YHCB - BACSU - GREMLIN Contacts

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YHCB - Uncharacterized protein YhcB

UniProt:	P54586	Sequences: MKIYVVYDSEGEHTKVLAEAIAEGARENDAAEVFIDHVDQADIRKLKDMDAIIWGCPGHFGTISSGLKTWIDRLGYLWAEGELINKVGAVFCTTATTHGGLEMTMHNLITPMFHQGMIVVGLPGNVPENALYGSYYGAGVTCPVDSDELMSEEGIQLGRALGRRVSQVTGNLTAGQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	176 (171)
Sequences:	2595 (1456)
Seq/√Len:	111.4

ECOLI - NQOR
BACSU - YHCB
SULSO - Q97U66

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
163_R	167_Q	3.089	1.00
27_E	163_R	2.951	1.00
53_I	165_V	2.845	1.00
89_A	161_L	2.816	1.00
8_D	64_S	2.618	1.00
17_L	158_G	2.576	1.00
103_M	106_H	2.404	1.00
22_A	26_R	2.384	1.00
23_E	159_R	2.226	1.00
15_K	19_E	2.137	1.00
53_I	89_A	2.098	1.00
87_V	172_L	2.079	1.00
25_A	33_V	2.071	1.00
74_L	115_Q	1.975	1.00
152_E	156_Q	1.940	1.00
162_G	166_S	1.937	1.00
89_A	165_V	1.931	1.00
77_L	82_E	1.858	1.00
24_G	162_G	1.804	1.00
27_E	159_R	1.800	1.00
88_G	112_M	1.799	1.00
56_C	64_S	1.773	1.00
92_C	139_G	1.758	1.00
3_I	51_A	1.749	1.00
84_I	125_N	1.748	1.00
4_Y	49_M	1.735	1.00
122_L	157_L	1.728	1.00
2_K	32_E	1.713	1.00
20_A	159_R	1.701	1.00
134_S	139_G	1.686	1.00
120_V	168_V	1.682	1.00
47_K	77_L	1.666	1.00
47_K	82_E	1.654	1.00
68_K	111_P	1.641	1.00
90_V	108_L	1.622	1.00
138_A	161_L	1.604	1.00
34_F	45_K	1.571	1.00
38_V	67_L	1.532	1.00
44_R	47_K	1.517	1.00
113_F	121_G	1.471	1.00
20_A	155_I	1.455	1.00
20_A	23_E	1.450	1.00
85_N	164_R	1.434	1.00
55_G	91_F	1.411	1.00
68_K	72_D	1.401	1.00
109_I	113_F	1.371	1.00
21_I	91_F	1.370	1.00
54_W	108_L	1.357	1.00
17_L	138_A	1.349	1.00
16_V	19_E	1.348	1.00
56_C	108_L	1.340	1.00
16_V	155_I	1.335	1.00
81_G	84_I	1.316	1.00
34_F	49_M	1.310	0.99
87_V	165_V	1.307	0.99
88_G	117_M	1.305	0.99
94_T	101_L	1.298	0.99
167_Q	171_N	1.219	0.99
4_Y	36_D	1.199	0.99
7_Y	15_K	1.198	0.99
89_A	138_A	1.194	0.99
92_C	105_M	1.191	0.99
169_T	173_T	1.187	0.99
93_T	142_C	1.179	0.99
126_V	157_L	1.164	0.99
62_T	107_N	1.164	0.99
85_N	167_Q	1.160	0.99
5_V	22_A	1.160	0.99
52_I	117_M	1.148	0.99
150_M	155_I	1.137	0.99
168_V	172_L	1.129	0.98
113_F	119_V	1.089	0.98
25_A	166_S	1.085	0.98
155_I	159_R	1.083	0.98
44_R	48_D	1.072	0.98
36_D	45_K	1.071	0.98
24_G	166_S	1.066	0.98
