HYBB - ECOLI - GREMLIN Contacts

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HYBB - Probable Ni/Fe-hydrogenase 2 b-type cytochrome subunit

UniProt:	P37180	Sequences: MSHDPQPLGGKIISKPVMIFGPLIVICMLLIVKRLVFGLGSVSDLNGGFPWGVWIAFDLLIGTGFACGGWALAWAVYVFNRGQYHPLVRPALLASLFGYSLGGLSITIDVGRYWNLPYFYIPGHFNVNSVLFETAVCMTIYIGVMALEFAPALFERLGWKVSLQRLNKVMFFIIALGALLPTMHQSSMGSLMISAGYKVHPLWQSYEMLPLFSLLTAFIMGFSIVIFEGSLVQAGLRGNGPDEKSLFVKLTNTISVLLAIFIVLRFGELIYRDKLSLAFAGDFYSVMFWIEVLLMLFPLVVLRVAKLRNDSRMLFLSALSALLGCATWRLTYSLVAFNPGGGYAYFPTWEELLISIGFVAIEICAYIVLIRLLPILPPLKQNDHNRHEASKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11800
Length:	392 (352)
Sequences:	1427 (1046)
Seq/√Len:	55.7

ECOLI - HYBB
HALSA - DMSC
SULSO - Q97V35

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_L	353_L	5.432	1.00
21_G	25_V	3.916	1.00
251_T	314_L	3.546	1.00
57_F	326_A	3.505	1.00
227_F	315_F	3.431	1.00
24_I	361_I	3.273	1.00
20_F	360_A	3.258	1.00
25_V	29_L	3.049	1.00
24_I	364_C	2.889	1.00
223_S	318_A	2.852	1.00
29_L	33_K	2.764	1.00
285_S	289_W	2.760	1.00
118_Y	121_I	2.665	1.00
34_R	54_W	2.583	1.00
208_M	264_L	2.561	1.00
44_D	348_T	2.484	1.00
319_L	323_L	2.436	1.00
23_L	360_A	2.323	1.00
301_V	317_S	2.313	1.00
42_V	350_E	2.309	1.00
345_Y	351_E	2.299	1.00
227_F	318_A	2.282	1.00
118_Y	122_P	2.247	1.00
115_N	118_Y	2.217	1.00
16_P	367_I	2.217	1.00
64_G	217_A	2.211	1.00
107_T	116_L	2.197	1.00
297_F	320_S	2.188	1.00
33_K	37_F	2.187	1.00
32_V	36_V	2.179	1.00
26_I	353_L	2.163	1.00
274_K	278_A	2.139	1.00
310_D	313_M	2.072	1.00
301_V	307_L	2.065	1.00
18_M	22_P	2.062	1.00
230_S	315_F	2.005	1.00
254_I	257_L	1.963	1.00
15_K	19_I	1.926	1.00
295_M	298_P	1.912	1.00
251_T	302_L	1.908	1.00
249_K	252_N	1.897	1.00
272_R	278_A	1.894	1.00
67_C	181_P	1.894	1.00
45_L	54_W	1.847	0.99
254_I	321_A	1.840	0.99
19_I	23_L	1.837	0.99
347_P	351_E	1.833	0.99
231_L	235_G	1.812	0.99
70_W	177_G	1.778	0.99
357_G	367_I	1.765	0.99
294_L	320_S	1.748	0.99
43_S	54_W	1.742	0.99
161_V	164_Q	1.734	0.99
205_S	335_V	1.732	0.99
352_L	356_I	1.731	0.99
272_R	276_S	1.725	0.99
288_F	291_E	1.707	0.99
219_I	321_A	1.705	0.99
15_K	18_M	1.700	0.99
17_V	364_C	1.664	0.99
307_L	313_M	1.647	0.99
368_V	372_L	1.626	0.99
90_P	229_G	1.621	0.99
