YFHB - BACSU - GREMLIN Contacts

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YFHB - Uncharacterized isomerase YfhB

UniProt:	O31570	Sequences: MKEAEVLKYEAFTSSPGKGNPAGVVLQGDDYTEDEMQIIAERAGYSETSFIRKSESADLELRYFTPGHEMNLCGHATVASLYALCEKGMLESGKTYSIQTKAGILPVKISEKDGRIHITLEQASPQFKPFTGDRKKLADALGITDEDFHEDLPIVFGSTGIWTAIVPLKSLEASKKMVPDNKQFPEVLVDLPKASVHPFTFETVHPDSDLHGRHFSSPYSGTIEDPVTGTASGVMGAYMKHYGNAEQHKFIIEQGQEIGKDGKVEIEMNEAGGHVKVNMTGTAVYSETRILKI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	293 (264)
Sequences:	4108 (3064)
Seq/√Len:	188.6

ECOLI - YDDE
BACSU - YFHB
HALSA - Q9HHG6 Q9HS99

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
249_K	267_E	3.642	1.00
82_Y	285_Y	3.636	1.00
32_T	35_E	3.379	1.00
177_M	198_P	3.253	1.00
227_V	262_G	3.086	1.00
170_S	173_A	2.736	1.00
172_E	176_K	2.674	1.00
9_Y	83_A	2.594	1.00
51_I	80_S	2.532	1.00
61_L	100_T	2.448	1.00
97_S	104_I	2.442	1.00
29_D	53_K	2.422	1.00
8_K	287_E	2.295	1.00
14_S	282_T	2.241	1.00
181_N	223_I	2.231	1.00
60_E	99_Q	2.223	1.00
15_S	18_K	2.221	1.00
95_T	108_K	2.016	1.00
71_N	101_K	2.009	1.00
236_G	266_I	1.990	1.00
267_E	278_N	1.979	1.00
54_S	60_E	1.916	1.00
171_L	175_K	1.907	1.00
95_T	106_P	1.884	1.00
251_I	263_K	1.844	1.00
5_E	290_I	1.827	1.00
253_E	261_D	1.824	1.00
169_K	173_A	1.790	1.00
10_E	42_R	1.775	1.00
212_G	232_S	1.768	1.00
5_E	288_T	1.761	1.00
39_I	291_L	1.742	1.00
180_D	183_Q	1.729	1.00
110_S	117_H	1.702	1.00
58_D	99_Q	1.695	1.00
49_S	80_S	1.681	1.00
26_L	51_I	1.678	1.00
13_T	18_K	1.669	1.00
251_I	265_E	1.662	1.00
227_V	264_V	1.644	1.00
115_R	282_T	1.615	1.00
54_S	99_Q	1.609	1.00
228_T	231_A	1.590	1.00
117_H	280_T	1.585	1.00
139_D	183_Q	1.568	1.00
31_Y	39_I	1.559	1.00
36_M	62_R	1.558	1.00
183_Q	186_E	1.551	1.00
119_T	276_K	1.541	1.00
232_S	252_I	1.526	1.00
236_G	268_M	1.513	1.00
168_L	173_A	1.510	1.00
6_V	287_E	1.502	1.00
141_L	166_V	1.498	1.00
7_L	83_A	1.493	1.00
13_T	284_V	1.487	1.00
60_E	101_K	1.479	1.00
163_T	194_A	1.475	1.00
40_A	48_T	1.447	1.00
269_N	278_N	1.438	1.00
31_Y	35_E	1.434	1.00
163_T	214_H	1.433	1.00
253_E	263_K	1.425	1.00
35_E	39_I	1.405	1.00
115_R	265_E	1.403	1.00
72_L	230_T	1.402	1.00
33_E	36_M	1.394	1.00
171_L	202_E	1.388	1.00
143_I	168_L	1.386	1.00
252_I	264_V	1.377	1.00
168_L	174_S	1.375	1.00
58_D	104_I	1.365	1.00
61_L	80_S	1.344	1.00
216_S	221_G	1.332	1.00
99_Q	104_I	1.327	1.00
7_L	288_T	1.314	1.00
256_Q	261_D	1.311	1.00
85_C	109_I	1.304	1.00
158_S	162_W	1.301	1.00
73_C	76_A	1.300	1.00
8_K	45_Y	1.299	1.00
147_D	169_K	1.283	1.00
110_S	113_D	1.265	1.00
