YGHQ - ECOLI - GREMLIN Contacts

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YGHQ - Inner membrane protein YghQ

UniProt:	Q46841	Sequences: MAGFNIKHWFADGAFRTIIRNSAWLGSSNVVSALLGLLALSCAGKGMTPAMFGVLVIVQSYAKSISDFIKFQTWQLVVQYGTPALTNNNPQQFRNVVSFSFSLDIVSGAVAIVGGIALLPFLSHSLGLDDQSFWLAALYCTLIPSMASSTPTGILRAVDRFDLIAVQQATKPFLRAAGSVVAWYFDFGFAGFVIAWYVSNLVGGTMYWWFAARELRRRNIHNAFKLNLFESARYIKGAWSFVWSTNIAHSIWSARNSCSTVLVGIVLGPAAAGLFKIAMTFFDAAGTPAGLLGKSFYPEVMRLDPRTTRPWLLGVKSGLLAGGIGILVALAVLIVGKPLISLVFGVKYLEAYDLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13001
Length:	355 (277)
Sequences:	24488 (19653)
Seq/√Len:	1180.8

ECOLI - YGHQ MURJ WZXC WZXE RFBX MDTK DINF YEEO
BACSU - EPSK YABM TUAB YTGP SP5B YKVU YOEA NORM YISQ YPNP
HALSA - Q9HRT3 Q9HSW2 Q9HQQ5 Q9HN79 Q9HRF2 Q9HMS7 Q9HRF7
SULSO - Q97XT3 Q97XG2 Q7LXE2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
160_R	163_L	4.359	1.00
89_N	92_Q	4.270	1.00
56_V	276_K	4.238	1.00
118_L	121_F	4.149	1.00
144_P	201_L	3.385	1.00
236_K	240_S	3.308	1.00
120_P	124_H	2.931	1.00
84_A	92_Q	2.659	1.00
77_V	100_S	2.506	1.00
162_D	166_V	2.483	1.00
179_S	182_A	2.262	1.00
121_F	124_H	2.229	1.00
95_N	231_S	2.210	1.00
16_R	20_R	2.172	1.00
231_S	234_Y	2.168	1.00
81_G	157_A	2.152	1.00
133_F	136_A	2.143	1.00
115_G	139_Y	2.082	1.00
232_A	236_K	2.059	1.00
268_G	271_A	2.031	1.00
48_T	51_M	1.990	1.00
167_Q	206_M	1.960	1.00
140_C	143_I	1.952	1.00
92_Q	95_N	1.950	1.00
84_A	89_N	1.946	1.00
97_V	154_I	1.935	1.00
79_Q	83_P	1.887	1.00
83_P	87_N	1.878	1.00
40_L	280_T	1.872	1.00
119_L	136_A	1.847	1.00
137_A	190_A	1.808	1.00
174_L	202_V	1.794	1.00
112_I	116_I	1.788	1.00
80_Y	241_F	1.755	1.00
147_A	204_G	1.722	1.00
42_C	180_V	1.719	1.00
209_W	213_R	1.707	1.00
205_T	209_W	1.698	1.00
133_F	190_A	1.651	1.00
84_A	87_N	1.648	1.00
99_F	235_I	1.640	1.00
167_Q	207_Y	1.634	1.00
92_Q	234_Y	1.623	1.00
121_F	125_S	1.602	1.00
163_L	210_F	1.591	1.00
208_W	212_A	1.564	1.00
188_G	191_G	1.555	1.00
26_G	291_L	1.551	1.00
116_I	136_A	1.534	1.00
154_I	158_V	1.531	1.00
190_A	194_I	1.529	1.00
178_G	195_A	1.521	1.00
259_S	275_F	1.517	1.00
171_K	203_G	1.506	1.00
270_A	274_L	1.485	1.00
104_D	150_T	1.475	1.00
95_N	99_F	1.474	1.00
96_V	234_Y	1.473	1.00
31_V	169_A	1.465	1.00
95_N	234_Y	1.464	1.00
263_V	275_F	1.463	1.00
24_W	162_D	1.462	1.00
160_R	214_E	1.461	1.00
90_P	94_R	1.441	1.00
94_R	98_S	1.430	1.00
261_V	265_I	1.424	1.00
151_P	207_Y	1.408	1.00
91_Q	95_N	1.397	1.00
17_T	20_R	1.395	1.00
181_V	185_F	1.388	1.00
49_P	270_A	1.381	1.00
57_I	264_G	1.366	1.00
100_S	238_A	1.366	1.00
41_S	45_K	1.361	1.00
177_A	181_V	1.336	1.00
159_D	299_E	1.333	1.00
243_W	247_I	1.330	1.00
76_L	241_F	1.330	1.00
137_A	194_I	1.323	1.00
250_S	254_A	1.319	1.00
103_L	235_I	1.319	1.00