248_V	309_N	1.610	0.98
126_N	129_S	1.610	0.98
102_G	148_E	1.603	0.98
53_V	56_A	1.593	0.98
248_V	252_N	1.586	0.98
215_L	260_I	1.580	0.98
304_V	307_L	1.575	0.98
103_G	107_T	1.569	0.98
348_T	351_E	1.544	0.98
52_G	56_A	1.539	0.98
272_R	277_L	1.536	0.98
274_K	277_L	1.525	0.98
216_T	329_R	1.497	0.98
257_L	260_I	1.496	0.98
284_Y	288_F	1.496	0.98
262_I	299_L	1.475	0.97
28_M	32_V	1.469	0.97
273_D	277_L	1.466	0.97
226_I	318_A	1.463	0.97
266_F	292_V	1.437	0.97
290_I	294_L	1.436	0.97
255_S	262_I	1.434	0.97
296_L	300_V	1.428	0.97
312_R	316_L	1.428	0.97
19_I	356_I	1.423	0.97
109_D	188_M	1.407	0.96
177_G	183_M	1.405	0.96
139_T	191_L	1.402	0.96
297_F	323_L	1.398	0.96
247_F	314_L	1.396	0.96
295_M	299_L	1.362	0.96
25_V	28_M	1.358	0.96
227_F	322_L	1.350	0.95
117_P	120_Y	1.345	0.95
34_R	39_L	1.341	0.95
22_P	28_M	1.340	0.95
213_S	332_Y	1.333	0.95
314_L	363_I	1.333	0.95
193_I	209_L	1.330	0.95
141_Y	185_Q	1.325	0.95
101_L	362_E	1.324	0.95
345_Y	348_T	1.321	0.95
93_L	369_L	1.320	0.95
22_P	25_V	1.314	0.95
260_I	264_L	1.311	0.95
299_L	303_R	1.298	0.94
232_V	366_Y	1.296	0.94
135_A	139_T	1.290	0.94
49_F	53_V	1.275	0.94
292_V	320_S	1.263	0.93
133_E	137_C	1.260	0.93
33_K	350_E	1.255	0.93
134_T	138_M	1.250	0.93
349_W	353_L	1.249	0.93
216_T	322_L	1.247	0.93
97_F	362_E	1.244	0.93
143_G	187_S	1.242	0.93
301_V	304_V	1.241	0.93
288_F	324_G	1.238	0.93
91_A	141_Y	1.224	0.92
91_A	225_V	1.223	0.92
306_K	309_N	1.214	0.92
325_C	328_W	1.213	0.92
70_W	95_S	1.213	0.92
59_L	329_R	1.211	0.92
223_S	322_L	1.209	0.92
73_A	91_A	1.204	0.92
262_I	266_F	1.198	0.92
369_L	373_L	1.197	0.92
81_R	84_Y	1.189	0.91
64_G	67_C	1.184	0.91
237_R	297_F	1.173	0.91
263_V	267_G	1.171	0.91
22_P	29_L	1.162	0.90
272_R	279_F	1.155	0.90
134_T	188_M	1.151	0.90
31_I	108_I	1.143	0.89
42_V	353_L	1.135	0.89
261_F	265_R	1.129	0.89
226_I	314_L	1.126	0.89
295_M	300_V	1.121	0.89
24_I	28_M	1.111	0.88
302_L	317_S	1.107	0.88
18_M	25_V	1.103	0.88
273_D	276_S	1.096	0.87
97_F	366_Y	1.084	0.87
18_M	24_I	1.077	0.86
21_G	36_V	1.072	0.86
38_G	52_G	1.070	0.86
112_R	115_N	1.070	0.86
275_L	278_A	1.059	0.86
293_L	298_P	1.059	0.86
125_F	128_N	1.057	0.85
131_L	191_L	1.056	0.85
217_A	329_R	1.055	0.85
37_F	42_V	1.049	0.85
184_H	188_M	1.049	0.85
