HYCD - ECOLI - GREMLIN Contacts

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HYCD - Formate hydrogenlyase subunit 4

UniProt:	P16430	Sequences: MSVLYPLIQALVLFAVAPLLSGITRVARARLHNRRGPGVLQEYRDIIKLLGRQSVGPDASGWVFRLTPYVMVGVMLTIATALPVVTVGSPLPQLGDLITLLYLFAIARFFFAISGLDTGSPFTAIGASREAMLGVLVEPMLLLGLWVAAQVAGSTNISNITDTVYHWPLSQSIPLVLALCACAFATFIEMGKLPFDLAEAEQELQEGPLSEYSGSGFGVMKWGISLKQLVVLQMFVGVFIPWGQMETFTAGGLLLALVIAIVKLVVGVLVIALFENSMARLRLDITPRITWAGFGFAFLAFVSLLAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10477
Length:	307 (288)
Sequences:	5370 (2506)
Seq/√Len:	147.7

ECOLI - HYCD HYFC NUOH
HALSA - Q9HRL8
SULSO - Q980H2 Q97ZA4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
154_S	159_N	4.733	1.00
179_L	235_F	3.994	1.00
28_R	276_N	3.846	1.00
233_Q	260_A	3.659	1.00
183_A	270_V	3.584	1.00
21_S	42_E	3.507	1.00
31_L	276_N	3.435	1.00
236_V	260_A	3.062	1.00
233_Q	264_L	2.655	1.00
123_T	210_S	2.653	1.00
43_Y	46_I	2.473	1.00
163_T	171_Q	2.456	1.00
54_S	216_G	2.439	1.00
152_A	171_Q	2.414	1.00
187_F	274_F	2.390	1.00
159_N	162_D	2.375	1.00
182_C	235_F	2.354	1.00
172_S	240_I	2.319	1.00
190_M	271_I	2.314	1.00
240_I	267_G	2.302	1.00
75_M	227_K	2.271	1.00
255_L	259_I	2.226	1.00
232_L	267_G	2.141	1.00
172_S	179_L	2.085	1.00
75_M	226_L	2.073	1.00
71_M	110_F	2.053	1.00
206_E	209_L	2.038	1.00
78_I	230_V	2.011	1.00
63_V	113_I	1.987	1.00
229_L	268_V	1.985	1.00
101_L	142_L	1.974	1.00
50_L	218_G	1.958	1.00
13_L	226_L	1.948	1.00
115_G	127_A	1.926	1.00
186_T	231_V	1.851	1.00
71_M	223_G	1.808	1.00
183_A	187_F	1.791	1.00
99_T	103_L	1.789	1.00
184_F	294_F	1.778	1.00
169_L	173_I	1.774	1.00
77_T	99_T	1.772	1.00
178_A	239_F	1.766	1.00
48_K	52_R	1.739	1.00
27_A	269_L	1.718	1.00
23_I	269_L	1.712	1.00
20_L	268_V	1.683	1.00
266_V	270_V	1.658	1.00
19_L	42_E	1.654	1.00
81_A	99_T	1.648	1.00
147_V	178_A	1.611	1.00
17_A	226_L	1.599	1.00
170_S	263_K	1.580	1.00
156_N	159_N	1.579	1.00
35_R	38_G	1.517	1.00
170_S	173_I	1.492	1.00
27_A	272_A	1.486	1.00
41_Q	45_D	1.469	1.00
130_E	198_A	1.468	1.00
255_L	258_V	1.462	1.00
89_S	158_S	1.458	1.00
30_R	35_R	1.454	1.00
100_L	104_F	1.453	1.00
133_L	286_T	1.447	1.00
175_L	305_L	1.441	1.00
140_M	185_A	1.439	1.00
217_F	221_K	1.438	1.00
31_L	273_L	1.430	1.00
200_A	204_L	1.430	1.00
178_A	301_F	1.418	1.00
209_L	217_F	1.414	1.00
186_T	235_F	1.407	1.00
197_L	281_L	1.402	1.00
7_L	11_L	1.373	1.00
148_A	160_I	1.357	1.00
197_L	286_T	1.344	1.00
70_V	74_V	1.336	1.00
93_Q	99_T	1.334	1.00
273_L	277_S	1.321	1.00
200_A	203_E	1.317	1.00
27_A	31_L	1.316	1.00
17_A	222_W	1.312	1.00
140_M	298_F	1.301	1.00
80_T	99_T	1.300	1.00
145_L	238_V	1.290	1.00
30_R	38_G	1.286	1.00
176_V	180_C	1.284	1.00
16_V	229_L	1.255	1.00
11_L	14_F	1.252	1.00
152_A	163_T	1.249	1.00
65_R	216_G	1.247	1.00
