YDHX - ECOLI - GREMLIN Contacts

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YDHX - Uncharacterized ferredoxin-like protein YdhX

UniProt:	P77375	Sequences: MSFTRRKFVLGMGTVIFFTGSASSLLANTRQEKEVRYAMIHDESRCNGCNICARACRKTNHVPAQGSRLSIAHIPVTDNDNETQYHFFRQSCQHCEDAPCIDVCPTGASWRDEQGIVRVEKSQCIGCSYCIGACPYQVRYLNPVTKVADKCDFCAESRLAKGFPPICVSACPEHALIFGREDSPEIQAWLQQNKYYQYQLPGAGKPHLYRRFGQHLIKKENV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13958
Length:	222 (177)
Sequences:	2599 (1477)
Seq/√Len:	111.0

ECOLI - YDHX NRFC HYBA FDOH YNFG FDNH DMSB YDHY HYFA HYDN YSAA HYCB YGFS NARY NARH
BACSU - NARH
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
59_T	156_E	2.944	1.00
78_D	81_N	2.914	1.00
128_S	141_L	2.795	1.00
165_P	168_V	2.722	1.00
96_E	207_H	2.697	1.00
103_V	133_A	2.622	1.00
101_I	109_S	2.500	1.00
109_S	139_R	2.478	1.00
39_M	153_F	2.440	1.00
183_S	186_I	2.197	1.00
131_I	148_A	2.128	1.00
98_A	111_R	2.067	1.00
41_H	176_L	1.965	1.00
68_R	149_D	1.951	1.00
112_D	160_A	1.939	1.00
35_V	182_D	1.938	1.00
35_V	180_R	1.890	1.00
103_V	129_Y	1.885	1.00
197_Q	200_L	1.863	1.00
38_A	181_E	1.821	1.00
109_S	119_V	1.799	1.00
128_S	131_I	1.785	1.00
46_C	52_C	1.721	1.00
40_I	211_R	1.719	1.00
142_N	149_D	1.699	1.00
46_C	49_C	1.685	1.00
153_F	208_L	1.681	1.00
46_C	171_C	1.678	1.00
168_V	176_L	1.677	1.00
116_I	159_L	1.657	1.00
112_D	118_R	1.652	1.00
158_R	163_F	1.641	1.00
141_L	148_A	1.622	1.00
197_Q	205_K	1.582	1.00
91_S	208_L	1.579	1.00
47_N	173_E	1.568	1.00
36_R	96_E	1.547	1.00
116_I	153_F	1.539	1.00
155_A	160_A	1.527	1.00
59_T	158_R	1.516	1.00
49_C	52_C	1.516	1.00
190_L	195_Y	1.511	1.00
158_R	169_S	1.503	1.00
104_C	124_C	1.488	1.00
49_C	171_C	1.465	1.00
55_A	170_A	1.462	1.00
60_N	156_E	1.445	1.00
179_G	183_S	1.413	1.00
104_C	130_C	1.404	1.00
99_P	204_G	1.398	1.00
97_D	102_D	1.395	1.00
128_S	143_P	1.387	1.00
194_K	201_P	1.378	1.00
101_I	111_R	1.370	1.00
124_C	130_C	1.368	1.00
188_A	191_Q	1.362	1.00
52_C	171_C	1.345	1.00
177_I	187_Q	1.331	1.00
120_E	123_Q	1.317	1.00
98_A	101_I	1.311	0.99
69_L	176_L	1.306	0.99
44_S	211_R	1.255	0.99
180_R	183_S	1.254	0.99
112_D	116_I	1.228	0.99
164_P	169_S	1.225	0.99
163_F	169_S	1.217	0.99
106_T	109_S	1.205	0.99
50_N	53_A	1.205	0.99
97_D	205_K	1.203	0.99
106_T	125_I	1.199	0.99
51_I	170_A	1.188	0.99
129_Y	132_G	1.182	0.99
91_S	176_L	1.181	0.99
90_Q	198_Y	1.176	0.99
118_R	155_A	1.171	0.99
36_R	207_H	1.169	0.99