240_K	268_M	1.261	1.00
22_A	79_A	1.261	1.00
118_I	121_E	1.260	1.00
167_P	199_F	1.254	1.00
62_R	69_E	1.244	1.00
82_Y	86_E	1.222	1.00
37_Q	40_A	1.219	1.00
171_L	200_T	1.218	1.00
195_S	214_H	1.210	1.00
108_K	278_N	1.207	1.00
23_G	43_A	1.205	1.00
18_K	261_D	1.203	1.00
6_V	43_A	1.201	1.00
107_V	118_I	1.195	1.00
33_E	37_Q	1.195	1.00
216_S	222_T	1.187	1.00
265_E	280_T	1.187	1.00
210_L	235_M	1.183	1.00
264_V	279_M	1.179	1.00
135_K	139_D	1.175	1.00
249_K	265_E	1.143	1.00
197_H	232_S	1.140	1.00
147_D	176_K	1.139	1.00
167_P	238_Y	1.120	1.00
171_L	211_H	1.117	1.00
143_I	177_M	1.117	1.00
7_L	26_L	1.116	1.00
232_S	264_V	1.112	1.00
30_D	52_R	1.097	1.00
46_S	226_P	1.090	1.00
165_I	234_V	1.085	1.00
255_G	261_D	1.085	1.00
122_Q	125_P	1.085	1.00
68_H	220_S	1.084	1.00
135_K	145_D	1.080	1.00
137_L	164_A	1.079	1.00
21_P	45_Y	1.079	1.00
114_G	282_T	1.075	1.00
218_P	222_T	1.071	1.00
140_A	183_Q	1.071	1.00
140_A	184_F	1.067	1.00
34_D	38_I	1.067	1.00
214_H	231_A	1.062	1.00
4_A	25_V	1.061	1.00
212_G	252_I	1.051	1.00
107_V	116_I	1.046	1.00
8_K	43_A	1.045	1.00
11_A	22_A	1.045	1.00
81_L	98_I	1.044	1.00
85_C	116_I	1.041	1.00
218_P	221_G	1.038	1.00
63_Y	76_A	1.038	1.00
136_K	139_D	1.030	1.00
37_Q	41_E	1.030	1.00
61_L	98_I	1.029	1.00
138_A	145_D	1.026	1.00
147_D	173_A	1.022	1.00
22_A	73_C	1.019	1.00
174_S	200_T	1.019	1.00
84_L	88_G	1.012	1.00
16_P	286_S	1.011	1.00
171_L	203_T	0.992	0.99
47_E	228_T	0.988	0.99
24_V	83_A	0.981	0.99
26_L	83_A	0.980	0.99
172_E	175_K	0.976	0.99
90_L	96_Y	0.974	0.99
23_G	45_Y	0.974	0.99
86_E	285_Y	0.968	0.99
179_P	215_F	0.965	0.99
268_M	277_V	0.962	0.99
47_E	226_P	0.958	0.99
168_L	198_P	0.957	0.99
11_A	79_A	0.953	0.99
201_F	210_L	0.947	0.99
137_L	166_V	0.947	0.99
216_S	220_S	0.947	0.99
163_T	195_S	0.945	0.99
25_V	291_L	0.942	0.99
174_S	211_H	0.938	0.99
6_V	289_R	0.937	0.99
165_I	235_M	0.935	0.99
71_N	163_T	0.929	0.99
27_Q	30_D	0.927	0.99
199_F	238_Y	0.918	0.99
52_R	60_E	0.918	0.99
286_S	291_L	0.917	0.99
228_T	254_Q	0.917	0.99
47_E	76_A	0.912	0.99
238_Y	242_Y	0.911	0.99
144_T	147_D	0.910	0.99
216_S	223_I	0.907	0.99
211_H	256_Q	0.896	0.99
9_Y	24_V	0.893	0.99
197_H	231_A	0.889	0.99
138_A	148_F	0.887	0.99
70_M	76_A	0.885	0.99
119_T	278_N	0.878	0.99
212_G	235_M	0.875	0.99
57_A	104_I	0.875	0.99
40_A	66_P	0.873	0.99
209_D	247_Q	0.866	0.99
51_I	84_L	0.865	0.98
208_S	255_G	0.862	0.98
63_Y	73_C	0.857	0.98
118_I	122_Q	0.857	0.98
4_A	30_D	0.856	0.98
72_L	102_A	0.856	0.98
120_L	233_G	0.855	0.98
54_S	58_D	0.854	0.98
54_S	57_A	0.853	0.98
70_M	161_I	0.852	0.98
