YOHD - ECOLI - GREMLIN Contacts

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YOHD - Inner membrane protein YohD

UniProt:	P33366	Sequences: MDLNTLISQYGYAALVIGSLAEGETVTLLGGVAAHQGLLKFPLVVLSVALGGMIGDQVLYLCGRRFGGKLLRRFSKHQDKIERAQKLIQRHPYLFVIGTRFMYGFRVIGPTLIGASQLPPKIFLPLNILGAFAWALIFTTIGYAGGQVIAPWLHNLDQHLKHWVWLILVVVLVVGVRWWLKRRGKKKPDHQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12017
Length:	192 (175)
Sequences:	6761 (4795)
Seq/√Len:	362.5

ECOLI - YOHD YABI DEDA YQJA YGHB YDJX YDJZ
BACSU - YKOX YNGC YBFM YHJE YQED YTXB
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
57_Q	120_P	3.409	1.00
40_K	43_L	3.265	1.00
49_A	132_F	2.720	1.00
34_A	143_Y	2.533	1.00
53_M	128_I	2.479	1.00
93_Y	122_I	2.478	1.00
97_I	129_L	2.467	1.00
91_H	94_L	2.455	1.00
57_Q	124_L	2.454	1.00
45_V	136_L	2.438	1.00
175_G	179_W	2.350	1.00
174_V	178_W	2.349	1.00
119_P	122_I	2.263	1.00
176_V	180_L	2.178	1.00
48_V	135_A	2.119	1.00
47_S	51_G	2.086	1.00
41_F	140_T	2.002	1.00
85_Q	89_Q	1.941	1.00
45_V	139_T	1.935	1.00
153_L	156_L	1.875	1.00
68_G	85_Q	1.875	1.00
93_Y	126_L	1.850	1.00
140_T	144_A	1.813	1.00
64_R	117_Q	1.809	1.00
27_T	139_T	1.730	1.00
162_H	166_L	1.701	1.00
30_G	44_V	1.679	1.00
41_F	45_V	1.678	1.00
120_P	124_L	1.645	1.00
173_V	177_R	1.622	1.00
41_F	139_T	1.609	1.00
165_W	169_V	1.594	1.00
94_L	98_G	1.585	1.00
72_R	78_Q	1.535	1.00
61_L	65_R	1.485	1.00
78_Q	82_E	1.482	1.00
82_E	86_K	1.473	1.00
179_W	182_R	1.442	1.00
174_V	177_R	1.440	1.00
159_H	162_H	1.439	1.00
53_M	131_A	1.424	1.00
56_D	100_R	1.412	1.00
43_L	47_S	1.386	1.00
44_V	139_T	1.369	1.00
63_G	115_A	1.369	1.00
10_Y	14_A	1.360	1.00
161_K	165_W	1.320	1.00
34_A	41_F	1.320	1.00
101_F	133_A	1.315	1.00
85_Q	116_S	1.313	1.00
68_G	72_R	1.266	1.00
42_P	140_T	1.260	1.00
61_L	120_P	1.244	1.00
79_D	83_R	1.237	1.00
121_K	125_P	1.233	1.00
99_T	109_G	1.227	1.00
46_L	50_L	1.208	1.00
27_T	31_G	1.177	1.00
42_P	46_L	1.174	1.00
177_R	180_L	1.170	1.00
59_L	111_T	1.168	1.00
170_V	174_V	1.168	1.00
88_I	113_I	1.168	1.00
11_G	15_L	1.156	1.00
177_R	181_K	1.151	1.00
65_R	69_K	1.147	1.00
24_E	106_R	1.145	1.00
71_L	81_I	1.137	1.00
27_T	48_V	1.132	1.00
97_I	133_A	1.129	1.00
178_W	181_K	1.104	1.00
39_L	44_V	1.103	1.00
171_V	174_V	1.093	1.00
178_W	182_R	1.074	1.00
18_G	59_L	1.059	1.00
96_V	118_L	1.058	1.00
45_V	140_T	1.057	1.00
