YEHY - ECOLI - GREMLIN Contacts

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YEHY - Putative osmoprotectant uptake system permease protein YehY

UniProt:	P33361	Sequences: MTYFRINPVLALLLLLTAIAAALPFISYAPNRLVSGEGRHLWQLWPQTIWMLVGVGCAWLTACFIPGKKGSICALILAQFVFVLLVWGAGKAATQLAQNGSALARTSLGSGFWLAAALALLACSDAIRRISTHPLWRWLLHMQIAIIPLWLLYSGTLNDLSLMKEYANRQDVFDDALAQHLTLLFGAVLPALVIGVPLGIWCYFSTARQGAIFSLLNVIQTVPSVALFGLLIAPLAALVTAFPWLGTLGIAGTGMTPALIALVLYALLPLVRGVVVGLNQIPRDVLESARAMGMSGAQRFLHVQLPLALPVFLRSLRVVMVQTVGMAVIAALIGAGGFGALVFQGLLSSAIDLVLLGVIPVIVLAVLTDALFDLLIALLKVKRND	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12011
Length:	385 (306)
Sequences:	3171 (2511)
Seq/√Len:	143.5

ECOLI - YEHY PROW YHDY CYST POTH CYSW PSTC
BACSU - GANP MDXF OPUAB OPUCB OPUBB SSUC
HALSA - Q9HPK3 Q9HML6 Q9HMT4 Q9HP01 Q9HNI9 Q9HR05
SULSO - Q97UZ0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
290_R	299_R	4.202	1.00
295_S	298_Q	3.599	1.00
128_R	132_T	3.113	1.00
289_A	299_R	2.718	1.00
129_R	132_T	2.716	1.00
155_G	159_D	2.699	1.00
155_G	158_N	2.673	1.00
136_W	140_L	2.613	1.00
126_A	129_R	2.573	1.00
297_A	301_L	2.504	1.00
125_D	128_R	2.435	1.00
286_L	299_R	2.323	1.00
140_L	144_I	2.312	1.00
134_P	137_R	2.228	1.00
126_A	132_T	2.179	1.00
122_A	125_D	2.154	1.00
192_L	316_L	2.092	1.00
122_A	126_A	2.090	1.00
128_R	131_S	2.023	1.00
157_L	161_S	2.022	1.00
110_S	113_W	2.020	1.00
151_L	155_G	2.017	1.00
188_V	320_M	2.007	1.00
141_H	144_I	1.992	1.00
66_P	70_G	1.988	1.00
124_S	130_I	1.976	1.00
147_I	150_W	1.961	1.00
122_A	127_I	1.953	1.00
140_L	147_I	1.946	1.00
118_L	121_L	1.907	1.00
95_Q	98_Q	1.884	1.00
137_R	147_I	1.858	1.00
156_T	159_D	1.856	1.00
143_Q	147_I	1.844	1.00
144_I	147_I	1.842	1.00
126_A	130_I	1.825	1.00
90_G	95_Q	1.803	1.00
126_A	133_H	1.790	1.00
201_W	212_I	1.778	1.00
99_N	103_L	1.770	1.00
123_C	129_R	1.739	1.00
87_W	90_G	1.737	1.00
144_I	148_P	1.730	1.00
112_F	119_A	1.729	1.00
148_P	157_L	1.708	1.00
250_I	253_T	1.697	1.00
89_A	92_A	1.691	1.00
137_R	140_L	1.689	1.00
154_S	157_L	1.675	1.00
163_M	168_N	1.657	1.00
147_I	151_L	1.653	1.00
145_A	151_L	1.620	1.00
68_K	71_S	1.611	1.00
68_K	72_I	1.606	1.00
128_R	133_H	1.600	1.00
123_C	126_A	1.599	1.00
158_N	161_S	1.575	1.00
125_D	129_R	1.571	1.00
138_W	141_H	1.570	1.00
155_G	161_S	1.554	1.00
130_I	133_H	1.553	1.00
158_N	162_L	1.550	1.00
146_I	150_W	1.533	1.00
140_L	143_Q	1.513	1.00