77_L	83_L	1.066	0.98
95_A	144_V	1.065	0.98
158_G	162_G	1.055	0.98
26_R	33_V	1.037	0.97
63_I	108_L	1.037	0.97
23_E	26_R	1.034	0.97
42_D	45_K	1.033	0.97
131_L	153_E	1.026	0.97
58_G	104_T	1.019	0.97
41_A	45_K	1.010	0.97
28_N	166_S	1.007	0.97
46_L	74_L	1.003	0.97
87_V	169_T	1.001	0.97
5_V	25_A	0.997	0.97
65_S	69_T	0.994	0.97
94_T	141_T	0.993	0.97
29_D	170_G	0.987	0.96
21_I	24_G	0.985	0.96
45_K	48_D	0.980	0.96
51_A	165_V	0.979	0.96
131_L	151_S	0.971	0.96
3_I	25_A	0.967	0.96
143_P	146_S	0.966	0.96
90_V	109_I	0.959	0.96
3_I	166_S	0.959	0.96
43_I	73_R	0.958	0.96
63_I	68_K	0.956	0.96
66_G	72_D	0.955	0.96
71_I	111_P	0.948	0.95
17_L	140_V	0.939	0.95
23_E	27_E	0.934	0.95
151_S	154_G	0.933	0.95
26_R	32_E	0.933	0.95
19_E	26_R	0.932	0.95
62_T	111_P	0.927	0.95
152_E	155_I	0.920	0.95
62_T	68_K	0.918	0.95
90_V	105_M	0.918	0.95
67_L	71_I	0.917	0.95
28_N	170_G	0.911	0.94
50_D	173_T	0.900	0.94
106_H	136_Y	0.896	0.94
21_I	162_G	0.895	0.94
28_N	167_Q	0.890	0.94
90_V	119_V	0.880	0.93
47_K	80_E	0.874	0.93
161_L	165_V	0.872	0.93
140_V	150_M	0.868	0.93
69_T	73_R	0.867	0.93
90_V	112_M	0.860	0.93
103_M	107_N	0.860	0.93
18_A	91_F	0.857	0.92
63_I	111_P	0.854	0.92
118_I	168_V	0.846	0.92
160_A	164_R	0.843	0.92
15_K	37_H	0.836	0.91
30_A	166_S	0.835	0.91
63_I	107_N	0.831	0.91
56_C	63_I	0.828	0.91
22_A	35_I	0.811	0.90
87_V	168_V	0.801	0.90
128_E	153_E	0.798	0.89
87_V	118_I	0.792	0.89
65_S	72_D	0.792	0.89
112_M	117_M	0.790	0.89
105_M	108_L	0.788	0.89
107_N	110_T	0.779	0.88
43_I	47_K	0.775	0.88
102_E	110_T	0.769	0.88
25_A	30_A	0.767	0.87
51_A	87_V	0.758	0.87
159_R	163_R	0.758	0.87
22_A	33_V	0.757	0.87
43_I	77_L	0.756	0.87
19_E	35_I	0.751	0.86
19_E	22_A	0.749	0.86
6_V	41_A	0.744	0.86
43_I	74_L	0.742	0.86
24_G	158_G	0.738	0.85
19_E	23_E	0.736	0.85
20_A	24_G	0.736	0.85
131_L	139_G	0.728	0.85
123_P	164_R	0.727	0.85
58_G	94_T	0.723	0.84
125_N	160_A	0.718	0.84
156_Q	159_R	0.716	0.84
21_I	161_L	0.714	0.83
113_F	123_P	0.708	0.83
118_I	171_N	0.700	0.82
54_W	71_I	0.699	0.82
16_V	149_L	0.696	0.82
126_V	160_A	0.696	0.82
2_K	48_D	0.690	0.81
120_V	165_V	0.683	0.81
56_C	62_T	0.677	0.80
3_I	169_T	0.675	0.80
109_I	119_V	0.674	0.80
21_I	158_G	0.674	0.80
114_H	136_Y	0.669	0.79
75_G	79_A	0.665	0.79
34_F	48_D	0.664	0.79
