YDHF - ECOLI - GREMLIN Contacts

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YDHF - Oxidoreductase YdhF

UniProt:	P76187	Sequences: MVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHADIYGGYQCEAAFGEALKLAPHLRERMEIVSKCGIATTAREENVIGHYITDRDHIIKSAEQSLINLATDHLDLLLIHRPDPLMDADEVADAFKHLHQSGKVRHFGVSNFTPAQFALLQSRLPFTLATNQVEISPVHQPLLLDGTLDQLQQLRVRPMAWSCLGGGRLFNDDYFQPLRDELAVVAEELNAGSIEQVVYAWVLRLPSQPLPIIGSGKIERVRAAVEAETLKMTRQQWFRIRKAALGYDVP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13420
Length:	298 (262)
Sequences:	32590 (20665)
Seq/√Len:	1276.7

ECOLI - YDHF TAS YDJG YAJO GPR YEAE DKGA YDBC DKGB
BACSU - YCSN YRPG GS69 YCCK IOLS YTBE YQKF GR
HALSA - Q9HPH9 Q9HNN3 Q9HQU7 Q9HS02 Q9HSE6 Q9HQT1
SULSO - Q97UG6 Q97UV9 Q97ZZ1 Q97UJ7 Q97V56 Q97U17

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_E	270_R	3.255	1.00
111_E	151_K	2.962	1.00
31_A	66_E	2.921	1.00
69_K	118_A	2.850	1.00
237_L	284_Q	2.750	1.00
281_T	284_Q	2.513	1.00
35_V	70_L	2.494	1.00
110_A	146_L	2.454	1.00
107_I	145_H	2.452	1.00
40_E	44_L	2.388	1.00
107_I	149_S	2.335	1.00
144_K	148_Q	2.146	1.00
236_E	287_R	2.126	1.00
35_V	66_E	2.078	1.00
121_H	153_R	2.048	1.00
112_Q	116_N	2.035	1.00
252_R	285_W	2.016	1.00
145_H	149_S	2.006	1.00
198_Q	202_L	1.992	1.00
231_A	235_E	1.987	1.00
266_I	270_R	1.986	1.00
199_L	206_P	1.935	1.00
40_E	266_I	1.935	1.00
236_E	284_Q	1.912	1.00
74_L	77_R	1.908	1.00
103_R	145_H	1.880	1.00
282_R	286_F	1.868	1.00
232_V	287_R	1.864	1.00
44_L	270_R	1.863	1.00
18_V	48_T	1.860	1.00
59_Q	62_A	1.821	1.00
253_L	289_R	1.737	1.00
126_L	178_T	1.703	1.00
166_A	170_S	1.696	1.00
145_H	148_Q	1.695	1.00
166_A	198_Q	1.693	1.00
103_R	107_I	1.677	1.00
41_H	46_V	1.660	1.00
229_E	232_V	1.656	1.00
62_A	116_N	1.646	1.00
239_A	278_L	1.636	1.00
44_L	273_V	1.628	1.00
84_C	125_L	1.624	1.00
35_V	39_E	1.619	1.00
40_E	43_D	1.616	1.00
142_A	145_H	1.604	1.00
30_S	33_Q	1.603	1.00
107_I	111_E	1.598	1.00
205_R	258_L	1.598	1.00
274_E	277_T	1.592	1.00
82_S	113_S	1.592	1.00
241_S	271_A	1.591	1.00
39_E	70_L	1.591	1.00
80_I	119_T	1.585	1.00
110_A	125_L	1.569	1.00
35_V	67_A	1.568	1.00
248_A	278_L	1.566	1.00
286_F	290_K	1.565	1.00
82_S	122_L	1.558	1.00
84_C	106_I	1.552	1.00
31_A	35_V	1.551	1.00
144_K	174_F	1.538	1.00
81_V	126_L	1.502	1.00
108_K	112_Q	1.493	1.00
21_Y	49_V	1.464	1.00
12_P	154_H	1.450	1.00
42_L	78_M	1.439	1.00
53_D	109_S	1.424	1.00
161_T	164_Q	1.423	1.00
197_D	201_Q	1.410	1.00
200_Q	254_P	1.406	1.00
111_E	115_I	1.403	1.00
194_G	197_D	1.395	1.00
169_Q	202_L	1.392	1.00
126_L	207_M	1.385	1.00
147_H	174_F	1.378	1.00
181_V	206_P	1.369	1.00