86_K	90_R	1.044	1.00
31_G	142_G	1.044	1.00
49_A	53_M	1.042	1.00
19_S	22_E	1.042	1.00
53_M	124_L	1.040	1.00
127_N	131_A	1.034	1.00
49_A	135_A	1.033	1.00
125_P	129_L	1.033	1.00
9_Q	12_Y	1.030	1.00
9_Q	13_A	1.029	1.00
35_H	143_Y	1.021	1.00
12_Y	43_L	1.020	1.00
45_V	49_A	1.016	1.00
175_G	178_W	1.015	1.00
156_L	159_H	1.007	1.00
48_V	139_T	1.007	1.00
167_I	171_V	1.006	1.00
12_Y	16_V	1.006	1.00
82_E	85_Q	1.005	1.00
180_L	183_R	1.000	1.00
16_V	50_L	0.999	1.00
157_D	161_K	0.996	1.00
7_I	11_G	0.988	1.00
166_L	170_V	0.986	1.00
57_Q	61_L	0.985	1.00
164_V	168_L	0.974	1.00
10_Y	13_A	0.971	1.00
70_L	75_S	0.964	1.00
46_L	49_A	0.956	1.00
31_G	139_T	0.954	1.00
169_V	173_V	0.941	1.00
74_F	77_H	0.939	1.00
16_V	54_I	0.933	1.00
16_V	47_S	0.929	1.00
110_P	127_N	0.928	1.00
56_D	127_N	0.927	1.00
80_K	83_R	0.927	1.00
62_C	66_F	0.926	1.00
121_K	124_L	0.909	1.00
179_W	183_R	0.909	1.00
61_L	64_R	0.905	1.00
52_G	131_A	0.904	1.00
32_V	35_H	0.893	1.00
69_K	73_R	0.881	1.00
157_D	160_L	0.880	1.00
32_V	149_I	0.877	1.00
35_H	147_Q	0.870	1.00
137_I	140_T	0.864	1.00
15_L	48_V	0.864	1.00
43_L	46_L	0.862	1.00
160_L	164_V	0.861	1.00
124_L	128_I	0.861	1.00
163_W	166_L	0.836	1.00
66_F	69_K	0.835	1.00
87_L	95_F	0.834	1.00
8_S	12_Y	0.832	1.00
53_M	127_N	0.829	1.00
133_A	136_L	0.828	1.00
12_Y	40_K	0.825	1.00
106_R	134_W	0.817	1.00
12_Y	15_L	0.816	1.00
176_V	179_W	0.815	1.00
92_P	118_L	0.812	1.00
171_V	175_G	0.810	1.00
100_R	106_R	0.807	1.00
34_A	44_V	0.807	1.00
125_P	128_I	0.803	1.00
94_L	126_L	0.802	1.00
31_G	44_V	0.799	1.00
160_L	163_W	0.796	1.00
163_W	167_I	0.795	1.00
42_P	45_V	0.788	1.00
23_G	103_Y	0.788	1.00
172_L	176_V	0.784	1.00
52_G	100_R	0.781	1.00
50_L	54_I	0.781	1.00
161_K	164_V	0.780	1.00
23_G	127_N	0.778	1.00
29_L	33_A	0.770	1.00
173_V	176_V	0.768	1.00
144_A	148_V	0.765	1.00
34_A	139_T	0.765	1.00
60_Y	120_P	0.754	1.00
86_K	89_Q	0.751	1.00
74_F	78_Q	0.745	1.00
162_H	165_W	0.743	1.00
113_I	118_L	0.739	1.00
141_I	144_A	0.737	1.00
22_E	103_Y	0.734	1.00
21_A	107_V	0.729	1.00
136_L	140_T	0.728	1.00
156_L	160_L	0.727	1.00
102_M	105_F	0.727	1.00
135_A	139_T	0.716	0.99
169_V	180_L	0.716	0.99
8_S	13_A	0.712	0.99
114_G	117_Q	0.708	0.99
145_G	148_V	0.703	0.99
143_Y	147_Q	0.703	0.99
59_L	107_V	0.700	0.99
84_A	116_S	0.697	0.99
132_F	136_L	0.691	0.99
149_I	152_W	0.690	0.99
99_T	103_Y	0.690	0.99
