CDS 230 - 1429 /gene="1" /product="gp1" /function="ParB-like nuclease domain" /locus tag="Kovu_1" /note=Original Glimmer call @bp 230 has strength 11.41; Genemark calls start at 230 /note=SSC: 230-1429 CP: yes SCS: both ST: NI BLAST-Start: [ParB-like nuclease domain protein [Arthrobacter phage Edmundo]],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.44, -3.5925599723783583, no F: ParB-like nuclease domain SIF-BLAST: ,,[ParB-like nuclease domain protein [Arthrobacter phage Edmundo]],,QGJ88076,83.9196,0.0 SIF-HHPRED: ParB family protein; DNA-binding protein, CTP, Myxococcus, DNA-segregation, DNA BINDING PROTEIN; HET: UFQ, GOL; 1.7A {Myxococcus xanthus (strain DK 1622)},,,7BNR_B,31.3283,99.3 SIF-Syn: Gene located in the same area in pham members. /note=Start called 100% of the time when present, best RBS score by far. Homologous genes in pham all call ParB-like nuclease domain as function. CDS 1429 - 1644 /gene="2" /product="gp2" /function="Hypothetical Protein" /locus tag="Kovu_2" /note=Original Glimmer call @bp 1429 has strength 13.83; Genemark calls start at 1429 /note=SSC: 1429-1644 CP: no SCS: both ST: NI BLAST-Start: GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.36, -5.932673762002171, no F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: DUF5327 ; Family of unknown function (DUF5327),,,PF17261.6,18.3099,58.0 SIF-Syn: synteny is unknown due to the gene being an orpham. Gene of similar size in same place in Wheelbite. CDS 1646 - 1930 /gene="3" /product="gp3" /function="Hypothetical Protein" /locus tag="Kovu_3" /note=Original Glimmer call @bp 1646 has strength 7.52; Genemark calls start at 1646 /note=SSC: 1646-1930 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_WALTZ_3 [Arthrobacter phage Waltz]],,NCBI, q25:s8 63.8298% 2.77442E-5 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.44, -3.513874779476501, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_WALTZ_3 [Arthrobacter phage Waltz]],,ATW59881,49.2958,2.77442E-5 SIF-HHPRED: SIF-Syn: Based on phages Waltz and Shrooms, we can expect a gene to be present in this area of the genome but both Waltz and Shrooms have slightly different proteins nearby which suggests some variation in function. /note=Protein is an orpham. CDS 2007 - 3386 /gene="4" /product="gp4" /function="Hypothetical Protein" /locus tag="Kovu_4" /note=Original Glimmer call @bp 2007 has strength 11.1; Genemark calls start at 2007 /note=SSC: 2007-3386 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein KMD21_gp04 [Arthrobacter phage LiSara] ],,NCBI, q176:s184 57.7342% 4.16755E-9 GAP: 76 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.292, -3.773970443115436, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein KMD21_gp04 [Arthrobacter phage LiSara] ],,YP_010082517,23.6111,4.16755E-9 SIF-HHPRED: SIF-Syn: Orpham, but similar lengths in general area of best matches CDS 3470 - 4075 /gene="5" /product="gp5" /function="ParB-like nuclease domain" /locus tag="Kovu_5" /note=Original Glimmer call @bp 3470 has strength 12.34; Genemark calls start at 3452 /note=SSC: 3470-4075 CP: no SCS: both-gl ST: NI BLAST-Start: [ParB-like nuclease domain protein [Arthrobacter phage Shrooms]],,NCBI, q1:s16 96.5174% 1.58533E-101 GAP: 83 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.652, -5.986297339340146, no F: ParB-like nuclease domain SIF-BLAST: ,,[ParB-like nuclease domain protein [Arthrobacter phage Shrooms]],,ASR83886,75.463,1.58533E-101 SIF-HHPRED: ParB family protein; DNA-binding protein, CTP, Myxococcus, DNA-segregation, DNA BINDING PROTEIN; HET: UFQ, GOL; 1.7A {Myxococcus xanthus (strain DK 1622)},,,7BNR_B,67.6617,99.6 SIF-Syn: A lot of synteny with other phages in Pham CDS 4075 - 5169 /gene="6" /product="gp6" /function="PAPS reductase-like domain" /locus tag="Kovu_6" /note=Original Glimmer call @bp 4075 has strength 12.0; Genemark calls start at 4075 /note=SSC: 4075-5169 CP: no SCS: both ST: NI BLAST-Start: [phosphoadenosine phosphosulfate reductase [Arthrobacter phage Laroye] ],,NCBI, q1:s1 98.9011% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.959, -4.5746484857543, no F: PAPS reductase-like domain SIF-BLAST: ,,[phosphoadenosine phosphosulfate reductase [Arthrobacter phage Laroye] ],,YP_009602996,93.6639,0.0 SIF-HHPRED: Phosphoadenosine phosphosulfate reductase; Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, CysH, OXIDOREDUCTASE; HET: P6G, PG4; 1.9A {Vibrio vulnificus (strain CMCP6)},,,6VPU_B,61.2637,99.8 SIF-Syn: Found in this region in other AL phages. CDS 5156 - 5716 /gene="7" /product="gp7" /function="ParB-like dsDNA partitioning protein" /locus tag="Kovu_7" /note=Original Glimmer call @bp 5156 has strength 12.35; Genemark calls start at 5156 /note=SSC: 5156-5716 CP: no SCS: both ST: NI BLAST-Start: [ParB-like partition protein [Arthrobacter phage Laroye] ],,NCBI, q6:s7 95.1613% 1.25608E-108 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.906, -2.970161406017234, yes F: ParB-like dsDNA partitioning protein SIF-BLAST: ,,[ParB-like partition protein [Arthrobacter phage Laroye] ],,YP_009602997,89.1892,1.25608E-108 SIF-HHPRED: ParB family protein; DNA-binding protein, CTP, Myxococcus, DNA-segregation, DNA BINDING PROTEIN; HET: UFQ, GOL; 1.7A {Myxococcus xanthus (strain DK 1622)},,,7BNR_B,80.6452,99.8 SIF-Syn: There is a similarity with the gene that precedes this one in all other homologous phages. /note=Start 4 /note= Found in 1 of 55 ( 1.8% ) of genes in pham. No Manual Annotations of this start. Called 100.0% of time when present. Phage (with cluster) where this start called: Kovu_7 (AL) CDS 5694 - 6116 /gene="8" /product="gp8" /function="acetyltransferase" /locus tag="Kovu_8" /note=Original Glimmer call @bp 5694 has strength 11.41; Genemark calls start at 5694 /note=SSC: 5694-6116 CP: no SCS: both ST: NI BLAST-Start: [GNAT family N-acetyltransferase [Chthonomonadaceae bacterium]],,NCBI, q1:s1 92.8571% 1.0912E-10 GAP: -23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.757, -3.4175091270247986, no F: acetyltransferase SIF-BLAST: ,,[GNAT family N-acetyltransferase [Chthonomonadaceae bacterium]],,HLK60326,51.2195,1.0912E-10 SIF-HHPRED: GCN5-related N-acetyltransferase; N-Acyltransferase superfamily, Structural Genomics, PSI-Biology, Midwest Center for Structural Genomics, MCSG, PFAM:PF00583, putative acetyltransferase, transferase; HET: MSE; 1.37A {Kribbella flavida},,,4H89_A,96.4286,99.8 SIF-Syn: While synteny not known due to orpham status, equivalent gene in related phages Wheelbite and Edmundo have a methyltransferase at this location, as well as being preceded by a Hypothetical protein in pham 85699 and followed by a gene in pham 6141 /note=While an Orpham, HHPred results highly implicate this gene being an acetyl transferase. CDS 6116 - 6694 /gene="9" /product="gp9" /function="terminase, small subunit" /locus tag="Kovu_9" /note=Original Glimmer call @bp 6116 has strength 11.08; Genemark calls start at 6116 /note=SSC: 6116-6694 CP: yes SCS: both ST: NI BLAST-Start: [terminase small subunit [Arthrobacter phage Edmundo]],,NCBI, q1:s1 97.3958% 1.6093E-94 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.502, -4.226420930929867, no F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Arthrobacter phage Edmundo]],,QGJ88083,83.9572,1.6093E-94 SIF-HHPRED: Phage_term_sma ; Putative bacteriophage terminase small subunit,,,PF07141.15,78.125,99.4 SIF-Syn: Gene is found in same area in homologous genes in pham. /note=Start is called 100% of the time when present, and has one of the best RBS scores without losing coding potential. Top HHPred and NCBI blast hits are terminase small subunits, including Edmundo which is in the same pham. CDS 6744 - 8342 /gene="10" /product="gp10" /function="terminase" /locus tag="Kovu_10" /note=Original Glimmer call @bp 6744 has strength 10.05; Genemark calls start at 6744 /note=SSC: 6744-8342 CP: no SCS: both ST: NI BLAST-Start: [terminase large subunit [Arthrobacter phage Wheelbite] ],,NCBI, q1:s21 97.3684% 0.0 GAP: 49 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.3, -3.8183153089559627, no F: terminase SIF-BLAST: ,,[terminase large subunit [Arthrobacter phage Wheelbite] ],,YP_010082718,87.5926,0.0 SIF-HHPRED: Gene 2 protein; DNA packaging, terminase, ATPase, nuclease, ATP binding, Magnesium binding, VIRAL PROTEIN; 1.69A {Shigella phage Sf6},,,4IDH_A,86.6541,100.0 SIF-Syn: CDS 8435 - 8806 /gene="11" /product="gp11" /function="Hypothetical Protein" /locus tag="Kovu_11" /note=Original Glimmer call @bp 8435 has strength 15.59; Genemark calls start at 8435 /note=SSC: 8435-8806 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein KMD23_gp11 [Arthrobacter phage Wheelbite] ],,NCBI, q24:s13 79.6748% 1.81462E-29 GAP: 92 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.906, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein KMD23_gp11 [Arthrobacter phage Wheelbite] ],,YP_010082719,57.377,1.81462E-29 SIF-HHPRED: DUF3037 ; Protein of unknown function (DUF3037),,,PF11236.12,17.8862,75.3 SIF-Syn: Has some synteny, gene before (10) matches, but the next gene (12) does not match that of in the other genes in the pham /note=- start 5 includes 100% of genes in pham /note=- No change, start is called by both glimmer and Genemark, includes all coding potential, and is found in 100% of genes in pham CDS 8859 - 9041 /gene="12" /product="gp12" /function="Hypothetical Protein" /locus tag="Kovu_12" /note=Original Glimmer call @bp 8859 has strength 7.83; Genemark calls start at 8859 /note=SSC: 8859-9041 CP: yes SCS: both ST: NI BLAST-Start: GAP: 52 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.89, -3.005970110175159, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: Dynactin subunit 3; Dynactin, Complex, Scaffold, Cytoskeleton, STRUCTURAL PROTEIN; HET: ATP, ADP; 3.8A {Sus scrofa},,,6ZNL_O,91.6667,55.9 SIF-Syn: none /note=none CDS 9095 - 9502 /gene="13" /product="gp13" /function="Hypothetical Protein" /locus tag="Kovu_13" /note=Original Glimmer call @bp 9095 has strength 11.47; Genemark calls start at 9116 /note=SSC: 9095-9502 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_WALTZ_12 [Arthrobacter phage Waltz]],,NCBI, q1:s1 82.2222% 7.98649E-32 GAP: 53 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.154, -4.598157131439597, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_WALTZ_12 [Arthrobacter phage Waltz]],,ATW59890,65.812,7.98649E-32 SIF-HHPRED: SIF-Syn: In the pham the gene location of 13 and it`s match in other genes (which is typically 12) are in roughly the same spot