YBET - ECOLI - GREMLIN Contacts

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YBET - Uncharacterized protein YbeT

UniProt:	P77296	Sequences: MNKKLMYIFAIFIVAAITCISQPKKTTLRDKAMVNYAFDYLSSPGSLPFTTAATELSAIHGHSTSQYRLGEFYLHGSDGKPLDYTQARYWYEQSAEQENPRAQSKLGWIYLKGLGVKPDTRKAILWYKEAAEQGYAHAQYTLGLIYRNGSGINVNHYESQKWLKLTAKQHYKNAERLLAGLPAH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13650
Length:	184 (145)
Sequences:	3103 (2576)
Seq/√Len:	213.9

ECOLI - YBET YIBG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
147_R	163_L	2.782	1.00
74_L	91_Y	2.587	1.00
139_Q	162_W	2.537	1.00
139_Q	169_Q	2.511	1.00
66_Q	97_Q	2.431	1.00
158_E	161_K	2.385	1.00
103_Q	126_W	2.304	1.00
103_Q	133_Q	2.241	1.00
167_A	175_E	2.212	1.00
111_L	127_Y	2.137	1.00
122_K	125_L	2.132	1.00
70_G	91_Y	2.127	1.00
46_S	49_F	2.019	1.00
95_A	103_Q	2.012	1.00
66_Q	90_W	2.004	1.00
86_Q	89_Y	1.985	1.00
58_A	66_Q	1.921	1.00
69_L	73_Y	1.892	1.00
88_R	106_L	1.860	1.00
107_G	127_Y	1.808	1.00
67_Y	99_N	1.739	1.00
155_N	158_E	1.704	1.00
128_K	158_E	1.704	1.00
53_A	57_S	1.697	1.00
128_K	132_E	1.659	1.00
159_S	163_L	1.616	1.00
35_N	38_F	1.573	1.00
162_W	165_L	1.520	1.00
123_A	127_Y	1.511	1.00
119_D	122_K	1.505	1.00
131_A	139_Q	1.496	1.00
143_G	163_L	1.494	1.00
124_I	152_I	1.493	1.00
54_T	68_R	1.486	1.00
164_K	168_K	1.484	1.00
104_S	138_A	1.441	1.00
67_Y	102_A	1.441	1.00
158_E	162_W	1.433	1.00
104_S	135_Y	1.420	1.00
88_R	92_E	1.393	1.00
94_S	102_A	1.385	1.00
87_A	91_Y	1.369	1.00
144_L	163_L	1.346	1.00
140_Y	177_L	1.337	1.00
47_L	50_T	1.310	1.00
55_E	59_I	1.308	1.00
90_W	93_Q	1.278	1.00
142_L	146_Y	1.275	1.00
130_A	138_A	1.213	1.00
92_E	96_E	1.204	1.00
50_T	54_T	1.202	1.00
95_A	126_W	1.189	1.00
140_Y	171_Y	1.186	1.00
106_L	110_Y	1.175	1.00
92_E	122_K	1.174	1.00
113_G	119_D	1.170	1.00
57_S	62_H	1.158	1.00
126_W	129_E	1.156	1.00
88_R	116_V	1.151	1.00
58_A	90_W	1.143	1.00
42_S	47_L	1.129	1.00
103_Q	129_E	1.124	1.00
122_K	126_W	1.118	1.00
51_T	55_E	1.117	1.00
58_A	61_G	1.113	1.00
160_Q	164_K	1.088	1.00
113_G	116_V	1.086	1.00
91_Y	105_K	1.066	1.00
139_Q	165_L	1.051	1.00
67_Y	105_K	1.036	1.00
95_A	131_A	1.035	1.00
93_Q	97_Q	1.027	1.00
166_T	174_A	1.022	1.00
104_S	108_W	1.019	1.00
113_G	118_P	1.011	1.00
85_T	121_R	1.000	1.00
64_T	99_N	0.993	1.00
145_I	151_G	0.985	1.00
143_G	162_W	0.978	1.00
88_R	110_Y	0.972	1.00
127_Y	141_T	0.956	1.00
131_A	134_G	0.951	1.00
124_I	128_K	0.950	1.00
110_Y	116_V	0.949	1.00
76_G	79_G	0.947	1.00
111_L	123_A	0.946	1.00
67_Y	71_E	0.940	0.99
104_S	141_T	0.937	0.99
58_A	65_S	0.932	0.99
38_F	42_S	0.928	0.99
124_I	142_L	0.927	0.99
55_E	86_Q	0.925	0.99
76_G	83_D	0.923	0.99
89_Y	93_Q	0.910	0.99
125_L	129_E	0.904	0.99
101_R	135_Y	0.899	0.99
83_D	86_Q	0.897	0.99
147_R	177_L	0.887	0.99
68_R	71_E	0.884	0.99
136_A	171_Y	0.879	0.99
107_G	126_W	0.872	0.99
66_Q	93_Q	0.866	0.99
131_A	162_W	0.865	0.99
62_H	65_S	0.861	0.99
108_W	127_Y	0.859	0.99
74_L	105_K	0.855	0.99
109_I	115_G	0.850	0.99
51_T	69_L	0.845	0.99
74_L	87_A	0.845	0.99