134_T	187_S	1.047	0.85
305_A	309_N	1.041	0.85
15_K	22_P	1.039	0.84
147_L	173_I	1.038	0.84
310_D	315_F	1.035	0.84
230_S	247_F	1.028	0.84
252_N	256_V	1.024	0.84
190_S	210_P	1.022	0.83
29_L	231_L	1.015	0.83
140_I	192_M	1.010	0.83
274_K	279_F	1.009	0.83
20_F	364_C	1.002	0.82
104_L	107_T	0.995	0.82
39_L	54_W	0.993	0.82
187_S	191_L	0.990	0.81
69_G	221_G	0.988	0.81
215_L	264_L	0.988	0.81
293_L	297_F	0.987	0.81
16_P	19_I	0.984	0.81
97_F	365_A	0.982	0.81
109_D	141_Y	0.982	0.81
29_L	36_V	0.981	0.81
255_S	303_R	0.979	0.81
103_G	138_M	0.977	0.81
185_Q	217_A	0.967	0.80
298_P	321_A	0.966	0.80
281_G	288_F	0.964	0.80
25_V	316_L	0.961	0.79
117_P	121_I	0.960	0.79
275_L	279_F	0.958	0.79
133_E	145_M	0.954	0.79
16_P	297_F	0.951	0.79
65_F	68_G	0.949	0.79
90_P	366_Y	0.948	0.79
244_K	248_V	0.948	0.79
39_L	43_S	0.947	0.78
29_L	355_S	0.943	0.78
281_G	289_W	0.943	0.78
139_T	143_G	0.942	0.78
33_K	36_V	0.941	0.78
252_N	267_G	0.933	0.77
261_F	328_W	0.930	0.77
170_M	173_I	0.930	0.77
143_G	284_Y	0.925	0.77
100_S	142_I	0.923	0.77
272_R	275_L	0.923	0.77
363_I	367_I	0.914	0.76
276_S	279_F	0.912	0.76
256_V	263_V	0.908	0.75
282_D	289_W	0.908	0.75
69_G	102_G	0.907	0.75
287_M	327_T	0.905	0.75
250_L	270_I	0.904	0.75
73_A	141_Y	0.902	0.75
17_V	20_F	0.902	0.75
83_Q	249_K	0.894	0.74
250_L	360_A	0.889	0.74
262_I	295_M	0.887	0.74
144_V	176_L	0.886	0.74
79_F	84_Y	0.885	0.74
18_M	21_G	0.880	0.73
30_L	350_E	0.879	0.73
31_I	35_L	0.876	0.73
52_G	55_I	0.871	0.72
66_A	221_G	0.869	0.72
261_F	264_L	0.863	0.72
19_I	22_P	0.862	0.72
57_F	355_S	0.861	0.72
100_S	365_A	0.860	0.71
66_A	141_Y	0.859	0.71
306_K	310_D	0.858	0.71
24_I	29_L	0.857	0.71
33_K	42_V	0.857	0.71
103_G	131_L	0.856	0.71
15_K	344_A	0.856	0.71
17_V	21_G	0.851	0.71
144_V	180_L	0.847	0.70
72_L	225_V	0.846	0.70
248_V	308_R	0.845	0.70
293_L	310_D	0.842	0.70
227_F	316_L	0.839	0.70
63_T	102_G	0.837	0.69
350_E	353_L	0.834	0.69
70_W	217_A	0.834	0.69
261_F	268_E	0.832	0.69
138_M	187_S	0.832	0.69
200_H	336_A	0.828	0.69
186_S	208_M	0.828	0.69
215_L	366_Y	0.827	0.68
279_F	287_M	0.823	0.68
89_R	92_L	0.818	0.68
264_L	267_G	0.818	0.68
54_W	134_T	0.814	0.67
22_P	26_I	0.813	0.67
73_A	148_E	0.809	0.67
295_M	302_L	0.809	0.67
146_A	310_D	0.808	0.67
293_L	312_R	0.807	0.67