and are roughly the same length. It is also surrounded by similar genes excluding the fact that Kovu has an orphan for gene 12. /note=- Start 1 (K-9095) is called 100 percent of time when present and conserved 100% of time in pham /note=- Start 9095 has all coding potential included in start; 9116 misses very minor coding potential CDS 9499 - 9852 /gene="14" /product="gp14" /function="Hypothetical Protein" /locus tag="Kovu_14" /note=Original Glimmer call @bp 9499 has strength 10.55; Genemark calls start at 9499 /note=SSC: 9499-9852 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_SHROOMS_13 [Arthrobacter phage Shrooms]],,NCBI, q1:s1 98.2906% 3.16372E-4 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.042, -4.394706008439538, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SHROOMS_13 [Arthrobacter phage Shrooms]],,ASR83894,57.0175,3.16372E-4 SIF-HHPRED: DUF3150 ; Protein of unknown function (DUF3150),,,PF11348.12,58.1197,73.9 SIF-Syn: Synteny is similar because it has a matching gene in another pham and is surrounded by similar genes Similar genes to the right in related phages, more contrast in genes to the left /note=The start is not conserved in all phams and Kovu is the only one with this start; However the start is called 100% of time when present CDS 9876 - 10469 /gene="15" /product="gp15" /function="SSB protein" /locus tag="Kovu_15" /note=Original Glimmer call @bp 9876 has strength 7.91; Genemark calls start at 9876 /note=SSC: 9876-10469 CP: yes SCS: both ST: NI BLAST-Start: [single-stranded DNA-binding protein [Arthrobacter sp. 49Tsu3.1M3] ],,NCBI, q1:s1 100.0% 3.50904E-92 GAP: 23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.693, -2.90473872338446, yes F: SSB protein SIF-BLAST: ,,[single-stranded DNA-binding protein [Arthrobacter sp. 49Tsu3.1M3] ],,WP_079555013,82.7225,3.50904E-92 SIF-HHPRED: Single-stranded DNA-binding protein 2; Single-stranded DNA-binding protein, Streptomyces Coelicolor, DNA damage, DNA repair, DNA replication, DNA-binding, Phosphoprotein, DNA BINDING PROTEIN; 2.141A {Streptomyces coelicolor} SCOP: b.40.4.3,,,3EIV_A,62.9442,100.0 SIF-Syn: Has no synteny, genes before and after do not match up to those of the other genes on the other phages in the pham /note=-Start 89 found in 47.5% of genes in this pham /note=-No change, Both Glimmer and Genemark called, and start includes all coding potential CDS 10642 - 10803 /gene="16" /product="gp16" /function="Hypothetical Protein" /locus tag="Kovu_16" /note=Original Glimmer call @bp 10642 has strength 5.37; Genemark calls start at 10666 /note=SSC: 10642-10803 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein UFOVP655_15 [uncultured Caudovirales phage]],,NCBI, q9:s14 67.9245% 1.28786E-4 GAP: 172 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.585, -3.966323606399536, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein UFOVP655_15 [uncultured Caudovirales phage]],,CAB4155723,48.0769,1.28786E-4 SIF-HHPRED: SIF-Syn: none /note=start 4, found in 2/2, called 100% of time, no MA /note=calling the start that glimmer calls because the RBS and the starterator best represents that this start is the best. CDS 10803 - 12257 /gene="17" /product="gp17" /function="portal protein" /locus tag="Kovu_17" /note=Original Glimmer call @bp 10803 has strength 12.32; Genemark calls start at 10803 /note=SSC: 10803-12257 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Arthrobacter phage Laroye] ],,NCBI, q8:s4 88.6364% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.042, -4.841864039781758, no F: portal protein SIF-BLAST: ,,[portal protein [Arthrobacter phage Laroye] ],,YP_009603006,79.1667,0.0 SIF-HHPRED: Portal protein; G20C, portal protein, bacteriophage, transport protein; 1.9A {Thermus phage P7426},,,5NGD_A,85.3306,100.0 SIF-Syn: Has good synteny - It (gene_17) is in a relatively same spot and surrounded by similar genes as in other phages in pham and cluster /note=- All pham considers this gene a portal protein - EX : Laroye_16 (portal protein), Laroye_16 (portal protein) /note=- Start includes all coding potential and is the longest possible open reading frame /note=- Kovu is the only one with this start of 10803 (1/292 or .3%) but is called 100% of time when present CDS 12190 - 13848 /gene="18" /product="gp18" /function="capsid maturation protease" /locus tag="Kovu_18" /note=Original Glimmer call @bp 12373 has strength 10.35; Genemark calls start at 12190 /note=SSC: 12190-13848 CP: yes SCS: both-gm ST: NI BLAST-Start: [head maturation protease [Arthrobacter phage LiSara] ],,NCBI, q21:s10 96.3768% 0.0 GAP: -68 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.032, -7.029966004414837, no F: capsid maturation protease SIF-BLAST: ,,[head maturation protease [Arthrobacter phage LiSara] ],,YP_010082530,73.8318,0.0 SIF-HHPRED: Phage_min_cap2 ; Phage minor capsid protein 2,,,PF06152.15,30.4348,99.6 SIF-Syn: - this function is expected in this part of the genome - surrounded by genes similar to other phages in pham /note=- Using start 12373 does not include all coding potential and leaves a gap of 115. Start 12190 has an atypical overlap of 68 base pairs /note=- Start 12373 has a gap of 115 ; Start 12190 has an overlap of 68 - Gap excludes significant amount of coding potential; A-typical overlap is preferred /note=- Score is better for start 12190 (e = 1.032 and final = -7.030) versus 12373 (e = .0703 and final = - 8.264) /note=- Start changed- Evidence is called start excluded coding potential and has worse scores CDS 13829 - 14026 /gene="19" /product="gp19" /function="Hypothetical Protein" /locus tag="Kovu_19" /note=Original Glimmer call @bp 13829 has strength 1.34; Genemark calls start at 13853 /note=SSC: 13829-14026 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein [Corynebacterium cyclohexanicum] ],,NCBI, q1:s3 80.0% 0.00243564 GAP: -20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.813, -3.7466128715229834, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Corynebacterium cyclohexanicum] ],,WP_229232662,40.7895,0.00243564 SIF-HHPRED: Ribosome modulation factor; solution NMR structure, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, UNKNOWN FUNCTION; NMR {Vibrio parahaemolyticus},,,2JRM_A,76.9231,99.3 SIF-Syn: yes , the genes doesn`t exit on other genes in the pham, but the genes around it stay the same /note=-start 6 found in 50% of genes in pham /note=-No change, start should remain @13829 as glimmer called because it includes the most coding potential CDS 14023 - 15156 /gene="20" /product="gp20" /function="RNA ligase" /locus tag="Kovu_20" /note=Original Glimmer call @bp 14023 has strength 11.98; Genemark calls start at 14023 /note=SSC: 14023-15156 CP: yes SCS: both ST: NI BLAST-Start: [RNA ligase [Arthrobacter phage LiSara] ],,NCBI, q2:s3 99.2042% 5.70713E-171 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.628, -5.27259541663274, no F: RNA ligase SIF-BLAST: ,,[RNA ligase [Arthrobacter phage LiSara] ],,YP_010082531,79.8928,5.70713E-171 SIF-HHPRED: d.61.1.2 (A:) 2`-5` RNA ligase LigT {Thermus thermophilus [TaxId: 274]} | CLASS: Alpha and beta proteins (a+b), FOLD: LigT-like, SUPFAM: LigT-like, FAM: 2`-5` RNA ligase LigT,,,SCOP_d1iuha_,44.5623,99.5 SIF-Syn: RNA ligase is found in the same location in other pham members. /note=Best RBS without losing significant coding potential. The start is called in 100% of genes in pham CDS 15137 - 15493 /gene="21" /product="gp21" /function="VRR-Nuc domain protein" /locus tag="Kovu_21" /note=Original Glimmer call @bp 15137 has strength 10.03; Genemark calls start at 15137 /note=SSC: 15137-15493 CP: no SCS: both ST: NI BLAST-Start: [nuclease [Arthrobacter phage Edmundo]],,NCBI, q1:s1 99.1525% 5.56656E-49 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.339, -3.7329837339109084, no F: VRR-Nuc domain protein SIF-BLAST: ,,[nuclease [Arthrobacter phage Edmundo]],,QGJ88093,73.7705,5.56656E-49 SIF-HHPRED: Nuclease; Nuclease, HYDROLASE; HET: SO4; 1.85A {Salmonella phage SETP3} SCOP: c.52.1.35,,,4QBN_A,83.8983,99.8 SIF-Syn: Yes, Has some synteny because gene before it is the same, but gene after it is different. /note=-start 18 found in 47.6% of genes in pham /note=-No change because it was called by both Glimmer and Genemark, and includes all coding potential CDS 15481 - 15873 /gene="22" /product="gp22" /function="nuclease" /locus tag="Kovu_22" /note=Original Glimmer call @bp 15481 has strength 11.23; Genemark calls start at 15481 /note=SSC: 15481-15873 CP: no SCS: both ST: NI BLAST-Start: [nuclease [Arthrobacter phage Altadena]],,NCBI, q6:s2 91.5385% 3.92385E-21 GAP: -13 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.144, -5.194122423817307, yes F: nuclease SIF-BLAST: ,,[nuclease [Arthrobacter phage Altadena]],,WNO25880,62.069,3.92385E-21 SIF-HHPRED: Thermonuclease; HYDROLASE, Calcium, Endonuclease, Membrane, Metal-binding, Nuclease, Secreted, Zymogen; NMR {Staphylococcus aureus} SCOP: b.40.1.1,,,2KHS_A,91.5385,99.3 SIF-Syn: It doesn`t have a lot of Synteny actually, it seems similar maybe at first but it is different from the rest of the genes. CDS 15942 - 16385 /gene="23" /product="gp23" /function="Hypothetical Protein" /locus tag="Kovu_23" /note=Original Glimmer call @bp 16032 has strength 13.63; Genemark calls start at 15942 /note=SSC: 15942-16385 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_WALTZ_20 [Arthrobacter phage Waltz]],,NCBI, q3:s4 98.6395% 1.24795E-30 GAP: 68 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.906, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_WALTZ_20 [Arthrobacter phage Waltz]],,ATW59898,58.1081,1.24795E-30 SIF-HHPRED: RiPP precursor (SonA); alpha-N-methyltransferase, borosin, natural products, TRANSFERASE; HET: SAM; 1.55A {Shewanella oneidensis},,,8T1T_D,40.8163,77.1 SIF-Syn: Would be expected to be in genome due to: waltz_20, Edmundo_20, wheelbite_20, shrooms_20,LiSara_20, /note=starterator calls start 7: found in 5/6, called 20%, /note=The starterator start begins on bp 16032. I am not in favor of this start and think it should be changed because DNA master for start 16032: z score: 2.875 /note= final score: -3.430 /note=DNA Master for start 15942: z score: 2.949 /note= final score:-2.505 /note=Since this start is only called 20% of the time when it is present and it removes a 90bp coding potential, which we know the 90bp is valid coding potential due to the DNA Master findings, I believe we should make the start at 15,942 (In favor of GeneMark) CDS 16375 - 16707 /gene="24" /product="gp24" /function="Hypothetical Protein" /locus tag="Kovu_24" /note=Original Glimmer call @bp 16438 has strength 4.61; Genemark calls start at 16438 /note=SSC: 16375-16707 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein FDH64_gp22 [Arthrobacter phage Laroye] ],,NCBI, q1:s1 94.5455% 1.59331E-17 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.883, -5.310715880084647, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH64_gp22 [Arthrobacter phage Laroye] ],,YP_009603012,52.459,1.59331E-17 SIF-HHPRED: SIF-Syn: this function is expected in this part of the genome /note=Justin: Start changed to include all coding potential. Initial call was much smaller than other called genes in the pham. Kovu does not have the most frequently called start. CDS 16704 - 17321 /gene="25" /product="gp25" /function="RNaseE" /locus tag="Kovu_25" /note=Original Glimmer call @bp 16704 has strength 16.09; Genemark calls start at 16704 /note=SSC: 16704-17321 CP: no SCS: both ST: NI BLAST-Start: [RNase [Arthrobacter phage Shrooms]],,NCBI, q1:s1 100.0% 1.51056E-66 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.059, -2.17469248771465, yes F: RNaseE SIF-BLAST: ,,[RNase [Arthrobacter phage Shrooms]],,ASR83903,69.8565,1.51056E-66 SIF-HHPRED: c.55.3.0 (A:136-286) automated matches {Human (Homo sapiens) [TaxId: 9606]} | CLASS: Alpha and beta proteins (a/b), FOLD: Ribonuclease H-like motif, SUPFAM: Ribonuclease H-like, FAM: automated matches,,,SCOP_d2qk9a1,68.2927,99.0 SIF-Syn: Gene located in the same area in pham members CDS complement (17326 - 17736) /gene="26" /product="gp26" /function="endonuclease VII" /locus tag="Kovu_26" /note=Genemark calls start at 17736 /note=SSC: 17736-17326 CP: yes SCS: genemark ST: NI BLAST-Start: [endonuclease VII domain-containing protein [Streptomyces gossypii] ],,NCBI, q49:s2 63.9706% 1.08375E-25 GAP: 128 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.026, -5.399187552617544, no F: endonuclease VII SIF-BLAST: ,,[endonuclease VII domain-containing protein [Streptomyces gossypii] ],,WP_260218469,62.3762,1.08375E-25 SIF-HHPRED: Restriction endonuclease Hpy99I; ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, HPY99I, PSEUDOPALINDROME, HYDROLASE-DNA COMPLEX; HET: 1PE; 1.5A {Helicobacter pylori},,,3GOX_A,90.4412,99.8 SIF-Syn: no matches in subcluster. /note=Very weak gene potential in S and host (better in host). Fills gap. Gene on forward strand will be deleted. CDS 17865 - 18647 /gene="27" /product="gp27" /function="Hypothetical Protein" /locus tag="Kovu_27" /note=Original Glimmer call @bp 17865 has strength 14.63; Genemark calls start at 17883 /note=SSC: 17865-18647 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_SHROOMS_23 [Arthrobacter phage Shrooms]],,NCBI, q1:s1 100.0% 1.50705E-70 GAP: 128 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.042, -4.455662434380964, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SHROOMS_23 [Arthrobacter phage Shrooms]],,ASR83904,67.7778,1.50705E-70 SIF-HHPRED: MGC84997 protein; nuclear pore complex, inner ring, Nup205, Nup93, Nup188, Nup155, NDC1, Aladin, STRUCTURAL PROTEIN; 4.2A {Xenopus laevis},,,7WKK_i,55.3846,91.9 SIF-Syn: YES Genes to the right are similar in related genomes. Genes on the left show more contrast, Kovu has two additional genes not seen in related genomes /note=Start matches with phages in different cluster (FM). Larger gap probably needed for direction change. CDS 18651 - 19028 /gene="28" /product="gp28" /function="head fiber protein" /locus tag="Kovu_28" /note=Original Glimmer call @bp 18651 has strength 12.34; Genemark calls start at 18651 /note=SSC: 18651-19028 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein FDH64_gp25 [Arthrobacter phage Laroye] ],,NCBI, q1:s1 93.6% 1.1388E-40 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.395, -3.6916801401915316, yes F: head fiber protein SIF-BLAST: ,,[hypothetical protein FDH64_gp25 [Arthrobacter phage Laroye] ],,YP_009603015,71.6535,1.1388E-40 SIF-HHPRED: Capsid fiber protein; bacteriophage, phi29, prohead, VIRUS; HET: SO4; 1.8A {Bacillus phage phi29},,,6QYY_A,91.2,99.7 SIF-Syn: Yes, sequence of preceding gene and following gene in same phams is conserved in phages Edmundo and Waltz, with prior gene being in pham 5650, and following gene in pham 5532. /note=Highly probable based off of HHPred results. CDS 19058 - 20017 /gene="29" /product="gp29" /function="major capsid protein" /locus tag="Kovu_29" /note=Original Glimmer call @bp 19058 has strength 12.24; Genemark calls start at 19058 /note=SSC: 19058-20017 CP: yes SCS: both ST: NI BLAST-Start: [major capsid protein [Arthrobacter phage Shrooms]],,NCBI, q1:s1 100.0% 0.0 GAP: 29 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.038, -2.156361006712914, yes F: major capsid protein SIF-BLAST: ,,[major capsid protein [Arthrobacter phage Shrooms]],,ASR83906,92.163,0.0 SIF-HHPRED: Phage-related protein; PHAGE-RELATED PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, VIRAL PROTEIN; HET: MSE, PG4; 2.05A {Bordetella bronchiseptica RB50},,,3BJQ_J,99.0596,100.0 SIF-Syn: this function is expected in this part of the genome CDS 20094 - 20372 /gene="30" /product="gp30" /function="Hypothetical Protein" /locus tag="Kovu_30" /note=Original Glimmer call @bp 20094 has strength 10.42; Genemark calls start at 20094 /note=SSC: 20094-20372 CP: yes SCS: both ST: NI BLAST-Start: GAP: 76 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.906, -2.794070146961553, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: To a degree, Other phages in AL have Major capsid protein in pham 5532 preceding, but don`t have a consistent pattern after. Similar sized gap preceding others. /note=Likely gene, no known function. Weak homology hit to Gene 26 in Wheelbite and Edmundo. This gene is in same spot in those genomes. CDS 20369 - 22672 /gene="31" /product="gp31" /function="Hypothetical Protein" /locus tag="Kovu_31" /note=Original Glimmer call @bp 20369 has strength 14.14; Genemark calls start at 20369 /note=SSC: 20369-22672 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_KHARCHO_102 [Arthrobacter phage Kharcho] ],,NCBI, q4:s3 99.6089% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.906, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_KHARCHO_102 [Arthrobacter phage Kharcho] ],,WIC89148,81.6167,0.0 SIF-HHPRED: End_beta_barrel ; Beta barrel domain of bacteriophage endosialidase,,,PF12195.12,8.73533,96.4 SIF-Syn: Gene located in the same area in pham members CDS 22675 - 23088 /gene="32" /product="gp32" /function="Hypothetical Protein" /locus tag="Kovu_32" /note=Original Glimmer call @bp 22675 has strength 9.72; Genemark calls start at 22675 /note=SSC: 22675-23088 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein KMD23_gp30 [Arthrobacter phage Wheelbite] ],,NCBI, q1:s1 91.9708% 1.68301E-39 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.504, -5.542591178556752, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein KMD23_gp30 [Arthrobacter phage Wheelbite] ],,YP_010082738,67.4074,1.68301E-39 SIF-HHPRED: SIF-Syn: Similar genes follow in other AL phages. Preceding genes differ in Kovu. CDS 23082 - 23408 /gene="33" /product="gp33" /function="head-to-tail stopper" /locus tag="Kovu_33" /note=Original Glimmer call @bp 23082 has strength 12.38; Genemark calls start at 23082 /note=SSC: 23082-23408 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein KMD22_gp32 [Arthrobacter phage Salgado] ],,NCBI, q2:s1 97.2222% 1.90119E-32 GAP: -7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.3, -3.8970005018578204, no F: head-to-tail stopper SIF-BLAST: ,,[hypothetical protein KMD22_gp32 [Arthrobacter phage Salgado] ],,YP_010082641,66.3551,1.90119E-32 SIF-HHPRED: Stopper protein Rcc01689; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_E,94.4444,98.9 SIF-Syn: Yes head-to-tail stoppers are found in the same area of pham members. /note=Does not have the most annotated start, only phage with the start that is called. Best RBS score. CDS 23412 - 23813 /gene="34" /product="gp34" /function="Hypothetical Protein" /locus tag="Kovu_34" /note=Original Glimmer call @bp 23412 has strength 8.68; Genemark calls start at 23412 /note=SSC: 23412-23813 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_WALTZ_29 [Arthrobacter phage Waltz]],,NCBI, q1:s1 97.7444% 1.40688E-48 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.969, -4.473102278738214, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_WALTZ_29 [Arthrobacter phage Waltz]],,ATW59907,71.2121,1.40688E-48 SIF-HHPRED: CdbA; nucleoid ribbon-helix-helix, DNA BINDING PROTEIN; 2.24A {Myxococcus xanthus DK 1622},,,6SBW_A,36.0902,84.5 SIF-Syn: Yes, Followed by a head-to-tail stopper in 5202, and followed by a hypothetical protein in pham 6170, same as in phages Waltz and Edmundo /note=Hypothetical protein, (There is a decent chance of it being a minor capsid or minor tail protein, but nothing, I`m exceptionally confident in.) CDS 23813 - 24256 /gene="35" /product="gp35" /function="tail terminator" /locus tag="Kovu_35" /note=Original Glimmer call @bp 23813 has strength 11.81; Genemark calls start at 23813 /note=SSC: 23813-24256 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_WALTZ_30 [Arthrobacter phage Waltz]],,NCBI, q1:s1 100.0% 4.51558E-45 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.339, -4.197870532213559, yes F: tail terminator SIF-BLAST: ,,[hypothetical protein SEA_WALTZ_30 [Arthrobacter phage Waltz]],,ATW59908,65.9864,4.51558E-45 SIF-HHPRED: Tail terminator protein Rcc01690; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_F,95.2381,99.6 SIF-Syn: -yes, synteny with waltz in pecaan and phamerator -this gene is in a section surrounded by other homologous genes in other subclusters in pham /note=start 1: found in 1/10, no MA, called 100% of the time when present (only kovu), walz_30 called start 3. /note= /note=- Z and final score for start: 2.339, -4.198. Not the lowest final score but the one with the lowest has the same z-score and is only a 3 base pair difference; No need to change start /note=- Start includes all coding potential and is the longest possible ORF CDS 24246 - 24524 /gene="36" /product="gp36" /function="Hypothetical Protein" /locus tag="Kovu_36" /note=Original Glimmer call @bp 24294 has strength 9.62; Genemark calls start at 24246 /note=SSC: 24246-24524 CP: yes SCS: both-gm ST: NI BLAST-Start: GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.006, -4.534089041695007, no F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: Matches with other genes in pham /note=Justin: start moved to 24246. Most frequently called in starterator. Fills gap, acceptable overlap. CDS 24521 - 24748 /gene="37" /product="gp37" /function="Hypothetical Protein" /locus tag="Kovu_37" /note=Original Glimmer call @bp 24521 has strength 6.63; Genemark calls start at 24521 /note=SSC: 24521-24748 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_EDMUNDO_35 [Arthrobacter phage Edmundo]],,NCBI, q1:s1 73.3333% 1.08896E-20 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.167, -4.105706954229964, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_EDMUNDO_35 [Arthrobacter phage Edmundo]],,QGJ88171,60.7595,1.08896E-20 SIF-HHPRED: Mu-like_Com ; Mu-like prophage protein Com,,,PF10122.13,52.0,98.7 SIF-Syn: N/A Orpham CDS 24900 - 25148 /gene="38" /product="gp38" /function="Hypothetical Protein" /locus tag="Kovu_38" /note=Original Glimmer call @bp 24900 has strength 11.23; Genemark calls start at 24900 /note=SSC: 24900-25148 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein [Micromonospora sp. WMMD1082] ],,NCBI, q6:s5 89.0244% 6.22521E-11 GAP: 151 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.762, -5.5736513488419765, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Micromonospora sp. WMMD1082] ],,WP_278179331,58.0247,6.22521E-11 SIF-HHPRED: DUF3203 ; Protein of unknown function (DUF3203),,,PF11462.12,84.1463,90.7 SIF-Syn: Orpham. This region of related genomes is filled with tightly packed, short-ish genes. This is a big gap, but no coding potential to suggest filling. /note=While there is a sizable gap between genes, the start includes all coding potential. No data on starterator. No coding potential in GeneMark S or host for the earlier start. CDS 25150 - 25533 /gene="39" /product="gp39" /function="Hypothetical Protein" /locus tag="Kovu_39" /note=Original Glimmer call @bp 25150 has strength 10.24; Genemark calls start at 25150 /note=SSC: 25150-25533 CP: yes SCS: both ST: NI BLAST-Start: GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.728, -6.29944796767998, no F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: a.4.5.0 (A:176-252) automated matches {Human (Homo sapiens) [TaxId: 9606]} | CLASS: All alpha proteins, FOLD: DNA/RNA-binding 3-helical bundle, SUPFAM: `Winged helix` DNA-binding domain, FAM: automated matches,,,SCOP_d3cuqa2,50.3937,93.4 SIF-Syn: No synteny. Other related phages are packed with genes in this area, but they don`t match other known genes. /note=Gene is an Orpham CDS 25625 - 26038 /gene="40" /product="gp40" /function="membrane protein" /locus tag="Kovu_40" /note=Original Glimmer call @bp 25625 has strength 10.5; Genemark calls start at 25625 /note=SSC: 25625-26038 CP: yes SCS: both ST: NI BLAST-Start: GAP: 91 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.734, -2.956683020935497, no F: membrane protein SIF-BLAST: SIF-HHPRED: RCR ; Chitin synthesis regulation, resistance to Congo red,,,PF12273.12,18.2482,91.9 SIF-Syn: N/A No synteny between related genomes Leaves a sizable gap, but no coding potential before the called start. /note=only member of pham /note=Most likely a transmembrane protein. DeepTMHMM finds one TM region. /note=Moving start to 25541 does not improve HHPred or BLAST hits. Does give a predicted signal sequence in DeepTMHMM. Left start at 25625. CDS 26055 - 26219 /gene="41" /product="gp41" /function="Hypothetical Protein" /locus tag="Kovu_41" /note=Original Glimmer call @bp 26055 has strength 6.8; Genemark calls start at 26031 /note=SSC: 26055-26219 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_SHROOMS_36 [Arthrobacter phage Shrooms]],,NCBI, q2:s7 98.1481% 6.45103E-20 GAP: 16 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.757, -3.1164791313608173, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SHROOMS_36 [Arthrobacter phage Shrooms]],,ASR83917,79.661,6.45103E-20 SIF-HHPRED: SIF-Syn: There is synteny because gene 42 is found in homologous phages (Waltz); However there are no other similar genes surrounded gene 42 in Kovu that also exists in Waltz /note=• Found in 1 of 8 ( 12.5% ) of genes in pham /note=• No Manual Annotations of this start. Not present in any other pham members. /note=* All coding potential is including in this start (26055) but it is not the longest possible ORF (start 26031 is) /note=* Phamerator calls CDD - deeptmhmm; Query Start (Amino Acid Position): 1; Query End (Amino Acid Position): 44; Type: signal CDS 26800 - 26916 /gene="42" /product="gp42" /function="Hypothetical Protein" /locus tag="Kovu_42" /note=Original Glimmer call @bp 26800 has strength 13.24; Genemark calls start at 26800 /note=SSC: 26800-26916 CP: yes SCS: both ST: NI BLAST-Start: GAP: 580 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.142, -1.993391246735709, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: No homologous genes. Other AL phages have similar sized genes in a similar order. /note=Large gap with previous gene. /note=Online HHPred has a hit to E. coli phage Mu tail fiber assembly protein at 85.5% probability but poor E value. CDS 26913 - 27383 /gene="43" /product="gp43" /function="Hypothetical Protein" /locus tag="Kovu_43" /note=Original Glimmer call @bp 26913 has strength 15.49; Genemark calls start at 26913 /note=SSC: 26913-27383 CP: yes SCS: both ST: NI BLAST-Start: GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.806, -4.905314844093283, no F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: Orphan, but gene of this size is expected. /note=Start site includes all coding potential. Best RBS scores without losing coding potential. CDS 27380 - 27667 /gene="44" /product="gp44" /function="Hypothetical Protein" /locus tag="Kovu_44" /note=Original Glimmer call @bp 27380 has strength 13.09; Genemark calls start at 27380 /note=SSC: 27380-27667 CP: yes SCS: both ST: NI BLAST-Start: GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.813, -2.7863799983944713, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: Similar genetic environment in related phages. /note=No match to anything. CDS 27664 - 28140 /gene="45" /product="gp45" /function="Hypothetical Protein" /locus tag="Kovu_45" /note=Original Glimmer call @bp 27664 has strength 13.49; Genemark calls start at 27664 /note=SSC: 27664-28140 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein KMD22_gp44 [Arthrobacter phage Salgado] ],,NCBI, q97:s94 27.8481% 5.45295E-4 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.666, -3.0248543014571307, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein KMD22_gp44 [Arthrobacter phage Salgado] ],,YP_010082653,20.8054,5.45295E-4 SIF-HHPRED: SIF-Syn: Gene is an orpham surrounded by other orphams; no synteny found. Similarly sized genes in the area. /note=Gene is an orpham. BLAST hits only match a small part of the gene. CDS 28143 - 28511 /gene="46" /product="gp46" /function="Hypothetical Protein" /locus tag="Kovu_46" /note=Original Glimmer call @bp 28143 has strength 8.39; Genemark calls start at 28143 /note=SSC: 28143-28511 CP: yes SCS: both ST: NI BLAST-Start: GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.127, -4.782222827850149, no F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: There is some sort of synteny; More so in size not function.... (There are no similar function genes including and surrounding this one in other subclusters, but there are similar size adjacent genes whose size looks similar to other pham members. Ex: Wheelbite) /note=- Start includes all coding potential and contains the longest possible ORF /note=- Start called 100% of time when present /note=- Start has the best scores (lowest final and highest Z) CDS 28495 - 28686 /gene="47" /product="gp47" /function="Hypothetical Protein" /locus tag="Kovu_47" /note=Original Glimmer call @bp 28495 has strength 6.28; Genemark calls start at 28495 /note=SSC: 28495-28686 CP: no SCS: both ST: NI BLAST-Start: GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.595, -3.1789026931375792, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: No Synteny /note=No Data on Starterator. CDS 28683 - 28967 /gene="48" /product="gp48" /function="Hypothetical Protein" /locus tag="Kovu_48" /note=Original Glimmer call @bp 28683 has strength 8.28; Genemark calls start at 28719 /note=SSC: 28683-28967 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein KMD23_gp47 [Arthrobacter phage Wheelbite] ],,NCBI, q1:s1 53.1915% 1.01422E-4 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.44, -3.513874779476501, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein KMD23_gp47 [Arthrobacter phage Wheelbite] ],,YP_010082755,51.8519,1.01422E-4 SIF-HHPRED: g.41.9.0 (L:) automated matches {Sus scrofa [TaxId: 9825]} | CLASS: Small proteins, FOLD: Rubredoxin-like, SUPFAM: RNA polymerase subunits, FAM: automated matches,,,SCOP_d7b7ul_,25.5319,95.4 SIF-Syn: /note=Conserved Domain with Rubredoxin protein. Also related to Lar antirestriction system in E. coli phage Rac. This doesn`t fit with approved antirestriction systems. CDS 28964 - 29254 /gene="49" /product="gp49" /function="Hypothetical Protein" /locus tag="Kovu_49" /note=Genemark calls start at 29012 /note=SSC: 28964-29254 CP: yes SCS: genemark-cs ST: NI BLAST-Start: [hypothetical protein SEA_WALTZ_45 [Arthrobacter phage Waltz]],,NCBI, q27:s3 72.9167% 0.00640454 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.356, -3.6333723343341213, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_WALTZ_45 [Arthrobacter phage Waltz]],,ATW59922,60.5634,0.00640454 SIF-HHPRED: SIF-Syn: Matches with other genes in pham /note=Gene number on PECAAN does not align with the gene number on Phamerator and PhagesDB. This gene aligns with gene #51 on Phamerator and PhagesDB. Weak HHpred hit to tail assembly chaperone. /note=First start makes most sense with -4 overlap. No coding potential to justify the move, but RBS scores are vastly better. Chose -4 overlap. CDS 29439 - 29768 /gene="50" /product="gp50" /function="Hypothetical Protein" /locus tag="Kovu_50" /note=Original Glimmer call @bp 29439 has strength 8.45; Genemark calls start at 29439 /note=SSC: 29439-29768 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_WALTZ_46 [Arthrobacter phage Waltz]],,NCBI, q8:s25 50.4587% 0.00773069 GAP: 184 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.574, -5.328146428608027, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_WALTZ_46 [Arthrobacter phage Waltz]],,ATW59923,18.4049,0.00773069 SIF-HHPRED: Early endosome antigen 1; PROTEIN-ZINC FINGER COMPLEX, BETA