YADH - ECOLI - GREMLIN Contacts

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YADH - Inner membrane transport permease YadH

UniProt:	P0AFN6	Sequences: MMHLYWVALKSIWAKEIHRFMRIWVQTLVPPVITMTLYFIIFGNLIGSRIGDMHGFSYMQFIVPGLIMMSVITNAYANVASSFFGAKFQRNIEELLVAPVPTHVIIAGYVGGGVARGLFVGILVTAISLFFVPFQVHSWVFVALTLVLTAVLFSLAGLLNGVFAKTFDDISLVPTFVLTPLTYLGGVFYSLTLLPPFWQGLSHLNPIVYMISGFRYGFLGINDVPLVTTFGVLVVFIVAFYLICWSLIQRGRGLRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12321
Length:	256 (237)
Sequences:	23594 (16286)
Seq/√Len:	1057.9

ECOLI - YADH YHHJ YBHR YBHS
BACSU - YVFS TAGG YFIM YFIN NATB YHAP
HALSA - Q9HRJ5 Q9HMU9
SULSO - Q97VH7 Q97U55 Q97WP5 Q97Z04 Q7LY08 Q97W41

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
145_T	213_G	5.355	1.00
14_A	18_H	4.110	1.00
159_L	243_I	3.617	1.00
149_T	210_M	3.409	1.00
12_I	108_G	3.251	1.00
13_W	115_A	3.193	1.00
9_L	111_G	2.963	1.00
10_K	14_A	2.726	1.00
122_I	143_A	2.695	1.00
16_E	109_Y	2.627	1.00
101_P	104_V	2.565	1.00
151_V	237_I	2.534	1.00
152_L	237_I	2.517	1.00
13_W	111_G	2.446	1.00
196_P	200_G	2.413	1.00
227_V	231_G	2.260	1.00
231_G	235_V	2.231	1.00
18_H	21_M	2.142	1.00
228_T	232_V	2.087	1.00
159_L	247_L	2.081	1.00
232_V	235_V	2.058	1.00
57_S	60_Q	2.051	1.00
148_L	234_V	2.044	1.00
199_Q	203_H	1.949	1.00
126_A	130_F	1.945	1.00
159_L	240_F	1.930	1.00
196_P	199_Q	1.911	1.00
209_Y	229_T	1.902	1.00
9_L	104_V	1.877	1.00
9_L	13_W	1.840	1.00
242_L	246_S	1.810	1.00
152_L	240_F	1.809	1.00
21_M	24_W	1.797	1.00
235_V	239_A	1.774	1.00
202_S	208_V	1.731	1.00
58_Y	61_F	1.712	1.00
127_I	131_F	1.691	1.00
197_F	200_G	1.688	1.00
118_L	147_V	1.660	1.00
141_F	217_G	1.658	1.00
155_L	241_Y	1.648	1.00
9_L	107_A	1.635	1.00
155_L	237_I	1.623	1.00
152_L	233_L	1.607	1.00
191_L	202_S	1.593	1.00
236_F	240_F	1.579	1.00
164_A	173_V	1.570	1.00
166_T	169_D	1.569	1.00
203_H	209_Y	1.568	1.00
212_S	229_T	1.529	1.00
209_Y	232_V	1.525	1.00
160_N	164_A	1.505	1.00
86_A	109_Y	1.503	1.00
148_L	237_I	1.503	1.00
140_V	144_L	1.497	1.00
145_T	230_F	1.480	1.00
149_T	153_F	1.468	1.00
141_F	226_L	1.456	1.00
239_A	243_I	1.453	1.00
15_K	86_A	1.449	1.00
13_W	108_G	1.442	1.00
9_L	108_G	1.413	1.00
230_F	234_V	1.410	1.00
141_F	144_L	1.398	1.00
200_G	204_L	1.364	1.00
148_L	230_F	1.335	1.00
181_L	205_N	1.321	1.00
10_K	13_W	1.302	1.00
232_V	236_F	1.291	1.00
18_H	22_R	1.286	1.00
