Skip to main content

Table 1 KS5 genome annotation

From: Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex

Gene Start End Putative function Strand Predicted RBS and start codon Length (no. of aa residues) Closest relative (excluding ATCC 17616) Alignment region (no. of aa residues) % ID Source GenBank accession no. ATCC 17616 locus tag ATCC 17616 GenBank accession no.
1 108 815 integrase - AGCAACAAGcacaaggcaTTG 235 integrase family protein 134-368/368 87 Burkholderia thailandensis MSMB43 ZP_02468407.1 BMULJ_03640 YP_001948048.1
2 2142 4937 zinc finger CHC2-family protein - GAGCAACAGcaataacgATG 931 conserved hypothetical protein 1-931/931 96 Burkholderia multivorans CGD1 ZP_03587581.1 BMULJ_03641 YP_001948049.1
3 4940 5200 unknown - GGGGGAAGccgcATG 86 conserved hypothetical protein 1-86/86 91 Burkholderia multivorans CGD1 ZP_03587582.1 BMULJ_03642 YP_001948050.1
4 5197 5556 unknown - GGGGGTGAtgtgATG 119 conserved hypothetical protein 1-119/119 97 Burkholderia multivorans CGD1 ZP_03587583.1 BMULJ_03643 YP_001948051.1
5 5561 5755 membrane protein - GGAGccaaaccATG 64 putative phage-encoded membrane protein 1-64/64 78 Burkholderia ambifaria MEX-5 ZP_02905725.1 BMULJ_03644 YP_001948052.1
6 5798 6001 unknown - GGATGcactgaccgATG 67 conserved hypothetical protein 1-67/67 92 Burkholderia multivorans CGD1 ZP_03587585.1 BMULJ_03645 YP_001948053.1
7 6005 6199 unknown - GGAGAGActcATG 64 conserved hypothetical protein 1-64/64 98 Burkholderia multivorans CGD1 ZP_03587586.1 BMULJ_03646 YP_001948054.1
8 6289 6537 transcriptional activator (Ogr) - GTAGGAGccccgaATG 82 transcriptional activator Ogr/delta 1-82/82 91 Burkholderia cenocepacia MC0-3 YP_001763475.1 BMULJ_03647 YP_001948055.1
9 6547 6825 DNA binding protein - GGGCGttgagtcATG 92 putative phage DNA-binding protein 1-92/92 98 Burkholderia ambifaria MEX-5 ZP_02905729.1 BMULJ_03648 YP_001948056.1
10 6829 7065 unknown - GAAGGGAAGtataccgtcATG 78 putative bacteriophage protein 1-77/78 80 Burkholderia sp. CCGE1001 ZP_06292840.1 BMULJ_03649 YP_001948057.1
11 7121 7603 repressor + GATAATACAcaccgatcgGTG 160 putative phage DNA-binding protein 12-166/167 79 Burkholderia pseudomallei K96243 YP_106769.1 BMULJ_03650 YP_001948058.1
12 7660 8406 membrane protein + AGGGAAttcaATG 248 putative phage-encoded membrane protein 1-241/249 43 Burkholderia pseudomallei K96243 YP_106770.1 BMULJ_03651 YP_001948059.1
  8971 8975 direct repeat flanking ISBmu 23           
ISBmu 23 8976 10185 ISBmu 23 insertion sequence           
  8976 8991 ISBmu 23 inverted repeat           
  9063 10055 ISBmu 23 transposase + GGAACGGAcccacgacgATG 330 transposase IS4 family protein 1-330/330 100 Burkholderia sp. Ch1-1 ZP_06846513.1 BMULJ_03652 YP_001948060.1
  10170 10185 ISBmu 23 inverted repeat           
  10185 10189 direct repeat flanking ISBmu 23           
13 10359 11510 tail protein (D) - AAGGAGGcgatctcgctATG 383 phage late control gene D protein 1-379/382 96 Burkholderia multivorans CGD1 ZP_03587594.1 BMULJ_03653 YP_001948061.1