228_Q	268_V	1.245	1.00
26_V	30_R	1.236	1.00
152_A	160_I	1.235	1.00
143_L	302_V	1.230	1.00
235_F	267_G	1.228	1.00
92_P	158_S	1.220	1.00
120_S	123_T	1.218	1.00
205_Q	210_S	1.218	1.00
112_A	131_A	1.216	1.00
188_I	195_F	1.212	1.00
162_D	167_W	1.196	1.00
283_L	287_P	1.193	1.00
126_G	198_A	1.183	1.00
164_V	171_Q	1.182	1.00
159_N	163_T	1.182	1.00
141_L	185_A	1.175	1.00
22_G	39_V	1.165	1.00
158_S	162_D	1.158	1.00
169_L	174_P	1.156	1.00
79_A	230_V	1.153	1.00
182_C	231_V	1.149	1.00
147_V	298_F	1.131	0.99
289_I	294_F	1.128	0.99
64_F	68_P	1.119	0.99
228_Q	271_I	1.117	0.99
151_V	175_L	1.116	0.99
15_A	43_Y	1.113	0.99
114_S	117_D	1.088	0.99
67_T	114_S	1.085	0.99
233_Q	237_G	1.074	0.99
197_L	204_L	1.070	0.99
50_L	215_S	1.070	0.99
16_V	265_V	1.069	0.99
260_A	264_L	1.066	0.99
269_L	273_L	1.065	0.99
92_P	156_N	1.065	0.99
23_I	27_A	1.062	0.99
140_M	290_T	1.050	0.99
244_Q	259_I	1.047	0.99
97_L	149_A	1.046	0.99
77_T	103_L	1.045	0.99
167_W	171_Q	1.042	0.99
47_I	51_G	1.036	0.99
180_C	184_F	1.035	0.99
19_L	39_V	1.034	0.99
204_L	208_P	1.030	0.99
242_W	263_K	1.029	0.99
24_T	275_E	1.023	0.99
197_L	285_I	1.020	0.99
67_T	113_I	1.020	0.99
72_V	76_L	1.019	0.99
143_L	299_L	1.018	0.99
236_V	240_I	1.017	0.99
43_Y	47_I	1.010	0.99
190_M	231_V	1.009	0.99
32_H	37_P	1.006	0.99
179_L	239_F	1.000	0.99
215_S	218_G	0.991	0.99
114_S	220_M	0.988	0.99
236_V	264_L	0.988	0.99
26_V	52_R	0.987	0.99
24_T	192_K	0.986	0.99
100_L	157_I	0.986	0.99
57_P	64_F	0.984	0.99
56_G	65_R	0.981	0.99
114_S	212_Y	0.981	0.99
196_D	280_R	0.980	0.98
181_A	297_A	0.979	0.98
140_M	295_G	0.974	0.98
154_S	160_I	0.972	0.98
241_P	263_K	0.971	0.98
108_R	134_G	0.968	0.98
71_M	220_M	0.967	0.98
128_S	198_A	0.966	0.98
270_V	274_F	0.966	0.98
22_G	42_E	0.963	0.98
81_A	100_L	0.961	0.98
67_T	117_D	0.960	0.98
147_V	302_V	0.957	0.98
67_T	110_F	0.946	0.98
267_G	270_V	0.938	0.98
11_L	15_A	0.929	0.98
281_L	285_I	0.917	0.98
282_R	287_P	0.915	0.98
72_V	223_G	0.914	0.98
75_M	230_V	0.913	0.98
200_A	280_R	0.913	0.98
21_S	225_S	0.911	0.98
26_V	38_G	0.909	0.98
147_V	175_L	0.907	0.98
183_A	271_I	0.904	0.97
273_L	278_M	0.902	0.97
240_I	263_K	0.902	0.97
46_I	51_G	0.901	0.97
23_I	272_A	0.892	0.97
176_V	179_L	0.889	0.97
74_V	103_L	0.887	0.97
175_L	301_F	0.887	0.97
144_G	185_A	0.883	0.97
28_R	275_E	0.875	0.97
301_F	305_L	0.870	0.97
46_I	50_L	0.868	0.97
101_L	145_L	0.865	0.97
109_F	283_L	0.864	0.97
72_V	219_V	0.861	0.97
164_V	241_P	0.859	0.97
144_G	181_A	0.858	0.97
49_L	218_G	0.853	0.96
81_A	96_D	0.847	0.96
46_I	222_W	0.838	0.96
29_A	35_R	0.838	0.96
130_E	200_A	0.826	0.96
49_L	221_K	0.825	0.96
89_S	92_P	0.823	0.96
96_D	156_N	0.821	0.96
116_L	119_G	0.820	0.95
84_V	90_P	0.819	0.95
140_M	294_F	0.816	0.95
193_L	278_M	0.810	0.95
297_A	301_F	0.808	0.95
63_V	67_T	0.808	0.95
183_A	235_F	0.806	0.95
