YABI - ECOLI - GREMLIN Contacts

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YABI - Inner membrane protein YabI

UniProt:	P30149	Sequences: MQALLEHFITQSTVYSLMAVVLVAFLESLALVGLILPGTVLMAGLGALIGSGELSFWHAWLAGIIGCLMGDWISFWLGWRFKKPLHRWSFLKKNKALLDKTEHALHQHSMFTILVGRFVGPTRPLVPMVAGMLDLPVAKFITPNIIGCLLWPPFYFLPGILAGAAIDIPAGMQSGEFKWLLLATAVFLWVGGWLCWRLWRSGKATDRLSHYLSRGRLLWLTPLISAIGVVALVVLIRHPLMPVYIDILRKVVGV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11571
Length:	254 (195)
Sequences:	4703 (3371)
Seq/√Len:	241.4

ECOLI - YABI YGHB DEDA YQJA YOHD
BACSU - YKOX YNGC YBFM
SULSO - Q97V45

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_W	137_V	3.420	1.00
55_S	58_H	3.260	1.00
64_I	149_L	3.080	1.00
114_L	146_I	2.944	1.00
191_G	195_C	2.866	1.00
49_I	160_I	2.625	1.00
108_H	111_F	2.590	1.00
68_L	145_I	2.549	1.00
60_W	153_P	2.505	1.00
193_W	197_R	2.494	1.00
25_F	73_I	2.460	1.00
192_G	196_W	2.398	1.00
179_W	183_A	2.376	1.00
63_G	152_P	2.347	1.00
94_N	97_L	2.328	1.00
110_M	139_K	2.282	1.00
72_W	141_I	2.261	1.00
102_E	106_H	2.182	1.00
194_L	198_L	2.150	1.00
136_P	139_K	2.063	1.00
190_V	194_L	1.943	1.00
56_F	60_W	1.930	1.00
56_F	157_L	1.912	1.00
62_A	66_G	1.907	1.00
60_W	156_F	1.891	1.00
12_S	16_S	1.883	1.00
181_L	185_A	1.878	1.00
96_A	100_K	1.783	1.00
42_M	156_F	1.760	1.00
83_K	102_E	1.723	1.00
157_L	161_L	1.719	1.00
99_D	103_H	1.700	1.00
25_F	69_M	1.697	1.00
17_L	58_H	1.694	1.00
192_G	195_C	1.691	1.00
79_W	134_D	1.683	1.00
110_M	143_P	1.663	1.00
45_L	59_A	1.626	1.00
95_K	99_D	1.619	1.00
189_W	193_W	1.614	1.00
56_F	156_F	1.609	1.00
137_V	141_I	1.574	1.00
86_H	95_K	1.562	1.00
68_L	148_C	1.551	1.00
21_V	65_I	1.512	1.00
90_F	93_K	1.511	1.00
17_L	55_S	1.472	1.00
20_V	63_G	1.422	1.00
27_E	38_G	1.413	1.00
59_A	156_F	1.406	1.00
24_A	66_G	1.394	1.00
118_F	150_L	1.387	1.00
138_A	142_T	1.379	1.00
60_W	157_L	1.375	1.00
80_R	84_P	1.344	1.00
33_G	74_S	1.300	1.00
194_L	197_R	1.299	1.00
15_Y	19_A	1.296	1.00
76_W	80_R	1.295	1.00
68_L	144_N	1.280	1.00
21_V	62_A	1.259	1.00
49_I	56_F	1.245	1.00
111_F	115_V	1.236	1.00
6_E	10_T	1.235	1.00
57_W	157_L	1.233	1.00
57_W	61_L	1.217	1.00
116_G	126_V	1.215	1.00
68_L	141_I	1.206	1.00
29_L	36_L	1.191	1.00
50_G	164_A	1.184	1.00
195_C	199_W	1.180	1.00
197_R	200_R	1.179	1.00
61_L	65_I	1.175	1.00
178_K	182_L	1.175	1.00
195_C	198_L	1.174	1.00
76_W	137_V	1.171	1.00
190_V	193_W	1.139	1.00
88_W	93_K	1.135	1.00
67_C	148_C	1.113	1.00
21_V	66_G	1.111	1.00
65_I	69_M	1.101	1.00
198_L	202_G	1.098	1.00
58_H	62_A	1.093	1.00
197_R	201_S	1.086	1.00
15_Y	18_M	1.082	1.00
186_V	190_V	1.081	1.00