190_P	263_V	1.511	1.00
129_R	133_H	1.503	1.00
143_Q	155_G	1.488	1.00
141_H	145_A	1.480	1.00
70_G	74_A	1.457	1.00
250_I	254_G	1.445	1.00
79_Q	82_F	1.429	1.00
137_R	148_P	1.424	1.00
152_L	156_T	1.420	1.00
88_G	92_A	1.409	1.00
159_D	162_L	1.398	1.00
136_W	141_H	1.397	1.00
298_Q	301_L	1.391	1.00
73_C	77_L	1.391	1.00
151_L	158_N	1.390	1.00
151_L	156_T	1.387	1.00
151_L	157_L	1.384	1.00
89_A	94_T	1.383	1.00
78_A	82_F	1.368	1.00
71_S	74_A	1.366	1.00
81_V	86_V	1.362	1.00
285_V	307_L	1.340	1.00
112_F	115_A	1.335	1.00
93_A	96_L	1.330	1.00
134_P	147_I	1.326	1.00
156_T	161_S	1.323	1.00
136_W	150_W	1.314	1.00
119_A	125_D	1.314	1.00
71_S	75_L	1.313	1.00
124_S	128_R	1.312	1.00
74_A	78_A	1.304	1.00
136_W	139_L	1.290	1.00
150_W	155_G	1.289	1.00
195_G	270_L	1.285	1.00
349_S	352_D	1.279	1.00
94_T	98_Q	1.279	1.00
67_G	70_G	1.275	1.00
140_L	150_W	1.274	1.00
103_L	106_T	1.273	1.00
91_K	98_Q	1.272	1.00
110_S	114_L	1.271	1.00
137_R	144_I	1.270	1.00
101_S	104_A	1.260	1.00
286_L	304_Q	1.251	1.00
324_V	364_L	1.249	1.00
126_A	131_S	1.248	1.00
151_L	154_S	1.241	1.00
125_D	131_S	1.233	1.00
75_L	79_Q	1.230	1.00
249_G	254_G	1.228	1.00
99_N	104_A	1.224	1.00
102_A	105_R	1.213	1.00
148_P	151_L	1.212	1.00
125_D	130_I	1.210	1.00
95_Q	99_N	1.207	1.00
127_I	132_T	1.205	1.00
75_L	78_A	1.205	1.00
84_L	88_G	1.199	1.00
144_I	150_W	1.198	1.00
196_V	274_V	1.192	1.00
100_G	105_R	1.189	1.00
141_H	152_L	1.182	1.00
150_W	153_Y	1.180	1.00
93_A	98_Q	1.179	1.00
72_I	76_I	1.179	1.00
134_P	144_I	1.178	1.00
145_A	148_P	1.172	1.00
72_I	82_F	1.171	1.00
138_W	143_Q	1.167	1.00
137_R	151_L	1.165	1.00
155_G	160_L	1.163	1.00
134_P	141_H	1.163	1.00
146_I	149_L	1.157	1.00
273_G	315_S	1.152	0.99
374_L	377_A	1.148	0.99
72_I	75_L	1.135	0.99
179_Q	335_A	1.135	0.99
127_I	130_I	1.128	0.99
97_A	108_L	1.110	0.99
97_A	100_G	1.099	0.99
135_L	140_L	1.088	0.99
152_L	155_G	1.085	0.99
125_D	132_T	1.083	0.99
115_A	118_L	1.078	0.99
337_G	348_S	1.073	0.99
341_L	345_G	1.072	0.99
66_P	69_K	1.070	0.99
135_L	139_L	1.064	0.99
102_A	106_T	1.063	0.99
195_G	274_V	1.056	0.99
227_L	261_A	1.051	0.99
134_P	145_A	1.049	0.99
125_D	133_H	1.047	0.99
122_A	131_S	1.042	0.99
95_Q	100_G	1.042	0.99
83_V	86_V	1.038	0.99
138_W	145_A	1.034	0.99
71_S	79_Q	1.025	0.99
122_A	129_R	1.021	0.99
134_P	138_W	1.016	0.99
143_Q	150_W	1.012	0.99
109_G	113_W	1.011	0.99
339_G	343_F	1.007	0.99
109_G	119_A	1.006	0.99