33_Q	36_S	1.367	1.00
239_A	244_Q	1.352	1.00
38_I	67_A	1.348	1.00
270_R	274_E	1.331	1.00
248_A	252_R	1.316	1.00
36_S	40_E	1.314	1.00
12_P	79_E	1.307	1.00
122_L	152_V	1.304	1.00
103_R	141_D	1.302	1.00
39_E	43_D	1.301	1.00
287_R	290_K	1.292	1.00
112_Q	115_I	1.290	1.00
154_H	177_A	1.281	1.00
229_E	287_R	1.275	1.00
239_A	245_V	1.271	1.00
169_Q	198_Q	1.261	1.00
107_I	142_A	1.257	1.00
146_L	152_V	1.240	1.00
263_S	268_R	1.238	1.00
79_E	124_L	1.237	1.00
117_L	122_L	1.237	1.00
65_G	118_A	1.234	1.00
103_R	142_A	1.234	1.00
152_V	155_F	1.222	1.00
162_P	198_Q	1.221	1.00
231_A	242_I	1.221	1.00
232_V	236_E	1.219	1.00
241_S	244_Q	1.212	1.00
263_S	269_V	1.210	1.00
66_E	118_A	1.203	1.00
75_R	119_T	1.192	1.00
196_L	200_Q	1.190	1.00
61_E	113_S	1.184	1.00
137_D	171_R	1.179	1.00
32_R	36_S	1.176	1.00
105_H	108_K	1.171	1.00
130_P	164_Q	1.162	1.00
183_I	253_L	1.153	1.00
62_A	66_E	1.148	1.00
124_L	178_T	1.136	1.00
104_D	108_K	1.135	1.00
48_T	81_V	1.129	1.00
49_V	64_F	1.125	1.00
148_Q	173_P	1.121	1.00
166_A	202_L	1.119	1.00
267_E	270_R	1.112	1.00
102_D	105_H	1.111	1.00
144_K	147_H	1.099	1.00
147_H	177_A	1.093	1.00
250_V	259_P	1.091	1.00
186_V	227_R	1.090	1.00
48_T	207_M	1.089	1.00
21_Y	64_F	1.089	1.00
111_E	149_S	1.088	1.00
182_E	187_H	1.075	1.00
143_F	155_F	1.075	1.00
75_R	121_H	1.071	1.00
138_E	141_D	1.062	1.00
166_A	201_Q	1.060	1.00
127_I	143_F	1.059	1.00
36_S	266_I	1.055	1.00
228_D	232_V	1.054	1.00
10_Q	154_H	1.050	1.00
47_T	79_E	1.048	1.00
110_A	122_L	1.038	1.00
146_L	151_K	1.029	1.00
233_V	245_V	1.028	1.00
167_L	171_R	1.027	1.00
37_F	269_V	1.019	1.00
162_P	166_A	1.018	1.00
185_P	288_I	1.013	1.00
232_V	235_E	1.008	1.00
39_E	67_A	1.004	1.00
244_Q	274_E	1.000	1.00
228_D	231_A	0.998	1.00
230_L	242_I	0.997	1.00
9_P	177_A	0.996	1.00
61_E	116_N	0.978	1.00
15_S	47_T	0.975	1.00
157_V	176_L	0.974	1.00
123_D	153_R	0.968	1.00
66_E	70_L	0.963	1.00
16_R	251_L	0.957	1.00
244_Q	271_A	0.953	1.00
193_D	197_D	0.953	1.00
185_P	246_V	0.948	1.00
141_D	145_H	0.944	1.00
251_L	275_A	0.944	1.00
207_M	258_L	0.943	1.00
142_A	146_L	0.941	1.00
178_T	207_M	0.933	1.00
16_R	276_E	0.932	1.00
68_L	78_M	0.927	1.00
36_S	39_E	0.924	1.00
108_K	111_E	0.924	1.00
197_D	200_Q	0.918	1.00
271_A	274_E	0.916	1.00
107_I	110_A	0.910	1.00
146_L	149_S	0.900	1.00
53_D	88_T	0.899	1.00
15_S	46_V	0.897	1.00
265_K	268_R	0.889	1.00
267_E	271_A	0.889	1.00
107_I	146_L	0.888	1.00
10_Q	177_A	0.888	1.00
286_F	289_R	0.887	1.00
198_Q	201_Q	0.886	1.00
137_D	167_L	0.885	1.00
269_V	273_V	0.884	1.00
200_Q	256_Q	0.871	1.00
155_F	176_L	0.870	1.00
252_R	279_K	0.868	1.00
38_I	49_V	0.868	1.00
