YBHG - ECOLI - GREMLIN Contacts

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YBHG - UPF0194 membrane protein YbhG

UniProt:	P75777	Sequences: MMKKPVVIGLAVVVLAAVVAGGYWWYQSRQDNGLTLYGNVDIRTVNLSFRVGGRVESLAVDEGDAIKAGQVLGELDHKPYEIALMQAKAGVSVAQAQYDLMLAGYRNEEIAQAAAAVKQAQAAYDYAQNFYNRQQGLWKSRTISANDLENARSSRDQAQATLKSAQDKLRQYRSGNREQDIAQAKASLEQAQAQLAQAELNLQDSTLIAPSDGTLLTRAVEPGTVLNEGGTVFTVSLTRPVWVRAYVDERNLDQAQPGRKVLLYTDGRPDKPYHGQIGFVSPTAEFTPKTVETPDLRTDLVYRLRIVVTDADDALRQGMPVTVQFGDEAGHE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13315
Length:	332 (269)
Sequences:	23881 (18588)
Seq/√Len:	1133.3

ECOLI - YBHG YHII EMRA MDTN YIBH EMRK YIAV YDHJ MACA AAEA ACRE ACRA MDTE MDTA CUSB
BACSU - YKNX YVRP YHBJ

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_S	74_E	3.105	1.00
71_V	206_T	2.867	1.00
67_K	212_D	2.826	1.00
278_G	307_V	2.535	1.00
152_R	156_D	2.404	1.00
128_Q	132_N	2.343	1.00
74_E	206_T	2.321	1.00
134_Q	143_I	2.266	1.00
260_K	274_H	2.260	1.00
59_A	74_E	2.256	1.00
134_Q	151_A	2.211	1.00
88_K	199_E	2.192	1.00
67_K	70_Q	2.122	1.00
77_H	81_E	2.115	1.00
41_D	244_R	2.096	1.00
275_G	306_I	2.058	1.00
50_R	204_D	2.056	1.00
155_R	159_Q	2.032	1.00
95_Q	192_Q	2.032	1.00
135_Q	152_R	2.002	1.00
135_Q	139_K	1.985	1.00
59_A	71_V	1.912	1.00
65_A	214_T	1.910	1.00
68_A	212_D	1.904	1.00
71_V	208_I	1.877	1.00
128_Q	159_Q	1.865	1.00
262_L	274_H	1.857	1.00
242_W	305_R	1.852	1.00
138_W	145_A	1.828	1.00
128_Q	155_R	1.819	1.00
84_L	199_E	1.815	1.00
216_L	236_S	1.814	1.00
147_D	150_N	1.788	1.00
244_R	303_R	1.772	1.00
126_Y	130_F	1.758	1.00
145_A	149_E	1.750	1.00
138_W	148_L	1.747	1.00
131_Y	148_L	1.743	1.00
84_L	195_L	1.740	1.00
91_V	195_L	1.738	1.00
189_E	192_Q	1.724	1.00
262_L	272_P	1.691	1.00
131_Y	135_Q	1.691	1.00
276_Q	309_T	1.659	1.00
84_L	88_K	1.652	1.00
85_M	88_K	1.647	1.00
121_Q	166_Q	1.641	1.00
81_E	85_M	1.623	1.00
260_K	276_Q	1.577	1.00
245_A	323_V	1.569	1.00
276_Q	307_V	1.562	1.00
131_Y	155_R	1.556	1.00
261_V	306_I	1.540	1.00
91_V	95_Q	1.530	1.00
81_E	202_L	1.525	1.00
196_A	199_E	1.514	1.00
61_D	64_D	1.509	1.00
245_A	306_I	1.499	1.00
88_K	195_L	1.493	1.00
131_Y	152_R	1.478	1.00
284_A	302_Y	1.477	1.00
86_Q	194_Q	1.473	1.00
40_V	243_V	1.449	1.00
279_F	305_R	1.442	1.00
92_S	95_Q	1.441	1.00
130_F	150_N	1.433	1.00
148_L	152_R	1.433	1.00
124_Y	155_R	1.424	1.00
163_K	166_Q	1.423	1.00
125_D	129_N	1.417	1.00
243_V	321_V	1.416	1.00
156_D	159_Q	1.416	1.00
91_V	192_Q	1.403	1.00
197_Q	201_N	1.396	1.00
56_E	76_D	1.380	1.00
83_A	86_Q	1.377	1.00
83_A	197_Q	1.374	1.00
227_N	230_G	1.371	1.00
55_V	220_V	1.371	1.00
150_N	154_S	1.365	1.00
55_V	73_G	1.360	1.00