148_P	156_T	1.003	0.99
82_F	86_V	0.999	0.99
73_C	82_F	0.998	0.99
141_H	147_I	0.996	0.99
181_L	185_F	0.994	0.98
121_L	125_D	0.990	0.98
156_T	160_L	0.989	0.98
139_L	143_Q	0.988	0.98
67_G	71_S	0.986	0.98
124_S	131_S	0.981	0.98
233_A	342_V	0.979	0.98
337_G	340_A	0.975	0.98
251_A	254_G	0.973	0.98
127_I	133_H	0.969	0.98
134_P	140_L	0.966	0.98
183_L	262_L	0.962	0.98
67_G	72_I	0.957	0.98
141_H	150_W	0.956	0.98
95_Q	102_A	0.955	0.98
117_A	120_L	0.949	0.98
115_A	119_A	0.948	0.98
143_Q	152_L	0.928	0.98
69_K	74_A	0.922	0.98
116_A	120_L	0.918	0.97
155_G	162_L	0.918	0.97
150_W	154_S	0.915	0.97
139_L	142_M	0.905	0.97
144_I	151_L	0.900	0.97
239_V	242_F	0.897	0.97
79_Q	84_L	0.893	0.97
79_Q	83_V	0.892	0.97
122_A	128_R	0.888	0.97
143_Q	146_I	0.885	0.97
186_G	259_L	0.885	0.97
91_K	97_A	0.877	0.97
186_G	190_P	0.875	0.97
337_G	343_F	0.875	0.97
152_L	159_D	0.874	0.97
136_W	146_I	0.867	0.96
290_R	296_G	0.866	0.96
148_P	155_G	0.862	0.96
69_K	72_I	0.858	0.96
127_I	131_S	0.857	0.96
123_C	132_T	0.857	0.96
138_W	144_I	0.854	0.96
99_N	106_T	0.854	0.96
134_P	156_T	0.850	0.96
110_S	128_R	0.847	0.96
66_P	73_C	0.843	0.96
136_W	151_L	0.840	0.96
178_A	182_T	0.837	0.96
66_P	74_A	0.835	0.96
157_L	160_L	0.832	0.95
142_M	145_A	0.831	0.95
345_G	348_S	0.829	0.95
370_A	373_D	0.829	0.95
315_S	319_V	0.827	0.95
93_A	97_A	0.825	0.95
258_A	333_I	0.825	0.95
143_Q	149_L	0.825	0.95
90_G	94_T	0.822	0.95
154_S	159_D	0.822	0.95
110_S	119_A	0.821	0.95
74_A	77_L	0.821	0.95
275_V	279_N	0.821	0.95
123_C	128_R	0.817	0.95
340_A	343_F	0.816	0.95
122_A	133_H	0.813	0.95
143_Q	151_L	0.812	0.95
184_L	320_M	0.811	0.95
134_P	150_W	0.810	0.95
325_G	328_V	0.809	0.95
89_A	93_A	0.808	0.95
217_N	272_R	0.807	0.95
289_A	294_M	0.804	0.95
99_N	108_L	0.803	0.95
238_L	241_A	0.803	0.95
79_Q	89_A	0.792	0.94
110_S	116_A	0.788	0.94
249_G	253_T	0.786	0.94
100_G	106_T	0.783	0.94
121_L	129_R	0.782	0.94
137_R	141_H	0.776	0.93
138_W	150_W	0.772	0.93
123_C	127_I	0.770	0.93
65_I	68_K	0.769	0.93
274_V	278_L	0.769	0.93
63_C	66_P	0.768	0.93
256_T	260_I	0.767	0.93
134_P	139_L	0.766	0.93
148_P	152_L	0.766	0.93
103_L	107_S	0.765	0.93
67_G	74_A	0.764	0.93
91_K	96_L	0.762	0.93
121_L	124_S	0.762	0.93
135_L	138_W	0.762	0.93
65_I	70_G	0.759	0.93
135_L	150_W	0.758	0.93
146_I	153_Y	0.754	0.92
75_L	80_F	0.754	0.92
72_I	79_Q	0.752	0.92
67_G	75_L	0.748	0.92
151_L	159_D	0.745	0.92
100_G	104_A	0.744	0.92
