YDIK - ECOLI - GREMLIN Contacts

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YDIK - UPF0118 inner membrane protein YdiK

UniProt:	P0AFS7	Sequences: MVNVRQPRDVAQILLSVLFLAIMIVACLWIVQPFILGFAWAGTVVIATWPVLLRLQKIMFGRRSLAVLVMTLLLVMVFIIPIALLVNSIVDGSGPLIKAISSGDMTLPDLAWLNTIPVIGAKLYAGWHNLLDMGGTAIMAKVRPYIGTTTTWFVGQAAHIGRFMVHCALMLLFSALLYWRGEQVAQGIRHFATRLAGVRGDAAVLLAAQAIRAVALGVVVTALVQAVLGGIGLAVSGVPYATLLTVLMILSCLVQLGPLPVLIPAIIWLYWTGDTTWGTVLLVWSGVVGTLDNVIRPMLIRMGADLPLILILSGVIGGLIAFGMIGLFIGPVLLAVSWRLFAAWVEEVPPPTDQPEEILEELGEIEKPNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13970
Length:	370 (329)
Sequences:	10985 (8618)
Seq/√Len:	475.1

ECOLI - YDIK PERM YHHT TQSA
BACSU - YUBA YUEF YTVI YRRI YDBI
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
232_G	284_W	5.386	1.00
230_G	245_T	5.203	1.00
54_R	58_I	5.002	1.00
314_G	334_L	3.322	1.00
46_I	208_A	2.985	1.00
56_Q	63_R	2.963	1.00
226_A	249_I	2.768	1.00
276_T	280_V	2.616	1.00
62_R	65_L	2.606	1.00
230_G	234_A	2.507	1.00
54_R	57_K	2.491	1.00
44_V	174_S	2.476	1.00
266_I	282_L	2.469	1.00
279_T	283_V	2.459	1.00
226_A	245_T	2.396	1.00
61_G	69_V	2.320	1.00
338_W	342_A	2.246	1.00
99_A	102_S	2.183	1.00
280_V	283_V	2.054	1.00
266_I	278_G	2.018	1.00
233_L	238_V	1.976	1.00
116_I	119_I	1.962	1.00
25_V	29_W	1.937	1.00
206_L	343_A	1.906	1.00
41_A	174_S	1.902	1.00
202_A	343_A	1.897	1.00
49_W	53_L	1.865	1.00
219_V	253_L	1.833	1.00
64_S	68_L	1.824	1.00
217_G	299_L	1.817	1.00
175_A	179_W	1.812	1.00
229_G	248_M	1.790	1.00
207_A	336_V	1.785	1.00
67_V	175_A	1.753	1.00
170_M	174_S	1.731	1.00
247_L	251_S	1.713	1.00
52_L	70_M	1.709	1.00
241_A	245_T	1.697	1.00
124_Y	128_H	1.696	1.00
189_R	201_D	1.689	1.00
114_N	117_P	1.684	1.00
52_L	67_V	1.683	1.00
67_V	71_T	1.678	1.00
137_A	140_A	1.673	1.00
29_W	32_Q	1.673	1.00
298_M	302_M	1.664	1.00
230_G	241_A	1.645	1.00
231_I	234_A	1.641	1.00
26_A	30_I	1.636	1.00
319_L	327_L	1.634	1.00
277_W	280_V	1.630	1.00
94_G	98_K	1.627	1.00
105_M	108_P	1.624	1.00
79_I	83_A	1.624	1.00
64_S	179_W	1.619	1.00
51_V	70_M	1.617	1.00
274_D	277_W	1.610	1.00
49_W	63_R	1.602	1.00
192_A	200_G	1.598	1.00
112_W	115_T	1.579	1.00
21_A	25_V	1.575	1.00
22_I	26_A	1.568	1.00
225_Q	252_C	1.561	1.00
180_R	307_P	1.558	1.00
173_F	309_I	1.526	1.00
55_L	73_L	1.525	1.00
239_P	272_T	1.523	1.00
173_F	177_L	1.519	1.00
52_L	63_R	1.490	1.00
106_T	109_D	1.473	1.00
251_S	261_V	1.472	1.00
234_A	241_A	1.452	1.00
38_F	313_S	1.441	1.00
133_M	136_T	1.430	1.00
112_W	116_I	1.427	1.00
286_G	289_G	1.421	1.00
295_I	299_L	1.418	1.00
229_G	287_V	1.399	1.00
275_T	279_T	1.381	1.00
262_L	266_I	1.350	1.00
290_T	295_I	1.334	1.00
180_R	183_Q	1.326	1.00
48_T	178_Y	1.322	1.00
139_M	143_R	1.320	1.00
86_V	90_V	1.317	1.00
102_S	105_M	1.302	1.00
14_L	18_L	1.301	1.00
228_L	287_V	1.291	1.00
193_T	197_G	1.290	1.00
210_A	335_A	1.289	1.00
64_S	175_A	1.277	1.00
52_L	66_A	1.274	1.00
48_T	74_L	1.271	1.00
269_L	281_L	1.269	1.00
