YGHU - ECOLI - GREMLIN Contacts

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YGHU - Disulfide-bond oxidoreductase YghU

UniProt:	Q46845	Sequences: MTDNTYQPAKVWTWDKSAGGAFANINRPVSGPTHEKTLPVGKHPLQLYSLGTPNGQKVTIMLEELLALGVTGAEYDAWLIRIGDGDQFSSGFVEVNPNSKIPALRDHTHNPPIRVFESGSILLYLAEKFGYFLPQDLAKRTETMNWLFWLQGAAPFLGGGFGHFYHYAPVKIEYAINRFTMEAKRLLDVLDKQLAQHKFVAGDEYTIADMAIWPWFGNVVLGGVYDAAEFLDAGSYKHVQRWAKEVGERPAVKRGRIVNRTNGPLNEQLHERHDASDFETNTEDKRQG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13005
Length:	288 (227)
Sequences:	3722 (2272)
Seq/√Len:	150.8

ECOLI - YGHU YFCG YNCG GSTA SSPA GSTB YFCF YIBF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
198_K	245_E	4.410	1.00
232_D	235_S	3.857	1.00
149_W	189_V	2.874	1.00
241_R	245_E	2.842	1.00
63_E	254_R	2.562	1.00
61_M	122_L	2.561	1.00
153_A	186_L	2.511	1.00
172_I	175_A	2.423	1.00
148_F	152_G	2.275	1.00
195_A	238_H	2.264	1.00
63_E	74_E	2.233	1.00
133_L	144_M	2.200	1.00
173_E	177_N	2.146	1.00
132_F	210_M	2.087	1.00
200_V	212_I	2.043	1.00
156_F	179_F	2.015	1.00
149_W	186_L	2.001	1.00
61_M	132_F	2.000	1.00
89_S	93_V	1.956	1.00
34_H	37_T	1.912	1.00
133_L	140_R	1.895	1.00
51_G	257_I	1.893	1.00
41_G	108_T	1.889	1.00
123_L	144_M	1.858	1.00
78_W	82_I	1.801	1.00
154_A	190_L	1.800	1.00
146_W	150_L	1.799	1.00
146_W	193_Q	1.748	1.00
152_G	160_G	1.720	1.00
191_D	237_K	1.718	1.00
234_G	240_Q	1.715	1.00
88_F	92_F	1.712	1.00
61_M	210_M	1.708	1.00
216_F	242_W	1.695	1.00
33_T	36_K	1.690	1.00
49_S	59_T	1.676	1.00
205_Y	249_R	1.654	1.00
245_E	249_R	1.644	1.00
210_M	246_V	1.640	1.00
190_L	239_V	1.626	1.00
88_F	91_G	1.613	1.00
79_L	82_I	1.590	1.00
90_S	94_E	1.576	1.00
240_Q	244_K	1.568	1.00
31_G	37_T	1.562	1.00
153_A	182_E	1.541	1.00
46_Q	78_W	1.536	1.00
32_P	36_K	1.530	1.00
191_D	238_H	1.512	1.00
45_L	62_L	1.472	1.00
136_D	139_K	1.464	1.00
193_Q	197_H	1.458	1.00
263_G	267_E	1.452	1.00
205_Y	246_V	1.448	1.00
64_E	249_R	1.443	1.00
225_Y	266_N	1.435	1.00
92_F	97_P	1.430	1.00
213_W	256_R	1.403	1.00
91_G	95_V	1.381	1.00
154_A	186_L	1.375	1.00
246_V	252_V	1.374	1.00
89_S	92_F	1.369	1.00
154_A	183_A	1.362	1.00
75_Y	82_I	1.341	1.00
146_W	201_A	1.336	1.00
136_D	204_E	1.328	1.00
78_W	84_D	1.325	1.00
245_E	248_E	1.324	1.00
