HYFI - ECOLI - GREMLIN Contacts

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HYFI - Hydrogenase-4 component I

UniProt:	P77668	Sequences: MSPVLTQHVSQPITLDEQTQKMKRHLLQDIRRSAYVYRVDCGGCNACEIEIFAAITPVFDAERFGIKVVSSPRHADILLFTGAVTRAMRMPALRAYESAPDHKICVSYGACGVGGGIFHDLYSVWGGSDTIVPIDVWIPGCPPTPAATIHGFAVALGLLQQKIHAVDYRDPTGVTMQPLWPQIPPSQRIAIEREARRLAGYRQGREICDRLLRHLSDDPTGNRVNTWLRDADDPRLNSIVQQLFRVLRGLHD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14217
Length:	252 (204)
Sequences:	241 (86)
Seq/√Len:	6.0

ECOLI - HYFI HYCG NUOB
HALSA - Q9HRM0
SULSO - Q7LXP2 Q97ZA8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
128_S	134_I	3.394	0.86
32_R	71_S	2.980	0.78
18_Q	64_F	2.979	0.78
17_E	25_H	2.979	0.78
12_P	18_Q	2.696	0.70
17_E	122_Y	2.641	0.68
27_L	136_V	2.589	0.67
45_N	122_Y	2.544	0.65
200_G	203_Q	2.422	0.61
45_N	124_V	2.281	0.56
103_K	118_F	2.256	0.55
91_P	144_T	2.235	0.55
22_M	79_L	2.224	0.54
150_H	154_V	2.213	0.54
122_Y	161_Q	2.072	0.49
11_Q	18_Q	2.069	0.49
75_A	118_F	2.060	0.48
24_R	211_L	1.999	0.46
80_F	128_S	1.970	0.45
15_L	174_V	1.935	0.44
18_Q	28_Q	1.905	0.43
57_P	151_G	1.896	0.43
110_A	120_D	1.859	0.41
91_P	94_R	1.842	0.41
18_Q	177_Q	1.831	0.40
62_E	67_K	1.818	0.40
80_F	92_A	1.758	0.38
92_A	132_V	1.739	0.37
14_T	18_Q	1.727	0.37
84_V	137_W	1.652	0.34
59_F	120_D	1.631	0.34
122_Y	183_I	1.602	0.33
42_G	52_F	1.597	0.33
48_E	52_F	1.586	0.32
185_P	206_E	1.583	0.32
49_I	118_F	1.575	0.32
33_S	67_K	1.566	0.32
84_V	132_V	1.516	0.30
33_S	56_T	1.508	0.30
19_T	23_K	1.507	0.30
53_A	64_F	1.497	0.30
45_N	161_Q	1.464	0.29
187_Q	190_A	1.462	0.29
37_Y	62_E	1.452	0.28
72_P	76_D	1.446	0.28
102_H	137_W	1.439	0.28
25_H	122_Y	1.409	0.27
64_F	124_V	1.399	0.27
72_P	127_G	1.385	0.26
61_A	66_I	1.375	0.26
17_E	124_V	1.374	0.26
112_G	131_I	1.371	0.26
99_A	146_A	1.358	0.26
35_Y	159_L	1.353	0.26
58_V	160_Q	1.351	0.25
59_F	110_A	1.335	0.25
11_Q	183_I	1.332	0.25
28_Q	64_F	1.330	0.25
11_Q	15_L	1.329	0.25
96_Y	105_C	1.317	0.25
84_V	88_M	1.310	0.24
17_E	45_N	1.294	0.24
78_L	94_R	1.288	0.24
91_P	161_Q	1.277	0.24
69_V	79_L	1.276	0.23
166_V	179_L	1.268	0.23
193_R	204_G	1.268	0.23
192_E	203_Q	1.257	0.23
11_Q	17_E	1.254	0.23
42_G	55_I	1.236	0.22
188_R	207_I	1.234	0.22
47_C	109_G	1.232	0.22
105_C	114_G	1.229	0.22
167_D	206_E	1.219	0.22
11_Q	16_D	1.210	0.22
93_L	97_E	1.207	0.22
18_Q	24_R	1.198	0.22
95_A	104_I	1.171	0.21
124_V	161_Q	1.164	0.21
202_R	206_E	1.163	0.21
200_G	204_G	1.156	0.21
22_M	34_A	1.154	0.21
176_M	182_Q	1.152	0.20
37_Y	90_M	1.145	0.20
146_A	155_A	1.141	0.20
90_M	132_V	1.113	0.20
107_S	176_M	1.106	0.19
203_Q	206_E	1.105	0.19
49_I	148_T	1.096	0.19
37_Y	87_A	1.094	0.19
12_P	15_L	1.086	0.19
76_D	127_G	1.080	0.19