50_G	160_I	1.067	1.00
17_L	62_A	1.065	1.00
42_M	46_G	1.058	1.00
169_P	172_M	1.045	1.00
71_D	137_V	1.044	1.00
166_I	169_P	1.043	1.00
99_D	102_E	1.043	1.00
105_L	130_A	1.037	1.00
26_L	33_G	1.031	1.00
88_W	91_L	1.025	1.00
78_G	132_M	1.025	1.00
42_M	63_G	1.022	1.00
141_I	145_I	1.018	1.00
64_I	152_P	1.017	1.00
71_D	117_R	1.009	1.00
10_T	13_T	1.002	1.00
20_V	59_A	0.994	1.00
191_G	194_L	0.993	1.00
71_D	144_N	0.989	1.00
72_W	76_W	0.984	1.00
199_W	202_G	0.979	1.00
74_S	124_P	0.979	1.00
138_A	141_I	0.975	1.00
144_N	148_C	0.968	1.00
198_L	201_S	0.964	1.00
114_L	150_L	0.964	1.00
165_A	168_I	0.948	1.00
39_T	123_R	0.927	1.00
102_E	133_L	0.922	1.00
74_S	128_M	0.921	1.00
185_A	188_L	0.919	1.00
46_G	159_G	0.914	1.00
89_S	92_K	0.906	1.00
76_W	79_W	0.906	1.00
64_I	68_L	0.903	1.00
196_W	199_W	0.900	1.00
165_A	169_P	0.898	1.00
58_H	61_L	0.888	1.00
167_D	171_G	0.881	0.99
188_L	192_G	0.875	0.99
54_L	59_A	0.875	0.99
49_I	156_F	0.875	0.99
36_L	124_P	0.870	0.99
127_P	144_N	0.870	0.99
47_A	166_I	0.843	0.99
57_W	60_W	0.842	0.99
60_W	64_I	0.838	0.99
169_P	173_Q	0.838	0.99
67_C	117_R	0.836	0.99
97_L	100_K	0.835	0.99
24_A	63_G	0.824	0.99
187_F	191_G	0.824	0.99
153_P	157_L	0.814	0.99
150_L	153_P	0.810	0.99
177_F	180_L	0.806	0.99
186_V	189_W	0.802	0.99
93_K	125_L	0.802	0.99
77_L	81_F	0.799	0.99
179_W	182_L	0.797	0.99
89_S	95_K	0.795	0.99
81_F	84_P	0.795	0.99
88_W	95_K	0.794	0.99
142_T	146_I	0.789	0.99
13_T	16_S	0.782	0.99
26_L	34_L	0.779	0.99
12_S	15_Y	0.778	0.99
91_L	98_L	0.775	0.99
168_I	171_G	0.771	0.99
16_S	19_A	0.767	0.99
17_L	54_L	0.766	0.99
166_I	170_A	0.761	0.98
6_E	9_I	0.757	0.98
27_E	117_R	0.757	0.98
69_M	73_I	0.756	0.98
84_P	87_R	0.753	0.98
196_W	200_R	0.752	0.98
11_Q	16_S	0.751	0.98
38_G	144_N	0.750	0.98
47_A	50_G	0.750	0.98
24_A	152_P	0.749	0.98
72_W	144_N	0.744	0.98
112_T	115_V	0.737	0.98
167_D	170_A	0.734	0.98
101_T	133_L	0.731	0.98
189_W	192_G	0.731	0.98
85_L	88_W	0.731	0.98
75_F	131_G	0.725	0.98
181_L	188_L	0.724	0.98
10_T	14_V	0.720	0.98
113_I	135_L	0.719	0.98
21_V	69_M	0.717	0.98
172_M	175_G	0.716	0.98
7_H	11_Q	0.714	0.98
34_L	74_S	0.704	0.97
23_V	41_L	0.701	0.97
75_F	137_V	0.701	0.97
28_S	117_R	0.700	0.97
103_H	107_Q	0.700	0.97
9_I	16_S	0.697	0.97
71_D	116_G	0.696	0.97
14_V	18_M	0.682	0.97
20_V	45_L	0.682	0.97
100_K	103_H	0.680	0.97
111_F	143_P	0.677	0.97
96_A	99_D	0.677	0.97
8_F	16_S	0.675	0.97
83_K	86_H	0.671	0.97
199_W	203_K	0.670	0.97
117_R	144_N	0.667	0.97
134_D	139_K	0.666	0.96
47_A	162_A	0.665	0.96
191_G	197_R	0.664	0.96
46_G	156_F	0.660	0.96
16_S	54_L	0.658	0.96
120_G	124_P	0.656	0.96
