Table 2 |
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|
Phage KS10 putative genes and homologues |
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|
GP |
Coding |
Str. |
Possible RBS* & Start Codon |
AA |
Putative Function |
Alignment Region |
% Identity |
Score |
% GC |
Sig. matches to proteins in NCBI's GenBank |
|
|
||||||||||
|
1 |
205–1437 |
- |
AGGCGcgtaaATG |
410 |
virion morphogenesis |
400(28–418)/248(16–263) |
30%/33% |
160/137 |
63.26 |
Pseudomonas bacteriophage B3 gp33/BcepMu gp30 |
|
2 |
1438–1698 |
- |
AAAGGAGccaacaATG |
86 |
hyp. protein |
- |
- |
- |
61.69 |
no sig. match |
|
3 |
1743–3278 |
- |
GGAAG//36 bp//cgtttATG |
511 |
portal |
354(35–374) |
32% |
182 |
62.57 |
BcepMu gp29 |
|
4 |
3268–4884 |
- |
AAGAGGcctgatccacgATG |
538 |
terminase large subunit** |
520(4–521) |
55% |
569 |
58.94 |
D3112 p26 |
|
5 |
4891–5388 |
- |
AAGGGttgacgcATG |
165 |
terminase small subunit** |
164(1–164) |
37% |
161 |
59.24 |
D3112 p24 |
|
6 |
5392–5682 |
- |
AGGGTATccgcgATG |
96 |
hyp. protein |
- |
- |
- |
59.45 |
no sig. match |
|
7 |
5679–5903 |
- |
GGATAacgATG |
74 |
dksA/traR C4-type zinc finger |
74(1–72) |
45% |
44.3 |
60.89 |
Enterobateria phage WPhi gp82 |
|
8 |
5893–6186 |
- |
GAGGAtgcccgtcATG |
102 |
hyp. protein |
- |
- |
- |
65.99 |
no sig. match |
|
9 |
6466–7137 |
- |
GTGGGcctcgcagcATG |
223 |
endolysin |
186(20–203) |
54% |
188 |
65.03 |
BcepMu gp22 |
|
10 |
7134–7535 |
- |
GGGTGccgccgtcgcgaATG |
133 |
holin |
119(1–111)/116(8–113) |
36%/39% |
72.4/63.5 |
58.96 |
Ralstonia solanacearum UW551***/BcepMu gp21 |
|
11 |
7650–8258 |
- |
GGGAAGcgcgaaATG |
202 |
hyp. protein |
177(53–211) |
26% |
45.4 |
53.53 |
Pseudomonas entomophila L48 |
|
12 |
8251–8784 |
- |
GGGAATAtgtaaagcATG |
177 |
hyp. protein |
- |
- |
- |
54.87 |
no sig. match |
|
13 |
8839–9309 |
- |
AAGAGGccgaccATG |
156 |
hyp. protein/phage repressor |
131(1–125)/137(2–127) |
39%/36% |
85.1/72.4 |
56.69 |
E. coli B171/BcepMu gp17 |
|
14 |
9391–9582 |
+ |
GGAGcaaatATG |
63 |
DNA binding protein/conserved hyp. protein |
62(5–65)/59(1–57) |
33%/52% |
38.1/65.1 |
58.85 |
BcepMu gp16/Ralstonia solanacearum UW551 |
|
15 |
9579–10631 |
+ |
GGGGAGGtggATG |
350 |
conserved hyp. protein |
141(49–186)/127(77–203) |
28%/28% |
38.1/44.7 |
64.71 |
BcepMu gp10/Ralstonia solanacearum UW551 |
|
16 |
10671–12296 |
+ |
AGGTGcgatATG |
541 |
transposase |
539(24–559) |
36% |
336 |
65.19 |
Ralstonia solanacearum UW551 |
|
17 |
12306–13298 |
+ |
GAATAAGGAGtgaccATG |
330 |
transposition protein |
309(7–311) |
42% |
222 |
64.15 |
Ralstonia solanacearum UW551 |
|
18 |
13306–13494 |
+ |
GTGAGGccatcATG |
62 |
hyp. protein |
- |
- |
- |
66.14 |
no sig. match |
|
19 |
13491–13796 |
+ |
GAGGTGAcggcATG |
101 |
hyp. protein |
- |
- |
- |
69.28 |
no sig. match |
|
20 |
13859–14371 |
+ |
TGGccgacgacagcATG |
170 |
hyp. protein |
172(55–187) |
60% |
180 |
67.25 |
Ralstonia solanacearum UW551 |
|
21 |
14368–14994 |
+ |
AAGGAAcccatcATG |
208 |
conserved protein |
200(9–210)/199(6–204) |
72%/55% |
210/205 |
63 |
Ralstonia solanacearum UW551/BcepMu gp05 |
|
22 |
15005–15397 |
+ |
GAGGGGctggccATG |
130 |
hyp. protein |
- |
- |
- |
66.16 |
no sig. match |
|
23 |
15460–15732 |
+ |
AGGAGAAAcaccctcATG |
90 |
DNA binding protein Hu-beta |
90(1–90) |
57% |
108 |
64.47 |
Bordetella pertussis Tohama I |
|
24 |
15809–16642 |
+ |
GAGGAAccccaaaATG |
277 |
hyp. protein |
117(51167)/58(344–401) |
53%/67% |
114 |
62.83 |
Burkholderia thailandensis E264 gp38 |
|
25 |
16806–17126 |
+ |
GGGGAGTGAcactgtgATG |
106 |
hyp. protein |
111(9–119) |
37% |
55.1 |
64.49 |
Burkholderia pseudomallei K96243 |
|
26 |
17128–17568 |
+ |
GGAGGcccgctgacATG |
146 |
modulation of host genes? |
129(9–135) |
30% |
58.5 |
64.17 |