132_S	136_A	1.307	1.00
116_I	120_P	1.302	1.00
190_A	193_V	1.288	1.00
166_V	170_T	1.284	1.00
191_G	195_A	1.283	1.00
143_I	146_M	1.281	1.00
23_A	27_S	1.278	1.00
106_V	110_V	1.268	1.00
234_Y	237_G	1.260	1.00
128_L	131_Q	1.257	1.00
233_R	236_K	1.253	1.00
257_S	260_T	1.246	1.00
139_Y	143_I	1.242	1.00
151_P	208_W	1.235	1.00
194_I	197_Y	1.220	1.00
85_L	158_V	1.215	1.00
210_F	214_E	1.211	1.00
187_F	191_G	1.208	1.00
85_L	93_F	1.198	1.00
80_Y	83_P	1.197	1.00
55_L	59_Q	1.191	1.00
152_T	156_R	1.176	1.00
181_V	184_Y	1.176	1.00
175_R	199_S	1.175	1.00
114_G	118_L	1.173	1.00
129_D	132_S	1.160	1.00
197_Y	200_N	1.159	1.00
230_E	235_I	1.153	1.00
83_P	237_G	1.153	1.00
49_P	274_L	1.148	1.00
84_A	96_V	1.147	1.00
50_A	131_Q	1.143	1.00
127_G	130_D	1.142	1.00
30_V	34_L	1.140	1.00
43_A	192_F	1.131	1.00
102_S	106_V	1.125	1.00
80_Y	96_V	1.121	1.00
44_G	277_I	1.115	1.00
140_C	144_P	1.105	1.00
173_F	177_A	1.097	1.00
29_N	33_A	1.094	1.00
37_L	41_S	1.094	1.00
144_P	204_G	1.091	1.00
46_G	183_W	1.084	1.00
141_T	197_Y	1.080	1.00
95_N	98_S	1.078	1.00
34_L	38_L	1.072	1.00
212_A	216_R	1.071	1.00
51_M	54_V	1.068	1.00
22_S	26_G	1.067	1.00
39_A	176_A	1.058	1.00
117_A	121_F	1.053	1.00
55_L	189_F	1.052	1.00
113_V	117_A	1.044	1.00
180_V	184_Y	1.039	1.00
77_V	81_G	1.037	1.00
85_L	90_P	1.033	1.00
194_I	198_V	1.030	1.00
262_L	266_V	1.023	1.00
105_I	109_A	1.016	1.00
137_A	193_V	1.015	1.00
112_I	143_I	1.008	1.00
98_S	102_S	1.006	1.00
179_S	195_A	1.005	1.00
99_F	230_E	1.002	1.00
47_M	51_M	1.001	1.00
209_W	212_A	0.997	1.00
19_I	23_A	0.994	1.00
167_Q	210_F	0.991	1.00
239_W	242_V	0.989	1.00
119_L	123_S	0.988	1.00
49_P	273_G	0.984	1.00
81_G	93_F	0.978	1.00
80_Y	237_G	0.974	1.00
109_A	113_V	0.972	1.00
22_S	295_S	0.970	1.00
63_K	67_D	0.966	1.00
195_A	199_S	0.966	1.00
297_Y	301_M	0.965	1.00
276_K	280_T	0.964	1.00
264_G	272_A	0.963	1.00
117_A	120_P	0.959	1.00
163_L	166_V	0.955	1.00
140_C	197_Y	0.954	1.00
239_W	243_W	0.953	1.00
93_F	158_V	0.952	1.00
39_A	196_W	0.948	1.00
199_S	203_G	0.937	1.00
272_A	276_K	0.936	1.00
196_W	200_N	0.931	1.00
263_V	272_A	0.927	1.00
279_M	283_D	0.923	1.00
78_V	153_G	0.923	1.00
55_L	192_F	0.918	1.00
60_S	260_T	0.915	1.00
18_I	22_S	0.912	1.00
92_Q	96_V	0.910	1.00
151_P	211_A	0.909	1.00
257_S	261_V	0.908	1.00
110_V	113_V	0.906	1.00
271_A	274_L	0.905	1.00
70_K	74_W	0.904	1.00
27_S	165_A	0.903	1.00
56_V	273_G	0.897	1.00
182_A	187_F	0.894	1.00
158_V	214_E	0.894	1.00
156_R	164_I	0.894	1.00
136_A	140_C	0.892	1.00
206_M	210_F	0.890	1.00
59_Q	63_K	0.883	1.00
128_L	132_S	0.869	1.00
160_R	210_F	0.866	1.00
115_G	119_L	0.863	1.00
197_Y	201_L	0.859	1.00
215_L	218_R	0.852	1.00
113_V	116_I	0.851	1.00
105_I	147_A	0.851	1.00
41_S	44_G	0.846	1.00
27_S	31_V	0.845	1.00
42_C	179_S	0.843	1.00