129_E	133_Q	0.844	0.99
163_L	177_L	0.835	0.99
53_A	56_L	0.833	0.99
88_R	109_I	0.824	0.99
172_K	176_R	0.823	0.99
90_W	126_W	0.820	0.99
72_F	145_I	0.813	0.99
105_K	108_W	0.813	0.99
108_W	111_L	0.811	0.98
41_L	46_S	0.810	0.98
129_E	165_L	0.807	0.98
130_A	135_Y	0.801	0.98
94_S	99_N	0.791	0.98
36_Y	39_D	0.791	0.98
171_Y	174_A	0.788	0.98
38_F	41_L	0.788	0.98
107_G	123_A	0.771	0.98
124_I	145_I	0.770	0.98
92_E	106_L	0.765	0.98
49_F	53_A	0.757	0.98
61_G	65_S	0.756	0.98
111_L	141_T	0.752	0.98
146_Y	149_G	0.747	0.97
95_A	98_E	0.745	0.97
91_Y	109_I	0.744	0.97
51_T	80_K	0.739	0.97
84_Y	114_L	0.737	0.97
172_K	175_E	0.734	0.97
76_G	82_L	0.733	0.97
63_S	94_S	0.729	0.97
141_T	144_L	0.727	0.97
86_Q	90_W	0.727	0.97
109_I	116_V	0.723	0.97
165_L	169_Q	0.723	0.97
76_G	80_K	0.722	0.97
38_F	45_G	0.717	0.97
71_E	75_H	0.711	0.97
120_T	150_S	0.710	0.97
100_P	130_A	0.708	0.96
170_H	174_A	0.704	0.96
32_A	36_Y	0.701	0.96
55_E	69_L	0.695	0.96
146_Y	158_E	0.693	0.96
149_G	152_I	0.687	0.96
106_L	126_W	0.687	0.96
99_N	102_A	0.686	0.96
49_F	52_A	0.683	0.96
41_L	49_F	0.679	0.96
146_Y	152_I	0.674	0.95
161_K	165_L	0.672	0.95
147_R	159_S	0.668	0.95
73_Y	86_Q	0.661	0.95
58_A	95_A	0.657	0.95
70_G	94_S	0.654	0.95
110_Y	122_K	0.652	0.94
56_L	59_I	0.652	0.94
166_T	171_Y	0.646	0.94
103_Q	139_Q	0.641	0.94
167_A	174_A	0.635	0.94
89_Y	125_L	0.634	0.94
47_L	77_S	0.634	0.94
149_G	155_N	0.634	0.94
58_A	131_A	0.626	0.93
34_V	37_A	0.626	0.93
151_G	155_N	0.624	0.93
85_T	157_Y	0.619	0.93
42_S	54_T	0.615	0.93
38_F	54_T	0.615	0.93
73_Y	80_K	0.615	0.93
108_W	141_T	0.606	0.92
37_A	40_Y	0.605	0.92
50_T	53_A	0.605	0.92
57_S	65_S	0.601	0.92
134_G	169_Q	0.588	0.91
63_S	99_N	0.585	0.91
33_M	37_A	0.578	0.90
54_T	65_S	0.578	0.90
129_E	132_E	0.576	0.90
121_R	124_I	0.576	0.90
142_L	162_W	0.575	0.90
72_F	79_G	0.574	0.90
149_G	154_V	0.571	0.90
71_E	105_K	0.568	0.89
110_Y	113_G	0.564	0.89
115_G	118_P	0.559	0.89
35_N	62_H	0.556	0.88
32_A	35_N	0.554	0.88
42_S	50_T	0.544	0.87
57_S	60_H	0.541	0.87
171_Y	175_E	0.535	0.86
71_E	74_L	0.534	0.86
140_Y	174_A	0.533	0.86
88_R	113_G	0.531	0.86
98_E	134_G	0.526	0.85
98_E	103_Q	0.522	0.85
32_A	39_D	0.519	0.85
72_F	80_K	0.516	0.84
162_W	166_T	0.516	0.84
38_F	50_T	0.516	0.84
71_E	91_Y	0.512	0.84
145_I	150_S	0.512	0.84
48_P	52_A	0.509	0.84
140_Y	144_L	0.507	0.83
45_G	56_L	0.506	0.83
136_A	143_G	0.504	0.83
100_P	133_Q	0.504	0.83
32_A	38_F	0.503	0.83
144_L	147_R	0.502	0.83
136_A	166_T	0.500	0.82

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
4bwrA	1	0.913	99.9	0.349	Contact Map
1ouvA	1	0.837	99.9	0.374	Contact Map
1klxA	1	0.7228	99.8	0.416	Contact Map
3e4bA	1	0.9728	99.7	0.499	Contact Map
3rjvA	1	0.9022	99.5	0.566	Contact Map
1hh8A	1	0.7826	99.1	0.642	Contact Map
4gywA	2	0.7826	99.1	0.647	Contact Map
3qkyA	1	0.788	99.1	0.65	Contact Map
2pziA	1	0.8913	99.1	0.653	Contact Map
2vsyA	1	0.6033	99	0.665	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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