YHHT - ECOLI - GREMLIN Contacts

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YHHT - UPF0118 inner membrane protein YhhT

UniProt:	P0AGM0	Sequences: METPQPDKTGMHILLKLASLVVILAGIHAAADIIVQLLLALFFAIVLNPLVTWFIRRGVQRPVAITIVVVVMLIALTALVGVLAASFNEFISMLPKFNKELTRKLFKLQEMLPFLNLHMSPERMLQRMDSEKVVTFTTALMTGLSGAMASVLLLVMTVVFMLFEVRHVPYKMRFALNNPQIHIAGLHRALKGVSHYLALKTLLSLWTGVIVWLGLELMGVQFALMWAVLAFLLNYVPNIGAVISAVPPMIQVLLFNGVYECILVGALFLVVHMVIGNILEPRMMGHRLGMSTMVVFLSLLIWGWLLGPVGMLLSVPLTSVCKIWMETTKGGSKLAILLGPGRPKSRLPG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12220
Length:	349 (316)
Sequences:	11019 (8605)
Seq/√Len:	484.0

ECOLI - YHHT TQSA YDIK PERM
BACSU - YUBA YUEF YTVI YDBI YRRI
HALSA - Q9HPX5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
212_W	227_A	5.162	1.00
214_G	267_L	4.972	1.00
53_W	57_R	4.537	1.00
85_A	90_F	3.128	1.00
298_S	318_T	3.071	1.00
45_I	190_L	3.071	1.00
86_S	90_F	2.954	1.00
55_I	61_R	2.681	1.00
208_G	231_F	2.665	1.00
60_Q	63_V	2.484	1.00
259_Y	263_L	2.435	1.00
212_W	216_E	2.391	1.00
262_I	266_A	2.357	1.00
53_W	56_R	2.328	1.00
90_F	95_P	2.242	1.00
43_F	158_V	2.235	1.00
249_M	265_G	2.232	1.00
322_K	326_E	2.217	1.00
208_G	227_A	2.193	1.00
93_M	96_K	2.171	1.00
120_S	123_R	2.115	1.00
59_V	67_I	2.102	1.00
215_L	220_V	1.974	1.00
159_V	163_F	1.944	1.00
40_A	158_V	1.889	1.00
199_L	283_M	1.882	1.00
201_T	235_Y	1.871	1.00
249_M	261_C	1.858	1.00
21_V	25_A	1.837	1.00
121_P	124_M	1.794	1.00
95_P	99_K	1.784	1.00
263_L	266_A	1.780	1.00
188_R	327_T	1.778	1.00
266_A	270_V	1.765	1.00
62_P	66_T	1.763	1.00
211_V	230_A	1.759	1.00
154_L	158_V	1.729	1.00
211_V	271_V	1.726	1.00
184_A	327_T	1.720	1.00
164_E	291_S	1.687	1.00
51_V	68_V	1.670	1.00
189_A	320_V	1.656	1.00
213_L	216_E	1.650	1.00
65_I	69_V	1.638	1.00
157_T	293_M	1.631	1.00
28_H	31_A	1.621	1.00
48_N	52_T	1.617	1.00
207_T	234_N	1.604	1.00
117_L	120_S	1.601	1.00
75_A	79_L	1.601	1.00
118_H	122_E	1.589	1.00
229_L	233_L	1.580	1.00
125_L	128_M	1.573	1.00
282_R	286_H	1.573	1.00
37_L	297_L	1.571	1.00
111_M	114_F	1.566	1.00
119_M	122_E	1.565	1.00
123_R	126_Q	1.547	1.00
212_W	223_A	1.527	1.00
303_G	311_M	1.525	1.00
157_T	161_M	1.522	1.00
223_A	227_A	1.498	1.00
65_I	159_V	1.498	1.00
260_E	263_L	1.493	1.00
119_M	123_R	1.490	1.00
203_L	275_I	1.486	1.00
210_I	271_V	1.480	1.00
20_L	24_L	1.464	1.00
216_E	223_A	1.449	1.00
50_L	68_V	1.431	1.00
77_T	81_G	1.421	1.00
48_N	61_R	1.420	1.00
221_Q	255_F	1.407	1.00