178_G	182_A	0.840	1.00
179_S	192_F	0.839	1.00
118_L	122_L	0.838	1.00
241_F	245_T	0.837	1.00
233_R	237_G	0.836	1.00
206_M	209_W	0.834	1.00
275_F	279_M	0.834	1.00
90_P	93_F	0.830	1.00
260_T	272_A	0.824	1.00
178_G	198_V	0.823	1.00
258_C	262_L	0.819	1.00
102_S	230_E	0.817	1.00
112_I	115_G	0.815	1.00
52_F	277_I	0.811	1.00
213_R	216_R	0.809	1.00
76_L	238_A	0.808	1.00
214_E	217_R	0.807	1.00
253_S	257_S	0.807	1.00
82_T	157_A	0.805	1.00
280_T	284_A	0.805	1.00
43_A	55_L	0.804	1.00
243_W	246_N	0.804	1.00
84_A	234_Y	0.803	1.00
28_S	165_A	0.793	1.00
119_L	139_Y	0.791	1.00
101_F	151_P	0.791	1.00
240_S	244_S	0.777	1.00
187_F	190_A	0.775	1.00
76_L	242_V	0.771	1.00
166_V	169_A	0.770	1.00
155_L	211_A	0.768	1.00
103_L	107_S	0.767	1.00
81_G	158_V	0.766	1.00
106_V	109_A	0.765	1.00
207_Y	211_A	0.762	1.00
99_F	103_L	0.760	1.00
290_G	294_K	0.758	1.00
175_R	179_S	0.758	1.00
57_I	272_A	0.757	1.00
289_A	293_G	0.754	1.00
161_F	295_S	0.754	1.00
19_I	22_S	0.751	1.00
104_D	146_M	0.749	1.00
282_F	285_A	0.747	1.00
77_V	96_V	0.746	1.00
72_Q	242_V	0.744	1.00
259_S	279_M	0.744	1.00
286_G	289_A	0.734	1.00
177_A	180_V	0.728	1.00
81_G	96_V	0.727	1.00
237_G	241_F	0.724	1.00
70_K	146_M	0.723	1.00
50_A	53_G	0.722	1.00
28_S	168_Q	0.722	1.00
170_T	174_L	0.722	1.00
130_D	134_W	0.720	1.00
91_Q	94_R	0.720	1.00
32_S	172_P	0.720	1.00
42_C	46_G	0.716	1.00
277_I	280_T	0.712	1.00
124_H	130_D	0.708	1.00
141_T	200_N	0.706	1.00
53_G	272_A	0.705	1.00
291_L	294_K	0.702	1.00
31_V	35_L	0.698	1.00
273_G	277_I	0.697	1.00
99_F	231_S	0.696	1.00
110_V	114_G	0.694	1.00
187_F	194_I	0.694	1.00
102_S	105_I	0.693	1.00
54_V	269_P	0.693	1.00
207_Y	210_F	0.687	1.00
240_S	243_W	0.684	1.00
120_P	136_A	0.684	1.00
127_G	132_S	0.682	1.00
153_G	156_R	0.682	1.00
127_G	131_Q	0.677	1.00
116_I	139_Y	0.677	1.00
58_V	138_L	0.677	1.00
192_F	195_A	0.675	1.00
237_G	240_S	0.674	1.00
130_D	133_F	0.669	1.00
167_Q	203_G	0.669	1.00
25_L	295_S	0.666	1.00
148_S	203_G	0.666	1.00
170_T	206_M	0.661	1.00
108_G	112_I	0.660	1.00
155_L	207_Y	0.659	1.00
278_A	282_F	0.656	1.00
40_L	44_G	0.655	1.00
211_A	215_L	0.653	1.00
80_Y	84_A	0.649	1.00
171_K	175_R	0.648	1.00
131_Q	134_W	0.647	1.00
142_L	146_M	0.644	1.00
99_F	234_Y	0.643	1.00
137_A	197_Y	0.641	1.00
285_A	288_P	0.641	1.00
52_F	56_V	0.639	1.00
148_S	204_G	0.638	1.00
97_V	151_P	0.636	1.00
137_A	140_C	0.636	1.00
260_T	276_K	0.636	1.00
280_T	283_D	0.635	1.00
163_L	167_Q	0.635	1.00
108_G	143_I	0.633	1.00
50_A	269_P	0.632	1.00
167_Q	171_K	0.631	1.00
22_S	292_L	0.629	1.00
25_L	294_K	0.629	1.00
279_M	282_F	0.629	1.00
247_I	250_S	0.628	1.00
191_G	194_I	0.627	1.00
273_G	276_K	0.627	1.00
254_A	258_C	0.626	1.00
98_S	101_F	0.626	1.00
139_Y	142_L	0.624	1.00
58_V	135_L	0.621	1.00
