Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes

Paul, Sandip; Bag, Sumit K; Das, Sabyasachi; Harvill, Eric T; Dutta, Chitra

doi:10.1186/gb-2008-9-4-r70

Table 3 Top 20 amino acid pairs of 4 orthologous groups according to differences and ratios in number of forward (non-halophiles to halophiles) and backward (halophiles to non-halophiles) replacements

From: Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes

	Most biased in gain					Most biased in ratio
	Pair	Ratio	Forward no.	Reverse no.	Gain	Pair	Ratio	Forward no.	Reverse no.	Gain
Set I (orthologous proteins	I→V	1.82	1,632	895	737	C→D	9	27	3	24*
of PLUT and SRUB)	I→L	1.85	1,195	647	548	I→D	8.5	34	4	30*
	K→E	4.09	704	172	532	I→P	8.43	59	7	52*
	K→R	2.06	856	416	440	K→D	6.35	438	69	369
	K→D	6.35	438	69	369	I→R	6.18	105	17	88
	E→D	1.39	1,214	874	340	L→D	4.46	107	24	83
	G→D	2.43	485	200	285	K→P	4.38	140	32	108
	S→A	1.53	818	534	284	K→E	4.09	704	172	532
	S→D	2.56	438	171	267	L→W	4.08	49	12	37
	N→D	2.45	431	176	255	M→P	3.43	48	14	34
	K→Q	2.84	330	116	214	M→E	3.28	95	29	66
	S→T	1.52	616	405	211	F→H	3.27	85	26	59
	L→V	1.31	833	635	198	I→E	3.03	94	31	63
	R→D	2.57	308	120	188	M→R	2.95	112	38	74
	S→E	1.82	403	221	182	L→E	2.91	201	69	132
	A→D	1.77	415	235	180	K→Q	2.84	330	116	214
	K→A	2.47	287	116	171	K→G	2.74	167	61	106
	L→R	2.65	252	95	157	L→R	2.65	252	95	157
	K→T	2.64	230	87	143	K→T	2.64	230	87	143
	R→E	1.39	497	357	140	R→D	2.57	308	120	188
Set II (orthologous proteins	K→E	5.19	306	59	247	K→D	8.56	214	25	189
of PPUT and HMAR1)	I→V	1.62	521	321	200	L→D	5.6	56	10	46
	L→V	1.75	462	264	198	K→E	5.19	306	59	247
	A→E	2.28	351	154	197	Q→D	5.11	189	37	152
	K→D	8.56	214	25	189	K→S	4.92	59	12	47
	A→D	2.93	264	90	174	H→D	4.44	80	18	62
	Q→E	2.44	266	109	157	I→D	4.2	21	5	16
	Q→D	5.11	189	37	152	I→Y	4	40	10	30
	G→D	2.41	210	87	123	P→H	3.8	19	5	14
	R→D	2.71	160	59	101	M→E	3.63	29	8	21
	R→E	1.95	207	106	101	L→P	3.43	48	14	34
	N→D	2.35	169	72	97	Y→D	3.38	27	8	19
	E→D	1.25	429	343	86	K→T	3.29	102	31	71
	S→T	1.46	249	170	79	C→A	3.24	81	25	56
	S→D*	1.9	152	80	72	L→E	3.13	100	32	68
	K→T	3.29	102	31	71	K→G	2.95	65	22	43
	A→T	1.55	198	128	70	A→D	2.93	264	90	174
	P→D	2.82	107	38	69	K→P	2.91	32	11	21
	L→I*	1.25	349	280	69	P→D	2.82	107	38	69
	L→E	3.13	100	32	68	I→E	2.75	44	16	28
Set III (orthologous proteins	I→V	2.23	3,368	1,513	1,855	C→Q	10.00	30	3	27*
of MTHP and HMAR1)	R→E	2.62	1,836	701	1,135	K→D	7.30	883	121	762
	R→D	4.34	1,306	301	1,005	M→D	7.28	182	25	158
	E→D	1.52	2,576	1,693	883	C→D	5.31	69	13	56
	K→E	4.11	1,162	283	879	I→Q	5.10	148	29	119
	I→L	1.70	2,087	1,230	857	M→Q	4.91	157	32	125
	S→D	2.84	1,312	462	850	C→E	4.86	68	14	54
	K→D	7.30	883	121	762	I→D	4.80	192	40	152
	L→V	1.60	1,978	1,237	741	L→D	4.49	337	75	262
	G→D	2.35	1,183	504	679	M→H	4.44	80	18	62
	S→A	1.61	1,556	967	589	K→Q	4.42	407	92	315
	S→E	2.00	1,054	527	527	R→D	4.34	1,306	301	1,005
	R→A	2.14	978	458	520	K→E	4.11	1,162	283	879
	R→T	3.10	740	239	501	K→G	4.04	331	82	249
	L→A	2.11	946	448	498	C→N	4.00	32	8	24*
	I→A	2.76	756	274	482	I→W	3.88	62	16	46
	I→T	3.84	572	149	423	I→T	3.84	572	149	423
	V→T	1.88	892	475	417	M→E	3.81	259	68	191
	N→D	2.23	753	337	416	K→T	3.79	425	112	313
	R→Q	2.45	697	284	413	W→D	3.69	48	13	35*
Set IV (orthologous proteins	I→V	2.58	3,584	1,389	2,195	K→D	12.93	1,461	113	1,348
of UMET and NPHA)	K→E	8.72	2,023	232	1,791	K→E	8.72	2,023	232	1,791
	K→D	12.93	1,461	113	1,348	K→A	8.28	993	120	873
	K→R	3.01	1,623	540	1,083	K→G	6.57	519	79	440
	I→L	1.95	2,135	1,096	1,039	M→D	6.50	130	20	110
	K→A	8.28	993	120	873	M→R	5.59	246	44	202
	N→D	3.20	1,024	320	704	K→T	5.44	685	126	559
	S→A	1.65	1,515	920	595	C→R	5.00	60	12	48
	K→T	5.44	685	126	559	K→P	4.92	300	61	239
	I→A	2.78	760	273	487	I→E	4.75	318	67	251
	M→L	1.93	1,000	517	483	I→H	4.48	103	23	80
	G→D	1.85	1,037	561	476	K→S	4.42	570	129	441
	S→D	1.98	915	462	453	I→D	4.05	174	43	131
	I→T	3.88	606	156	450	C→N	4.00	32	8	24*
	K→S	4.42	570	129	441	K→Q	3.95	510	129	381
	K→G	6.57	519	79	440	I→T	3.88	606	156	450
	V→A	1.41	1,464	1,040	424	M→H	3.82	65	17	48
	L→V	1.32	1,753	1,329	424	I→R	3.81	278	73	205
	R→E	1.57	1,136	724	412	M→E	3.48	212	61	151
	E→D	1.23	2,181	1,774	407	M→P	3.41	75	22	53

All the replacements of amino acid pairs are significant at p < 10^-3 for set I, p < 10^-2 for set II, and p < 10^-6 for sets III and IV, except replacements marked with asterisks. Organism abbreviations are listed in Table 1.

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