99_K	102_T	1.382	1.00
54_F	71_V	1.375	1.00
88_N	92_S	1.369	1.00
233_L	244_S	1.355	1.00
126_Q	129_D	1.348	1.00
51_V	65_I	1.347	1.00
269_L	273_M	1.346	1.00
113_P	116_N	1.332	1.00
100_E	103_R	1.327	1.00
87_F	90_F	1.323	1.00
173_R	183_I	1.312	1.00
47_L	162_L	1.308	1.00
170_Y	174_F	1.308	1.00
62_P	163_F	1.300	1.00
248_P	264_V	1.297	1.00
226_W	248_P	1.294	1.00
122_E	126_Q	1.291	1.00
245_A	249_M	1.290	1.00
121_P	125_L	1.289	1.00
294_V	318_T	1.281	1.00
51_V	61_R	1.262	1.00
274_V	279_L	1.252	1.00
73_L	77_T	1.247	1.00
44_A	161_M	1.247	1.00
207_T	271_V	1.245	1.00
192_G	319_S	1.243	1.00
259_Y	262_I	1.239	1.00
279_L	283_M	1.235	1.00
99_K	103_R	1.232	1.00
299_L	311_M	1.232	1.00
111_M	115_L	1.231	1.00
272_H	276_G	1.231	1.00
252_V	264_V	1.227	1.00
104_K	107_K	1.221	1.00
302_W	318_T	1.220	1.00
256_N	260_E	1.217	1.00
122_E	125_L	1.216	1.00
13_I	17_L	1.209	1.00
17_L	21_V	1.206	1.00
258_V	261_C	1.202	1.00
265_G	269_L	1.192	1.00
107_K	111_M	1.191	1.00
104_K	108_L	1.186	1.00
96_K	99_K	1.180	1.00
302_W	306_L	1.180	1.00
100_E	104_K	1.179	1.00
51_V	162_L	1.170	1.00
97_F	101_L	1.170	1.00
14_L	18_A	1.168	1.00
96_K	100_E	1.164	1.00
214_G	263_L	1.154	1.00
48_N	165_V	1.146	1.00
106_F	109_Q	1.144	1.00
204_S	234_N	1.143	1.00
203_L	207_T	1.142	1.00
59_V	63_V	1.140	1.00
252_V	261_C	1.138	1.00
40_A	154_L	1.137	1.00
298_S	302_W	1.132	1.00
214_G	218_M	1.130	1.00
109_Q	113_P	1.126	1.00
227_A	231_F	1.126	1.00
36_Q	40_A	1.125	1.00
276_G	280_E	1.123	1.00
215_L	230_A	1.123	1.00
107_K	110_E	1.119	1.00
188_R	326_E	1.116	1.00
43_F	154_L	1.115	1.00
123_R	127_R	1.106	1.00
65_I	79_L	1.094	1.00
51_V	64_A	1.082	1.00
24_L	28_H	1.080	1.00
213_L	217_L	1.078	1.00
185_G	324_W	1.071	1.00
203_L	279_L	1.070	1.00
201_T	205_L	1.070	1.00
85_A	89_E	1.066	1.00
61_R	166_R	1.062	1.00
90_F	94_L	1.062	1.00
50_L	53_W	1.060	1.00
294_V	322_K	1.059	1.00
120_S	124_M	1.054	1.00
220_V	252_V	1.043	1.00
118_H	125_L	1.040	1.00
218_M	267_L	1.039	1.00
178_N	181_I	1.036	1.00
120_S	125_L	1.032	1.00
40_A	44_A	1.029	1.00
93_M	97_F	1.029	1.00
261_C	265_G	1.024	1.00
25_A	29_A	1.018	1.00
55_I	64_A	1.013	1.00
207_T	211_V	1.010	1.00
198_A	202_L	1.009	1.00
195_H	199_L	1.008	1.00
200_K	280_E	1.006	1.00
153_L	157_T	1.003	1.00
164_E	167_H	1.002	1.00
171_K	174_F	0.999	1.00
69_V	158_V	0.997	1.00
157_T	297_L	0.994	1.00
208_G	212_W	0.994	1.00
110_E	113_P	0.991	1.00
231_F	235_Y	0.989	1.00
39_L	154_L	0.989	1.00
37_L	157_T	0.989	1.00