259_N	263_G	1.323	1.00
205_Y	210_M	1.319	1.00
153_A	189_V	1.317	1.00
82_I	85_G	1.314	1.00
92_F	95_V	1.302	1.00
231_L	236_Y	1.293	1.00
87_Q	90_S	1.286	1.00
193_Q	200_V	1.269	1.00
240_Q	243_A	1.267	1.00
31_G	36_K	1.249	1.00
81_R	84_D	1.234	1.00
127_E	140_R	1.229	1.00
60_I	252_V	1.227	1.00
33_T	37_T	1.224	1.00
123_L	207_I	1.220	1.00
31_G	34_H	1.208	1.00
46_Q	76_D	1.200	1.00
46_Q	107_H	1.191	1.00
149_W	153_A	1.189	1.00
32_P	35_E	1.188	1.00
120_S	145_N	1.186	1.00
88_F	95_V	1.185	1.00
115_V	124_Y	1.185	1.00
65_L	126_A	1.184	1.00
93_V	97_P	1.182	1.00
92_F	96_N	1.172	1.00
114_R	142_E	1.169	1.00
142_E	193_Q	1.168	1.00
38_L	110_N	1.167	1.00
87_Q	96_N	1.152	1.00
141_T	145_N	1.149	1.00
32_P	40_V	1.143	1.00
56_Q	214_P	1.141	1.00
51_G	59_T	1.139	1.00
160_G	182_E	1.137	1.00
198_K	203_D	1.126	1.00
180_T	230_F	1.124	0.99
161_F	180_T	1.117	0.99
91_G	94_E	1.115	0.99
233_A	243_A	1.095	0.99
126_A	131_Y	1.093	0.99
32_P	37_T	1.093	0.99
37_T	40_V	1.091	0.99
80_I	84_D	1.090	0.99
175_A	179_F	1.088	0.99
60_I	210_M	1.085	0.99
88_F	97_P	1.085	0.99
143_T	201_A	1.075	0.99
186_L	189_V	1.073	0.99
31_G	35_E	1.065	0.99
198_K	241_R	1.063	0.99
90_S	93_V	1.044	0.99
49_S	55_G	1.039	0.99
135_Q	140_R	1.035	0.99
75_Y	80_I	1.034	0.99
89_S	95_V	1.027	0.99
147_L	211_A	1.010	0.99
198_K	248_E	1.009	0.99
75_Y	84_D	1.006	0.99
267_E	270_H	1.006	0.99
75_Y	79_L	1.004	0.99
161_F	183_A	1.002	0.99
87_Q	93_V	0.991	0.99
143_T	206_T	0.983	0.99
142_E	145_N	0.982	0.99
89_S	94_E	0.981	0.99
35_E	40_V	0.981	0.99
93_V	96_N	0.966	0.98
192_K	196_Q	0.960	0.98
80_I	83_G	0.948	0.98
193_Q	201_A	0.946	0.98
133_L	143_T	0.945	0.98
201_A	208_A	0.934	0.98
37_T	110_N	0.928	0.98
79_L	84_D	0.925	0.98
238_H	241_R	0.921	0.98
60_I	214_P	0.917	0.98
200_V	208_A	0.914	0.98
192_K	195_A	0.914	0.98
59_T	77_A	0.912	0.98
95_V	105_R	0.908	0.98
264_P	269_L	0.901	0.98
56_Q	60_I	0.895	0.97
197_H	201_A	0.890	0.97
56_Q	256_R	0.890	0.97
181_M	185_R	0.886	0.97
39_P	110_N	0.885	0.97
188_D	236_Y	0.879	0.97
76_D	82_I	0.874	0.97
75_Y	78_W	0.871	0.97
241_R	248_E	0.869	0.97
88_F	96_N	0.864	0.97
244_K	248_E	0.862	0.97
264_P	268_Q	0.857	0.97
89_S	96_N	0.849	0.97
88_F	99_S	0.841	0.96
87_Q	91_G	0.841	0.96
217_G	256_R	0.837	0.96
87_Q	94_E	0.836	0.96