96_E	205_K	1.166	0.99
38_A	184_P	1.157	0.99
185_E	188_A	1.145	0.99
195_Y	211_R	1.142	0.99
143_P	146_K	1.137	0.99
55_A	166_I	1.118	0.98
38_A	207_H	1.111	0.98
110_W	118_R	1.096	0.98
99_P	133_A	1.089	0.98
190_L	209_Y	1.086	0.98
112_D	155_A	1.085	0.98
118_R	152_D	1.085	0.98
110_W	120_E	1.083	0.98
89_R	210_R	1.083	0.98
140_Y	149_D	1.077	0.98
78_D	82_E	1.071	0.98
143_P	149_D	1.043	0.97
136_Y	206_P	1.039	0.97
177_I	189_W	1.038	0.97
159_L	178_F	1.012	0.97
199_Q	202_G	1.008	0.97
59_T	166_I	1.003	0.97
116_I	155_A	1.003	0.97
139_R	148_A	0.999	0.97
198_Y	204_G	0.996	0.97
34_E	182_D	0.977	0.96
121_K	147_V	0.975	0.96
193_N	211_R	0.971	0.96
41_H	89_R	0.969	0.96
111_R	117_V	0.968	0.96
197_Q	209_Y	0.959	0.96
69_L	89_R	0.955	0.96
41_H	208_L	0.949	0.95
89_R	176_L	0.948	0.95
190_L	193_N	0.948	0.95
41_H	91_S	0.946	0.95
39_M	168_V	0.940	0.95
119_V	139_R	0.925	0.95
67_S	70_S	0.925	0.95
62_V	68_R	0.921	0.95
188_A	192_Q	0.921	0.95
44_S	193_N	0.907	0.94
70_S	90_Q	0.906	0.94
114_Q	160_A	0.905	0.94
60_N	152_D	0.893	0.94
129_Y	133_A	0.880	0.93
37_Y	159_L	0.874	0.93
70_S	140_Y	0.867	0.93
104_C	127_C	0.846	0.92
43_E	89_R	0.842	0.92
37_Y	178_F	0.838	0.91
181_E	185_E	0.835	0.91
40_I	189_W	0.835	0.91
152_D	156_E	0.832	0.91
153_F	178_F	0.831	0.91
180_R	186_I	0.820	0.91
128_S	148_A	0.818	0.90
124_C	127_C	0.817	0.90
111_R	207_H	0.811	0.90
106_T	123_Q	0.811	0.90
37_Y	116_I	0.810	0.90
91_S	153_F	0.808	0.90
189_W	193_N	0.806	0.90
142_N	145_T	0.806	0.90
106_T	127_C	0.805	0.90
105_P	130_C	0.804	0.90
57_R	62_V	0.783	0.88
36_R	182_D	0.782	0.88
105_P	124_C	0.779	0.88
48_G	175_A	0.774	0.88
197_Q	202_G	0.767	0.87
125_I	129_Y	0.760	0.87
68_R	75_P	0.755	0.87
73_H	85_Y	0.753	0.86
56_C	151_C	0.748	0.86
195_Y	199_Q	0.748	0.86
94_H	117_V	0.743	0.86
51_I	173_E	0.743	0.86
43_E	88_F	0.742	0.86
36_R	111_R	0.741	0.86
101_I	110_W	0.740	0.85
119_V	148_A	0.733	0.85
96_E	111_R	0.731	0.85
106_T	110_W	0.727	0.84
68_R	71_I	0.722	0.84
121_K	145_T	0.721	0.84
131_I	141_L	0.720	0.84
127_C	130_C	0.719	0.84
103_V	109_S	0.718	0.84
78_D	83_T	0.718	0.84
151_C	154_C	0.715	0.83
44_S	209_Y	0.712	0.83
174_H	177_I	0.706	0.83
103_V	132_G	0.704	0.83
153_F	159_L	0.702	0.82
56_C	154_C	0.694	0.82
51_I	54_R	0.690	0.81
199_Q	204_G	0.687	0.81
42_D	178_F	0.677	0.80
48_G	71_I	0.674	0.80
66_G	69_L	0.672	0.80
203_A	210_R	0.671	0.79
73_H	87_F	0.670	0.79
192_Q	195_Y	0.669	0.79
41_H	210_R	0.667	0.79
164_P	168_V	0.654	0.78
69_L	91_S	0.653	0.78