47_L	72_M	0.989	1.00
215_L	264_V	0.989	1.00
89_E	93_M	0.988	1.00
167_H	170_Y	0.987	1.00
59_V	64_A	0.985	1.00
275_I	280_E	0.983	1.00
51_V	55_I	0.982	1.00
19_S	23_I	0.981	1.00
203_L	234_N	0.979	1.00
127_R	130_S	0.975	1.00
41_L	161_M	0.969	1.00
17_L	20_L	0.966	1.00
207_T	241_A	0.961	1.00
278_I	282_R	0.961	1.00
137_T	141_M	0.961	1.00
258_V	262_I	0.958	1.00
203_L	280_E	0.955	1.00
214_G	271_V	0.954	1.00
309_V	313_L	0.953	1.00
253_L	261_C	0.952	1.00
218_M	260_E	0.952	1.00
298_S	314_S	0.951	1.00
64_A	68_V	0.951	1.00
126_Q	130_S	0.946	1.00
177_N	181_I	0.943	1.00
124_M	128_M	0.943	1.00
267_L	271_V	0.942	1.00
106_F	110_E	0.940	1.00
147_A	151_V	0.937	1.00
102_T	106_F	0.935	1.00
263_L	267_L	0.930	1.00
66_T	70_V	0.930	1.00
205_L	231_F	0.928	1.00
212_W	224_L	0.926	1.00
243_I	247_P	0.923	1.00
110_E	114_F	0.921	1.00
84_A	87_F	0.917	1.00
222_F	225_M	0.913	1.00
125_L	129_D	0.910	1.00
229_L	244_S	0.903	1.00
85_A	95_P	0.901	1.00
270_V	274_V	0.901	1.00
321_C	325_M	0.899	1.00
165_V	169_P	0.898	1.00
105_L	109_Q	0.898	1.00
211_V	215_L	0.890	1.00
112_L	115_L	0.887	1.00
234_N	241_A	0.882	1.00
53_W	58_G	0.880	1.00
290_M	318_T	0.877	1.00
227_A	230_A	0.874	1.00
167_H	171_K	0.872	1.00
18_A	22_V	0.871	1.00
21_V	24_L	0.870	1.00
206_W	210_I	0.864	1.00
63_V	66_T	0.861	1.00
140_L	144_L	0.860	1.00
52_T	55_I	0.858	1.00
176_L	180_Q	0.856	1.00
94_L	97_F	0.854	1.00
324_W	328_T	0.852	1.00
184_A	188_R	0.850	1.00
234_N	280_E	0.850	1.00
209_V	212_W	0.850	1.00
33_I	301_I	0.849	1.00
40_A	157_T	0.845	1.00
124_M	127_R	0.844	1.00
202_L	206_W	0.842	1.00
203_L	284_M	0.839	1.00
215_L	226_W	0.839	1.00
89_E	92_S	0.834	1.00
273_M	277_N	0.833	1.00
141_M	145_S	0.824	1.00
195_H	287_R	0.820	1.00
250_I	254_L	0.820	1.00
218_M	263_L	0.820	1.00
209_V	213_L	0.819	1.00
101_L	104_K	0.817	1.00
314_S	318_T	0.815	1.00
245_A	268_F	0.807	1.00
173_R	181_I	0.807	1.00
272_H	275_I	0.806	1.00
253_L	258_V	0.804	1.00
216_E	219_G	0.798	1.00
29_A	32_D	0.798	1.00
118_H	121_P	0.794	1.00
92_S	95_P	0.791	1.00
44_A	158_V	0.791	1.00
251_Q	255_F	0.790	1.00
23_I	26_G	0.790	1.00
121_P	128_M	0.788	1.00
171_K	175_A	0.788	1.00
112_L	116_N	0.784	1.00
230_A	234_N	0.784	1.00
15_L	19_S	0.783	1.00
288_L	315_V	0.773	1.00
117_L	122_E	0.772	1.00
86_S	89_E	0.771	1.00
218_M	264_V	0.770	1.00
109_Q	116_N	0.766	1.00
62_P	159_V	0.760	1.00
60_Q	64_A	0.756	1.00
52_T	56_R	0.753	1.00
119_M	124_M	0.750	1.00
177_N	180_Q	0.747	1.00
16_K	20_L	0.747	1.00
207_T	280_E	0.746	1.00