14 11507 11935 tail protein (U) - GAAGGAGGGAttgtcATG 142 bacteriophage gpU 1-142/142 95 Burkholderia multivorans CGD1 ZP_03587595.1 BMULJ_03654 YP_001948062.1
15 11949 14711 tail tape measure protein (T) - GAGCGAGGcgacgaATG 920 putative phage-related tail transmembrane protein 1-919/919 91 Burkholderia cenocepacia MC0-3 YP_001763483.1 BMULJ_03655 YP_001948063.1
16 14827 15138 tail protein (E) - AGAGGAAccatacgATG 103 phage tail protein E 1-103/103 97 Burkholderia multivorans CGD1 ZP_03587598.1 BMULJ_03657 YP_001948065.1
17 14708 15138 tail protein (E+E') - AGAGGAAccatacgATG 143 phage tail protein E 1-87/103 97 Burkholderia multivorans CGD1 ZP_03587598.1 BMULJ_03656
BMULJ_03657
YP_001948064.1
YP_001948065.1
18 15171 15680 tail tube protein (FII) - AGGGAAAcgcaATG 169 phage major tail tube protein 1-169/169 94 Burkholderia multivorans CGD1 ZP_03587599.1 BMULJ_03658 YP_001948066.1
19 15710 16882 tail sheath protein (FI) - GGGAGAttgcATG 390 tail sheath protein 1-390/390 94 Burkholderia cenocepacia MC0-3 YP_001763487.1 BMULJ_03659 YP_001948067.1
20 16993 17742 N-4/N-6 DNA methylase - GAGGGAAtcgccccATG 249 DNA methylase N-4/N-6 domain protein 1-249/249 89 Burkholderia ambifaria MEX-5 ZP_02905740.1 BMULJ_03660 YP_001948068.1
21 17720 17902 Com translational regulator - AAGCAGGAAtcacccgATG 60 hypothetical protein Bcenmc03_0187 1-60/60 85 Burkholderia cenocepacia MC0-3 YP_001763489.1 BMULJ_03661 YP_001948069.1
22 18049 18927 tail fiber assembly protein - GAGACACAcctATG 292 gp31, bacteriophage-acquired protein 1-272/278 89 Burkholderia multivorans CGD1 ZP_03587603.1 BMULJ_03662 YP_001948070.1
23 18937 20547 tail fiber protein - GGATAcctgaacATG 536 bacteriophage protein 1-536/536 99 Burkholderia multivorans CGD1 ZP_03587604.1 BMULJ_03663 YP_001948071.1
24 20550 21104 baseplate assembly protein (I) - GGGGTGGccgATG 184 ZP_03587605.1 1-184/184 92 Burkholderia multivorans CGD1 ZP_03587605.1 BMULJ_03664 YP_001948072.1
25 21097 22002 baseplate assembly protein (J) - GAGGCAcggcATG 301 ZP_03587606.1 1-301/301 94 Burkholderia multivorans CGD1 ZP_03587606.1 BMULJ_03665 YP_001948073.1
26 21999 22376 ZP_03587607.1 - GAAGGGGcacggATG 125 baseplate assembly protein W (GpW) 1-125/125 89 Burkholderia multivorans CGD1 ZP_03587607.1 BMULJ_03666 YP_001948074.1
27 22373 23005 baseplate assembly protein (V) - GCGGCAtccttgccgcATG 210 YP_001763496.1 1-137/234 78 Burkholderia cenocepacia MC0-3 YP_001763496.1 BMULJ_03667 YP_001948075.1
28 23206 25086 exonuclease (Old) - AAGTGGGGAccaactATG 626 ATP-dependent endonuclease 1-625/626 72 Cupriavidus metallidurans CH34 YP_586772.1 BMULJ_03668 YP_001948076.1
29 25269 25718 tail completion protein (S) - GGGGAcgtgATG 149 phage virion morphogenesis protein 1-148/149 89 Burkholderia multivorans CGD1 ZP_03587610.1 BMULJ_03669 YP_001948077.1
30 25718 26128 tail completion protein (R) - AGGAGGcgccGTG 136 P2 phage tail completion protein R (GpR) 1-136/136 96 Burkholderia multivorans CGD1 ZP_03587611.1 BMULJ_03670 YP_001948078.1