203_A	206_P	0.652	0.77
51_I	58_K	0.651	0.77
69_L	72_A	0.651	0.77
98_A	139_R	0.647	0.77
165_P	176_L	0.645	0.77
48_G	138_V	0.643	0.76
69_L	73_H	0.636	0.76
181_E	190_L	0.636	0.76
189_W	192_Q	0.631	0.75
200_L	203_A	0.630	0.75
39_M	178_F	0.618	0.74
48_G	52_C	0.618	0.74
149_D	152_D	0.616	0.73
128_S	132_G	0.615	0.73
128_S	149_D	0.615	0.73
180_R	184_P	0.615	0.73
48_G	171_C	0.613	0.73
43_E	210_R	0.613	0.73
158_R	166_I	0.612	0.73
45_R	175_A	0.608	0.72
68_R	140_Y	0.607	0.72
141_L	145_T	0.605	0.72
108_A	123_Q	0.602	0.72
195_Y	209_Y	0.598	0.71
78_D	84_Q	0.596	0.71
194_K	200_L	0.595	0.71
195_Y	198_Y	0.594	0.71
79_N	82_E	0.593	0.71
160_A	163_F	0.591	0.70
131_I	143_P	0.588	0.70
37_Y	114_Q	0.587	0.70
60_N	166_I	0.587	0.70
63_P	66_G	0.586	0.70
194_K	197_Q	0.583	0.69
48_G	87_F	0.581	0.69
51_I	172_P	0.579	0.69
36_R	181_E	0.575	0.68
190_L	194_K	0.574	0.68
202_G	207_H	0.573	0.68
121_K	149_D	0.572	0.68
199_Q	203_A	0.570	0.68
114_Q	118_R	0.568	0.67
76_V	85_Y	0.568	0.67
159_L	162_G	0.567	0.67
60_N	68_R	0.567	0.67
47_N	172_P	0.567	0.67
68_R	152_D	0.565	0.67
39_M	69_L	0.562	0.66
94_H	159_L	0.561	0.66
68_R	72_A	0.561	0.66
203_A	211_R	0.558	0.66
39_M	91_S	0.554	0.65
181_E	184_P	0.551	0.65
65_Q	75_P	0.548	0.65
42_D	211_R	0.547	0.64
198_Y	202_G	0.543	0.64
58_K	170_A	0.543	0.64
162_G	190_L	0.539	0.63
197_Q	207_H	0.538	0.63
192_Q	200_L	0.535	0.63
51_I	166_I	0.532	0.62
152_D	155_A	0.530	0.62
63_P	144_V	0.529	0.62
200_L	210_R	0.528	0.62
42_D	45_R	0.527	0.62
140_Y	148_A	0.527	0.62
110_W	123_Q	0.524	0.61
137_Q	141_L	0.521	0.61
120_E	164_P	0.521	0.61
191_Q	194_K	0.517	0.60
59_T	169_S	0.516	0.60
66_G	70_S	0.512	0.59
194_K	211_R	0.512	0.59
139_R	184_P	0.510	0.59
39_M	89_R	0.509	0.59
40_I	206_P	0.508	0.59
35_V	79_N	0.506	0.58
111_R	116_I	0.502	0.58
158_R	162_G	0.501	0.58
79_N	191_Q	0.501	0.58
181_E	207_H	0.500	0.58
165_P	178_F	0.500	0.58
94_H	111_R	0.500	0.58

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	0.8378	100	0.413	Contact Map
2ivfB	1	0.8468	100	0.427	Contact Map
1kqfB	3	0.9324	100	0.477	Contact Map
2vpzB	2	0.8378	100	0.483	Contact Map
1h0hB	1	0.8378	100	0.487	Contact Map
1q16B	2	0.8604	100	0.533	Contact Map
4z3xE	2	0.7342	100	0.622	Contact Map
3mm5B	2	0.9685	99.8	0.73	Contact Map
1jnrB	1	0.6261	99.5	0.789	Contact Map
3gyxB	1	0.6261	99.5	0.791	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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