120_S	129_D	0.746	1.00
297_L	301_I	0.740	1.00
226_W	251_Q	0.740	1.00
285_G	295_V	0.740	1.00
36_Q	285_G	0.739	1.00
158_V	162_L	0.737	1.00
83_L	86_S	0.734	1.00
111_M	116_N	0.734	1.00
204_S	235_Y	0.732	1.00
284_M	295_V	0.732	1.00
216_E	227_A	0.731	1.00
52_T	166_R	0.729	1.00
176_L	181_I	0.728	1.00
191_K	195_H	0.725	1.00
90_F	97_F	0.724	1.00
75_A	78_A	0.723	1.00
54_F	68_V	0.720	1.00
280_E	284_M	0.718	1.00
103_R	107_K	0.717	1.00
117_L	121_P	0.716	1.00
249_M	253_L	0.716	1.00
87_F	91_I	0.713	1.00
14_L	17_L	0.712	1.00
204_S	207_T	0.708	1.00
274_V	278_I	0.698	1.00
204_S	208_G	0.696	1.00
206_W	279_L	0.696	1.00
280_E	283_M	0.695	1.00
203_L	283_M	0.692	1.00
26_G	30_A	0.689	1.00
60_Q	65_I	0.688	1.00
205_L	209_V	0.687	1.00
91_I	95_P	0.680	1.00
61_R	65_I	0.675	1.00
185_G	327_T	0.674	1.00
108_L	111_M	0.673	1.00
230_A	244_S	0.669	1.00
169_P	173_R	0.668	1.00
84_A	88_N	0.667	1.00
88_N	91_I	0.664	1.00
173_R	176_L	0.662	1.00
189_A	323_I	0.660	1.00
241_A	244_S	0.659	1.00
36_Q	150_S	0.657	1.00
188_R	192_G	0.656	1.00
188_R	323_I	0.654	1.00
299_L	315_V	0.648	1.00
101_L	105_L	0.645	1.00
234_N	275_I	0.645	1.00
48_N	162_L	0.644	1.00
318_T	322_K	0.642	1.00
98_N	102_T	0.641	1.00
183_I	187_H	0.640	1.00
189_A	193_V	0.639	1.00
234_N	272_H	0.639	1.00
241_A	272_H	0.638	1.00
146_G	150_S	0.636	1.00
202_L	283_M	0.635	1.00
108_L	112_L	0.634	1.00
207_T	275_I	0.633	1.00
74_I	77_T	0.629	1.00
200_K	204_S	0.629	1.00
90_F	101_L	0.625	1.00
302_W	317_L	0.624	1.00
133_V	137_T	0.624	1.00
134_V	137_T	0.624	1.00
194_S	198_A	0.624	1.00
231_F	234_N	0.621	1.00
133_V	136_F	0.620	0.99
98_N	101_L	0.620	0.99
211_V	267_L	0.619	0.99
71_V	74_I	0.618	0.99
244_S	248_P	0.617	0.99
208_G	224_L	0.616	0.99
204_S	231_F	0.614	0.99
59_V	68_V	0.613	0.99
175_A	325_M	0.612	0.99
109_Q	112_L	0.608	0.99
39_L	43_F	0.606	0.99
292_T	296_F	0.605	0.99
234_N	276_G	0.605	0.99
203_L	241_A	0.604	0.99
125_L	130_S	0.604	0.99
143_G	146_G	0.602	0.99
200_K	203_L	0.601	0.99
13_I	16_K	0.600	0.99
244_S	275_I	0.599	0.99
198_A	287_R	0.599	0.99
200_K	234_N	0.599	0.99
97_F	104_K	0.597	0.99
141_M	144_L	0.596	0.99
131_E	135_T	0.593	0.99
170_Y	183_I	0.592	0.99
121_P	127_R	0.591	0.99
193_V	196_Y	0.590	0.99
143_G	147_A	0.586	0.99
192_G	195_H	0.585	0.99
238_N	292_T	0.582	0.99
196_Y	316_P	0.582	0.99
54_F	59_V	0.582	0.99
62_P	65_I	0.581	0.99
87_F	95_P	0.580	0.99
47_L	158_V	0.579	0.99
208_G	228_V	0.579	0.99
308_P	311_M	0.578	0.99