BETA ALPHA FOLD, BETA HAIRPIN, Rab5A GTPase, EEA1, PROTEIN TRANSPORT; HET: GTP; 2.03A {Homo sapiens},,,3MJH_B,27.5229,89.9 SIF-Syn: Gene of this size in this area consistent with pham members. /note=Start site LORF and best Z score. CDS 29765 - 30076 /gene="51" /product="gp51" /function="Hypothetical Protein" /locus tag="Kovu_51" /note=Original Glimmer call @bp 29765 has strength 7.57; Genemark calls start at 29765 /note=SSC: 29765-30076 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein QDA10_gp096 [Microbacterium phage Ariadne] ],,NCBI, q9:s14 87.3786% 1.71E-4 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.757, -2.8454123590742793, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein QDA10_gp096 [Microbacterium phage Ariadne] ],,YP_010751932,46.1538,1.71E-4 SIF-HHPRED: uncharacterized protein XF2673; solution NMR structure, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, unknown function; NMR {Xylella fastidiosa Temecula1},,,2K5R_A,48.5437,98.5 SIF-Syn: Gene is surrounded by orphams; no synteny observed CDS 30066 - 30437 /gene="52" /product="gp52" /function="Hypothetical Protein" /locus tag="Kovu_52" /note=Original Glimmer call @bp 30066 has strength 6.66; Genemark calls start at 30066 /note=SSC: 30066-30437 CP: yes SCS: both ST: NI BLAST-Start: GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.224, -4.447172733638442, no F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: All genes in area are unique to Kovu, except one that has pham members in other clusters /note=Excellent coding potential CDS 30579 - 31544 /gene="53" /product="gp53" /function="ribonucleotide reductase" /locus tag="Kovu_53" /note=Original Glimmer call @bp 30579 has strength 13.62; Genemark calls start at 30579 /note=SSC: 30579-31544 CP: yes SCS: both ST: NI BLAST-Start: [class 1b ribonucleoside-diphosphate reductase subunit beta [Zafaria cholistanensis] ],,NCBI, q4:s7 99.0654% 0.0 GAP: 141 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.813, -2.707694805492614, yes F: ribonucleotide reductase SIF-BLAST: ,,[class 1b ribonucleoside-diphosphate reductase subunit beta [Zafaria cholistanensis] ],,WP_149958005,88.2716,0.0 SIF-HHPRED: Ribonucleotide reductase subunit R2F; metal free, ribonucleotide reductase, hydrogen bond, Metal Binding Protein; 1.63A {Corynebacterium ammoniagenes} SCOP: a.25.1.2,,,3DHZ_A,99.0654,100.0 SIF-Syn: None /note=For some reason GenemarkS didn`t call the start, may be why starterator results were weak CDS 31604 - 32269 /gene="54" /product="gp54" /function="DNA methyltransferase" /locus tag="Kovu_54" /note=Original Glimmer call @bp 31604 has strength 9.78; Genemark calls start at 31604 /note=SSC: 31604-32269 CP: yes SCS: both ST: NI BLAST-Start: [DNA methylase [Arthrobacter phage Sarge] ],,NCBI, q7:s3 97.2851% 1.01303E-123 GAP: 59 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.688, -5.160958035523474, no F: DNA methyltransferase SIF-BLAST: ,,[DNA methylase [Arthrobacter phage Sarge] ],,YP_010649608,84.7926,1.01303E-123 SIF-HHPRED: DNA (cytosine-5)-methyltransferase 1; DNMT1, DNA methytransferase1, DNA methylation, TRANSFERASE; HET: ZN, SAH; 2.622A {Homo sapiens},,,4WXX_A,72.8507,99.7 SIF-Syn: This function matches with other genes in pham. /note=includes 20 nt with little to no coding potential, but minimizes gap. CDS 32319 - 33014 /gene="55" /product="gp55" /function="Hypothetical Protein" /locus tag="Kovu_55" /note=Original Glimmer call @bp 32319 has strength 8.06; Genemark calls start at 32319 /note=SSC: 32319-33014 CP: yes SCS: both ST: NI BLAST-Start: GAP: 49 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.965, -2.66590822473965, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: b.34.20.1 (A:7-71) Uncharacterized protein YorP {Bacillus subtilis [TaxId: 1423]} | CLASS: All beta proteins, FOLD: SH3-like barrel, SUPFAM: YorP-like, FAM: YorP-like,,,SCOP_d2heqa1,17.7489,92.9 SIF-Syn: no homologous genes /note=-orphan /note=-Dna sequence for Laroye_59 shares similarity to Kovu_57 CDS 33011 - 33289 /gene="56" /product="gp56" /function="Hypothetical Protein" /locus tag="Kovu_56" /note= /note=SSC: 33011-33289 CP: yes SCS: neither ST: NI BLAST-Start: [hypothetical protein SEA_TUCK_38 [Arthrobacter phage Tuck]],,NCBI, q1:s1 70.6522% 1.99658E-18 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.504, -5.62127637145861, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_TUCK_38 [Arthrobacter phage Tuck]],,WAB10812,71.6418,1.99658E-18 SIF-HHPRED: SIF-Syn: In an area of poor synteny to other AL phages. /note=Fills relatively large gap. Good gene potential. Relatively large overlap at end with next gene. CDS 33213 - 33443 /gene="57" /product="gp57" /function="helix-turn-helix DNA binding domain" /locus tag="Kovu_57" /note=Original Glimmer call @bp 33210 has strength 8.45; Genemark calls start at 33204 /note=SSC: 33213-33443 CP: yes SCS: both-cs ST: NI BLAST-Start: GAP: -77 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.757, -2.9063687850157054, no F: helix-turn-helix DNA binding domain SIF-BLAST: SIF-HHPRED: SIF-Syn: related genomes in pham have same function in similar spot LiSara_57 and Laroye_60 both call HTH binding domain protein, they are in cluster AL /note=no starterator because it is an orpham but the start at 33210 ( glimmer start) should be called due to its rbs score and its coding potential represented on gene mark. /note=Justin: moved to 33213 because there are two starts back to back. Call the second. CDS 33436 - 33810 /gene="58" /product="gp58" /function="Hypothetical Protein" /locus tag="Kovu_58" /note=Original Glimmer call @bp 33436 has strength 4.99; Genemark calls start at 33436 /note=SSC: 33436-33810 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_RIZWANA_42 [Arthrobacter phage Rizwana]],,NCBI, q1:s3 79.8387% 2.22103E-25 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.3, -5.061353357642258, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_RIZWANA_42 [Arthrobacter phage Rizwana]],,QWY81339,63.2075,2.22103E-25 SIF-HHPRED: Peptide synthetase XpsB (Modular protein); PROTEIN, PROTEIN BINDING; NMR {Xenorhabdus cabanillasii JM26},,,7B2F_A,8.06452,8.4 SIF-Syn: this function is not expected in other parts of the genome CDS 33848 - 34150 /gene="59" /product="gp59" /function="Hypothetical Protein" /locus tag="Kovu_59" /note=Original Glimmer call @bp 33848 has strength 16.44; Genemark calls start at 33932 /note=SSC: 33848-34150 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein KDJ02_gp35 [Arthrobacter phage Litotes] ],,NCBI, q30:s3 71.0% 7.12422E-13 GAP: 37 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.826, -4.863117164298828, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein KDJ02_gp35 [Arthrobacter phage Litotes] ],,YP_010050204,62.1622,7.12422E-13 SIF-HHPRED: b.34.5.0 (A:3-65) automated matches {Coxiella burnetii [TaxId: 777]} | CLASS: All beta proteins, FOLD: SH3-like barrel, SUPFAM: Translation proteins SH3-like domain, FAM: automated matches,,,SCOP_d3trea1,61.0,89.6 SIF-Syn: Pham members with homologous gene is found in this area of the genome. /note=Does not have the start that is celled in all other pham members. Called start includes all coding potential. Better RBS scores with -53 overlap doesn`t make sense. CDS 34296 - 34448 /gene="60" /product="gp60" /function="Hypothetical Protein" /locus tag="Kovu_60" /note=Original Glimmer call @bp 34296 has strength 12.68; Genemark calls start at 34296 /note=SSC: 34296-34448 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein FDH64_gp63 [Arthrobacter phage Laroye] ],,NCBI, q8:s6 86.0% 2.67789E-12 GAP: 145 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.994, -2.394485424036831, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDH64_gp63 [Arthrobacter phage Laroye] ],,YP_009603053,72.9167,2.67789E-12 SIF-HHPRED: GINS_B_archaea_Gins23; beta-strand (B) domain of archaeal GINS complex protein Gins23. The GINS (named from the Japanese go-ichi-ni-san, meaning 5-1-2-3 for the Sld5, Psf1, Psf2, and Psf3 subunits) complex is involved in both initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork.,,,cd21697,80.0,97.1 SIF-Syn: synteny with edmundo_62, LiSara_60, waltz_60 /note=start 3: found in 3/10 of genes in pham, 2MA, called 100% of the time when present /note=no start change CDS 34448 - 35200 /gene="61" /product="gp61" /function="major tail protein" /locus tag="Kovu_61" /note=Original Glimmer call @bp 34448 has strength 17.41; Genemark calls start at 34457 /note=SSC: 34448-35200 CP: yes SCS: both-gl ST: SS BLAST-Start: [major tail protein [Arthrobacter phage Wheelbite] ],,NCBI, q1:s1 100.0% 6.40944E-81 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.757, -3.6727816321281046, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage Wheelbite] ],,YP_010082768,69.7581,6.40944E-81 SIF-HHPRED: Major tail protein; Marine bacteriophage, Cryo-EM, Siphophage, Baseplate, Megatron protein, Tail fibre protein, Distal tail protein, Hub protein, VIRAL; 4.5A {Dinoroseobacter phage vB_DshS-R4C},,,8GTC_F,52.4,99.5 SIF-Syn: Synteny with: LiSara_61, Salgao_64, Wheelbite_60, Laroye_64, Shrooms_62, Waltz_61; all are major tail protein /note=Starterator says the best start is start 1 (34448) which is the glimmer start that I decided to go with. Found in 8/11 genes, 7/10MA, called 100% of the time when present CDS 35210 - 35638 /gene="62" /product="gp62" /function="major tail protein" /locus tag="Kovu_62" /note=Original Glimmer call @bp 35210 has strength 13.96; Genemark calls start at 35210 /note=SSC: 35210-35638 CP: yes SCS: both ST: NI BLAST-Start: [major tail protein [Arthrobacter phage Waltz]],,NCBI, q1:s1 99.2958% 6.36759E-74 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.943, -4.52809571235251, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage Waltz]],,ATW59939,88.0282,6.36759E-74 SIF-HHPRED: Major tail protein; Marine bacteriophage, Cryo-EM, Siphophage, Baseplate, Megatron protein, Tail fibre protein, Distal tail protein, Hub protein, VIRAL; 4.5A {Dinoroseobacter phage vB_DshS-R4C},,,8GTC_F,95.7747,99.8 SIF-Syn: Homologous genes have same function. CDS 35665 - 36174 /gene="63" /product="gp63" /function="tail assembly chaperone" /locus tag="Kovu_63" /note=Original Glimmer call @bp 35677 has strength 10.79; Genemark calls start at 35677 /note=SSC: 35665-36174 CP: yes SCS: both-cs ST: NI BLAST-Start: [tail assembly chaperone [Arthrobacter phage Wheelbite] ],,NCBI, q1:s1 100.0% 3.42947E-68 GAP: 