YBHB - ECOLI - GREMLIN Contacts

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YBHB - UPF0098 protein YbhB

UniProt:	P12994	Sequences: MKLISNDLRDGDKLPHRHVFNGMGYDGDNISPHLAWDDVPAGTKSFVVTCYDPDAPTGSGWWHWVVVNLPADTRVLPQGFGSGLVAMPDGVLQTRTDFGKTGYDGAAPPKGETHRYIFTVHALDIERIDVDEGASGAMVGFNVHFHSLASASITAMFS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11238
Length:	158 (147)
Sequences:	2558 (1767)
Seq/√Len:	145.8

ECOLI - YBHB YBCL
BACSU - YXKA
HALSA - Q9HND1
SULSO - Q7LXJ9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
124_D	146_H	4.976	1.00
39_V	46_F	3.934	1.00
25_Y	107_A	3.508	1.00
98_F	104_D	2.956	1.00
50_C	118_F	2.827	1.00
17_R	78_Q	2.570	1.00
48_V	120_V	2.567	1.00
13_K	156_M	2.485	1.00
68_N	129_D	2.481	1.00
6_N	33_H	2.331	1.00
7_D	78_Q	2.277	1.00
7_D	33_H	2.127	1.00
9_R	12_D	2.006	1.00
117_I	154_T	1.973	1.00
46_F	71_A	1.903	1.00
119_T	152_S	1.845	1.00
8_L	155_A	1.843	1.00
47_V	139_V	1.779	1.00
14_L	106_A	1.738	1.00
17_R	28_D	1.734	1.00
39_V	74_R	1.732	1.00
123_L	143_V	1.683	1.00
67_V	94_T	1.667	1.00
94_T	139_V	1.627	1.00
29_N	105_G	1.627	1.00
33_H	75_V	1.575	1.00
35_A	75_V	1.454	1.00
31_S	76_L	1.437	1.00
3_L	151_A	1.422	1.00
119_T	150_S	1.422	1.00
47_V	143_V	1.407	1.00
66_V	91_V	1.405	1.00
3_L	120_V	1.398	1.00
36_W	76_L	1.396	1.00
54_D	115_R	1.325	1.00
45_S	125_I	1.323	1.00
88_P	91_V	1.322	1.00
69_L	73_T	1.320	1.00
79_G	82_S	1.306	1.00
67_V	139_V	1.275	1.00
139_V	143_V	1.264	1.00
68_N	127_R	1.256	1.00
14_L	155_A	1.247	1.00
8_L	15_P	1.216	1.00
45_S	68_N	1.210	1.00
142_N	145_F	1.198	1.00
62_W	136_G	1.192	1.00
143_V	147_S	1.188	1.00
52_D	63_H	1.186	1.00
65_V	94_T	1.154	1.00
81_G	93_Q	1.153	1.00
5_S	153_I	1.141	0.99
121_H	143_V	1.137	0.99
135_S	138_M	1.135	0.99
93_Q	102_G	1.126	0.99
40_P	122_A	1.111	0.99
2_K	37_D	1.109	0.99
45_S	127_R	1.099	0.99
125_I	146_H	1.094	0.99
18_H	78_Q	1.088	0.99
61_W	98_F	1.086	0.99
39_V	43_T	1.081	0.99
17_R	30_I	1.079	0.99
65_V	139_V	1.073	0.99
77_P	80_F	1.069	0.99
6_N	35_A	1.066	0.99
47_V	123_L	1.063	0.99
117_I	152_S	1.058	0.99
103_Y	106_A	1.057	0.99
68_N	92_L	1.055	0.99
87_M	91_V	1.054	0.99
42_G	148_L	1.043	0.99
46_F	120_V	1.039	0.99
3_L	34_L	1.037	0.99
67_V	134_A	1.030	0.99
128_I	143_V	1.020	0.99
10_D	154_T	1.008	0.99
121_H	147_S	1.006	0.99
40_P	43_T	0.990	0.99
46_F	74_R	0.978	0.98
63_H	108_P	0.976	0.98
18_H	33_H	0.969	0.98
120_V	151_A	0.967	0.98
43_T	148_L	0.966	0.98
63_H	114_H	0.941	0.98
134_A	139_V	0.936	0.98
51_Y	62_W	0.934	0.98
51_Y	119_T	0.925	0.98
68_N	128_I	0.919	0.98
51_Y	59_S	0.918	0.98
67_V	92_L	0.914	0.98
108_P	114_H	0.904	0.97
5_S	34_L	0.900	0.97
115_R	154_T	0.900	0.97
43_T	46_F	0.900	0.97
52_D	114_H	0.897	0.97
30_I	78_Q	0.896	0.97
50_C	103_Y	0.894	0.97
19_V	157_F	0.879	0.97
36_W	46_F	0.875	0.97
19_V	26_D	0.872	0.97
59_S	137_A	0.869	0.97
32_P	118_F	0.864	0.97
13_K	16_H	0.864	0.97
95_R	133_G	0.863	0.96
13_K	113_T	0.862	0.96
3_L	153_I	0.857	0.96
31_S	64_W	0.853	0.96
39_V	42_G	0.844	0.96
64_W	93_Q	0.839	0.96
