HYFA - ECOLI - GREMLIN Contacts

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HYFA - Hydrogenase-4 component A

UniProt:	P23481	Sequences: MNRFVVAEPLWCTGCNTCLAACSDVHKTQGLQQHPRLALAKTSTITAPVVCHHCEEAPCLQVCPVNAISQRDDAIQLNESLCIGCKLCAVVCPFGAISASGSRPVNAHAQYVFQAEGSLKDGEENAPTQHALLRWEPGVQTVAVKCDLCDFLPEGPACVRACPNQALRLITGDSLQRQMKEKQRLAASWFANGGEDPLSLTQEQR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11150
Length:	205 (173)
Sequences:	1230 (809)
Seq/√Len:	61.5

ECOLI - HYFA HYCB NRFC HYDN YDHX YNFG DMSB YGFS FDOH YSAA FDNH HYBA YDHY AEGA
HALSA - DMSB
SULSO - Q97XX9 Q97V38 Q97V75

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_C	18_C	3.426	1.00
5_V	148_L	3.188	1.00
152_L	160_R	3.021	1.00
68_I	97_I	2.970	1.00
12_C	18_C	2.636	1.00
67_A	70_Q	2.619	1.00
37_L	40_A	2.499	1.00
12_C	15_C	2.485	1.00
176_Q	181_E	2.463	1.00
62_V	87_L	2.457	1.00
174_S	177_R	2.408	1.00
12_C	162_C	2.195	1.00
156_P	159_V	2.161	1.00
25_V	151_F	2.133	1.00
32_Q	35_P	2.023	1.00
6_V	179_M	1.980	1.00
183_Q	188_S	1.967	1.00
86_K	99_A	1.949	1.00
168_R	182_K	1.948	1.00
4_F	172_G	1.940	1.00
15_C	162_C	1.901	1.00
7_A	167_L	1.895	1.00
43_S	103_R	1.855	1.00
179_M	182_K	1.852	1.00
62_V	91_V	1.836	1.00
10_L	186_A	1.832	1.00
31_L	35_P	1.784	1.00
178_Q	181_E	1.769	0.99
6_V	182_K	1.765	0.99
138_G	144_V	1.724	0.99
60_L	143_A	1.703	0.99
21_A	161_A	1.641	0.99
86_K	101_G	1.614	0.99
32_Q	39_L	1.607	0.99
69_S	78_N	1.588	0.99
65_V	68_I	1.576	0.99
63_C	88_C	1.555	0.99
110_Q	113_F	1.554	0.99
7_A	50_V	1.505	0.98
32_Q	40_A	1.501	0.98
63_C	82_C	1.498	0.98
23_S	28_T	1.497	0.98
180_K	184_R	1.496	0.98
18_C	162_C	1.421	0.98
65_V	69_S	1.415	0.97
34_H	37_L	1.411	0.97
70_Q	75_I	1.405	0.97
65_V	70_Q	1.386	0.97
177_R	180_K	1.378	0.97
62_V	84_G	1.374	0.97
181_E	185_L	1.348	0.97
13_T	164_N	1.339	0.96
82_C	88_C	1.337	0.96
35_P	38_A	1.321	0.96
32_Q	36_R	1.313	0.96
175_L	180_K	1.307	0.96
63_C	85_C	1.299	0.96
159_V	167_L	1.297	0.96
35_P	39_L	1.296	0.96
86_K	89_A	1.255	0.95
100_S	144_V	1.234	0.94
103_R	106_N	1.222	0.94
61_Q	101_G	1.215	0.94
185_L	190_F	1.207	0.94
17_T	21_A	1.172	0.93
31_L	34_H	1.152	0.92
4_F	190_F	1.148	0.92
33_Q	39_L	1.139	0.92
32_Q	37_L	1.132	0.91
106_N	109_A	1.119	0.91
27_K	144_V	1.113	0.91
181_E	184_R	1.110	0.90
171_T	174_S	1.107	0.90
82_C	85_C	1.106	0.90
85_C	88_C	1.101	0.90