153_A	185_R	0.834	0.96
160_G	179_F	0.832	0.96
180_T	231_L	0.827	0.96
77_A	82_I	0.817	0.96
213_W	252_V	0.817	0.96
178_R	182_E	0.808	0.95
65_L	130_G	0.807	0.95
233_A	240_Q	0.807	0.95
262_N	266_N	0.806	0.95
185_R	189_V	0.803	0.95
55_G	101_I	0.799	0.95
87_Q	92_F	0.797	0.95
78_W	83_G	0.791	0.95
250_P	254_R	0.791	0.95
47_L	104_L	0.790	0.95
222_G	264_P	0.787	0.95
32_P	128_K	0.787	0.95
152_G	182_E	0.786	0.95
56_Q	255_G	0.785	0.95
226_D	264_P	0.777	0.94
90_S	97_P	0.775	0.94
188_D	231_L	0.772	0.94
45_L	104_L	0.771	0.94
32_P	39_P	0.771	0.94
33_T	39_P	0.770	0.94
222_G	226_D	0.767	0.94
91_G	96_N	0.767	0.94
191_D	241_R	0.766	0.94
95_V	103_A	0.766	0.94
146_W	189_V	0.765	0.94
81_R	85_G	0.762	0.94
199_F	246_V	0.758	0.94
88_F	93_V	0.745	0.93
78_W	81_R	0.745	0.93
213_W	217_G	0.744	0.93
201_A	206_T	0.743	0.93
174_Y	178_R	0.726	0.92
143_T	147_L	0.726	0.92
90_S	95_V	0.719	0.92
35_E	110_N	0.717	0.92
146_W	190_L	0.717	0.92
119_G	147_L	0.716	0.91
148_F	151_Q	0.715	0.91
190_L	193_Q	0.715	0.91
145_N	149_W	0.715	0.91
34_H	40_V	0.713	0.91
217_G	258_V	0.710	0.91
248_E	253_K	0.709	0.91
223_G	247_G	0.706	0.91
76_D	84_D	0.705	0.91
126_A	130_G	0.701	0.91
257_I	260_R	0.698	0.90
190_L	212_I	0.695	0.90
251_A	254_R	0.694	0.90
246_V	249_R	0.691	0.90
177_N	180_T	0.691	0.90
210_M	249_R	0.688	0.90
140_R	144_M	0.688	0.90
105_R	112_P	0.685	0.90
94_E	97_P	0.682	0.89
123_L	148_F	0.682	0.89
157_L	183_A	0.681	0.89
91_G	97_P	0.674	0.89
198_K	201_A	0.671	0.89
177_N	181_M	0.670	0.89
88_F	94_E	0.669	0.89
217_G	243_A	0.668	0.88
146_W	149_W	0.665	0.88
171_K	176_I	0.665	0.88
90_S	96_N	0.664	0.88
80_I	86_D	0.659	0.88
59_T	255_G	0.658	0.88
191_D	195_A	0.658	0.88
87_Q	97_P	0.653	0.87
80_I	85_G	0.651	0.87
134_P	143_T	0.649	0.87
63_E	75_Y	0.647	0.87
64_E	205_Y	0.642	0.86
54_N	57_K	0.633	0.86
45_L	73_A	0.632	0.86
189_V	193_Q	0.631	0.85
124_Y	128_K	0.629	0.85
147_L	207_I	0.628	0.85
82_I	86_D	0.628	0.85
193_Q	196_Q	0.627	0.85
142_E	197_H	0.627	0.85
159_G	163_H	0.626	0.85
186_L	190_L	0.625	0.85
120_S	123_L	0.623	0.85
64_E	251_A	0.622	0.85
207_I	211_A	0.622	0.85
197_H	203_D	0.621	0.85
119_G	211_A	0.619	0.84
182_E	185_R	0.615	0.84
150_L	208_A	0.614	0.84
82_I	263_G	0.613	0.84
231_L	234_G	0.612	0.84
85_G	88_F	0.610	0.83