22_G	26_Y	1.360	1.00
21_G	25_W	1.359	1.00
53_G	75_L	1.354	1.00
121_Q	162_L	1.343	1.00
98_Y	188_L	1.325	1.00
162_L	166_Q	1.303	1.00
23_Y	27_Q	1.290	1.00
132_N	136_G	1.282	1.00
65_A	238_T	1.279	1.00
73_G	207_L	1.271	1.00
56_E	74_E	1.267	1.00
23_Y	26_Y	1.265	1.00
195_L	199_E	1.262	1.00
133_R	149_E	1.259	1.00
240_P	307_V	1.258	1.00
135_Q	148_L	1.247	1.00
262_L	326_G	1.245	1.00
154_S	157_Q	1.240	1.00
85_M	196_A	1.226	1.00
136_G	140_S	1.225	1.00
192_Q	196_A	1.225	1.00
146_N	150_N	1.217	1.00
127_A	158_A	1.216	1.00
83_A	201_N	1.212	1.00
200_L	204_D	1.210	1.00
124_Y	128_Q	1.210	1.00
71_V	74_E	1.203	1.00
159_Q	163_K	1.202	1.00
209_A	235_V	1.201	1.00
60_V	70_Q	1.200	1.00
80_Y	205_S	1.199	1.00
199_E	203_Q	1.198	1.00
271_K	314_A	1.173	1.00
215_L	233_F	1.170	1.00
57_S	222_P	1.168	1.00
90_G	190_Q	1.167	1.00
264_Y	324_Q	1.163	1.00
125_D	128_Q	1.162	1.00
132_N	135_Q	1.158	1.00
20_A	24_W	1.158	1.00
136_G	139_K	1.146	1.00
265_T	321_V	1.141	1.00
248_D	251_N	1.137	1.00
237_L	240_P	1.134	1.00
72_L	233_F	1.130	1.00
262_L	324_Q	1.126	1.00
84_L	202_L	1.126	1.00
213_G	235_V	1.123	1.00
244_R	305_R	1.120	1.00
246_Y	303_R	1.119	1.00
88_K	92_S	1.118	1.00
124_Y	159_Q	1.115	1.00
124_Y	162_L	1.093	1.00
43_R	237_L	1.088	1.00
44_T	234_T	1.085	1.00
90_G	93_V	1.084	1.00
121_Q	125_D	1.081	1.00
77_H	205_S	1.077	1.00
19_V	23_Y	1.075	1.00
130_F	146_N	1.072	1.00
125_D	156_D	1.070	1.00
91_V	188_L	1.069	1.00
87_A	191_A	1.058	1.00
86_Q	90_G	1.057	1.00
49_F	207_L	1.050	1.00
149_E	152_R	1.042	1.00
218_R	221_E	1.042	1.00
129_N	149_E	1.032	1.00
46_N	234_T	1.032	1.00
52_G	228_E	1.029	1.00
95_Q	188_L	1.023	1.00
94_A	191_A	1.020	1.00
35_T	324_Q	1.001	1.00
45_V	211_S	1.000	1.00
154_S	158_A	0.993	1.00
92_S	189_E	0.993	1.00
93_V	97_Q	0.992	1.00
50_R	54_R	0.983	1.00
94_A	97_Q	0.982	1.00
217_T	234_T	0.982	1.00
62_E	217_T	0.979	1.00
65_A	212_D	0.977	1.00
274_H	309_T	0.977	1.00
97_Q	187_S	0.972	1.00
89_A	193_A	0.963	1.00
152_R	155_R	0.962	1.00
263_L	308_V	0.957	1.00
264_Y	272_P	0.949	1.00
73_G	233_F	0.949	1.00
126_Y	153_S	0.947	1.00
134_Q	147_D	0.946	1.00
247_V	255_A	0.946	1.00
256_Q	259_R	0.944	1.00
40_V	241_V	0.943	1.00
46_N	231_T	0.941	1.00
157_Q	161_T	0.941	1.00
73_G	232_V	0.936	1.00
64_D	70_Q	0.932	1.00
226_L	232_V	0.930	1.00
281_S	303_R	0.929	1.00
243_V	263_L	0.927	1.00
58_L	222_P	0.927	1.00
126_Y	150_N	0.925	1.00
187_S	190_Q	0.919	1.00
130_F	134_Q	0.917	1.00
120_A	123_A	0.915	1.00
35_T	322_T	0.915	1.00
90_G	194_Q	0.914	1.00
82_I	200_L	0.910	1.00
60_V	233_F	0.910	1.00
33_G	324_Q	0.908	1.00
54_R	225_V	0.908	1.00
78_K	200_L	0.904	1.00
61_D	218_R	0.903	1.00
209_A	212_D	0.898	1.00