33_Q	40_A	1.101	0.90
34_H	40_A	1.086	0.89
12_C	163_P	1.083	0.89
33_Q	38_A	1.068	0.89
34_H	38_A	1.066	0.89
131_A	134_R	1.064	0.89
57_A	70_Q	1.063	0.88
5_V	9_P	1.059	0.88
57_A	60_L	1.057	0.88
93_P	145_K	1.051	0.88
178_Q	182_K	1.048	0.88
68_I	77_L	1.042	0.87
13_T	19_L	0.997	0.85
183_Q	187_A	0.996	0.85
3_R	72_D	0.994	0.85
31_L	37_L	0.987	0.84
138_G	142_V	0.981	0.84
26_H	151_F	0.971	0.83
165_Q	168_R	0.968	0.83
34_H	39_L	0.966	0.83
14_G	18_C	0.962	0.83
182_K	185_L	0.960	0.83
187_A	190_F	0.960	0.83
180_K	183_Q	0.946	0.82
79_E	100_S	0.939	0.81
36_R	109_A	0.938	0.81
60_L	70_Q	0.926	0.80
79_E	142_V	0.925	0.80
48_P	145_K	0.913	0.79
13_T	163_P	0.912	0.79
33_Q	36_R	0.910	0.79
14_G	162_C	0.904	0.79
62_V	90_V	0.897	0.78
185_L	188_S	0.897	0.78
48_P	166_A	0.892	0.78
145_K	166_A	0.877	0.77
182_K	186_A	0.872	0.76
36_R	40_A	0.869	0.76
77_L	97_I	0.859	0.75
168_R	178_Q	0.855	0.75
18_C	163_P	0.854	0.75
78_N	81_L	0.852	0.75
72_D	75_I	0.849	0.74
112_V	185_L	0.840	0.74
106_N	111_Y	0.836	0.73
175_L	183_Q	0.828	0.72
45_I	185_L	0.827	0.72
22_C	27_K	0.825	0.72
75_I	85_C	0.824	0.72
152_L	157_A	0.821	0.72
93_P	156_P	0.816	0.71
155_G	159_V	0.813	0.71
31_L	40_A	0.812	0.71
109_A	113_F	0.811	0.71
58_P	93_P	0.808	0.71
50_V	148_L	0.807	0.71
67_A	81_L	0.799	0.70
21_A	83_I	0.797	0.70
87_L	90_V	0.790	0.69
89_A	99_A	0.789	0.69
6_V	159_V	0.789	0.69
89_A	143_A	0.787	0.69
103_R	111_Y	0.782	0.68
70_Q	73_D	0.776	0.68
183_Q	189_W	0.772	0.67
89_A	100_S	0.766	0.67
31_L	39_L	0.765	0.66
86_K	95_G	0.755	0.65
12_C	22_C	0.752	0.65
84_G	93_P	0.751	0.65
65_V	71_R	0.748	0.65
27_K	138_G	0.748	0.65
94_F	145_K	0.741	0.64
99_A	140_Q	0.739	0.64
32_Q	38_A	0.738	0.64
71_R	76_Q	0.738	0.64
53_H	76_Q	0.737	0.64
146_C	149_C	0.736	0.63
68_I	75_I	0.733	0.63
47_A	50_V	0.731	0.63
6_V	188_S	0.729	0.63
26_H	29_Q	0.728	0.63
60_L	75_I	0.725	0.62
58_P	145_K	0.713	0.61
89_A	95_G	0.713	0.61
35_P	40_A	0.709	0.61
64_P	88_C	0.707	0.60
12_C	16_N	0.704	0.60
129_Q	181_E	0.702	0.60
52_H	148_L	0.701	0.60
27_K	30_G	0.699	0.59
87_L	91_V	0.695	0.59
42_T	45_I	0.673	0.57
62_V	79_E	0.671	0.56
13_T	182_K	0.671	0.56
83_I	88_C	0.669	0.56
183_Q	190_F	0.666	0.56
11_W	107_A	0.665	0.56
148_L	169_L	0.665	0.56
83_I	93_P	0.663	0.55
24_D	161_A	0.662	0.55
26_H	147_D	0.661	0.55
17_T	171_T	0.657	0.55
65_V	84_G	0.657	0.55
49_V	148_L	0.657	0.55