155_L	240_F	1.273	1.00
125_T	142_V	1.269	1.00
114_V	147_V	1.268	1.00
106_I	244_C	1.254	1.00
159_L	244_C	1.244	1.00
228_T	231_G	1.242	1.00
212_S	216_Y	1.232	1.00
17_I	21_M	1.227	1.00
187_V	211_I	1.225	1.00
145_T	217_G	1.224	1.00
17_I	112_G	1.200	1.00
108_G	112_G	1.197	1.00
200_G	203_H	1.195	1.00
117_G	150_A	1.185	1.00
162_V	247_L	1.176	1.00
243_I	247_L	1.170	1.00
81_S	84_F	1.169	1.00
44_N	47_G	1.163	1.00
165_K	169_D	1.161	1.00
203_H	208_V	1.159	1.00
114_V	151_V	1.159	1.00
175_T	179_T	1.153	1.00
239_A	242_L	1.148	1.00
103_H	107_A	1.147	1.00
146_L	210_M	1.130	1.00
234_V	238_V	1.129	1.00
40_I	44_N	1.126	1.00
155_L	244_C	1.121	1.00
34_T	38_Y	1.111	1.00
152_L	236_F	1.110	1.00
208_V	212_S	1.106	1.00
194_L	199_Q	1.100	1.00
163_F	247_L	1.092	1.00
106_I	245_W	1.089	1.00
88_F	167_F	1.089	1.00
197_F	201_L	1.082	1.00
216_Y	220_G	1.081	1.00
144_L	230_F	1.074	1.00
65_G	68_M	1.058	1.00
43_G	131_F	1.055	1.00
63_V	66_L	1.054	1.00
13_W	112_G	1.051	1.00
205_N	208_V	1.051	1.00
146_L	214_F	1.049	1.00
16_E	112_G	1.044	1.00
209_Y	213_G	1.043	1.00
13_W	17_I	1.039	1.00
209_Y	212_S	1.039	1.00
237_I	241_Y	1.033	1.00
221_I	224_V	1.030	1.00
60_Q	63_V	1.028	1.00
58_Y	62_I	1.027	1.00
80_A	170_I	1.010	1.00
164_A	169_D	1.010	1.00
140_V	143_A	1.004	1.00
109_Y	113_G	0.999	1.00
191_L	199_Q	0.998	1.00
11_S	14_A	0.986	1.00
176_F	180_P	0.980	1.00
139_W	143_A	0.970	1.00
150_A	154_S	0.965	1.00
135_Q	138_S	0.955	1.00
199_Q	202_S	0.951	1.00
158_L	244_C	0.946	1.00
126_A	129_L	0.942	1.00
138_S	141_F	0.938	1.00
86_A	91_N	0.934	1.00
16_E	19_R	0.928	1.00
144_L	148_L	0.918	1.00
217_G	226_L	0.910	1.00
156_A	240_F	0.909	1.00
137_H	140_V	0.908	1.00
43_G	132_V	0.907	1.00
133_P	136_V	0.902	1.00
36_T	127_I	0.900	1.00
210_M	233_L	0.896	1.00
160_N	174_P	0.887	1.00
156_A	177_V	0.885	1.00
195_P	199_Q	0.885	1.00
226_L	229_T	0.880	1.00
80_A	84_F	0.879	1.00
65_G	69_M	0.869	1.00
246_S	249_Q	0.858	1.00
157_G	161_G	0.857	1.00
29_V	33_I	0.857	1.00
110_V	155_L	0.855	1.00
23_I	26_Q	0.851	1.00
103_H	245_W	0.850	1.00
68_M	207_I	0.847	1.00
191_L	203_H	0.846	1.00
100_V	105_I	0.844	1.00
227_V	230_F	0.839	1.00
110_V	241_Y	0.839	1.00
222_N	225_P	0.838	1.00
91_N	94_E	0.835	1.00
191_L	208_V	0.834	1.00
64_P	69_M	0.827	1.00
169_D	172_L	0.823	1.00
80_A	83_F	0.821	1.00
229_T	233_L	0.819	1.00
171_S	175_T	0.819	1.00
66_L	69_M	0.816	1.00