26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.635, -6.501868165458011, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage Wheelbite] ],,YP_010082770,71.6578,3.42947E-68 SIF-HHPRED: Tail assembly chaperone; Bacteriophage HK97, morphogenesis, tail assembly chaperone, CHAPERONE; HET: MSE; 2.3A {Enterobacteria phage HK97},,,2OB9_B,69.8225,99.8 SIF-Syn: There is synteny because the gene and surrounding genes are found throughout homologous phages in the same area. /note=I think the start should be changed to the first start in 64 because it shortens the gap by 12 nucleotides and it includes more coding potential. /note=Start 5: /note=• Found in 1 of 10 ( 10.0% ) of genes in pham /note=• No Manual Annotations of this start. /note=• Called 100.0% of time when present CDS 36246 - 36326 /gene="64" /product="gp64" /function="tail assembly chaperone" /locus tag="Kovu_64" /note= /note=SSC: 36246-36326 CP: no SCS: neither ST: NI BLAST-Start: [tail assembly chaperone [Arthrobacter phage Kharcho] ],,NCBI, q1:s200 88.4615% 6.34059E-5 GAP: 71 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.826, -7.010287268468504, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage Kharcho] ],,WIC89088,9.52381,6.34059E-5 SIF-HHPRED: SIF-Syn: /note=ribosomal frameshift /note=CDS join(35665..36141;36141..36326) CDS 36350 - 40081 /gene="65" /product="gp65" /function="tape measure protein" /locus tag="Kovu_65" /note=Original Glimmer call @bp 36350 has strength 12.93; Genemark calls start at 36398 /note=SSC: 36350-40081 CP: yes SCS: both-gl ST: NI BLAST-Start: [tail length tape measure protein [Arthrobacter phage Sonali] ],,NCBI, q35:s261 84.6339% 0.0 GAP: 23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.757, -2.7653702713535186, yes F: tape measure protein SIF-BLAST: ,,[tail length tape measure protein [Arthrobacter phage Sonali] ],,YP_009819689,54.0664,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BF,6.91875,100.0 SIF-Syn: Yes, has some synteny because gene before it is the same, but gene after it is different. /note=-Start 21 found in 25% of genes in pham. Start @36350 /note=-no change, start is @36350 where Glimmer called it to be, this start includes the most coding potential. CDS 40087 - 42081 /gene="66" /product="gp66" /function="minor tail protein" /locus tag="Kovu_66" /note=Original Glimmer call @bp 40087 has strength 11.54; Genemark calls start at 40087 /note=SSC: 40087-42081 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Kharcho] ],,NCBI, q1:s1 100.0% 0.0 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.069, -4.319174984166765, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Kharcho] ],,WIC89090,65.0842,0.0 SIF-HHPRED: Endo-1,4-beta-xylanase C; Binding Site, Carbohydrates, Enzyme Stability, Substrate Specificity, Endo-1, 4-beta-xylanase, Xylan-binding domain, Thermophilic enzymes, Thermostabilizing Domains, sugar; HET: CA, GOL; 2.43A {Paenibacillus barcinonensis},,,4XUP_D,50.0,99.6 SIF-Syn: Similar genes were observed in related phages; tape measure protein - minor tail protein - minor tail protein (similar to Laroye and Salgado) Better synenty observed when compared to Karcho_44 and Ottawa_44 (both members of FM) TMP - MTP - MTP arrangement the same but TMP is more similar in these genes to the TMP in Kovu /note=start site called 100% of the time when present in pham. CDS 42081 - 43256 /gene="67" /product="gp67" /function="minor tail protein" /locus tag="Kovu_67" /note=Original Glimmer call @bp 42102 has strength 10.05; Genemark calls start at 42102 /note=SSC: 42081-43256 CP: yes SCS: both-cs ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Kharcho] ],,NCBI, q1:s1 99.7442% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.456, -5.664406167576407, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Kharcho] ],,WIC89091,86.445,0.0 SIF-HHPRED: SIF-Syn: this function is expected in most parts of the genome /note=Justin: moved start to 42081. A -1 overlap makes more sense than a 21bp gap. Other phages in the cluster start this gene right at the stop of the previous. CDS 43241 - 44224 /gene="68" /product="gp68" /function="minor tail protein" /locus tag="Kovu_68" /note=Original Glimmer call @bp 43241 has strength 12.9; Genemark calls start at 43241 /note=SSC: 43241-44224 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Kharcho] ],,NCBI, q1:s1 100.0% 5.34343E-122 GAP: -16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.994, -2.253486910374644, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Kharcho] ],,WIC89092,71.988,5.34343E-122 SIF-HHPRED: Proteasome-associated ATPase; coil coil with 5 beta-strand barrel inter domain, CHAPERONE; 3.94A {Mycobacterium tuberculosis},,,3M9B_H,42.5076,89.4 SIF-Syn: This function matches with other phages in this pham. /note=-Start 2 if found in 70% of genes in pham /note=-No change, start includes the most coding potential, and was called by both Glimmer and Genemark CDS 44228 - 44797 /gene="69" /product="gp69" /function="minor tail protein" /locus tag="Kovu_69" /note=Original Glimmer call @bp 44228 has strength 13.1; Genemark calls start at 44228 /note=SSC: 44228-44797 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Kharcho] ],,NCBI, q1:s1 100.0% 1.33154E-73 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.404, -4.182126921701495, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Kharcho] ],,WIC89093,77.7778,1.33154E-73 SIF-HHPRED: Gp15 protein; Listeria, homotrimeric, receptor binding protein, Bacteriophage, VIRAL PROTEIN; HET: ACT, 1PE; 1.7A {Listeria phage PSA},,,6R5W_A,53.9683,98.1 SIF-Syn: Gene should be found here. /note=Start 1: Found in 3 of 3 ( 100.0% ) of genes in pham Called 100.0% of time when present • Phage (with cluster) where this start called: Kharcho_47 (FM), Kovu_69 (AL), Ottawa_47 (FM), CDS 44816 - 45061 /gene="70" /product="gp70" /function="membrane protein" /locus tag="Kovu_70" /note=Original Glimmer call @bp 44816 has strength 6.0; Genemark calls start at 44837 /note=SSC: 44816-45061 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_KHARCHO_48 [Arthrobacter phage Kharcho] ],,NCBI, q13:s12 85.1852% 1.57559E-17 GAP: 18 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.595, -4.421940741823874, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_KHARCHO_48 [Arthrobacter phage Kharcho] ],,WIC89094,57.5,1.57559E-17 SIF-HHPRED: Cell division protein FtsB; Bacterial cell division, divisome, FtsB, FtsL, FtsQ, FtsBLQ, FtsQLB, membrane protein complex, heterotrimer, MEMBRANE PROTEIN; 3.04A {Escherichia coli},,,8HHF_B,85.1852,97.4 SIF-Syn: No synteny observed between related phage genomes Synteny observed between Kovu_70 and Karcho_48 and Ottawa_48 (both in FM). Karcho and Ottawa exhibit minor tail protein - hypothetical protein - hypothetical protein whereas Kovu exhibits MTP - HP - orpham /note=Most likely a transmembrane protein. DeepTMHMM calls single transmembrane domain. CDS 45058 - 45423 /gene="71" /product="gp71" /function="membrane protein" /locus tag="Kovu_71" /note=Original Glimmer call @bp 45058 has strength 7.68; Genemark calls start at 45079 /note=SSC: 45058-45423 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein GCM10023233_22570 [Brevibacterium otitidis]],,NCBI, q8:s1 61.9835% 1.94421E-4 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.703, -2.9619179281457164, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein GCM10023233_22570 [Brevibacterium otitidis]],,BFF07288,21.1009,1.94421E-4 SIF-HHPRED: Cell division protein FtsL; bacterial cell division, peptidoglycan synthesis, membrane protein complex, MEMBRANE PROTEIN;{Pseudomonas aeruginosa PAO1},,,8BH1_D,41.3223,93.4 SIF-Syn: No homologous genes. /note=Likely hypothetical intermembrane protein, supported by HHPred and DeepTMHMM /note= /note=-Potential function in cell division or related membrane functions. CDS 45436 - 46323 /gene="72" /product="gp72" /function="endolysin" /locus tag="Kovu_72" /note=Original Glimmer call @bp 45436 has strength 14.84; Genemark calls start at 45436 /note=SSC: 45436-46323 CP: no SCS: both ST: NI BLAST-Start: [endolysin [Arthrobacter phage Kharcho] ],,NCBI, q4:s1 97.9661% 1.22055E-128 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.44, -3.5316035464369326, yes F: endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Kharcho] ],,WIC89096,82.5623,1.22055E-128 SIF-HHPRED: Peptidase M23; membrane protein, enzyme, TRANSPORT PROTEIN; HET: ADP;{Vibrio cholerae},,,8TZL_E,48.4746,99.2 SIF-Syn: Has no synteny, genes before and after do not match up to those of the other genes on the other phages in the pham /note=-Start 3 found in 40% of genes in pham /note=-No change, both glimmer and genemark called the same start, and it includes almost all coding potential CDS 46323 - 46700 /gene="73" /product="gp73" /function="holin" /locus tag="Kovu_73" /note=Genemark calls start at 46323 /note=SSC: 46323-46700 CP: yes SCS: genemark ST: NI BLAST-Start: [holin [Arthrobacter phage Kharcho] ],,NCBI, q1:s1 100.0% 1.36509E-44 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.027, -4.408951082954879, yes F: holin SIF-BLAST: ,,[holin [Arthrobacter phage Kharcho] ],,WIC89097,79.3651,1.36509E-44 SIF-HHPRED: SIF-Syn: This function matches with other phages in this pham. Genes in related phages match to the left /note=This gene is #74 on Phamerator and PhagesDB. /note=Membrane protein CDS complement (46755 - 47078) /gene="74" /product="gp74" /function="Hypothetical Protein" /locus tag="Kovu_74" /note=Original Glimmer call @bp 47078 has strength 7.69; Genemark calls start at 47078 /note=SSC: 47078-46755 CP: yes SCS: both ST: NI BLAST-Start: GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.44, -3.5316035464369326, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: Uncharacterized lipoprotein YifL; Lipopolysaccharide, Lipoprotein, LptDE, MEMBRANE PROTEIN; HET: PCJ; 2.98A {Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)},,,8H1R_F,28.972,98.6 SIF-Syn: no not in this cluster but it is adjacent to "exhile draft (48)" in cluster AZ /note=no start change; has the best rbs CDS complement (47075 - 47326) /gene="75" /product="gp75" /function="membrane protein" /locus tag="Kovu_75" /note=Original Glimmer call @bp 47326 has strength 9.13; Genemark calls start at 47326 /note=SSC: 47326-47075 CP: no SCS: both ST: NI BLAST-Start: GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.327, -5.86209866121396, no F: membrane protein SIF-BLAST: SIF-HHPRED: DUF2244 ; Integral membrane protein (DUF2244),,,PF10003.13,66.2651,65.3 SIF-Syn: no homologous genes /note=orphan. Very weak