263_V	266_F	0.805	0.66
177_G	210_P	0.804	0.66
24_I	30_L	0.803	0.66
44_D	264_L	0.802	0.66
28_M	361_I	0.801	0.66
132_F	136_V	0.798	0.66
301_V	313_M	0.795	0.65
21_G	29_L	0.792	0.65
222_F	253_T	0.790	0.65
73_A	184_H	0.789	0.65
21_G	28_M	0.789	0.65
24_I	37_F	0.786	0.64
173_I	179_L	0.785	0.64
134_T	137_C	0.782	0.64
113_Y	129_S	0.781	0.64
55_I	141_Y	0.776	0.63
168_K	171_F	0.775	0.63
59_L	217_A	0.773	0.63
129_S	210_P	0.772	0.63
207_E	271_Y	0.771	0.63
208_M	215_L	0.769	0.63
336_A	351_E	0.769	0.63
56_A	334_L	0.766	0.62
70_W	145_M	0.765	0.62
212_F	318_A	0.764	0.62
334_L	337_F	0.762	0.62
296_L	316_L	0.758	0.62
245_S	249_K	0.756	0.61
137_C	187_S	0.756	0.61
226_I	250_L	0.754	0.61
146_A	150_A	0.752	0.61
294_L	297_F	0.750	0.61
17_V	27_C	0.750	0.61
59_L	67_C	0.749	0.61
290_I	318_A	0.748	0.61
21_G	364_C	0.748	0.61
17_V	24_I	0.747	0.61
348_T	352_L	0.746	0.60
23_L	357_G	0.744	0.60
167_N	170_M	0.744	0.60
177_G	180_L	0.742	0.60
37_F	40_G	0.740	0.60
52_G	129_S	0.738	0.60
28_M	276_S	0.737	0.59
298_P	320_S	0.736	0.59
95_S	149_F	0.735	0.59
18_M	26_I	0.734	0.59
49_F	334_L	0.734	0.59
368_V	371_R	0.729	0.59
53_V	355_S	0.728	0.59
212_F	328_W	0.727	0.58
45_L	52_G	0.724	0.58
115_N	119_F	0.724	0.58
296_L	299_L	0.723	0.58
301_V	309_N	0.721	0.58
61_I	326_A	0.719	0.58
76_V	88_V	0.718	0.58
84_Y	249_K	0.717	0.57
79_F	194_S	0.717	0.57
284_Y	289_W	0.714	0.57
68_G	292_V	0.714	0.57
69_G	90_P	0.711	0.57
27_C	30_L	0.710	0.57
173_I	177_G	0.708	0.56
29_L	35_L	0.707	0.56
234_A	237_R	0.705	0.56
28_M	36_V	0.704	0.56
101_L	105_S	0.703	0.56
270_I	275_L	0.702	0.56
230_S	318_A	0.702	0.56
138_M	220_M	0.701	0.56
31_I	34_R	0.700	0.56
96_L	146_A	0.699	0.55
266_F	270_I	0.698	0.55
161_V	165_R	0.698	0.55
96_L	142_I	0.688	0.54
75_A	218_F	0.687	0.54
101_L	361_I	0.686	0.54
34_R	42_V	0.686	0.54
26_I	356_I	0.684	0.54
243_E	246_L	0.681	0.54
137_C	145_M	0.680	0.53
89_R	156_R	0.678	0.53
62_G	101_L	0.678	0.53
293_L	306_K	0.678	0.53
355_S	359_V	0.676	0.53
301_V	323_L	0.675	0.53
51_W	129_S	0.675	0.53
69_G	91_A	0.674	0.53
18_M	35_L	0.673	0.53
76_V	84_Y	0.673	0.53
226_I	254_I	0.672	0.53
153_L	157_L	0.672	0.53
277_L	344_A	0.670	0.52
245_S	356_I	0.670	0.52
45_L	128_N	0.666	0.52
281_G	285_S	0.664	0.52
253_T	263_V	0.663	0.52
