Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

Saunders, Nigel J; Boonmee, Prawit; Peden, John F; Jarvis, Stephen A

doi:10.1186/1471-2164-6-9

Table 5 Top 50 most divergent genes by TNS in H. pylori strain 26695 plus those additional genes > 2 SD greater than the mean by DNS and the 50 most divergent by HNS

From: Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

TNS order	annotation	HP#	J99 #	DNS order	HNS order
1	cag pathogenicity island protein (cag7)	HP0527	JHP0476	1	1
2	vacuolating cytotoxin (vacA) paralog	HP0289	JHP0274	2	4
3	hypothetical protein	HP0427	JHP0952	14	737
4	hypothetical protein	HP1408	JHP1300	15	738
5	vacuolating cytotoxin (vacA) paralog	HP0922	JHP0856	6	3
6	hypothetical protein	HP0609	JHP0556*	4	9
7	hypothetical protein	HP0119	NAH	17	2
8	poly E-rich hypothetical protein	HP0322	JHP0305	3	5
9	histidine and glutamine-rich metal-binding protein	HP1432	JHP1321	46	1432
10	hypothetical protein	HP0488	JHP0440	7	12
11	hypothetical protein	HP1116	JHP1044	8	13
12	vacuolating cytotoxin (vacA) paralog	HP0610	JHP0556*	13	17
13	secreted protein involved in flagellar motility	HP1192	JHP1117	410	1256
14	hypothetical protein	HP0996	JHP0942	5	46
15	cag island protein (cagA)	HP0547	JHP0495	31	7
16	hypothetical protein	HP0058	JHP0051	121	53
17	outer membrane protein (omp26)	HP1157	JHP1084	34	25
18	hypothetical protein	HP0080	JHP0074	9	122
19	hypothetical protein	HP1142	JHP1070	91	6
20	hypothetical protein	HP1520	NAH	167	33
21	hypothetical protein	HP0059	JHP0052	43	320
22	hypothetical protein	HP0906	JHP0842	42	16
23	DNA-directed RNA polymerase, beta subunit (rpoB)	HP1198	JHP1121	84	19
24	hypothetical protein	HP0030	JHP0026	45	39
25	vacuolating cytotoxin (vacA)	HP0887	JHP0819	18	34
26	histidine-rich, metal binding polypeptide (hpn)	HP1427	NAH	39	1449
27	hypothetical protein	HP0118	JHP0110	179	36
28	hypothetical protein	HP0513	JHP0462	122	15
29	hypothetical protein	HP1143	JHP1071	58	41
30	type III restriction enzyme R protein (res)	HP0592	NAH	16	35
31	hypothetical protein	HP1187	JHP1113	142	38
32	hypothetical protein	HP0508	JHP0458	139	77
33	hypothetical protein	HP1115	JHP1042	20	866
34	hypothetical protein	HP1516	NAH	593	1090
35	N-methylhydantoinase	HP0696	JHP0632	19	43
36	hypothetical protein	HP0489	JHP0441	10	582
37	hypothetical protein	HP0611	JHP0299	230	1129
38	urease beta subunit (urea amidohydrolase) (ureB)	HP0072	JHP0067	21	87
39	integrase/recombinase (xerD)	HP0995	JHP0941	25	448
40	flagellin A (flaA)	HP0601	JHP0548	33	180
41	multidrug resistance protein (spaB)	HP0600	JHP0547	97	30
42	type IIS restriction enzyme R and M protein (ECO57IR)	HP1517	NAH	28	14
43	fucosyltransferase	HP0651	JHP0596	48	75
44	hypothetical protein	HP0120	NAH	283	50
45	outer membrane protein (omp3)	HP0079	JHP0073	68	99
46	hypothetical protein	HP0345	NAH	249	1338
47	outer membrane protein (omp17)	HP0725	JHP0662	209	101
48	cag pathogenicity island protein (cag3)	HP0522	JHP0471	11	100
49	virB4 homolog (virB4)	HP0459	NAH	53	28
50	cag pathogenicity island protein (cag8)	HP0528	JHP0477	74	27
51	DNA transfer protein (cagE)	HP0441	JHP0492	29	22
53	hypothetical protein	HP1333	JHP1253	40	296
55	RNA polymerase sigma-70 factor (rpoD)	HP0088	JHP0081	56	31
58	hypothetical protein	HP0453	NAH	75	10
60	hypothetical protein	HP0669	JHP0613	69	42
61	hypothetical protein	HP1003	NAH	38	170
64	translation elongation factor EF-Tu (tufB)	HP1205	JHP1128	49	166
67	hypothetical protein	HP1089	JHP0336	12	59
71	hypothetical protein	HP0756	JHP0693	24	1548
72	hypothetical protein	HP0788	JHP0725	41	256
73	2',3'-cyclic-nucleotide 2'-phosphodiesterase (cpdB)	HP0104	JHP0096	54	68
77	DNA polymerase I (polA)	HP1470	JHP1363	30	54
78	hypothetical protein	HP0205	JHP0191	57	8
80	hypothetical protein	HP0731	JHP0668	132	32
81	hypothetical protein	HP0449	NAH	51	449
86	type I restriction enzyme R protein (hsdR)	HP1402	JHP1424	103	21
87	cag pathogenicity island protein (cag12)	HP0532	JHP0481	23	693
90	type I restriction enzyme R protein (hsdR)	HP0464	NAH	36	26
99	iron(III) dicitrate transport protein (fecA)	HP1400	JHP1426	32	129
101	type I restriction enzyme R protein (hsdR)	HP0846	JHP0784	342	37
102	cytochrome oxidase (cbb3 type) (fixN)	HP0144	JHP0132	27	168
119	type III restriction enzyme R protein	HP1371	JHP1285	52	23
120	adenine/cytosine DNA methyltransferase	HP0054	NAH	109	20
130	hypothetical protein	HP0186	JHP0174	47	276
137	DNA mismatch repair protein (MutS)	HP0621	JHP0565	22	64
147	outer membrane protein	HP0486	JHP0438	26	142
149	DNA topoisomerase I (topA)	HP0440	NAH	63	24
153	hypothetical protein	HP1479	JHP1372	55	127
154	DNA repair protein (recN)	HP1393	JHP1434	35	207
163	hypothetical protein	HP0586	JHP0534	631	29
164	virulence associated protein homolog (vacB)	HP1248	JHP1169	50	160
169	GMP reductase (guaC)	HP0854	JHP0790	44	451
176	preprotein translocase subunit (secA)	HP0786	JHP0723	119	49
181	cell division protein (ftsK)	HP1090	JHP0335	37	90
207	adenine specific DNA methyltransferase (mod)	HP1522	JHP1411	363	11
210	type III restriction enzyme R protein (res)	HP1521	JHP1410	195	18
219	DNA polymerase III alpha-subunit (dnaE)	HP1460	JHP1353	297	47
220	type II restriction enzyme (methyltransferase)	HP0478	JHP0430	1080	40
222	hypothetical protein	HP0733	JHP0670	224	48
225	cag pathogenicity island protein (cag13)	HP0534	JHP0482	60	1021
272	hypothetical protein	HP1106	JHP1033	59	277
332	translation initiation factor IF-2 (infB)	HP1048	JHP0377	291	45
340	type I restriction enzyme M protein (hsdM)	HP1403	JHP1423	125	44

* probably frame shifted components of the same vacA related gene
Genes with > 2 SD divergence in each analysis are indicated in bold
NAH indicates No Annotated Homologue in the other sequence

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ISSN: 1471-2164

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