22_M	31_R	1.071	0.19
92_A	128_S	1.064	0.18
11_Q	64_F	1.061	0.18
206_E	210_R	1.055	0.18
76_D	96_Y	1.053	0.18
103_K	112_G	1.047	0.18
168_Y	174_V	1.045	0.18
166_V	206_E	1.029	0.18
132_V	144_T	1.029	0.18
37_Y	89_R	1.022	0.18
47_C	133_P	1.020	0.18
17_E	20_Q	1.009	0.17
16_D	173_G	1.009	0.17
71_S	193_R	1.009	0.17
44_C	104_I	1.007	0.17
44_C	51_I	1.006	0.17
68_V	114_G	1.006	0.17
43_G	108_Y	1.005	0.17
93_L	112_G	0.996	0.17
52_F	78_L	0.992	0.17
14_T	17_E	0.991	0.17
15_L	28_Q	0.982	0.17
19_T	185_P	0.970	0.17
107_S	184_P	0.969	0.17
19_T	136_V	0.967	0.16
12_P	64_F	0.962	0.16
14_T	197_R	0.960	0.16
24_R	27_L	0.960	0.16
47_C	142_P	0.956	0.16
205_R	209_D	0.954	0.16
84_V	122_Y	0.946	0.16
109_G	133_P	0.943	0.16
76_D	129_D	0.942	0.16
12_P	28_Q	0.940	0.16
49_I	75_A	0.938	0.16
11_Q	179_L	0.933	0.16
56_T	62_E	0.932	0.16
25_H	84_V	0.932	0.16
190_A	194_E	0.926	0.16
73_R	143_P	0.916	0.16
32_R	72_P	0.916	0.16
55_I	114_G	0.916	0.16
27_L	179_L	0.914	0.15
135_D	158_L	0.910	0.15
92_A	134_I	0.909	0.15
110_A	118_F	0.903	0.15
159_L	193_R	0.900	0.15
43_G	76_D	0.897	0.15
75_A	127_G	0.895	0.15
18_Q	144_T	0.891	0.15
24_R	170_D	0.888	0.15
171_P	197_R	0.886	0.15
171_P	187_Q	0.881	0.15
109_G	142_P	0.880	0.15
49_I	55_I	0.880	0.15
41_C	52_F	0.878	0.15
51_I	148_T	0.872	0.15
18_Q	21_K	0.870	0.15
46_A	98_S	0.869	0.15
12_P	195_A	0.857	0.14
68_V	207_I	0.854	0.14
22_M	175_T	0.853	0.14
30_I	74_H	0.850	0.14
179_L	182_Q	0.846	0.14
166_V	170_D	0.842	0.14
172_T	206_E	0.841	0.14
172_T	186_S	0.837	0.14
178_P	203_Q	0.835	0.14
171_P	175_T	0.835	0.14
37_Y	122_Y	0.835	0.14
166_V	213_R	0.829	0.14
42_G	67_K	0.824	0.14
197_R	207_I	0.824	0.14
62_E	66_I	0.796	0.13
52_F	67_K	0.795	0.13
85_T	124_V	0.793	0.13
56_T	149_I	0.792	0.13
80_F	93_L	0.787	0.13
18_Q	53_A	0.784	0.13
172_T	175_T	0.780	0.13
15_L	18_Q	0.779	0.13
58_V	162_K	0.774	0.13
35_Y	52_F	0.772	0.13
96_Y	160_Q	0.772	0.13
17_E	183_I	0.764	0.13
103_K	110_A	0.763	0.13
11_Q	177_Q	0.760	0.13
192_E	195_A	0.759	0.13
16_D	189_I	0.758	0.13
149_I	189_I	0.757	0.13
188_R	193_R	0.755	0.13
34_A	144_T	0.748	0.13
132_V	177_Q	0.748	0.13
54_A	62_E	0.747	0.13
15_L	53_A	0.747	0.13
185_P	215_L	0.744	0.13
91_P	138_I	0.743	0.13
41_C	124_V	0.742	0.13
64_F	195_A	0.737	0.12
170_D	173_G	0.734	0.12
15_L	185_P	0.729	0.12
204_G	207_I	0.729	0.12
73_R	142_P	0.727	0.12
146_A	154_V	0.725	0.12
25_H	113_V	0.724	0.12
15_L	184_P	0.720	0.12
17_E	173_G	0.717	0.12
80_F	144_T	0.715	0.12
211_L	215_L	0.709	0.12
31_R	46_A	0.707	0.12
38_R	146_A	0.705	0.12
191_I	194_E	0.696	0.12
173_G	206_E	0.693	0.12
78_L	148_T	0.692	0.12
122_Y	163_I	0.690	0.12
39_V	67_K	0.688	0.12
149_I	203_Q	0.687	0.12
35_Y	99_A	0.684	0.12
43_G	127_G	0.682	0.12