231_G	234_V	0.815	1.00
39_F	124_V	0.813	1.00
211_I	215_R	0.811	1.00
94_E	98_A	0.805	1.00
84_F	170_I	0.802	1.00
122_I	126_A	0.800	1.00
9_L	103_H	0.798	1.00
123_L	126_A	0.796	1.00
178_L	182_T	0.790	1.00
210_M	213_G	0.787	1.00
234_V	237_I	0.784	1.00
132_V	136_V	0.783	1.00
121_G	146_L	0.783	1.00
16_E	113_G	0.780	1.00
118_L	122_I	0.777	1.00
213_G	229_T	0.775	1.00
82_S	85_G	0.775	1.00
63_V	77_A	0.774	1.00
143_A	147_V	0.772	1.00
63_V	128_S	0.766	1.00
65_G	74_N	0.763	1.00
57_S	61_F	0.761	1.00
127_I	130_F	0.755	1.00
17_I	115_A	0.751	1.00
145_T	210_M	0.751	1.00
243_I	246_S	0.748	1.00
113_G	117_G	0.747	1.00
40_I	127_I	0.739	1.00
104_V	108_G	0.739	1.00
91_N	95_L	0.736	1.00
209_Y	236_F	0.728	1.00
142_V	214_F	0.728	1.00
82_S	86_A	0.726	1.00
148_L	233_L	0.724	1.00
66_L	70_S	0.720	1.00
84_F	88_F	0.716	1.00
238_V	242_L	0.714	1.00
115_A	118_L	0.713	1.00
81_S	85_G	0.711	1.00
226_L	230_F	0.708	1.00
59_M	63_V	0.703	1.00
126_A	139_W	0.703	1.00
220_G	224_V	0.701	1.00
60_Q	65_G	0.697	1.00
85_G	88_F	0.696	1.00
79_V	113_G	0.692	1.00
56_F	60_Q	0.691	1.00
121_G	147_V	0.691	1.00
115_A	119_F	0.690	1.00
39_F	128_S	0.683	1.00
111_G	115_A	0.682	1.00
36_T	40_I	0.680	1.00
20_F	31_P	0.675	1.00
162_V	244_C	0.672	1.00
122_I	125_T	0.669	1.00
73_T	178_L	0.666	1.00
191_L	194_L	0.663	1.00
242_L	245_W	0.662	1.00
107_A	111_G	0.660	1.00
151_V	155_L	0.659	1.00
44_N	131_F	0.658	1.00
194_L	202_S	0.656	1.00
87_K	165_K	0.656	1.00
236_F	239_A	0.651	1.00
30_P	34_T	0.651	1.00
80_A	85_G	0.650	1.00
168_D	172_L	0.649	1.00
15_K	19_R	0.648	1.00
81_S	86_A	0.646	1.00
66_L	71_V	0.641	1.00
61_F	65_G	0.637	1.00
64_P	215_R	0.636	1.00
203_H	206_P	0.635	1.00
15_K	94_E	0.634	1.00
125_T	146_L	0.631	1.00
189_Y	193_L	0.631	1.00
245_W	249_Q	0.629	1.00
229_T	232_V	0.624	1.00
14_A	17_I	0.621	1.00
190_S	194_L	0.620	1.00
240_F	244_C	0.615	1.00
63_V	74_N	0.613	1.00
92_I	96_L	0.610	1.00
175_T	180_P	0.610	1.00
215_R	219_L	0.610	1.00
70_S	74_N	0.609	1.00
186_G	190_S	0.608	1.00
64_P	67_I	0.608	1.00
201_L	205_N	0.607	1.00
34_T	180_P	0.604	1.00
228_T	235_V	0.604	1.00
94_E	157_G	0.604	1.00
41_I	45_L	0.600	1.00
12_I	104_V	0.597	1.00
106_I	158_L	0.592	1.00
64_P	68_M	0.590	1.00
56_F	59_M	0.587	1.00
137_H	141_F	0.587	1.00
39_F	43_G	0.587	1.00
114_V	154_S	0.585	1.00
110_V	154_S	0.584	1.00
95_L	98_A	0.582	1.00
40_I	131_F	0.580	1.00
182_T	185_G	0.580	1.00