31 26172 26366 Rz1 - AAGGAGGttccggtttATG 64 Ribonuclease, Rne/Rng family 15-48/928 47 Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1 YP_003687809.1 none  
32 26125 26616 Rz - GGGTGGccgcATG 163 conserved hypothetical protein 1-163/163 85 Burkholderia ambifaria MEX-5 ZP_02905751.1 BMULJ_03671 YP_001948079.1
33 26613 27413 endolysin - GGGGGcgccATG 266 peptidoglycan binding domain-containing protein 1-266/266 90 Burkholderia cenocepacia MC0-3 YP_001763501.1 BMULJ_03672 YP_001948080.1
34 27406 27726 holin - AAGGGGAGGGAcaagtgATG 106 protein of unknown function DUF754 1-106/106 88 Burkholderia ambifaria MEX-5 ZP_02905753.1 BMULJ_03673 YP_001948081.1
35 27726 28100 putative antiholin - ATGGGActgagaATG 124 phage-related transmembrane protein 1-124/124 96 Burkholderia multivorans CGD1 ZP_03587615.1 BMULJ_03674 YP_001948082.1
36 28103 28315 tail protein (X) - AGGGAGctgtcctgATG 70 tail X family protein 1-70/70 94 Burkholderia cenocepacia MC0-3 YP_001763504.1 BMULJ_03675 YP_001948083.1
37 28315 28557 unknown - GTGGAGctcatctgATG 80 conserved hypothetical protein 1-80/80 72 Burkholderia multivorans CGD1 ZP_03587617.1 BMULJ_03676 YP_001948084.1
38 28557 29033 capsid completion protein (L) - AACGTGACGAAcccgaccATG 158 head completion protein 1-160/160 85 Burkholderia ambifaria MEX-5 ZP_02905755.1 BMULJ_03677 YP_001948085.1
39 29138 29824 terminase endonuclease subunit (M) - GGGTGGcgcATG 228 terminase 1-228/228 93 Burkholderia multivorans CGD1 ZP_03587619.1 BMULJ_03678 YP_001948086.1
40 29821 30846 capsid protein (N) - AAACGGAGAAtccATG 341 phage major capsid protein, P2 family 1-339/339 77 Burkholderia ambifaria MEX-5 ZP_02905757.1 BMULJ_03679 YP_001948087.1
41 30884 31705 capsid scaffolding protein (O) - AGAGGtttcgcacATG 273 phage capsid scaffolding protein GpO 1-273/273 95 Burkholderia multivorans CGD1 ZP_03587621.1 BMULJ_03680 YP_001948088.1
42 31855 33621 terminase ATPase subunit (P) + GGTAGccttgctgcATG 588 putative ATPase subunit of terminase (gpP-like) 1-583/583 92 Burkholderia multivorans CGD1 ZP_03587622.1 BMULJ_03681 YP_001948089.1
43 33621 34673 portal vertex protein (Q) + ATGGAGAttttctgATG 350 phage portal protein, pbsx family 1-348/349 92 Burkholderia multivorans CGD1 ZP_03587623.1 BMULJ_03682 YP_001948090.1
44 35144 36163 reverse transcriptase - GAATGGAtttccgaaaATG 339 putative reverse transcriptase 2-285/292 42 Sideroxydans lithotrophicus ES-1 YP_003522714.1 BMULJ_03683 YP_001948091.1
45 36120 36443 transcriptional regulator - GAAGGAGttgcatATG 107 transcriptional regulator 1-97/97 52 Acinetobacter baumannii ACICU YP_001840883.1 BMULJ_03684 YP_001948092.1
  1. Abbreviations: RBS, ribosome-binding site; aa, amino acid, % ID, percent identity. The P2 proteins that are similar to KS5 proteins based on CoreGenes analysis are shown in brackets in the putative function column. Excluding genes 17 and 31, annotations were based on those of the B. multivorans ATCC 17616 chromosome 2 sequence (NC_010805.1; BMULJ_03640 - BMULJ_03684, bp 477496-514731).