86_T	162_D	0.804	0.95
93_Q	220_M	0.802	0.95
32_H	36_G	0.802	0.95
192_K	196_D	0.800	0.95
164_V	170_S	0.796	0.95
14_F	76_L	0.791	0.95
187_F	271_I	0.789	0.94
22_G	30_R	0.787	0.94
59_A	64_F	0.785	0.94
133_L	191_G	0.782	0.94
196_D	199_E	0.782	0.94
90_P	222_W	0.780	0.94
196_D	203_E	0.775	0.94
295_G	298_F	0.770	0.94
188_I	286_T	0.769	0.94
260_A	263_K	0.769	0.94
70_V	73_G	0.758	0.93
133_L	137_V	0.756	0.93
22_G	28_R	0.753	0.93
203_E	280_R	0.752	0.93
144_G	147_V	0.751	0.93
97_L	157_I	0.749	0.93
256_A	259_I	0.746	0.93
45_D	48_K	0.742	0.92
19_L	43_Y	0.742	0.92
170_S	241_P	0.739	0.92
172_S	176_V	0.739	0.92
209_L	221_K	0.739	0.92
40_L	43_Y	0.737	0.92
149_A	155_T	0.737	0.92
73_G	304_L	0.735	0.92
181_A	184_F	0.733	0.92
10_A	14_F	0.729	0.92
218_G	222_W	0.727	0.92
77_T	159_N	0.726	0.92
65_R	69_Y	0.723	0.91
189_E	192_K	0.722	0.91
21_S	24_T	0.721	0.91
104_F	107_A	0.720	0.91
72_V	210_S	0.719	0.91
157_I	234_M	0.718	0.91
183_A	267_G	0.717	0.91
182_C	239_F	0.716	0.91
264_L	268_V	0.714	0.91
97_L	160_I	0.713	0.91
202_Q	206_E	0.711	0.91
56_G	61_G	0.710	0.91
231_V	235_F	0.709	0.91
118_T	212_Y	0.708	0.91
257_L	261_I	0.708	0.91
236_V	263_K	0.707	0.91
29_A	34_R	0.706	0.90
182_C	186_T	0.703	0.90
179_L	240_I	0.703	0.90
74_V	107_A	0.703	0.90
9_Q	90_P	0.700	0.90
24_T	225_S	0.698	0.90
18_P	46_I	0.697	0.90
16_V	19_L	0.696	0.90
18_P	28_R	0.695	0.90
136_L	287_P	0.694	0.90
71_M	107_A	0.694	0.90
198_A	208_P	0.693	0.90
45_D	280_R	0.691	0.90
202_Q	205_Q	0.689	0.89
258_V	262_V	0.688	0.89
37_P	41_Q	0.687	0.89
28_R	33_N	0.687	0.89
284_D	287_P	0.687	0.89
221_K	275_E	0.686	0.89
32_H	211_E	0.685	0.89
214_G	218_G	0.684	0.89
82_L	233_Q	0.683	0.89
41_Q	48_K	0.683	0.89
262_V	265_V	0.682	0.89
93_Q	100_L	0.681	0.89
120_S	271_I	0.675	0.88
280_R	284_D	0.673	0.88
196_D	204_L	0.671	0.88
71_M	111_F	0.670	0.88
57_P	68_P	0.668	0.88
16_V	268_V	0.668	0.88
167_W	172_S	0.668	0.88
147_V	301_F	0.666	0.88
137_V	188_I	0.665	0.88
25_R	34_R	0.664	0.88
236_V	256_A	0.662	0.87
141_L	144_G	0.660	0.87
82_L	90_P	0.658	0.87
26_V	39_V	0.657	0.87
15_A	18_P	0.657	0.87
126_G	130_E	0.653	0.87
147_V	305_L	0.653	0.87
177_L	301_F	0.653	0.87
110_F	113_I	0.650	0.86
25_R	36_G	0.647	0.86
288_R	292_A	0.646	0.86
268_V	272_A	0.646	0.86
133_L	136_L	0.645	0.86
64_F	212_Y	0.643	0.86
52_R	292_A	0.642	0.86
86_T	89_S	0.641	0.86
193_L	202_Q	0.637	0.85
19_L	22_G	0.636	0.85
289_I	293_G	0.633	0.85
18_P	22_G	0.631	0.85
17_A	29_A	0.630	0.85
25_R	45_D	0.628	0.85
84_V	233_Q	0.628	0.85
123_T	206_E	0.627	0.84
144_G	178_A	0.625	0.84
244_Q	255_L	0.621	0.84
281_L	290_T	0.619	0.84
46_I	218_G	0.618	0.84
54_S	64_F	0.617	0.84
141_L	290_T	0.614	0.83
266_V	269_L	0.614	0.83
6_P	91_L	0.614	0.83
126_G	205_Q	0.613	0.83
92_P	96_D	0.609	0.83
5_Y	131_A	0.609	0.83
173_I	176_V	0.608	0.83