95_L	100_V	0.578	1.00
68_M	71_V	0.577	1.00
96_L	102_T	0.575	1.00
241_Y	245_W	0.575	1.00
68_M	149_T	0.572	1.00
20_F	116_R	0.569	1.00
94_E	97_V	0.567	1.00
158_L	161_G	0.565	1.00
213_G	230_F	0.564	1.00
208_V	215_R	0.559	1.00
195_P	198_W	0.557	1.00
68_M	210_M	0.555	1.00
126_A	143_A	0.555	1.00
172_L	175_T	0.554	1.00
65_G	215_R	0.554	1.00
67_I	70_S	0.554	1.00
90_R	93_E	0.553	1.00
192_T	199_Q	0.552	1.00
94_E	100_V	0.551	1.00
40_I	43_G	0.551	1.00
160_N	163_F	0.550	1.00
213_G	226_L	0.550	1.00
11_S	18_H	0.550	1.00
160_N	173_V	0.549	1.00
181_L	207_I	0.548	1.00
80_A	174_P	0.548	1.00
238_V	241_Y	0.544	1.00
41_I	183_Y	0.542	1.00
41_I	44_N	0.541	1.00
94_E	99_P	0.541	1.00
87_K	92_I	0.540	1.00
216_Y	222_N	0.539	1.00
156_A	159_L	0.539	1.00
184_L	198_W	0.538	1.00
143_A	146_L	0.535	1.00
38_Y	58_Y	0.534	1.00
31_P	116_R	0.533	1.00
158_L	162_V	0.532	1.00
203_H	212_S	0.532	1.00
119_F	122_I	0.531	1.00
194_L	198_W	0.529	1.00
145_T	226_L	0.527	1.00
198_W	201_L	0.527	1.00
141_F	213_G	0.527	1.00
216_Y	226_L	0.525	1.00
47_G	131_F	0.525	1.00
216_Y	229_T	0.524	1.00
217_G	220_G	0.523	1.00
206_P	210_M	0.523	1.00
15_K	34_T	0.523	1.00
125_T	143_A	0.521	1.00
135_Q	222_N	0.521	1.00
204_L	209_Y	0.520	1.00
83_F	86_A	0.519	1.00
175_T	178_L	0.519	1.00
59_M	68_M	0.518	1.00
159_L	163_F	0.518	1.00
12_I	100_V	0.517	1.00
161_G	181_L	0.517	1.00
159_L	162_V	0.516	1.00
183_Y	186_G	0.516	1.00
59_M	62_I	0.516	1.00
146_L	150_A	0.514	1.00
147_V	151_V	0.514	1.00
179_T	182_T	0.513	1.00
80_A	86_A	0.513	1.00
175_T	181_L	0.511	1.00
213_G	216_Y	0.511	1.00
68_M	76_Y	0.509	1.00
163_F	243_I	0.509	1.00
21_M	28_L	0.507	1.00
59_M	64_P	0.507	1.00
20_F	112_G	0.504	1.00
70_S	73_T	0.504	1.00
128_S	142_V	0.504	1.00
186_G	191_L	0.504	1.00
164_A	170_I	0.503	1.00
65_G	187_V	0.502	1.00
142_V	218_F	0.502	1.00
63_V	69_M	0.500	1.00

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
2jwaA	2	0.168	12.1	0.928	Contact Map
2l2tA	2	0.1641	11.8	0.929	Contact Map
2m20A	2	0.1367	10.1	0.931	Contact Map
2kv5A	1	0.1289	9.5	0.932	Contact Map
2a65A	2	0.3477	7.7	0.935	Contact Map
2kluA	1	0.1406	6.4	0.937	Contact Map
2ks1B	1	0.168	6.2	0.937	Contact Map
2rddB	1	0.125	5.9	0.938	Contact Map
4b19A	1	0.1172	3.9	0.943	Contact Map
2l6wA	2	0.1484	3.7	0.944	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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