42_G	149_A	0.833	0.96
31_S	80_F	0.823	0.95
134_A	138_M	0.813	0.95
101_T	133_G	0.808	0.95
43_T	122_A	0.808	0.95
26_D	157_F	0.804	0.95
8_L	12_D	0.801	0.95
7_D	18_H	0.801	0.95
58_G	140_G	0.783	0.94
14_L	18_H	0.774	0.94
16_H	26_D	0.766	0.93
16_H	19_V	0.761	0.93
11_G	154_T	0.752	0.93
37_D	74_R	0.748	0.92
52_D	108_P	0.747	0.92
4_I	35_A	0.746	0.92
53_P	117_I	0.744	0.92
96_T	104_D	0.739	0.92
138_M	142_N	0.738	0.92
124_D	147_S	0.737	0.92
66_V	93_Q	0.736	0.92
4_I	37_D	0.733	0.92
68_N	125_I	0.730	0.92
61_W	104_D	0.722	0.91
29_N	98_F	0.712	0.91
29_N	104_D	0.704	0.90
64_W	81_G	0.702	0.90
110_K	113_T	0.701	0.90
27_G	107_A	0.697	0.90
30_I	79_G	0.694	0.89
40_P	46_F	0.693	0.89
147_S	150_S	0.692	0.89
55_A	61_W	0.691	0.89
19_V	25_Y	0.680	0.88
55_A	58_G	0.679	0.88
12_D	156_M	0.679	0.88
138_M	141_F	0.671	0.88
49_T	143_V	0.671	0.88
130_V	139_V	0.670	0.88
94_T	136_G	0.669	0.88
100_K	104_D	0.660	0.87
34_L	153_I	0.658	0.87
8_L	153_I	0.656	0.87
34_L	118_F	0.656	0.87
95_R	99_G	0.656	0.87
108_P	111_G	0.655	0.87
65_V	136_G	0.648	0.86
131_D	134_A	0.646	0.86
34_L	48_V	0.637	0.85
8_L	14_L	0.634	0.85
38_D	46_F	0.629	0.84
136_G	140_G	0.625	0.84
130_V	134_A	0.621	0.83
144_H	150_S	0.620	0.83
40_P	149_A	0.619	0.83
93_Q	101_T	0.617	0.83
96_T	100_K	0.617	0.83
13_K	19_V	0.615	0.83
18_H	30_I	0.613	0.83
113_T	156_M	0.612	0.83
63_H	105_G	0.609	0.82
51_Y	117_I	0.605	0.82
66_V	87_M	0.605	0.82
5_S	8_L	0.602	0.82
82_S	93_Q	0.599	0.81
12_D	155_A	0.595	0.81
143_V	146_H	0.592	0.81
48_V	69_L	0.590	0.80
66_V	81_G	0.590	0.80
55_A	60_G	0.590	0.80
55_A	109_P	0.585	0.80
51_Y	136_G	0.581	0.79
61_W	141_F	0.580	0.79
63_H	109_P	0.579	0.79
145_F	148_L	0.578	0.79
36_W	149_A	0.575	0.79
55_A	59_S	0.574	0.78
16_H	28_D	0.569	0.78
51_Y	140_G	0.567	0.78
35_A	74_R	0.564	0.77
53_P	109_P	0.560	0.77
47_V	121_H	0.559	0.77
47_V	94_T	0.559	0.77
29_N	100_K	0.555	0.76
15_P	18_H	0.554	0.76
76_L	80_F	0.552	0.76
11_G	156_M	0.549	0.75
49_T	121_H	0.549	0.75
119_T	140_G	0.548	0.75
36_W	67_V	0.543	0.75
54_D	63_H	0.542	0.74
109_P	114_H	0.542	0.74
66_V	69_L	0.541	0.74
51_Y	60_G	0.541	0.74
2_K	38_D	0.536	0.74
61_W	138_M	0.533	0.73
14_L	118_F	0.529	0.73
52_D	55_A	0.525	0.72
55_A	114_H	0.524	0.72
95_R	101_T	0.522	0.72
15_P	103_Y	0.520	0.71
70_P	74_R	0.520	0.71
123_L	145_F	0.518	0.71
62_W	97_D	0.513	0.70
25_Y	104_D	0.508	0.70
55_A	97_D	0.507	0.69
54_D	114_H	0.506	0.69
36_W	120_V	0.504	0.69
31_S	79_G	0.500	0.68
130_V	133_G	0.500	0.68

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
1fjjA	2	1	100	0.125	Contact Map
1fuxA	2	1	100	0.146	Contact Map
4begA	4	0.9937	100	0.159	Contact Map
3n08A	2	0.9114	100	0.169	Contact Map
2evvA	2	0.943	100	0.222	Contact Map
1wpxB	1	0.8671	99.9	0.51	Contact Map
2jyzA	1	0.8165	99.9	0.545	Contact Map
3axyA	1	0.7911	99.9	0.558	Contact Map
1vw41	1	0.8924	99.9	0.561	Contact Map
2gzqA	1	0.8354	99.9	0.565	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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