93_V	187_S	0.897	1.00
90_G	94_A	0.891	1.00
277_I	304_L	0.890	1.00
161_T	164_S	0.886	1.00
190_Q	194_Q	0.884	1.00
265_T	268_R	0.869	1.00
120_A	158_A	0.867	1.00
252_L	302_Y	0.858	1.00
268_R	273_Y	0.851	1.00
87_A	198_A	0.848	1.00
247_V	304_L	0.846	1.00
77_H	206_T	0.846	1.00
55_V	226_L	0.844	1.00
188_L	192_Q	0.834	1.00
151_A	154_S	0.826	1.00
50_R	79_P	0.823	1.00
40_V	315_L	0.817	1.00
277_I	306_I	0.817	1.00
58_L	73_G	0.816	1.00
141_R	145_A	0.814	1.00
218_R	233_F	0.813	1.00
123_A	157_Q	0.810	1.00
60_V	215_L	0.805	1.00
95_Q	98_Y	0.800	1.00
242_W	307_V	0.799	1.00
83_A	87_A	0.799	1.00
38_G	321_V	0.797	1.00
129_N	132_N	0.793	1.00
52_G	227_N	0.791	1.00
56_E	59_A	0.791	1.00
242_W	278_G	0.787	1.00
255_A	325_F	0.787	1.00
200_L	203_Q	0.786	1.00
191_A	194_Q	0.783	1.00
49_F	226_L	0.782	1.00
246_Y	301_V	0.781	1.00
74_E	77_H	0.779	1.00
87_A	90_G	0.779	1.00
82_I	193_A	0.776	1.00
66_I	72_L	0.774	1.00
56_E	77_H	0.771	1.00
73_G	218_R	0.769	1.00
263_L	275_G	0.766	1.00
310_D	313_D	0.762	1.00
68_A	210_P	0.761	1.00
255_A	277_I	0.760	1.00
264_Y	322_T	0.760	1.00
84_L	198_A	0.759	1.00
219_A	234_T	0.755	1.00
83_A	198_A	0.748	1.00
120_A	165_A	0.747	1.00
95_Q	99_D	0.745	1.00
143_I	147_D	0.743	1.00
203_Q	208_I	0.742	1.00
268_R	271_K	0.741	1.00
87_A	91_V	0.739	1.00
158_A	161_T	0.739	1.00
264_Y	270_D	0.738	1.00
211_S	235_V	0.732	1.00
194_Q	197_Q	0.731	1.00
153_S	157_Q	0.727	1.00
243_V	323_V	0.726	1.00
147_D	151_A	0.725	1.00
198_A	201_N	0.719	1.00
90_G	187_S	0.717	1.00
60_V	218_R	0.716	1.00
193_A	196_A	0.714	1.00
138_W	143_I	0.712	1.00
20_A	23_Y	0.711	1.00
21_G	26_Y	0.706	1.00
79_P	83_A	0.704	1.00
88_K	91_V	0.704	1.00
260_K	326_G	0.700	1.00
126_Y	129_N	0.699	1.00
49_F	73_G	0.692	1.00
158_A	162_L	0.690	1.00
134_Q	146_N	0.689	1.00
49_F	232_V	0.687	1.00
52_G	225_V	0.686	1.00
127_A	154_S	0.686	1.00
43_R	221_E	0.686	1.00
31_D	326_G	0.683	1.00
79_P	201_N	0.676	1.00
285_E	303_R	0.670	1.00
36_L	245_A	0.664	1.00
82_I	85_M	0.664	1.00
247_V	325_F	0.660	1.00
161_T	165_A	0.659	1.00
24_W	27_Q	0.659	1.00
87_A	195_L	0.659	1.00
12_V	16_A	0.658	1.00
187_S	191_A	0.657	1.00
214_T	238_T	0.654	1.00
54_R	76_D	0.653	1.00
80_Y	198_A	0.653	1.00
16_A	20_A	0.651	1.00
123_A	126_Y	0.648	1.00
135_Q	138_W	0.644	1.00
241_V	317_Q	0.643	1.00
47_L	210_P	0.643	1.00
81_E	84_L	0.642	1.00
79_P	200_L	0.640	1.00
257_P	280_V	0.638	1.00
316_R	319_M	0.637	1.00
22_G	25_W	0.635	1.00
47_L	233_F	0.633	1.00
278_G	305_R	0.628	1.00
51_V	80_Y	0.625	1.00
144_S	147_D	0.623	1.00
94_A	98_Y	0.622	1.00
77_H	202_L	0.620	1.00
123_A	154_S	0.618	1.00
191_A	195_L	0.617	1.00
46_N	224_T	0.614	1.00
263_L	321_V	0.614	1.00
86_Q	197_Q	0.612	1.00