142_L	145_L	0.608	0.83
31_L	269_L	0.608	0.83
177_L	181_A	0.608	0.83
60_S	119_G	0.607	0.83
82_L	230_V	0.607	0.83
199_E	207_G	0.606	0.82
68_P	212_Y	0.605	0.82
197_L	200_A	0.605	0.82
206_E	221_K	0.604	0.82
113_I	143_L	0.604	0.82
171_Q	174_P	0.598	0.82
160_I	238_V	0.597	0.81
104_F	235_F	0.597	0.81
25_R	199_E	0.595	0.81
162_D	168_P	0.592	0.81
76_L	226_L	0.592	0.81
81_A	84_V	0.589	0.81
34_R	207_G	0.587	0.80
74_V	106_I	0.586	0.80
66_L	70_V	0.585	0.80
298_F	305_L	0.582	0.80
47_I	50_L	0.581	0.80
40_L	44_R	0.581	0.80
24_T	28_R	0.581	0.80
22_G	26_V	0.579	0.79
13_L	17_A	0.575	0.79
168_P	172_S	0.574	0.79
237_G	242_W	0.573	0.79
90_P	95_G	0.572	0.79
9_Q	84_V	0.571	0.79
96_D	103_L	0.570	0.78
97_L	145_L	0.567	0.78
73_G	162_D	0.565	0.78
136_L	275_E	0.565	0.78
234_M	238_V	0.563	0.78
42_E	272_A	0.562	0.77
208_P	221_K	0.561	0.77
17_A	28_R	0.559	0.77
131_A	140_M	0.559	0.77
118_T	199_E	0.559	0.77
111_F	130_E	0.559	0.77
151_V	174_P	0.558	0.77
201_E	221_K	0.556	0.77
192_K	225_S	0.555	0.77
44_R	121_P	0.554	0.76
187_F	231_V	0.553	0.76
286_T	295_G	0.547	0.76
113_I	117_D	0.546	0.75
146_W	149_A	0.546	0.75
272_A	275_E	0.545	0.75
118_T	123_T	0.544	0.75
111_F	191_G	0.542	0.75
90_P	303_S	0.542	0.75
136_L	295_G	0.542	0.75
144_G	239_F	0.541	0.75
187_F	190_M	0.539	0.75
16_V	20_L	0.538	0.74
30_R	272_A	0.538	0.74
64_F	114_S	0.537	0.74
30_R	142_L	0.537	0.74
27_A	273_L	0.535	0.74
25_R	201_E	0.534	0.74
236_V	267_G	0.534	0.74
134_G	142_L	0.533	0.74
232_L	271_I	0.533	0.74
261_I	265_V	0.532	0.74
21_S	46_I	0.529	0.73
25_R	32_H	0.528	0.73
129_R	207_G	0.524	0.72
180_C	302_V	0.523	0.72
282_R	285_I	0.523	0.72
225_S	275_E	0.520	0.72
58_D	113_I	0.520	0.72
300_A	304_L	0.517	0.71
127_A	223_G	0.517	0.71
104_F	134_G	0.517	0.71
84_V	261_I	0.517	0.71
259_I	270_V	0.517	0.71
14_F	18_P	0.516	0.71
232_L	236_V	0.515	0.71
16_V	226_L	0.515	0.71
183_A	273_L	0.515	0.71
176_V	301_F	0.513	0.71
272_A	276_N	0.512	0.71
53_Q	64_F	0.512	0.71
199_E	203_E	0.508	0.70
189_E	224_I	0.506	0.70
85_V	244_Q	0.506	0.70
225_S	286_T	0.506	0.70
190_M	227_K	0.505	0.70
147_V	171_Q	0.504	0.70
233_Q	298_F	0.503	0.69
197_L	280_R	0.502	0.69
262_V	266_V	0.502	0.69
71_M	78_I	0.501	0.69
18_P	42_E	0.501	0.69
110_F	127_A	0.500	0.69
280_R	283_L	0.500	0.69

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
4he8H	1	0.8176	100	0.076	Contact Map
1q2fA	1	0.101	6.5	0.97	Contact Map
2jpkA	1	0.1107	3.7	0.973	Contact Map
4uisB	1	0.1336	2.9	0.975	Contact Map
2m7gA	1	0.1954	2.7	0.975	Contact Map
4he8M	1	0.9088	2.6	0.975	Contact Map
4ogqG	1	0.1205	2.6	0.975	Contact Map
1vryA	1	0.1792	2.6	0.975	Contact Map
1q90G	1	0.0977	2.6	0.975	Contact Map
2kncA	1	0.1498	2.1	0.976	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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