58_V	121_I	0.607	0.83
79_L	83_G	0.607	0.83
230_F	236_Y	0.605	0.83
37_T	124_Y	0.604	0.83
54_N	155_P	0.604	0.83
56_Q	218_N	0.602	0.83
222_G	269_L	0.601	0.83
225_Y	262_N	0.601	0.83
188_D	192_K	0.599	0.82
139_K	204_E	0.598	0.82
146_W	200_V	0.592	0.82
113_I	138_A	0.590	0.81
76_D	85_G	0.588	0.81
143_T	208_A	0.588	0.81
78_W	85_G	0.582	0.81
175_A	182_E	0.578	0.80
78_W	86_D	0.574	0.80
149_W	190_L	0.574	0.80
87_Q	95_V	0.573	0.80
127_E	144_M	0.570	0.79
122_L	207_I	0.567	0.79
54_N	156_F	0.565	0.79
62_L	75_Y	0.561	0.78
35_E	38_L	0.561	0.78
213_W	246_V	0.560	0.78
115_V	141_T	0.558	0.78
220_V	233_A	0.556	0.77
54_N	151_Q	0.554	0.77
181_M	230_F	0.553	0.77
106_D	113_I	0.553	0.77
141_T	144_M	0.552	0.77
81_R	263_G	0.552	0.77
65_L	129_F	0.549	0.77
226_D	269_L	0.547	0.76
38_L	124_Y	0.545	0.76
55_G	58_V	0.545	0.76
81_R	86_D	0.544	0.76
199_F	245_E	0.543	0.76
44_P	107_H	0.543	0.76
93_V	99_S	0.543	0.76
252_V	256_R	0.538	0.75
199_F	205_Y	0.536	0.75
76_D	80_I	0.536	0.75
264_P	267_E	0.535	0.75
88_F	112_P	0.533	0.74
120_S	144_M	0.531	0.74
105_R	114_R	0.529	0.74
89_S	97_P	0.528	0.74
58_V	125_L	0.527	0.74
103_A	113_I	0.526	0.74
33_T	40_V	0.525	0.73
249_R	254_R	0.525	0.73
221_L	224_V	0.523	0.73
86_D	89_S	0.523	0.73
153_A	190_L	0.522	0.73
63_E	125_L	0.522	0.73
33_T	120_S	0.521	0.73
31_G	128_K	0.520	0.73
229_E	262_N	0.520	0.73
154_A	212_I	0.519	0.73
39_P	108_T	0.519	0.73
221_L	244_K	0.518	0.72
35_E	39_P	0.516	0.72
60_I	246_V	0.515	0.72
77_A	80_I	0.513	0.72
139_K	142_E	0.513	0.72
50_L	264_P	0.510	0.71
184_K	235_S	0.509	0.71
218_N	223_G	0.508	0.71
94_E	111_P	0.507	0.71
40_V	105_R	0.506	0.71
220_V	223_G	0.504	0.70
155_P	215_W	0.504	0.70
76_D	83_G	0.503	0.70
150_L	212_I	0.500	0.70

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
3c8eA	2	0.9826	100	0.299	Contact Map
4puaA	2	0.9028	100	0.375	Contact Map
3gx0A	2	0.6979	100	0.383	Contact Map
1k0dA	2	0.7569	100	0.385	Contact Map
4mf5A	2	0.8125	100	0.391	Contact Map
4ecjA	2	0.7118	100	0.393	Contact Map
4ri6A	2	0.7188	100	0.394	Contact Map
1pn9A	2	0.7083	100	0.395	Contact Map
4pngA	2	0.7569	100	0.395	Contact Map
2imiA	2	0.7535	100	0.395	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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