hits to lysin B genes in pham 161434. Two transmembrane regions predicted. CDS complement (47323 - 47520) /gene="76" /product="gp76" /function="helix-turn-helix DNA binding domain" /locus tag="Kovu_76" /note=Original Glimmer call @bp 47520 has strength 12.39; Genemark calls start at 47520 /note=SSC: 47520-47323 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_SHROOMS_76 [Arthrobacter phage Shrooms]],,NCBI, q5:s1 87.6923% 7.02278E-26 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.813, -2.707694805492614, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein SEA_SHROOMS_76 [Arthrobacter phage Shrooms]],,ASR83955,81.9672,7.02278E-26 SIF-HHPRED: a.6.1.5 (B:1-69) automated matches {Escherichia phage [TaxId: 10710]} | CLASS: All alpha proteins, FOLD: Putative DNA-binding domain, SUPFAM: Putative DNA-binding domain, FAM: Terminase gpNU1 subunit domain,,,SCOP_d6hn7b1,83.0769,99.2 SIF-Syn: homologous genes found in same region of genome in pham members /note=Online HHpred has decent hits to excisionase in other phages. Also many HTH proteins, some merR like. CDS complement (47523 - 47801) /gene="77" /product="gp77" /function="Hypothetical Protein" /locus tag="Kovu_77" /note=Original Glimmer call @bp 47801 has strength 11.94; Genemark calls start at 47801 /note=SSC: 47801-47523 CP: yes SCS: both ST: NI BLAST-Start: GAP: 98 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.666, -2.9625409806968013, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: HTH_36 ; Helix-turn-helix domain,,,PF13730.10,20.6522,86.1 SIF-Syn: There is not any noticeable synteny for gene 78 /note=Not enough info to determine, since its an Orpham with no data. Weak evidence for HTH or other DNA-binding domains. CDS complement (47900 - 48145) /gene="78" /product="gp78" /function="Hypothetical Protein" /locus tag="Kovu_78" /note=Original Glimmer call @bp 48145 has strength 13.87; Genemark calls start at 48145 /note=SSC: 48145-47900 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_SHROOMS_77 [Arthrobacter phage Shrooms]],,NCBI, q3:s5 97.5309% 1.33482E-19 GAP: 104 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.983, -2.417348306996335, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SHROOMS_77 [Arthrobacter phage Shrooms]],,ASR83956,60.241,1.33482E-19 SIF-HHPRED: SIF-Syn: Yes, other genomes in pham have related genes in similar spot /note=Outside signal protein CDS complement (48250 - 48573) /gene="79" /product="gp79" /function="Hypothetical Protein" /locus tag="Kovu_79" /note=Original Glimmer call @bp 48573 has strength 16.08; Genemark calls start at 48573 /note=SSC: 48573-48250 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein [Actinomycetota bacterium]],,NCBI, q49:s4 47.6636% 1.75153E-4 GAP: 200 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.508, -3.3861058366776207, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Actinomycetota bacterium]],,MDP9435981,58.1818,1.75153E-4 SIF-HHPRED: DUF2188 ; Uncharacterized protein conserved in bacteria (DUF2188),,,PF09954.13,43.9252,81.4 SIF-Syn: No homologous genes /note=no data on starterator. Big gap, but direction change. CDS 48774 - 48965 /gene="80" /product="gp80" /function="Hypothetical Protein" /locus tag="Kovu_80" /note=Original Glimmer call @bp 48774 has strength 14.49; Genemark calls start at 48774 /note=SSC: 48774-48965 CP: yes SCS: both ST: NI BLAST-Start: GAP: 200 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.906, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: Surrounding genes are found throughout homologous phages /note=Yes because it shortens the gap and includes more coding potential from the atypical p.s.. I changed it to the first start with the longest possible orf. /note=Justin: moved start back to 48774. No coding potential between this and the first start (S or host). Gap ok since direction change. CDS 48980 - 49183 /gene="81" /product="gp81" /function="Hypothetical Protein" /locus tag="Kovu_81" /note=Original Glimmer call @bp 48980 has strength 17.58; Genemark calls start at 48980 /note=SSC: 48980-49183 CP: yes SCS: both ST: NI BLAST-Start: GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.757, -2.8454123590742793, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: Look into edmundo, gene 81; it seems like they made it into a whole gene /note=no data CDS 49335 - 50213 /gene="82" /product="gp82" /function="endolysin" /locus tag="Kovu_82" /note=Original Glimmer call @bp 49335 has strength 9.97; Genemark calls start at 49335 /note=SSC: 49335-50213 CP: yes SCS: both ST: NI BLAST-Start: [endolysin [Arthrobacter phage Laroye] ],,NCBI, q1:s1 97.9452% 4.30757E-123 GAP: 151 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.747, -4.954064444624791, no F: endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Laroye] ],,YP_009603072,73.913,4.30757E-123 SIF-HHPRED: Putative peptidoglycan-binding/hydrolysing protein; Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, Peptidoglycan-Binding Protein, Glutamine Hydroxamate, HYDROLASE; HET: CME, HGA, MSE; 2.05A {Peptoclostridium difficile (strain 630)},,,5TV7_A,47.9452,96.4 SIF-Syn: Similar function in homologous genes of same location. /note=Added amidase domain as another endolysin was identified. CDS 50281 - 50874 /gene="83" /product="gp83" /function="host nuclease inhibitor" /locus tag="Kovu_83" /note=Original Glimmer call @bp 50281 has strength 12.68; Genemark calls start at 50281 /note=SSC: 50281-50874 CP: yes SCS: both ST: NI BLAST-Start: [host nuclease inhibitor [Arthrobacter phage Waltz]],,NCBI, q4:s3 97.9695% 1.11959E-85 GAP: 67 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.599, -3.635743271219807, yes F: host nuclease inhibitor SIF-BLAST: ,,[host nuclease inhibitor [Arthrobacter phage Waltz]],,ATW59957,77.9487,1.11959E-85 SIF-HHPRED: Host-nuclease inhibitor protein Gam, putative; STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics; HET: MSE; 2.75A {Desulfovibrio vulgaris} SCOP: h.4.18.1,,,2P2U_A,82.2335,99.9 SIF-Syn: Has some synteny, although numbers of genes are different genes before and after match up /note=-start 2 is found in 80% of genes in pham /note=-No change, both Gene mark and glimmer called , start includes all coding potential, and start 2 if found in 80% of genes in pham CDS 50885 - 51901 /gene="84" /product="gp84" /function="ASCE ATPase" /locus tag="Kovu_84" /note=Original Glimmer call @bp 50885 has strength 12.0; Genemark calls start at 50885 /note=SSC: 50885-51901 CP: yes SCS: both ST: NI BLAST-Start: [ATPase [Arthrobacter phage Shrooms]],,NCBI, q1:s1 99.7041% 0.0 GAP: 10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.049, -2.13349812375341, yes F: ASCE ATPase SIF-BLAST: ,,[ATPase [Arthrobacter phage Shrooms]],,ASR83962,82.5137,0.0 SIF-HHPRED: c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]} | CLASS: Alpha and beta proteins (a/b), FOLD: P-loop containing nucleoside triphosphate hydrolases, SUPFAM: P-loop containing nucleoside triphosphate hydrolases, FAM: RecA protein-like (ATPase-domain),,,SCOP_d1xp8a1,59.1716,99.4 SIF-Syn: ASCE ATPase found in the same region of genome in pham members /note=start always called when present, captures all coding potential, and good rbs score /note=N and C termini do not match up with RecA recombinase. not a good hydrolytic KNK motif. CDS 51894 - 52127 /gene="85" /product="gp85" /function="Hypothetical Protein" /locus tag="Kovu_85" /note=Original Glimmer call @bp 51894 has strength 4.36; Genemark calls start at 51894 /note=SSC: 51894-52127 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_WALTZ_82 [Arthrobacter phage Waltz]],,NCBI, q22:s13 67.5325% 1.21954E-4 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.833, -2.66371296573402, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_WALTZ_82 [Arthrobacter phage Waltz]],,ATW59959,41.6667,1.21954E-4 SIF-HHPRED: SIF-Syn: No homologous genes. /note=Orpham. No TM domains. CDS 52352 - 52591 /gene="86" /product="gp86" /function="helix-turn-helix DNA binding domain" /locus tag="Kovu_86" /note=Original Glimmer call @bp 52352 has strength 13.4; Genemark calls start at 52352 /note=SSC: 52352-52591 CP: yes SCS: both ST: NI BLAST-Start: [HTH DNA binding protein [Arthrobacter phage Laroye] ],,NCBI, q1:s1 93.6709% 4.63918E-14 GAP: 224 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.965, -2.394841452453112, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding protein [Arthrobacter phage Laroye] ],,YP_009603076,56.4706,4.63918E-14 SIF-HHPRED: Z-DNA-binding protein 1; Structural Genomics, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-BIOLOGY, Protein Structure Initiative, IMMUNE SYSTEM; NMR {Homo sapiens} SCOP: a.4.5.0, l.1.1.1,,,2LNB_A,89.8734,97.4 SIF-Syn: Yes, Similar genes found in similar places in Laroye_86, and LiSara_83 CDS 52588 - 52920 /gene="87" /product="gp87" /function="helix-turn-helix DNA binding domain" /locus tag="Kovu_87" /note=Original Glimmer call @bp 52588 has strength 13.7; Genemark calls start at 52588 /note=SSC: 52588-52920 CP: yes SCS: both ST: NI BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage Waltz]],,NCBI, q37:s22 59.0909% 1.46314E-6 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.349, -3.790975366313636, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage Waltz]],,ATW59961,43.8202,1.46314E-6 SIF-HHPRED: DNA REPLICATION PROTEIN DNAD; PRIMOSOME, DNA-BINDING PROTEIN, DNA BINDING PROTEIN; HET: CL; 2.0A {BACILLUS SUBTILIS},,,2V79_B,62.7273,97.7 SIF-Syn: Yes - surrounded by similar genes that are found in Waltz /note=2.349, -3.791 (not highest z and lowest final but the start with highest z and lowest final has an extreme gap of over 100 NT) CDS 52910 - 53806 /gene="88" /product="gp88" /function="RepA-like replication initiator" /locus tag="Kovu_88" /note=Original Glimmer call @bp 52910 has strength 10.05; Genemark calls start at 53417 /note=SSC: 52910-53806 CP: yes SCS: both-gl ST: NI BLAST-Start: [transcriptional repressor [Arthrobacter phage Laroye] ],,NCBI, q4:s6 91.6107% 5.13062E-27 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.73, -5.643396235448333, no F: RepA-like replication initiator SIF-BLAST: ,,[transcriptional repressor [Arthrobacter phage Laroye] ],,YP_009603078,45.3968,5.13062E-27 SIF-HHPRED: DNA REPLICATION PROTEIN DNAD; PRIMOSOME, DNA-BINDING PROTEIN, DNA BINDING PROTEIN; HET: CL; 2.0A {BACILLUS SUBTILIS},,,2V79_B,30.8725,98.2 SIF-Syn: It may seem like waltz combined gene 89 and 91 for them; look into this (we have diff stops), possible Sydney with LiSara_85 /note=No data but went with the start that glimmer called. /note=Justin: an odd gene, with two regions of high gene potential, separated by about 200bp of no potential. Definitely some sort of DNA-binding domain, with a decent hit to RepA. Remaining protein has no matches. CDS 53803 - 54279 /gene="89" /product="gp89" /function="helicase loader" /locus tag="Kovu_89" /note=Original Glimmer call @bp 53803 has strength 9.99; Genemark calls start at 53803 /note=SSC: 53803-54279 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein KMD23_gp85 [Arthrobacter phage Wheelbite] ],,NCBI, q1:s1 87.3418% 4.31397E-12 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.331, -3.8294249377118383, no F: helicase loader SIF-BLAST: ,,[hypothetical protein KMD23_gp85 [Arthrobacter phage Wheelbite] ],,YP_010082793,47.8571,4.31397E-12 SIF-HHPRED: replisome organizer; helical bipartite natively unfolded domain, replication; HET: MSE; 2.4A {Bacillus phage SPP1} SCOP: a.179.1.1, l.1.1.1,,,1NO1_A,47.4684,99.0 SIF-Syn: there is similarity with the genes downstream but not with the gene upstream. /note=Start 4: • Found in 8 of 8 ( 100.0% ) of genes in Pham • Manual Annotations of this start: 6 of 7 • Called 87.5% of time when present. CDS 54276 - 54623 /gene="90" /product="gp90" /function="HNH endonuclease" /locus tag="Kovu_90" /note=Original Glimmer call @bp 54309 has strength 2.68; Genemark calls start at 54276 /note=SSC: 54276-54623 CP: yes SCS: both-gm ST: NI BLAST-Start: [HNH endonuclease [Arthrobacter phage Edmundo]],,NCBI, q1:s1 91.3043% 7.41992E-33 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.103, -6.347770337501965, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage Edmundo]],,QGJ88160,66.087,7.41992E-33 SIF-HHPRED: HNH endonuclease; Thermophilic bacteriophage, HNH Endonuclease, DNA nicking, HYDROLASE; 1.52A {Geobacillus virus E2},,,5H0M_A,60.8696,98.3 SIF-Syn: -Preceded by a Hypothetical protein in pham 87994 and followed by a Helix-Turn-Helix DNA binding protein in pham 87656, just like in phages Salgado and Shrooms /note=-start 4 is found in 100% of genes in pham /note=-Start should be changed to 54276 as Genemark called because this start includes more coding potential /note= /note=-Start should be changed to 54276 due to a better 4 bp overlap, which is well supported for being the correct gene, as well as being commonly called in other phages in pham. Having a worse RBS site doesn`t really matter in this case because of the 4 bp overlap. CDS 54642 - 54896 /gene="91" /product="gp91" /function="helix-turn-helix DNA binding domain" /locus tag="Kovu_91" /note=Original Glimmer call @bp 54642 has strength 9.36; Genemark calls start at 54642 /note=SSC: 54642-54896 CP: no SCS: both ST: NI BLAST-Start: [HTH DNA binding protein [Arthrobacter phage Salgado] ],,NCBI, q6:s3 92.8571% 1.94625E-30 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.611, -6.154904741023137, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding protein [Arthrobacter phage Salgado] ],,YP_010082700,77.1084,1.94625E-30 SIF-HHPRED: RNA polymerase sigma factor SIGMA-28 (FliA); TRANSCRIPTION, SIGMA FACTOR; 2.3A {Aquifex aeolicus} SCOP: a.4.13.1, a.177.1.1, a.4.13.2,,,1RP3_C,83.3333,99.0 SIF-Syn: There is synteny with phage Wheelbite`s gene 87 for example. /note=Hits to sigma factor, but also HTH. CDS 54976 - 55128 /gene="92" /product="gp92" /function="membrane protein" /locus tag="Kovu_92" /note=Original Glimmer call @bp 54976 has strength 14.21; Genemark calls start at 54976 /note=SSC: 54976-55128 CP: yes SCS: both ST: NA BLAST-Start: GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.508, -3.3060637489568596, yes F: membrane protein SIF-BLAST: SIF-HHPRED: SIF-Syn: No true syntenty but looks similar to area in Waltz /note=Phamerator says this about transmembrane domains: deeptmhmm; Query Start (Amino Acid Position): 23-Query End; (Amino Acid Position): 44; Type: transmembrane /note=Justin: agree. Changed to Membrane protein CDS 55122 - 55448 /gene="93" /product="gp93" /function="WhiB family transcription factor" /locus tag="Kovu_93" /note=Original Glimmer call @bp 55122 has strength 3.59; Genemark calls start at 55122 /note=SSC: 55122-55448 CP: yes SCS: both ST: NI BLAST-Start: [transcriptional regulator WhiB-like [Arthrobacter phage Laroye] ],,NCBI, q10:s7 87.963% 3.31479E-35 GAP: -7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.34, -5.9139150158552, no F: WhiB family transcription factor SIF-BLAST: ,,[transcriptional regulator WhiB-like [Arthrobacter phage Laroye] ],,YP_009603083,79.0,3.31479E-35 SIF-HHPRED: Transcriptional regulator WhiB; RNA polymerase, Transcription factor, Iron cluster, TRANSCRIPTION-TRANSFERASE-DNA complex;{Streptomyces venezuelae},,,8DY7_H,60.1852,99.7 SIF-Syn: Found in area in some other AL phages. CDS 55384 - 56145 /gene="94" /product="gp94" /function="Cas4 exonuclease" /locus tag="Kovu_94" /note=Original Glimmer call @bp 55519 has strength 11.66; Genemark calls start at 55519 /note=SSC: 55384-56145 CP: yes SCS: both-cs ST: NI BLAST-Start: [exonuclease [Arthrobacter phage Shrooms]],,NCBI, q5:s18 94.4664% 1.81108E-130 GAP: -65 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.593, -3.201021426436999, yes F: Cas4 exonuclease SIF-BLAST: ,,[exonuclease [Arthrobacter phage Shrooms]],,ASR83971,70.6093,1.81108E-130 SIF-HHPRED: Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA.,,,cd09637,81.4229,99.8 SIF-Syn: Similar genes seen in related phages but not strong synteny /note=helicase match present, so calling Cas4 exonuclease. CDS 56142 - 57803 /gene="95" /product="gp95" /function="DNA helicase" /locus tag="Kovu_95" /note=Original Glimmer call @bp 56142 has strength 12.05; Genemark calls start at 56142 /note=SSC: 56142-57803 CP: yes SCS: both ST: NI BLAST-Start: [DNA helicase [Arthrobacter phage Edmundo]],,NCBI, q1:s2 99.6383% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.65, -3.1379842619144376, no F: DNA helicase SIF-BLAST: ,,[DNA helicase [Arthrobacter phage Edmundo]],,QGJ88164,89.7112,0.0 SIF-HHPRED: Chromatin-remodeling ATPase INO80; Chromatin Remodeler, hexasome, DNA BINDING PROTEIN, DNA BINDING PROTEIN-Hydrolase complex; HET: ADP; 3.41A {Saccharomyces cerevisiae S288C},,,8EUF_Q,78.8427,100.0 SIF-Syn: Has some synteny, although numbers of genes are different genes before and after match up /note=-N/A (orpham) /note=-No change, both Glimmer and Genemark called, and start includes all coding potential CDS 57881 - 58312 /gene="96" /product="gp96" /function="Hypothetical Protein" /locus tag="Kovu_96" /note=Original Glimmer call @bp 57881 has strength 11.22; Genemark calls start at 57881 /note=SSC: 57881-58312 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_SHROOMS_96 [Arthrobacter phage Shrooms]],,NCBI, q2:s10 97.2028% 2.15632E-35 GAP: 77 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.081, -4.229395370396053, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SHROOMS_96 [Arthrobacter phage Shrooms]],,ASR83975,54.1936,2.15632E-35 SIF-HHPRED: d.269.1.1 (A:7-116) Hypothetical protein PH0828 {Pyrococcus horikoshii [TaxId: 53953]} | CLASS: Alpha and beta proteins (a+b), FOLD: Gamma-glutamyl cyclotransferase-like, SUPFAM: Gamma-glutamyl cyclotransferase-like, FAM: Gamma-glutamyl cyclotransferase-like,,,SCOP_d1v30a1,86.7133,99.7 SIF-Syn: related genes found in this region of genome in pham members. similarity in the genes downstream and upstream of this gene /note=good RBS score, all coding potential. Start 7: /note=• Found in 1 of 10 ( 10.0% ) of genes in pham /note=• No Manual Annotations of this start. /note=• Called 100.0% of time when present /note= /note=Matches gamma-glutamylamine cyclotransferase, but not on approved function (though previously called by other phages) CDS 58424 - 59440 /gene="97" /product="gp97" /function="carboxylate amine ligase" /locus tag="Kovu_97" /note=Original Glimmer call @bp 58424 has strength 16.42; Genemark calls start at 58424 /note=SSC: 58424-59440 CP: yes SCS: both ST: NI BLAST-Start: [amidoligase enzyme [Arthrobacter phage Laroye] ],,NCBI, q1:s1 100.0% 6.90511E-162 GAP: 111 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.154, -4.133270333136946, no F: carboxylate amine ligase SIF-BLAST: ,,[amidoligase enzyme [Arthrobacter phage Laroye] ],,YP_009603088,80.1187,6.90511E-162 SIF-HHPRED: Amidoligase_2 ; Putative amidoligase enzyme,,,PF12224.12,61.8343,100.0 SIF-Syn: This gene has synteny because is it, and similar surrounding genes, are found throughout homologous phages in the same area. /note=Summary by start number: /note=Start 2: /note=• Found in 8 of 10 ( 80.0% ) of genes in pham /note=• Manual Annotations of this start: 7 of 9 /note=• Called 100.0% of time when present CDS 59539 - 60345 /gene="98" /product="gp98" /function="glutamine amidotransferase domain" /locus tag="Kovu_98" /note=Original Glimmer call @bp 59539 has strength 13.33; Genemark calls start at 59539 /note=SSC: 59539-60345 CP: yes SCS: both ST: NI BLAST-Start: [glutamine amidotransferase [Arthrobacter phage Laroye] ],,NCBI, q1:s1 94.7761% 2.67521E-134 GAP: 98 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.059, -2.17469248771465, yes F: glutamine amidotransferase domain SIF-BLAST: ,,[glutamine amidotransferase [Arthrobacter phage Laroye] ],,YP_009603089,70.5085,2.67521E-134 SIF-HHPRED: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE; TRANSFERASE, GLUTAMINE AMIDOTRANSFERASE, PRTASE, PURINE BIOSYNTHESIS, PHOSPHORIBOSYLTRANSFERASE, GLYCOSYLTRANSFERASE; HET: ADP, 5GP, SF4; 2.8A {Bacillus subtilis} SCOP: d.153.1.1, c.61.1.1,,,1AO0_B,85.0746,99.9 SIF-Syn: Preceded by an gene in pham 6034 like in Salgado and Edmundo. /note=All of the other genes in this pham were also glutamine amidotransferase domain proteins CDS join(60371. .60393;1. .229) /gene="99" /product="gp99" /function="Hypothetical Protein" /locus tag="Kovu_99" /note=Original Glimmer call @bp 60371 has strength 8.94 /note=SSC: 60371-229 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein SEA_KHARCHO_67 [Arthrobacter phage Kharcho] ],,NCBI, q1:s1 97.5904% 1.14644E-19 GAP: 25 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.498, -4.155797982979146, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_KHARCHO_67 [Arthrobacter phage Kharcho] ],,WIC89113,63.2184,1.14644E-19 SIF-HHPRED: Polysaccharide deacetylase; deacetylase, beta alpha barrel, carbohydrate binding, family 4 carbohydrate esterase, HYDROLASE; 1.7A {Ammonifex degensii},,,4WCJ_A,92.7711,67.8 SIF-Syn: N/a gene not found in other AL phages