112_F	121_L	0.743	0.92
94_T	99_N	0.741	0.92
154_S	158_N	0.740	0.92
113_W	119_A	0.740	0.92
118_L	132_T	0.739	0.92
198_L	216_L	0.737	0.92
188_V	323_T	0.735	0.92
87_W	95_Q	0.734	0.91
72_I	86_V	0.733	0.91
193_V	197_P	0.732	0.91
140_L	145_A	0.728	0.91
105_R	108_L	0.728	0.91
144_I	156_T	0.722	0.91
78_A	89_A	0.722	0.91
113_W	120_L	0.721	0.91
153_Y	159_D	0.720	0.91
123_C	133_H	0.717	0.90
143_Q	154_S	0.716	0.90
93_A	101_S	0.713	0.90
124_S	132_T	0.709	0.90
272_R	369_D	0.709	0.90
154_S	162_L	0.708	0.90
85_L	89_A	0.707	0.90
83_V	87_W	0.705	0.90
228_F	322_Q	0.704	0.90
98_Q	102_A	0.703	0.90
70_G	73_C	0.699	0.89
112_F	118_L	0.698	0.89
66_P	79_Q	0.698	0.89
66_P	71_S	0.695	0.89
208_R	211_A	0.694	0.89
75_L	92_A	0.694	0.89
143_Q	148_P	0.693	0.89
124_S	129_R	0.693	0.89
109_G	118_L	0.692	0.89
343_F	346_L	0.691	0.89
313_L	375_L	0.690	0.89
196_V	305_L	0.689	0.89
88_G	91_K	0.688	0.89
70_G	77_L	0.686	0.88
110_S	121_L	0.685	0.88
203_Y	279_N	0.685	0.88
80_F	84_L	0.684	0.88
219_I	227_L	0.684	0.88
115_A	121_L	0.680	0.88
141_H	151_L	0.679	0.88
367_L	371_L	0.678	0.88
70_G	75_L	0.677	0.88
111_G	114_L	0.674	0.88
87_W	98_Q	0.674	0.88
136_W	143_Q	0.671	0.87
100_G	107_S	0.668	0.87
286_L	290_R	0.667	0.87
87_W	91_K	0.664	0.87
145_A	150_W	0.663	0.87
77_L	81_V	0.661	0.87
192_L	320_M	0.659	0.86
109_G	112_F	0.659	0.86
137_R	150_W	0.658	0.86
283_R	290_R	0.657	0.86
315_S	353_L	0.656	0.86
342_V	357_G	0.656	0.86
338_F	357_G	0.655	0.86
104_A	107_S	0.655	0.86
140_L	151_L	0.653	0.86
123_C	131_S	0.652	0.86
89_A	96_L	0.651	0.86
281_I	308_A	0.650	0.86
101_S	106_T	0.649	0.86
273_G	318_V	0.642	0.85
96_L	99_N	0.642	0.85
140_L	153_Y	0.641	0.85
69_K	86_V	0.638	0.85
64_F	70_G	0.636	0.84
96_L	100_G	0.636	0.84
321_V	329_I	0.634	0.84
141_H	149_L	0.633	0.84
82_F	91_K	0.633	0.84
144_I	152_L	0.631	0.84
124_S	133_H	0.629	0.84
71_S	78_A	0.627	0.84
75_L	103_L	0.627	0.84
317_R	320_M	0.626	0.83
199_G	203_Y	0.626	0.83
124_S	127_I	0.623	0.83
63_C	68_K	0.622	0.83
63_C	67_G	0.621	0.83
281_I	286_L	0.619	0.83
344_Q	348_S	0.619	0.83
77_L	94_T	0.617	0.83
135_L	144_I	0.615	0.82
66_P	72_I	0.615	0.82
119_A	122_A	0.614	0.82
259_L	263_V	0.610	0.82
257_P	356_L	0.610	0.82
111_G	119_A	0.608	0.82
149_L	153_Y	0.607	0.82
113_W	128_R	0.602	0.81
63_C	74_A	0.600	0.81
289_A	303_V	0.598	0.81
119_A	123_C	0.598	0.81
144_I	159_D	0.597	0.81
92_A	95_Q	0.594	0.80
154_S	161_S	0.593	0.80