178_A	186_S	0.662	0.51
111_G	354_I	0.661	0.51
116_L	182_T	0.658	0.51
101_L	150_A	0.658	0.51
59_L	106_I	0.657	0.51
65_F	98_G	0.656	0.51
229_G	242_D	0.656	0.51
257_L	294_L	0.654	0.51
102_G	141_Y	0.653	0.51
23_L	27_C	0.651	0.50
291_E	331_T	0.649	0.50
113_Y	116_L	0.648	0.50
82_G	85_H	0.647	0.50
59_L	188_M	0.647	0.50
69_G	141_Y	0.647	0.50
69_G	94_A	0.645	0.50
278_A	281_G	0.641	0.49
287_M	290_I	0.640	0.49
106_I	109_D	0.640	0.49
298_P	302_L	0.639	0.49
116_L	122_P	0.638	0.49
106_I	110_V	0.638	0.49
96_L	357_G	0.637	0.49
318_A	322_L	0.634	0.48
18_M	28_M	0.634	0.48
110_V	122_P	0.634	0.48
109_D	130_V	0.629	0.48
185_Q	188_M	0.629	0.48
87_L	178_A	0.626	0.48
96_L	155_E	0.623	0.47
67_C	189_G	0.621	0.47
24_I	36_V	0.621	0.47
92_L	186_S	0.618	0.47
18_M	29_L	0.618	0.47
136_V	139_T	0.616	0.47
23_L	29_L	0.614	0.46
313_M	317_S	0.613	0.46
134_T	184_H	0.610	0.46
120_Y	139_T	0.610	0.46
115_N	120_Y	0.610	0.46
141_Y	217_A	0.607	0.46
66_A	224_I	0.606	0.45
66_A	111_G	0.605	0.45
264_L	271_Y	0.603	0.45
148_E	188_M	0.601	0.45
175_A	179_L	0.597	0.44
262_I	305_A	0.595	0.44
59_L	186_S	0.595	0.44
54_W	57_F	0.595	0.44
70_W	325_C	0.593	0.44
181_P	188_M	0.593	0.44
34_R	40_G	0.592	0.44
148_E	167_N	0.592	0.44
195_A	199_V	0.591	0.44
71_A	210_P	0.590	0.44
226_I	230_S	0.590	0.44
127_V	130_V	0.588	0.44
25_V	37_F	0.588	0.44
22_P	37_F	0.586	0.43
194_S	199_V	0.585	0.43
208_M	335_V	0.583	0.43
66_A	184_H	0.582	0.43
26_I	29_L	0.582	0.43
134_T	185_Q	0.582	0.43
22_P	110_V	0.581	0.43
252_N	309_N	0.581	0.43
154_F	275_L	0.579	0.43
286_V	289_W	0.579	0.43
144_V	220_M	0.578	0.42
51_W	56_A	0.577	0.42
309_N	360_A	0.577	0.42
338_N	351_E	0.576	0.42
266_F	303_R	0.574	0.42
273_D	278_A	0.573	0.42
55_I	111_G	0.571	0.42
171_F	299_L	0.571	0.42
181_P	210_P	0.569	0.42
244_K	260_I	0.568	0.41
252_N	319_L	0.568	0.41
141_Y	184_H	0.568	0.41
290_I	320_S	0.567	0.41
107_T	138_M	0.567	0.41
69_G	95_S	0.566	0.41
306_K	313_M	0.565	0.41
255_S	266_F	0.565	0.41
323_L	326_A	0.562	0.41
298_P	324_G	0.562	0.41
350_E	365_A	0.562	0.41
77_Y	88_V	0.561	0.41
53_V	57_F	0.561	0.41
127_V	131_L	0.560	0.41
24_I	365_A	0.560	0.41
142_I	146_A	0.559	0.40
114_W	120_Y	0.559	0.40
288_F	293_L	0.558	0.40
218_F	221_G	0.557	0.40
264_L	377_P	0.557	0.40
79_F	316_L	0.556	0.40