165_F	204_V	0.868	1.00
179_N	199_L	0.865	1.00
157_V	165_F	0.863	1.00
42_L	74_L	0.861	1.00
141_D	144_K	0.860	1.00
167_L	170_S	0.857	1.00
53_D	105_H	0.849	1.00
283_Q	287_R	0.845	1.00
103_R	138_E	0.844	1.00
81_V	124_L	0.841	1.00
53_D	116_N	0.836	1.00
144_K	173_P	0.836	1.00
62_A	115_I	0.830	1.00
81_V	207_M	0.830	1.00
188_Q	289_R	0.826	1.00
31_A	63_A	0.825	1.00
283_Q	286_F	0.824	1.00
144_K	155_F	0.823	1.00
233_V	237_L	0.819	1.00
253_L	285_W	0.810	1.00
19_M	41_H	0.800	1.00
237_L	281_T	0.799	1.00
31_A	59_Q	0.798	1.00
40_E	269_V	0.793	1.00
53_D	112_Q	0.789	1.00
247_Y	275_A	0.788	1.00
32_R	35_V	0.771	1.00
196_L	206_P	0.771	1.00
162_P	195_T	0.768	1.00
159_N	209_W	0.762	1.00
44_L	274_E	0.762	1.00
10_Q	147_H	0.761	1.00
183_I	196_L	0.760	1.00
114_L	151_K	0.755	1.00
246_V	250_V	0.753	1.00
82_S	125_L	0.752	1.00
211_C	261_I	0.746	1.00
236_E	281_T	0.743	1.00
169_Q	175_T	0.741	1.00
264_G	268_R	0.739	1.00
51_H	64_F	0.738	1.00
252_R	282_R	0.738	1.00
229_E	291_A	0.737	1.00
39_E	74_L	0.731	1.00
34_L	63_A	0.730	1.00
129_R	159_N	0.726	1.00
46_V	273_V	0.723	1.00
17_F	251_L	0.720	1.00
114_L	119_T	0.717	1.00
21_Y	60_C	0.716	1.00
162_P	194_G	0.715	1.00
208_A	211_C	0.714	1.00
195_T	199_L	0.713	1.00
70_L	74_L	0.712	1.00
140_A	155_F	0.710	1.00
42_L	49_V	0.707	1.00
196_L	253_L	0.707	1.00
140_A	168_L	0.702	1.00
221_D	225_P	0.699	1.00
135_D	138_E	0.697	1.00
109_S	112_Q	0.697	1.00
126_L	156_G	0.692	1.00
208_A	259_P	0.692	1.00
106_I	146_L	0.690	1.00
188_Q	192_L	0.688	1.00
249_W	289_R	0.687	1.00
188_Q	193_D	0.686	1.00
110_A	151_K	0.681	1.00
113_S	125_L	0.679	1.00
224_Q	228_D	0.675	1.00
19_M	24_L	0.672	1.00
18_V	261_I	0.670	1.00
243_E	271_A	0.668	1.00
205_R	257_P	0.668	1.00
134_M	138_E	0.665	1.00
37_F	266_I	0.662	1.00
157_V	160_F	0.657	1.00
192_L	197_D	0.656	1.00
144_K	172_L	0.653	1.00
248_A	275_A	0.653	1.00
86_I	89_T	0.651	1.00
227_R	231_A	0.651	1.00
47_T	77_R	0.650	1.00
18_V	258_L	0.650	1.00
250_V	257_P	0.649	1.00
14_F	258_L	0.646	1.00
199_L	204_V	0.646	1.00
233_V	284_Q	0.645	1.00
54_I	85_G	0.645	1.00
280_M	285_W	0.642	1.00
140_A	176_L	0.642	1.00
101_T	127_I	0.640	1.00
183_I	250_V	0.640	1.00
225_P	228_D	0.640	1.00
23_R	214_G	0.639	1.00
76_E	121_H	0.638	1.00
131_D	134_M	0.637	1.00
106_I	142_A	0.636	1.00
12_P	153_R	0.635	1.00
268_R	271_A	0.628	1.00
230_L	288_I	0.625	1.00
237_L	245_V	0.623	1.00
42_L	47_T	0.621	1.00
157_V	179_N	0.621	1.00
106_I	139_V	0.621	1.00
122_L	125_L	0.620	1.00
245_V	280_M	0.620	1.00
59_Q	63_A	0.616	1.00
73_H	78_M	0.615	1.00
42_L	77_R	0.614	1.00
211_C	250_V	0.613	1.00
88_T	105_H	0.613	1.00
234_A	245_V	0.613	1.00