46_L	83_L	0.664	0.79
38_V	41_A	0.664	0.79
37_H	40_Q	0.661	0.79
52_I	88_G	0.661	0.79
14_T	91_F	0.659	0.78
48_D	152_E	0.654	0.78
21_I	138_A	0.650	0.77
156_Q	160_A	0.641	0.76
118_I	121_G	0.641	0.76
70_W	74_L	0.637	0.76
6_V	36_D	0.627	0.75
54_W	90_V	0.623	0.74
102_E	136_Y	0.622	0.74
57_P	104_T	0.620	0.74
14_T	56_C	0.619	0.74
36_D	49_M	0.617	0.74
98_H	139_G	0.615	0.73
102_E	106_H	0.614	0.73
26_R	29_D	0.608	0.73
4_Y	41_A	0.607	0.72
6_V	49_M	0.603	0.72
14_T	55_G	0.602	0.72
46_L	52_I	0.596	0.71
148_E	151_S	0.595	0.71
66_G	69_T	0.594	0.71
8_D	40_Q	0.593	0.71
27_E	30_A	0.591	0.70
7_Y	10_E	0.589	0.70
10_E	40_Q	0.587	0.70
21_I	53_I	0.586	0.70
122_L	138_A	0.581	0.69
81_G	116_G	0.577	0.69
126_V	164_R	0.576	0.68
59_H	94_T	0.574	0.68
36_D	41_A	0.574	0.68
98_H	102_E	0.573	0.68
9_S	12_E	0.571	0.68
11_G	40_Q	0.570	0.68
13_H	140_V	0.569	0.68
43_I	76_Y	0.565	0.67
46_L	70_W	0.563	0.67
63_I	67_L	0.562	0.67
8_D	66_G	0.560	0.66
51_A	169_T	0.559	0.66
70_W	115_Q	0.558	0.66
142_C	155_I	0.556	0.66
169_T	172_L	0.555	0.66
106_H	110_T	0.553	0.65
40_Q	50_D	0.552	0.65
111_P	115_Q	0.550	0.65
97_T	141_T	0.549	0.65
76_Y	80_E	0.548	0.65
129_N	153_E	0.548	0.65
2_K	34_F	0.547	0.65
168_V	171_N	0.545	0.64
98_H	131_L	0.545	0.64
56_C	90_V	0.543	0.64
71_I	107_N	0.543	0.64
164_R	168_V	0.541	0.64
53_I	87_V	0.541	0.64
40_Q	66_G	0.541	0.64
30_A	170_G	0.541	0.64
102_E	134_S	0.537	0.63
114_H	135_Y	0.536	0.63
161_L	164_R	0.536	0.63
14_T	53_I	0.532	0.62
21_I	55_G	0.530	0.62
56_C	92_C	0.528	0.62
74_L	77_L	0.528	0.62
150_M	154_G	0.516	0.60
101_L	141_T	0.514	0.60
118_I	172_L	0.512	0.59
44_R	77_L	0.508	0.59
131_L	141_T	0.505	0.58
56_C	115_Q	0.504	0.58
106_H	109_I	0.502	0.58
71_I	74_L	0.501	0.58
41_A	44_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
3d7nA	4	0.858	100	0.449	Contact Map
4lafA	4	0.9943	100	0.466	Contact Map
2a5lA	4	0.9489	100	0.471	Contact Map
3zhoA	4	0.9602	100	0.472	Contact Map
1ydgA	4	0.9773	100	0.479	Contact Map
2zkiA	7	0.9716	100	0.494	Contact Map
2arkA	4	0.9375	100	0.52	Contact Map
2q62A	4	0.9261	99.9	0.592	Contact Map
2fzvA	5	0.9261	99.9	0.6	Contact Map
3svlA	4	0.9034	99.9	0.614	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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