25_V	152_L	0.650	0.54
15_C	20_A	0.645	0.53
79_E	135_W	0.645	0.53
14_G	22_C	0.645	0.53
49_V	52_H	0.644	0.53
22_C	26_H	0.635	0.52
26_H	93_P	0.634	0.52
10_L	178_Q	0.633	0.52
43_S	155_G	0.632	0.52
85_C	156_P	0.631	0.52
36_R	39_L	0.628	0.51
67_A	71_R	0.622	0.51
86_K	103_R	0.620	0.51
182_K	190_F	0.618	0.50
76_Q	150_D	0.618	0.50
33_Q	37_L	0.616	0.50
78_N	89_A	0.612	0.50
180_K	187_A	0.607	0.49
24_D	164_N	0.607	0.49
78_N	105_V	0.606	0.49
45_I	184_R	0.603	0.49
106_N	110_Q	0.602	0.49
26_H	145_K	0.598	0.48
103_R	109_A	0.595	0.48
21_A	25_V	0.594	0.48
21_A	160_R	0.594	0.48
178_Q	186_A	0.592	0.47
87_L	100_S	0.590	0.47
60_L	68_I	0.590	0.47
73_D	93_P	0.589	0.47
98_S	101_G	0.586	0.47
67_A	73_D	0.585	0.47
145_K	171_T	0.582	0.46
31_L	38_A	0.577	0.46
17_T	161_A	0.574	0.45
112_V	188_S	0.573	0.45
17_T	169_L	0.570	0.45
178_Q	188_S	0.568	0.45
87_L	99_A	0.563	0.44
148_L	188_S	0.560	0.44
27_K	135_W	0.559	0.44
5_V	8_E	0.558	0.44
56_E	66_N	0.556	0.43
76_Q	134_R	0.556	0.43
65_V	81_L	0.555	0.43
6_V	183_Q	0.555	0.43
155_G	178_Q	0.553	0.43
142_V	145_K	0.550	0.43
65_V	73_D	0.549	0.43
4_F	189_W	0.546	0.42
179_M	187_A	0.545	0.42
23_S	29_Q	0.545	0.42
20_A	30_G	0.540	0.42
97_I	100_S	0.538	0.41
58_P	67_A	0.538	0.41
29_Q	153_P	0.534	0.41
38_A	184_R	0.532	0.41
4_F	56_E	0.530	0.40
12_C	187_A	0.528	0.40
45_I	155_G	0.526	0.40
23_S	26_H	0.525	0.40
41_K	107_A	0.521	0.39
78_N	83_I	0.520	0.39
179_M	185_L	0.518	0.39
77_L	104_P	0.517	0.39
15_C	163_P	0.514	0.39
37_L	42_T	0.511	0.38
13_T	16_N	0.511	0.38
100_S	138_G	0.509	0.38
84_G	88_C	0.507	0.38
67_A	93_P	0.506	0.38
157_A	160_R	0.506	0.38
186_A	189_W	0.505	0.38
145_K	169_L	0.503	0.38
75_I	91_V	0.502	0.37
4_F	7_A	0.502	0.37
18_C	189_W	0.502	0.37
38_A	105_V	0.501	0.37
138_G	141_T	0.501	0.37
68_I	73_D	0.500	0.37

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
1ti6B	2	0.8049	100	0.452	Contact Map
2ivfB	1	0.8195	100	0.457	Contact Map
2vpzB	2	0.8146	100	0.499	Contact Map
1h0hB	1	0.8146	100	0.519	Contact Map
1kqfB	3	0.8195	100	0.53	Contact Map
1q16B	2	0.8195	100	0.581	Contact Map
4z3xE	2	0.7512	99.9	0.646	Contact Map
3mm5B	2	0.8049	99.7	0.737	Contact Map
3i9v9	1	0.6146	99.3	0.801	Contact Map
3or1B	2	0.9366	99.3	0.801	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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