9_Y	283_A	0.852	0.98
14_S	263_K	0.851	0.98
83_A	87_K	0.845	0.98
154_I	166_V	0.843	0.98
35_E	38_I	0.843	0.98
137_L	140_A	0.842	0.98
197_H	214_H	0.842	0.98
58_D	97_S	0.841	0.98
43_A	287_E	0.841	0.98
227_V	252_I	0.839	0.98
253_E	256_Q	0.839	0.98
146_E	169_K	0.838	0.98
117_H	278_N	0.834	0.98
122_Q	233_G	0.828	0.98
97_S	106_P	0.828	0.98
175_K	211_H	0.825	0.98
10_E	17_G	0.822	0.98
13_T	282_T	0.821	0.98
49_S	61_L	0.820	0.98
4_A	27_Q	0.820	0.98
9_Y	285_Y	0.818	0.98
141_L	198_P	0.816	0.98
138_A	143_I	0.814	0.98
165_I	238_Y	0.813	0.98
49_S	76_A	0.812	0.98
17_G	42_R	0.809	0.98
267_E	280_T	0.805	0.98
116_I	121_E	0.805	0.98
210_L	252_I	0.803	0.98
202_E	206_P	0.801	0.98
174_S	177_M	0.796	0.97
85_C	96_Y	0.796	0.97
167_P	242_Y	0.792	0.97
36_M	64_F	0.787	0.97
87_K	288_T	0.785	0.97
184_F	196_V	0.784	0.97
11_A	63_Y	0.777	0.97
72_L	105_L	0.773	0.97
25_V	43_A	0.773	0.97
173_A	176_K	0.772	0.97
81_L	96_Y	0.772	0.97
5_E	87_K	0.768	0.97
133_D	136_K	0.766	0.97
82_Y	283_A	0.762	0.97
202_E	208_S	0.758	0.97
182_K	185_P	0.750	0.96
140_A	187_V	0.746	0.96
10_E	13_T	0.741	0.96
140_A	196_V	0.739	0.96
41_E	67_G	0.738	0.96
22_A	63_Y	0.737	0.96
134_R	138_A	0.737	0.96
51_I	88_G	0.735	0.96
78_V	230_T	0.733	0.96
100_T	118_I	0.732	0.96
22_A	76_A	0.731	0.96
30_D	33_E	0.729	0.96
63_Y	79_A	0.728	0.96
63_Y	70_M	0.728	0.96
84_L	96_Y	0.724	0.96
132_G	145_D	0.723	0.95
227_V	256_Q	0.722	0.95
161_I	234_V	0.720	0.95
175_K	255_G	0.717	0.95
38_I	41_E	0.717	0.95
127_F	157_G	0.716	0.95
57_A	99_Q	0.715	0.95
214_H	228_T	0.712	0.95
119_T	280_T	0.705	0.95
42_R	260_K	0.703	0.95
179_P	184_F	0.703	0.95
248_H	268_M	0.699	0.95
285_Y	288_T	0.697	0.95
271_A	276_K	0.694	0.94
17_G	260_K	0.685	0.94
20_N	228_T	0.683	0.94
209_D	250_F	0.682	0.94
33_E	62_R	0.682	0.94
218_P	223_I	0.680	0.94
162_W	194_A	0.676	0.94
121_E	276_K	0.676	0.94
136_K	183_Q	0.671	0.93
181_N	184_F	0.670	0.93
63_Y	98_I	0.668	0.93
171_L	174_S	0.667	0.93
47_E	70_M	0.667	0.93
136_K	186_E	0.666	0.93
214_H	235_M	0.664	0.93
181_N	218_P	0.660	0.93
168_L	177_M	0.658	0.93
227_V	232_S	0.658	0.93
115_R	280_T	0.657	0.93
7_L	285_Y	0.655	0.92
7_L	87_K	0.654	0.92
71_N	161_I	0.654	0.92
119_T	123_A	0.653	0.92
195_S	199_F	0.649	0.92
138_A	144_T	0.648	0.92
36_M	52_R	0.645	0.92
167_P	201_F	0.645	0.92
199_F	202_E	0.644	0.92
199_F	239_M	0.639	0.92
8_K	21_P	0.635	0.91
210_L	255_G	0.632	0.91
127_F	155_V	0.630	0.91
185_P	219_Y	0.629	0.91
236_G	279_M	0.628	0.91
29_D	52_R	0.628	0.91
11_A	76_A	0.626	0.91
208_S	253_E	0.624	0.91
256_Q	262_G	0.624	0.91
20_N	229_G	0.623	0.91