80_Y	238_A	0.621	1.00
141_T	145_S	0.619	1.00
201_L	205_T	0.619	1.00
259_S	262_L	0.619	1.00
268_G	272_A	0.619	1.00
21_N	161_F	0.618	1.00
109_A	143_I	0.617	1.00
24_W	28_S	0.617	1.00
204_G	208_W	0.616	1.00
47_M	189_F	0.616	1.00
198_V	202_V	0.615	1.00
16_R	19_I	0.611	1.00
170_T	173_F	0.611	1.00
35_L	38_L	0.610	1.00
292_L	296_F	0.607	1.00
39_A	179_S	0.605	1.00
153_G	157_A	0.604	1.00
147_A	151_P	0.602	1.00
186_D	190_A	0.602	1.00
112_I	139_Y	0.598	1.00
100_S	150_T	0.592	1.00
99_F	232_A	0.590	1.00
99_F	102_S	0.590	1.00
93_F	97_V	0.589	1.00
75_Q	78_V	0.589	1.00
270_A	273_G	0.589	1.00
39_A	175_R	0.588	1.00
151_P	204_G	0.587	1.00
47_M	53_G	0.587	1.00
57_I	128_L	0.586	1.00
252_W	256_N	0.584	1.00
180_V	183_W	0.583	1.00
251_I	255_R	0.581	1.00
94_R	218_R	0.580	1.00
296_F	300_V	0.579	1.00
180_V	185_F	0.578	1.00
17_T	159_D	0.578	1.00
79_Q	241_F	0.577	1.00
59_Q	62_A	0.576	1.00
38_L	41_S	0.576	1.00
152_T	164_I	0.576	1.00
176_A	180_V	0.574	1.00
78_V	157_A	0.574	1.00
174_L	199_S	0.565	1.00
155_L	163_L	0.565	1.00
182_A	195_A	0.565	1.00
40_L	52_F	0.564	1.00
20_R	162_D	0.560	1.00
152_T	168_Q	0.560	1.00
248_A	252_W	0.558	1.00
212_A	215_L	0.555	1.00
44_G	52_F	0.554	1.00
200_N	203_G	0.547	1.00
175_R	178_G	0.542	1.00
198_V	201_L	0.542	1.00
96_V	238_A	0.540	1.00
264_G	269_P	0.537	1.00
262_L	265_I	0.537	1.00
81_G	97_V	0.536	1.00
28_S	31_V	0.536	1.00
246_N	251_I	0.536	1.00
232_A	235_I	0.536	1.00
108_G	139_Y	0.536	1.00
174_L	177_A	0.534	1.00
182_A	185_F	0.531	1.00
295_S	298_P	0.530	1.00
175_R	195_A	0.529	1.00
150_T	153_G	0.528	1.00
108_G	146_M	0.527	1.00
135_L	139_Y	0.527	1.00
101_F	104_D	0.527	1.00
212_A	217_R	0.526	1.00
34_L	37_L	0.524	1.00
76_L	80_Y	0.523	1.00
116_I	140_C	0.522	1.00
161_F	165_A	0.520	1.00
131_Q	136_A	0.519	1.00
25_L	161_F	0.519	1.00
101_F	150_T	0.518	1.00
179_S	183_W	0.515	1.00
109_A	112_I	0.514	1.00
77_V	154_I	0.513	1.00
21_N	295_S	0.513	1.00
169_A	173_F	0.511	1.00
26_G	30_V	0.510	1.00
111_A	115_G	0.507	1.00
78_V	82_T	0.506	1.00
35_L	39_A	0.506	1.00
241_F	244_S	0.506	1.00
260_T	264_G	0.503	1.00
202_V	206_M	0.502	1.00
175_R	196_W	0.502	1.00
256_N	279_M	0.502	1.00
21_N	159_D	0.501	1.00
260_T	279_M	0.501	1.00
51_M	188_G	0.500	1.00
112_I	140_C	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
4lz6A	1	0.9859	100	0.271	Contact Map
3w4tA	1	0.9662	100	0.296	Contact Map
4humA	1	0.9831	100	0.3	Contact Map
3mktA	1	0.9746	100	0.302	Contact Map
3wdoA	1	0.8592	49.7	0.925	Contact Map
4ikvA	1	0.9183	40.8	0.929	Contact Map
4xnjA	1	0.9014	36.7	0.931	Contact Map
3o7qA	1	0.8535	33	0.933	Contact Map
4tphA	2	0.8479	29.4	0.934	Contact Map
1pw4A	1	0.8789	28.8	0.935	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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