137_R	156_T	0.590	0.80
116_A	127_I	0.590	0.80
94_T	103_L	0.589	0.80
77_L	87_W	0.588	0.80
81_V	84_L	0.586	0.79
110_S	117_A	0.584	0.79
237_A	241_A	0.581	0.79
203_Y	278_L	0.579	0.78
81_V	91_K	0.579	0.78
296_G	299_R	0.578	0.78
97_A	102_A	0.578	0.78
104_A	108_L	0.578	0.78
76_I	79_Q	0.578	0.78
72_I	91_K	0.577	0.78
267_L	271_V	0.575	0.78
134_P	143_Q	0.573	0.78
68_K	75_L	0.570	0.77
123_C	130_I	0.567	0.77
111_G	127_I	0.566	0.77
85_L	96_L	0.564	0.77
134_P	152_L	0.562	0.76
220_Q	269_P	0.562	0.76
94_T	100_G	0.560	0.76
257_P	277_G	0.560	0.76
97_A	112_F	0.559	0.76
101_S	105_R	0.558	0.76
314_R	318_V	0.557	0.76
140_L	148_P	0.556	0.76
134_P	158_N	0.554	0.75
341_L	344_Q	0.554	0.75
322_Q	326_M	0.553	0.75
93_A	104_A	0.552	0.75
118_L	122_A	0.549	0.75
147_I	159_D	0.549	0.75
111_G	128_R	0.548	0.75
268_L	354_V	0.547	0.75
113_W	124_S	0.545	0.74
114_L	121_L	0.544	0.74
171_D	174_D	0.543	0.74
121_L	126_A	0.542	0.74
63_C	69_K	0.542	0.74
120_L	127_I	0.540	0.74
70_G	79_Q	0.540	0.74
120_L	128_R	0.539	0.73
151_L	162_L	0.537	0.73
191_A	270_L	0.533	0.73
69_K	82_F	0.531	0.72
68_K	79_Q	0.530	0.72
78_A	86_V	0.530	0.72
98_Q	104_A	0.530	0.72
86_V	93_A	0.527	0.72
79_Q	86_V	0.527	0.72
78_A	90_G	0.527	0.72
68_K	73_C	0.525	0.71
72_I	83_V	0.525	0.71
75_L	82_F	0.523	0.71
134_P	151_L	0.523	0.71
143_Q	157_L	0.523	0.71
209_Q	279_N	0.521	0.71
199_G	330_A	0.521	0.71
86_V	90_G	0.520	0.71
95_Q	106_T	0.518	0.70
98_Q	103_L	0.517	0.70
281_I	304_Q	0.517	0.70
70_G	76_I	0.517	0.70
119_A	128_R	0.514	0.70
145_A	153_Y	0.513	0.70
249_G	252_G	0.511	0.69
324_V	369_D	0.511	0.69
98_Q	105_R	0.509	0.69
109_G	117_A	0.508	0.69
115_A	132_T	0.507	0.69
359_I	363_V	0.506	0.69
270_L	319_V	0.506	0.69
75_L	96_L	0.504	0.68
90_G	93_A	0.504	0.68
321_V	365_A	0.503	0.68
75_L	86_V	0.503	0.68
145_A	157_L	0.501	0.68
91_K	95_Q	0.501	0.68
228_F	265_Y	0.500	0.68
204_F	296_G	0.500	0.68
150_W	157_L	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
2onkC	2	0.626	100	0.492	Contact Map
4tquM	1	0.6519	100	0.5	Contact Map
3d31C	2	0.613	100	0.5	Contact Map
3rlfG	1	0.6416	100	0.555	Contact Map
4ymuD	2	0.5506	100	0.556	Contact Map
3tuiA	2	0.5377	100	0.559	Contact Map
3rlfF	1	0.8312	100	0.586	Contact Map
4tquN	1	0.6208	100	0.592	Contact Map
4mrsA	2	0.2442	11	0.959	Contact Map
4ev6A	3	0.1714	7.9	0.962	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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