27_E	144_N	0.644	0.96
180_L	183_A	0.638	0.96
24_A	147_G	0.636	0.95
193_W	196_W	0.632	0.95
9_I	48_L	0.632	0.95
44_G	47_A	0.628	0.95
27_E	124_P	0.627	0.95
44_G	48_L	0.625	0.95
42_M	152_P	0.620	0.95
139_K	143_P	0.616	0.95
119_V	122_T	0.615	0.95
71_D	113_I	0.615	0.95
28_S	113_I	0.613	0.94
101_T	122_T	0.608	0.94
154_F	158_P	0.606	0.94
112_T	126_V	0.605	0.94
11_Q	19_A	0.602	0.94
27_E	127_P	0.602	0.94
114_L	118_F	0.600	0.94
46_G	59_A	0.600	0.94
117_R	123_R	0.600	0.94
123_R	151_W	0.599	0.94
38_G	120_G	0.599	0.94
142_T	145_I	0.599	0.94
79_W	82_K	0.598	0.94
24_A	124_P	0.598	0.94
28_S	71_D	0.598	0.94
185_A	192_G	0.594	0.94
130_A	135_L	0.594	0.94
85_L	90_F	0.591	0.93
43_A	162_A	0.589	0.93
24_A	28_S	0.589	0.93
171_G	175_G	0.587	0.93
63_G	156_F	0.585	0.93
11_Q	15_Y	0.584	0.93
89_S	93_K	0.582	0.93
28_S	112_T	0.581	0.93
178_K	185_A	0.580	0.93
105_L	126_V	0.579	0.93
168_I	172_M	0.578	0.93
21_V	25_F	0.578	0.93
191_G	202_G	0.577	0.93
73_I	76_W	0.577	0.93
158_P	161_L	0.575	0.92
29_L	34_L	0.572	0.92
35_I	121_P	0.571	0.92
68_L	149_L	0.569	0.92
61_L	64_I	0.566	0.92
149_L	153_P	0.563	0.92
186_V	197_R	0.556	0.91
29_L	66_G	0.551	0.91
71_D	141_I	0.549	0.91
93_K	97_L	0.548	0.90
39_T	155_Y	0.546	0.90
29_L	124_P	0.544	0.90
129_V	135_L	0.543	0.90
136_P	193_W	0.541	0.90
102_E	134_D	0.541	0.90
72_W	145_I	0.541	0.90
190_V	197_R	0.537	0.90
104_A	109_S	0.537	0.90
155_Y	173_Q	0.536	0.90
154_F	157_L	0.536	0.90
67_C	124_P	0.534	0.89
183_A	187_F	0.534	0.89
161_L	164_A	0.533	0.89
167_D	173_Q	0.530	0.89
28_S	34_L	0.529	0.89
25_F	29_L	0.528	0.89
45_L	54_L	0.525	0.89
152_P	156_F	0.524	0.88
93_K	98_L	0.524	0.88
116_G	130_A	0.524	0.88
28_S	127_P	0.523	0.88
28_S	74_S	0.522	0.88
36_L	40_V	0.522	0.88
170_A	173_Q	0.521	0.88
184_T	196_W	0.520	0.88
28_S	144_N	0.518	0.88
103_H	106_H	0.518	0.88
145_I	149_L	0.512	0.87
24_A	36_L	0.512	0.87
113_I	130_A	0.511	0.87
166_I	173_Q	0.511	0.87
27_E	123_R	0.510	0.87
190_V	199_W	0.509	0.87
67_C	71_D	0.509	0.87
194_L	200_R	0.506	0.87
162_A	166_I	0.502	0.86
178_K	183_A	0.501	0.86
118_F	147_G	0.500	0.86

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
4dx5A	3	0.6772	52.3	0.935	Contact Map
4k0jA	3	0.6063	29	0.943	Contact Map
3wdoA	1	0.9528	27	0.944	Contact Map
4m64A	1	0.7953	26.4	0.945	Contact Map
3ne5A	3	0.6496	23.5	0.946	Contact Map
3w9iA	3	0.6378	20.7	0.947	Contact Map
2m20A	2	0.2362	19.9	0.948	Contact Map
2kluA	1	0.2756	16.1	0.95	Contact Map
2kncA	1	0.2087	14.3	0.951	Contact Map
4pypA	1	0.7205	14.3	0.951	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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