34_R	43_S	0.556	0.40
19_I	26_I	0.555	0.40
214_L	225_V	0.553	0.40
245_S	252_N	0.553	0.40
355_S	358_F	0.552	0.40
187_S	194_S	0.552	0.40
190_S	194_S	0.552	0.40
151_P	154_F	0.550	0.40
229_G	232_V	0.549	0.39
284_Y	324_G	0.548	0.39
38_G	111_G	0.547	0.39
287_M	292_V	0.546	0.39
247_F	276_S	0.545	0.39
346_F	349_W	0.544	0.39
130_V	135_A	0.543	0.39
181_P	185_Q	0.542	0.39
287_M	352_L	0.541	0.39
216_T	325_C	0.540	0.38
253_T	260_I	0.540	0.38
70_W	328_W	0.540	0.38
106_I	121_I	0.540	0.38
22_P	323_L	0.540	0.38
59_L	193_I	0.539	0.38
139_T	194_S	0.539	0.38
69_G	110_V	0.539	0.38
73_A	213_S	0.539	0.38
290_I	309_N	0.538	0.38
303_R	306_K	0.538	0.38
66_A	174_I	0.536	0.38
162_S	165_R	0.535	0.38
265_R	325_C	0.533	0.38
145_M	148_E	0.533	0.38
149_F	369_L	0.531	0.38
22_P	356_I	0.531	0.38
87_L	249_K	0.531	0.38
209_L	332_Y	0.530	0.37
144_V	149_F	0.530	0.37
49_F	55_I	0.530	0.37
74_W	326_A	0.529	0.37
102_G	217_A	0.527	0.37
51_W	203_W	0.527	0.37
59_L	134_T	0.524	0.37
232_V	302_L	0.524	0.37
211_L	264_L	0.523	0.37
365_A	378_P	0.523	0.37
236_L	370_I	0.522	0.37
355_S	363_I	0.521	0.37
245_S	257_L	0.521	0.37
42_V	361_I	0.518	0.36
220_M	320_S	0.517	0.36
89_R	332_Y	0.517	0.36
300_V	319_L	0.516	0.36
275_L	370_I	0.516	0.36
28_M	368_V	0.515	0.36
25_V	310_D	0.514	0.36
56_A	330_L	0.512	0.36
78_V	193_I	0.512	0.36
20_F	24_I	0.512	0.36
22_P	36_V	0.511	0.36
365_A	373_L	0.511	0.36
226_I	251_T	0.511	0.36
24_I	31_I	0.510	0.35
17_V	32_V	0.508	0.35
54_W	59_L	0.508	0.35
90_P	232_V	0.505	0.35
87_L	291_E	0.505	0.35
92_L	137_C	0.504	0.35
49_F	73_A	0.504	0.35
172_F	175_A	0.503	0.35
66_A	355_S	0.502	0.35
42_V	143_G	0.501	0.35
84_Y	253_T	0.501	0.35
274_K	282_D	0.500	0.34
259_A	262_I	0.500	0.34

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2vpzC	2	0.6301	100	0.629	Contact Map
4o6yA	2	0.523	68.9	0.951	Contact Map
3mk7A	1	0.574	47.2	0.957	Contact Map
4djkA	2	0.8673	23.7	0.963	Contact Map
4ev6A	3	0.1862	23.5	0.963	Contact Map
3l1lA	2	0.8444	21.3	0.964	Contact Map
3s8fA	1	0.7117	21.2	0.964	Contact Map
4i0uA	4	0.1811	20.8	0.964	Contact Map
2l8sA	1	0.1148	19.9	0.965	Contact Map
2a65A	2	0.7168	17.7	0.966	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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