286_F	300_L	0.609	1.00
145_A	148_L	0.606	1.00
60_V	64_D	0.605	1.00
9_G	13_V	0.605	1.00
42_I	240_P	0.603	1.00
80_Y	84_L	0.603	1.00
201_N	204_D	0.600	1.00
267_G	319_M	0.597	1.00
51_V	201_N	0.594	1.00
59_A	70_Q	0.594	1.00
126_Y	154_S	0.594	1.00
261_V	275_G	0.594	1.00
42_I	242_W	0.593	1.00
268_R	319_M	0.588	1.00
130_F	151_A	0.588	1.00
65_A	313_D	0.587	1.00
192_Q	195_L	0.587	1.00
196_A	200_L	0.584	1.00
9_G	12_V	0.584	1.00
145_A	152_R	0.584	1.00
90_G	191_A	0.583	1.00
285_E	299_D	0.578	1.00
62_E	218_R	0.577	1.00
236_S	317_Q	0.571	1.00
18_V	21_G	0.569	1.00
127_A	151_A	0.569	1.00
36_L	247_V	0.568	1.00
130_F	154_S	0.567	1.00
123_A	127_A	0.567	1.00
249_E	320_P	0.566	1.00
17_A	21_G	0.565	1.00
78_K	203_Q	0.561	1.00
21_G	24_W	0.557	1.00
159_Q	162_L	0.557	1.00
245_A	325_F	0.555	1.00
20_A	26_Y	0.554	1.00
245_A	304_L	0.553	1.00
127_A	130_F	0.548	1.00
138_W	141_R	0.544	1.00
219_A	231_T	0.543	1.00
257_P	278_G	0.542	1.00
160_A	163_K	0.541	1.00
49_F	52_G	0.540	1.00
82_I	197_Q	0.539	1.00
40_V	321_V	0.537	1.00
207_L	232_V	0.537	1.00
246_Y	287_T	0.534	1.00
284_A	300_L	0.534	1.00
32_N	254_Q	0.533	1.00
48_S	225_V	0.532	1.00
258_G	276_Q	0.531	1.00
153_S	160_A	0.531	1.00
120_A	162_L	0.530	1.00
263_L	306_I	0.529	1.00
302_Y	319_M	0.529	1.00
62_E	305_R	0.527	1.00
197_Q	200_L	0.526	1.00
143_I	148_L	0.526	1.00
142_T	146_N	0.524	1.00
58_L	218_R	0.523	1.00
251_N	254_Q	0.522	1.00
203_Q	206_T	0.522	1.00
44_T	236_S	0.519	1.00
306_I	323_V	0.517	1.00
93_V	161_T	0.517	1.00
123_A	161_T	0.517	1.00
212_D	239_R	0.516	1.00
56_E	222_P	0.514	1.00
51_V	204_D	0.514	1.00
80_Y	201_N	0.514	1.00
146_N	149_E	0.514	1.00
87_A	194_Q	0.513	1.00
39_N	300_L	0.513	1.00
133_R	146_N	0.512	1.00
243_V	308_V	0.512	1.00
186_A	189_E	0.510	1.00
85_M	193_A	0.510	1.00
132_N	155_R	0.509	1.00
231_T	234_T	0.507	1.00
269_P	273_Y	0.507	1.00
45_V	235_V	0.507	1.00
202_L	205_S	0.506	1.00
69_G	208_I	0.506	1.00
49_F	75_L	0.506	1.00
96_A	186_A	0.504	1.00
270_D	273_Y	0.503	1.00
36_L	323_V	0.503	1.00
263_L	323_V	0.502	1.00
89_A	92_S	0.501	1.00
82_I	86_Q	0.500	1.00
121_Q	124_Y	0.500	1.00
198_A	202_L	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
4tkoB	1	0.8584	100	0.28	Contact Map
4dk0A	5	0.8042	100	0.356	Contact Map
3fppA	3	0.7831	100	0.359	Contact Map
2f1mA	2	0.6988	100	0.38	Contact Map
3lnnA	6	0.7952	100	0.406	Contact Map
1vf7A	5	0.6777	100	0.432	Contact Map
4l8jA	2	0.7259	100	0.437	Contact Map
3ne5B	3	0.6566	100	0.449	Contact Map
4kkuA	1	0.5452	100	0.525	Contact Map
2k32A	1	0.3464	99.8	0.657	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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