62, YP_009602743, 100%, 2e-57] [HNH endonuclease, PhagesDB, Oxynfrius_62, 100%, 5e-49] SIF-HHPred: [HNH endonuclease, HHPred, 5H0M_A, 98%] SIF-Syn: [HNH endonuclease, Oxynfrius_62] BASE COUNT 9287 a 13177 c 13607 g 7947 t ORIGIN