5_E	23_G	0.623	0.91
47_E	66_P	0.622	0.90
200_T	211_H	0.621	0.90
76_A	79_A	0.619	0.90
108_K	117_H	0.617	0.90
266_I	279_M	0.616	0.90
158_S	161_I	0.615	0.90
21_P	46_S	0.607	0.89
164_A	193_K	0.606	0.89
197_H	235_M	0.605	0.89
65_T	70_M	0.605	0.89
203_T	206_P	0.602	0.89
5_E	289_R	0.599	0.89
25_V	48_T	0.599	0.89
197_H	212_G	0.598	0.89
235_M	239_M	0.597	0.89
110_S	115_R	0.596	0.89
66_P	222_T	0.592	0.88
165_I	197_H	0.591	0.88
214_H	234_V	0.590	0.88
123_A	126_Q	0.589	0.88
110_S	267_E	0.589	0.88
18_K	38_I	0.587	0.88
141_L	177_M	0.585	0.88
157_G	165_I	0.585	0.88
32_T	36_M	0.585	0.88
155_V	242_Y	0.584	0.87
154_I	164_A	0.580	0.87
123_A	161_I	0.579	0.87
147_D	167_P	0.579	0.87
55_E	99_Q	0.579	0.87
226_P	262_G	0.577	0.87
65_T	222_T	0.574	0.87
78_V	120_L	0.572	0.86
14_S	18_K	0.572	0.86
11_A	49_S	0.572	0.86
67_G	221_G	0.571	0.86
250_F	266_I	0.570	0.86
123_A	160_G	0.569	0.86
166_V	196_V	0.565	0.86
141_L	196_V	0.564	0.86
171_L	253_E	0.563	0.86
22_A	283_A	0.560	0.85
75_H	229_G	0.558	0.85
162_W	234_V	0.557	0.85
41_E	259_G	0.556	0.85
9_Y	82_Y	0.556	0.85
22_A	61_L	0.555	0.85
216_S	231_A	0.553	0.85
187_V	193_K	0.551	0.84
6_V	286_S	0.550	0.84
81_L	107_V	0.550	0.84
198_P	215_F	0.550	0.84
100_T	103_G	0.548	0.84
117_H	267_E	0.541	0.83
248_H	267_E	0.537	0.83
11_A	73_C	0.537	0.83
123_A	234_V	0.535	0.83
163_T	231_A	0.534	0.82
127_F	237_A	0.533	0.82
202_E	211_H	0.532	0.82
134_R	145_D	0.530	0.82
73_C	77_T	0.530	0.82
122_Q	277_V	0.529	0.82
63_Y	230_T	0.529	0.82
11_A	227_V	0.528	0.82
215_F	222_T	0.527	0.82
89_M	92_S	0.525	0.81
106_P	109_I	0.525	0.81
84_L	90_L	0.524	0.81
26_L	30_D	0.523	0.81
49_S	73_C	0.522	0.81
23_G	73_C	0.520	0.81
120_L	125_P	0.520	0.81
185_P	223_I	0.519	0.81
63_Y	72_L	0.518	0.81
240_K	250_F	0.518	0.81
71_N	194_A	0.517	0.80
27_Q	31_Y	0.516	0.80
86_E	288_T	0.512	0.80
76_A	225_D	0.511	0.80
43_A	286_S	0.511	0.80
209_D	253_E	0.511	0.80
208_S	263_K	0.508	0.79
36_M	50_F	0.506	0.79
240_K	244_N	0.505	0.79
83_A	86_E	0.502	0.78
207_D	263_K	0.501	0.78
143_I	147_D	0.500	0.78

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
3ednA	2	0.9966	100	0.244	Contact Map
1qyaA	2	0.9829	100	0.255	Contact Map
1ym5A	2	0.9659	100	0.255	Contact Map
1xubA	2	0.9352	100	0.263	Contact Map
1s7jA	1	0.8874	100	0.292	Contact Map
1u0kA	2	0.9454	100	0.299	Contact Map
4dunA	2	0.8805	100	0.303	Contact Map
4jbdA	2	0.884	100	0.406	Contact Map
3ejxA	5	0.9181	100	0.417	Contact Map
4juuA	2	0.9113	100	0.424	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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