67_G	71_L	0.677	0.99
60_Y	114_G	0.676	0.99
29_L	32_V	0.674	0.99
85_Q	117_Q	0.669	0.99
56_D	120_P	0.668	0.99
168_L	171_V	0.668	0.99
15_L	44_V	0.666	0.99
158_Q	161_K	0.666	0.99
57_Q	127_N	0.663	0.99
80_K	84_A	0.663	0.99
73_R	77_H	0.659	0.99
55_G	59_L	0.654	0.99
95_F	98_G	0.654	0.99
75_S	78_Q	0.653	0.99
28_L	32_V	0.652	0.99
152_W	156_L	0.650	0.99
71_L	74_F	0.631	0.99
30_G	39_L	0.631	0.99
72_R	79_D	0.630	0.99
58_V	61_L	0.630	0.99
52_G	134_W	0.624	0.99
103_Y	107_V	0.620	0.99
70_L	76_K	0.616	0.98
159_H	164_V	0.616	0.98
13_A	16_V	0.612	0.98
16_V	51_G	0.611	0.98
123_F	127_N	0.608	0.98
157_D	162_H	0.605	0.98
54_I	58_V	0.605	0.98
128_I	132_F	0.598	0.98
19_S	59_L	0.598	0.98
95_F	109_G	0.597	0.98
96_V	113_I	0.596	0.98
12_Y	39_L	0.589	0.98
68_G	71_L	0.586	0.98
38_L	42_P	0.577	0.98
177_R	183_R	0.576	0.98
78_Q	81_I	0.572	0.97
71_L	115_A	0.568	0.97
100_R	127_N	0.568	0.97
94_L	112_L	0.566	0.97
103_Y	127_N	0.566	0.97
133_A	137_I	0.565	0.97
24_E	130_G	0.565	0.97
153_L	157_D	0.563	0.97
122_I	126_L	0.562	0.97
23_G	123_F	0.562	0.97
27_T	135_A	0.559	0.97
73_R	76_K	0.557	0.97
150_A	153_L	0.557	0.97
24_E	100_R	0.556	0.97
166_L	169_V	0.555	0.97
8_S	11_G	0.554	0.97
24_E	138_F	0.553	0.97
52_G	106_R	0.544	0.97
66_F	70_L	0.543	0.97
52_G	107_V	0.543	0.97
88_I	95_F	0.542	0.97
31_G	138_F	0.538	0.96
7_I	14_A	0.535	0.96
70_L	73_R	0.532	0.96
6_L	10_Y	0.529	0.96
68_G	117_Q	0.525	0.96
159_H	163_W	0.525	0.96
24_E	107_V	0.524	0.96
52_G	55_G	0.523	0.96
168_L	172_L	0.521	0.96
22_E	27_T	0.519	0.96
107_V	138_F	0.516	0.95
83_R	86_K	0.516	0.95
30_G	139_T	0.515	0.95
129_L	132_F	0.514	0.95
70_L	74_F	0.513	0.95
59_L	104_G	0.510	0.95
111_T	115_A	0.507	0.95
109_G	127_N	0.506	0.95
79_D	82_E	0.504	0.95
60_Y	113_I	0.503	0.95
69_K	72_R	0.503	0.95
35_H	38_L	0.500	0.95
84_A	105_F	0.500	0.95

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
2l2tA	2	0.224	38.3	0.922	Contact Map
2kluA	1	0.2188	35.1	0.923	Contact Map
2m20A	2	0.1979	29.1	0.927	Contact Map
2micA	2	0.2135	21.7	0.931	Contact Map
2kv5A	1	0.1719	21.5	0.931	Contact Map
3w9iA	3	0.7656	21.2	0.931	Contact Map
2jwaA	2	0.224	19.1	0.933	Contact Map
4dx5A	3	0.8229	18.9	0.933	Contact Map
2ks1B	1	0.224	17	0.934	Contact Map
2gfpA	2	0.9271	15.3	0.936	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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