43_D	266_I	0.612	1.00
143_F	147_H	0.611	1.00
44_L	269_V	0.607	1.00
230_L	246_V	0.606	1.00
9_P	203_R	0.603	1.00
139_V	142_A	0.600	1.00
183_I	206_P	0.599	1.00
235_E	238_N	0.599	1.00
50_D	180_Q	0.598	1.00
166_A	169_Q	0.595	1.00
164_Q	167_L	0.594	1.00
210_S	214_G	0.593	1.00
74_L	78_M	0.590	1.00
147_H	152_V	0.590	1.00
24_L	34_L	0.588	1.00
37_F	263_S	0.588	1.00
114_L	121_H	0.588	1.00
223_F	226_L	0.588	1.00
220_D	223_F	0.587	1.00
284_Q	287_R	0.585	1.00
224_Q	227_R	0.584	1.00
26_D	63_A	0.582	1.00
253_L	257_P	0.582	1.00
38_I	42_L	0.581	1.00
147_H	154_H	0.581	1.00
33_Q	266_I	0.580	1.00
239_A	277_T	0.579	1.00
107_I	151_K	0.578	1.00
136_A	171_R	0.577	1.00
183_I	257_P	0.575	1.00
245_V	284_Q	0.575	1.00
22_W	210_S	0.575	1.00
114_L	122_L	0.575	1.00
38_I	64_F	0.572	1.00
110_A	114_L	0.572	1.00
9_P	175_T	0.571	1.00
234_A	237_L	0.571	1.00
24_L	37_F	0.570	1.00
234_A	242_I	0.569	1.00
84_C	101_T	0.566	1.00
244_Q	278_L	0.564	1.00
102_D	139_V	0.563	1.00
25_M	60_C	0.560	1.00
251_L	259_P	0.559	1.00
186_V	216_R	0.559	1.00
280_M	284_Q	0.556	1.00
18_V	260_I	0.552	1.00
8_A	205_R	0.549	1.00
225_P	229_E	0.549	1.00
125_L	152_V	0.548	1.00
137_D	141_D	0.548	1.00
239_A	274_E	0.545	1.00
245_V	288_I	0.544	1.00
233_V	287_R	0.542	1.00
136_A	164_Q	0.540	1.00
245_V	278_L	0.538	1.00
263_S	272_A	0.538	1.00
66_E	69_K	0.537	1.00
148_Q	174_F	0.537	1.00
114_L	120_D	0.536	1.00
125_L	143_F	0.536	1.00
84_C	109_S	0.535	1.00
216_R	227_R	0.531	1.00
19_M	37_F	0.529	1.00
248_A	279_K	0.528	1.00
110_A	142_A	0.525	1.00
51_H	60_C	0.524	1.00
136_A	167_L	0.524	1.00
56_G	59_Q	0.523	1.00
135_D	139_V	0.521	1.00
53_D	85_G	0.520	1.00
208_A	256_Q	0.520	1.00
14_F	48_T	0.518	1.00
130_P	160_F	0.518	1.00
136_A	139_V	0.517	1.00
42_L	67_A	0.514	1.00
49_V	68_L	0.512	1.00
86_I	129_R	0.512	1.00
41_H	49_V	0.511	1.00
239_A	248_A	0.510	1.00
64_F	67_A	0.509	1.00
169_Q	204_V	0.508	1.00
8_A	14_F	0.508	1.00
147_H	175_T	0.507	1.00
157_V	168_L	0.507	1.00
127_I	139_V	0.506	1.00
183_I	188_Q	0.505	1.00
226_L	231_A	0.502	1.00
208_A	250_V	0.501	1.00
17_F	276_E	0.500	1.00

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
4r9oA	5	0.9866	100	0.039	Contact Map
4xk2A	5	0.9497	100	0.071	Contact Map
1pyfA	1	0.9497	100	0.071	Contact Map
1lqaA	2	0.9832	100	0.073	Contact Map
3eauA	3	0.9799	100	0.074	Contact Map
1pz1A	1	0.9664	100	0.075	Contact Map
3v0sA	1	0.8993	100	0.076	Contact Map
3lutA	3	0.9765	100	0.078	Contact Map
3n6qA	5	0.9799	100	0.079	Contact Map
3n2tA	1	0.9732	100	0.082	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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