44_A	48_N	0.577	0.99
171_K	294_V	0.576	0.99
230_A	268_F	0.574	0.99
132_K	135_T	0.574	0.99
255_F	260_E	0.570	0.99
160_F	164_E	0.570	0.99
41_L	165_V	0.568	0.99
230_A	241_A	0.567	0.99
117_L	124_M	0.567	0.99
161_M	293_M	0.567	0.99
120_S	127_R	0.566	0.99
211_V	231_F	0.565	0.99
295_V	315_V	0.564	0.99
94_L	98_N	0.564	0.99
47_L	68_V	0.562	0.99
244_S	316_P	0.562	0.99
64_A	75_A	0.561	0.99
76_L	80_V	0.560	0.99
91_I	94_L	0.559	0.99
207_T	272_H	0.559	0.99
136_F	140_L	0.558	0.99
153_L	300_L	0.555	0.99
77_T	80_V	0.554	0.99
291_S	322_K	0.553	0.99
185_G	189_A	0.551	0.99
37_L	161_M	0.550	0.99
47_L	50_L	0.550	0.99
103_R	106_F	0.550	0.99
244_S	272_H	0.549	0.99
200_K	235_Y	0.549	0.99
78_A	82_V	0.549	0.99
157_T	296_F	0.547	0.99
15_L	18_A	0.541	0.99
229_L	247_P	0.540	0.99
60_Q	79_L	0.540	0.99
121_P	129_D	0.540	0.99
168_V	171_K	0.539	0.99
170_Y	173_R	0.538	0.99
169_P	187_H	0.537	0.99
195_H	198_A	0.536	0.99
285_G	289_G	0.536	0.99
306_L	310_G	0.536	0.99
202_L	205_L	0.534	0.98
199_L	319_S	0.533	0.98
54_F	67_I	0.532	0.98
290_M	295_V	0.531	0.98
192_G	323_I	0.531	0.98
200_K	284_M	0.531	0.98
207_T	210_I	0.529	0.98
95_P	101_L	0.528	0.98
255_F	258_V	0.527	0.98
276_G	300_L	0.525	0.98
120_S	130_S	0.525	0.98
272_H	303_G	0.524	0.98
302_W	314_S	0.523	0.98
55_I	60_Q	0.522	0.98
28_H	32_D	0.521	0.98
233_L	247_P	0.518	0.98
277_N	300_L	0.518	0.98
200_K	275_I	0.518	0.98
172_M	175_A	0.518	0.98
279_L	282_R	0.518	0.98
220_V	248_P	0.518	0.98
44_A	162_L	0.516	0.98
324_W	329_K	0.516	0.98
303_G	316_P	0.513	0.98
18_A	21_V	0.512	0.98
244_S	315_V	0.511	0.98
231_F	238_N	0.510	0.98
215_L	268_F	0.509	0.98
25_A	28_H	0.507	0.98
92_S	96_K	0.506	0.98
220_V	255_F	0.506	0.98
323_I	327_T	0.506	0.98
156_M	292_T	0.505	0.98
273_M	276_G	0.505	0.98
151_V	155_V	0.505	0.98
157_T	300_L	0.503	0.98
83_L	87_F	0.503	0.98
85_A	99_K	0.502	0.98
138_T	142_T	0.501	0.98
207_T	238_N	0.500	0.98
207_T	231_F	0.500	0.98

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
3mktA	1	0.9799	77.1	0.934	Contact Map
4lz6A	1	0.9656	44.3	0.947	Contact Map
4humA	1	0.9799	41.5	0.947	Contact Map
3w4tA	1	0.8625	37.8	0.949	Contact Map
3tx3A	2	0.6275	19.6	0.955	Contact Map
2kluA	1	0.1547	17.7	0.956	Contact Map
4ltoA	3	0.3181	17.6	0.956	Contact Map
4rp9A	2	0.8768	17.2	0.957	Contact Map
2kv5A	1	0.0946	14.4	0.958	Contact Map
3qe7A	2	0.7851	10.7	0.96	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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