24_R	169_R	0.677	0.12
11_Q	195_A	0.673	0.11
36_V	79_L	0.672	0.11
67_K	138_I	0.671	0.11
54_A	61_A	0.669	0.11
112_G	134_I	0.668	0.11
44_C	126_G	0.667	0.11
64_F	91_P	0.667	0.11
110_A	130_T	0.664	0.11
14_T	171_P	0.658	0.11
133_P	142_P	0.658	0.11
46_A	87_A	0.656	0.11
186_S	203_Q	0.649	0.11
13_I	171_P	0.645	0.11
190_A	195_A	0.644	0.11
206_E	211_L	0.644	0.11
41_C	94_R	0.638	0.11
38_R	125_W	0.637	0.11
121_L	155_A	0.635	0.11
41_C	88_M	0.634	0.11
90_M	134_I	0.633	0.11
31_R	156_L	0.633	0.11
106_V	147_A	0.632	0.11
152_F	196_R	0.626	0.11
54_A	57_P	0.626	0.11
192_E	206_E	0.624	0.11
64_F	177_Q	0.624	0.11
46_A	74_H	0.623	0.11
88_M	103_K	0.622	0.11
62_E	100_P	0.620	0.11
62_E	138_I	0.614	0.11
32_R	127_G	0.613	0.11
166_V	193_R	0.611	0.11
189_I	199_A	0.607	0.11
15_L	64_F	0.606	0.11
19_T	169_R	0.604	0.11
174_V	183_I	0.601	0.10
204_G	215_L	0.600	0.10
49_I	53_A	0.599	0.10
30_I	46_A	0.592	0.10
24_R	164_H	0.592	0.10
91_P	112_G	0.591	0.10
118_F	145_P	0.591	0.10
189_I	196_R	0.590	0.10
179_L	212_L	0.589	0.10
120_D	145_P	0.588	0.10
19_T	206_E	0.588	0.10
57_P	117_I	0.587	0.10
39_V	83_A	0.587	0.10
51_I	104_I	0.586	0.10
43_G	87_A	0.585	0.10
97_E	110_A	0.584	0.10
47_C	127_G	0.584	0.10
16_D	21_K	0.582	0.10
84_V	205_R	0.579	0.10
102_H	134_I	0.574	0.10
87_A	125_W	0.573	0.10
45_N	91_P	0.568	0.10
84_V	130_T	0.564	0.10
49_I	127_G	0.563	0.10
88_M	94_R	0.560	0.10
196_R	199_A	0.557	0.10
23_K	200_G	0.557	0.10
187_Q	210_R	0.555	0.10
210_R	213_R	0.552	0.10
30_I	155_A	0.552	0.10
190_A	207_I	0.544	0.10
94_R	161_Q	0.542	0.10
15_L	213_R	0.539	0.10
18_Q	164_H	0.537	0.10
35_Y	126_G	0.536	0.10
17_E	165_A	0.530	0.10
19_T	28_Q	0.530	0.10
195_A	200_G	0.529	0.10
121_L	147_A	0.529	0.10
149_I	166_V	0.526	0.10
81_T	108_Y	0.523	0.09
149_I	161_Q	0.523	0.09
107_S	131_I	0.521	0.09
190_A	213_R	0.520	0.09
161_Q	204_G	0.519	0.09
79_L	172_T	0.518	0.09
11_Q	14_T	0.518	0.09
29_D	105_C	0.515	0.09
52_F	55_I	0.514	0.09
32_R	88_M	0.510	0.09
17_E	163_I	0.509	0.09
38_R	108_Y	0.507	0.09
109_G	127_G	0.506	0.09
171_P	205_R	0.506	0.09
122_Y	165_A	0.505	0.09
15_L	190_A	0.505	0.09
94_R	103_K	0.503	0.09
44_C	113_V	0.500	0.09
41_C	122_Y	0.500	0.09

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
3i9v6	1	0.5754	100	0.508	Contact Map
1h2aS	1	0.8135	100	0.657	Contact Map
2wpnA	1	0.8373	100	0.663	Contact Map
4ue3S	2	0.7262	100	0.663	Contact Map
3ayxB	2	0.7817	100	0.664	Contact Map
4uqlA	1	0.8016	100	0.67	Contact Map
4kn9S	1	0.8294	100	0.676	Contact Map
3myrA	3	0.7698	100	0.677	Contact Map
4u9hS	1	0.754	100	0.678	Contact Map
4iucS	1	0.7302	100	0.678	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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