Escherichia coli B7A/Mu gp16 |
|
27 |
17565–17963 |
+ |
GAAACGAccgcATG |
132 |
middle operon regulator (Mor)**** |
106(14–118) |
31% |
52.8 |
64.91 |
Pseudomonas entomophila L48 |
|
28 |
18120–19322 |
+ |
AGAGAAccatTTG |
400 |
protease |
330(10–322) |
33% |
147 |
65.59 |
BcepMu gp32 |
|
29 |
18876–19322 |
+ |
AGGAagccATG |
148 |
scaffold |
- |
- |
- |
67.11 |
BcepMu gp33 |
|
30 |
19368–19724 |
+ |
AGAGGATtcacATG |
118 |
conserved hyp. protein |
77(41–117)/80(32–109) |
54%/42% |
72.4/44.3 |
71.71 |
Bacteriophage B3 gp37/BcepMu gp35 |
|
31 |
19775–20722 |
+ |
GGAGctatccATG |
315 |
major head subunit |
311(4–307) |
47% |
243 |
64.87 |
Bacteriophage B3 gp34 |
|
32 |
20797–21186 |
+ |
AAGAGAGatcATG |
129 |
hyp. protein |
- |
- |
- |
66.92 |
no sig. match |
|
33 |
21183–21686 |
+ |
GAAGGGccgcaaATG |
167 |
hyp. protein |
- |
- |
- |
65.48 |
no sig. match |
|
34 |
21683–22114 |
+ |
GGATAGGTAcgggaaATG |
143 |
virion morph. |
161(8–156) 121(7–124) |
31%/36% |
161/52.4 |
60.19 |
Thermus aquaticus Y51MC23/Escherichia coli 53638 (MuG) |
|
35 |
22114–22716 |
+ |
GGTGAGGATGAtgtgATG |
200 |
phage-related conserved hyp. protein |
165(1–164) |
24% |
41.2 |
61.36 |
Burkholderia thailandensis MSMB43 |
|
36 |
22700–22978 |
+ |
ACGGG//25 bp//gatATG |
92 |
hyp. protein |
- |
- |
- |
64.52 |
no sig. match |
|
37 |
23022–24500 |
+ |
AAGGGAcattcgacATG |
492 |
tail sheath protein |
472(12–481) |
34% |
188 |
63.15 |
Prophage MuSo2 (Marinomonas sp.)/MuL (gp39) |
|
38 |
24546–24917 |
+ |
AAGGGAGTGaaacATG |
123 |
hyp. protein |
- |
- |
- |
62.9 |
no sig. match |
|
39 |
25000–25554 |
+ |
TGAGATTcccaccATG |
184 |
tail assembly chaperone |
- |
- |
- |
62.88 |
FluMu gp41** |
|
40 |
25603–28038 |
+ |
GAGGAAGAgacgATG |
811 |
tail tape measure (TP109 fam.) |
484(3–458) |
38% |
265 |
64.2 |
Burkholderia vietnamiensis G4 |
|
41 |
28038–29408 |
+ |
GGAGGAAcgaactgATG |
456 |
DNA circulation protein |
455(3–412) |
27% |
150 |
65.43 |
Polaromonas sp. JS666/MuN (gp47) |
|
42 |
29414–30571 |
+ |
TGAcccctATG |
385 |
tail protein |
352(96–337) |
33% |
153 |
63.04 |
Polaromonas sp. JS666/MuP (gp44) |
|
43 |
30571–31092 |
+ |
GGAGcaaactgATG |
173 |
baseplate assembly |
60(36–188) |
30% |
63.5 |
61.88 |
Escherichia. coli 0157:H7 str. EC4501/MuQ (gp45) |
|
44 |
31177–31758 |
+ |
AGGccatcATG |
193 |
tail protein |
99(25–112) |
47% |
70.9 |
64.6 |
MuV (gp46) |
|
45 |
31755–32876 |
+ |
GGAAAAcatcATG |
476 |
tail protein |
306(24–325) |
36% |
144 |
65.86 |
Pseudomonas entomophila L48/MuW (gp47) |
|
46 |
32879–33478 |
+ |
AGGAGTgaccGTG |
173 |
tail protein |
197(5–192) |
26% |
57 |
65.17 |
Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough |
|
47 |
33478–34455 |
+ |
GGAcatcgactgATG |
325 |
tail fiber protein |
229(310–534) |
42% |
140 |
62.47 |
Burkholderia multivorans ATCC 17616 |
|
48 |
34463–36691 |
+ |
TGAGGcacgcATG |
742 |
ABC-type phosphate transport sys. |
459(40–493) |
46% |
364 |
60 |
Pseudomonas stutzeri A1501 |
|
49 |
36711–37475 |
+ |
GAGGTAcaaATG |
254 |
hyp. protein |
270(1–248) |
28% |
81.3 |
59.48 |
Klebsiella pneumoniae 342 KPK_4114 |
|
|
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|
Abbreviations: GP, gene product; Str., strand; RBS, ribosome-binding site; AA, amino acid; hyp, hypothetical; sig, significant; subsp, subspecies; *Putative RBS binding sites for gp1, gp4, and gp37 were identified using RBS finder. **Function predicted using PSI-BLAST ***All R. solanacearum UW551 references refer to unfinished DNA segment NZ_AAKL01000024.1 ****Function predicted using PHYRE database |
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|
Goudie et al. BMC Genomics 2008 9:615 doi:10.1186/1471-2164-9-615 |
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