265_A	281_L	1.268	1.00
63_R	182_E	1.263	1.00
137_A	141_K	1.261	1.00
288_V	292_D	1.256	1.00
282_L	286_G	1.255	1.00
61_G	65_L	1.248	1.00
97_I	101_S	1.239	1.00
221_T	291_L	1.237	1.00
15_L	19_F	1.233	1.00
18_L	22_I	1.232	1.00
244_L	265_A	1.230	1.00
102_S	106_T	1.229	1.00
193_T	196_A	1.222	1.00
194_R	197_G	1.221	1.00
315_V	327_L	1.221	1.00
45_V	177_L	1.219	1.00
310_L	334_L	1.212	1.00
112_W	117_P	1.211	1.00
41_A	170_M	1.210	1.00
276_T	279_T	1.206	1.00
122_K	125_A	1.205	1.00
278_G	282_L	1.201	1.00
232_G	236_S	1.200	1.00
101_S	105_M	1.197	1.00
216_L	220_V	1.195	1.00
121_A	124_Y	1.191	1.00
232_G	280_V	1.185	1.00
44_V	170_M	1.183	1.00
51_V	54_R	1.176	1.00
275_T	278_G	1.173	1.00
52_L	178_Y	1.170	1.00
49_W	181_G	1.167	1.00
68_L	72_L	1.164	1.00
125_A	129_N	1.164	1.00
26_A	29_W	1.163	1.00
238_V	269_L	1.162	1.00
75_V	79_I	1.158	1.00
314_G	318_G	1.156	1.00
186_Q	190_H	1.153	1.00
206_L	342_A	1.149	1.00
225_Q	287_V	1.148	1.00
141_K	144_P	1.136	1.00
318_G	334_L	1.136	1.00
125_A	128_H	1.136	1.00
231_I	235_V	1.135	1.00
61_G	66_A	1.133	1.00
37_G	41_A	1.130	1.00
52_L	56_Q	1.129	1.00
222_A	252_C	1.129	1.00
66_A	70_M	1.127	1.00
203_A	340_L	1.126	1.00
269_L	278_G	1.118	1.00
140_A	144_P	1.103	1.00
126_G	129_N	1.103	1.00
183_Q	186_Q	1.081	1.00
140_A	143_R	1.080	1.00
273_G	277_W	1.074	1.00
318_G	322_F	1.066	1.00
270_Y	278_G	1.065	1.00
221_T	225_Q	1.062	1.00
236_S	281_L	1.061	1.00
202_A	206_L	1.061	1.00
280_V	284_W	1.058	1.00
230_G	242_T	1.053	1.00
38_F	173_F	1.050	1.00
292_D	296_R	1.048	1.00
245_T	249_I	1.046	1.00
226_A	230_G	1.046	1.00
187_G	190_H	1.044	1.00
65_L	68_L	1.043	1.00
144_P	147_G	1.043	1.00
91_D	95_P	1.043	1.00
103_G	107_L	1.041	1.00
56_Q	66_A	1.037	1.00
219_V	223_L	1.035	1.00
233_L	248_M	1.035	1.00
314_G	330_G	1.027	1.00
294_V	298_M	1.025	1.00
133_M	137_A	1.020	1.00
218_V	296_R	1.020	1.00
122_K	126_G	1.019	1.00
163_F	167_C	1.017	1.00
117_P	121_A	1.015	1.00
136_T	139_M	1.013	1.00
20_L	24_I	1.012	1.00
42_G	177_L	1.010	1.00
40_W	170_M	1.008	1.00
95_P	98_K	1.002	1.00
128_H	132_D	1.001	1.00
181_G	185_A	1.000	1.00
223_L	249_I	0.992	1.00
83_A	87_N	0.988	1.00
213_A	217_G	0.985	1.00
153_F	157_A	0.980	1.00
249_I	253_L	0.979	1.00
225_Q	229_G	0.976	1.00
236_S	277_W	0.976	1.00
236_S	284_W	0.975	1.00
135_G	138_I	0.975	1.00
169_L	173_F	0.973	1.00
105_M	109_D	0.970	1.00
54_R	60_F	0.969	1.00
325_I	329_I	0.968	1.00
142_V	145_Y	0.967	1.00
220_V	224_V	0.963	1.00
71_T	174_S	0.962	1.00
113_L	117_P	0.960	1.00
247_L	261_V	0.955	1.00
41_A	45_V	0.953	1.00
173_F	313_S	0.950	1.00
157_A	161_G	0.950	1.00
53_L	57_K	0.947	1.00
34_F	317_G	0.941	1.00
15_L	18_L	0.940	1.00
225_Q	258_P	0.939	1.00
268_W	272_T	0.937	1.00
99_A	103_G	0.934	1.00
240_Y	243_L	0.933	1.00
145_Y	149_T	0.932	1.00
17_V	21_A	0.930	1.00
233_L	281_L	0.927	1.00
245_T	248_M	0.925	1.00
221_T	295_I	0.922	1.00
221_T	296_R	0.922	1.00
262_L	285_S	0.918	1.00
156_Q	160_I	0.916	1.00
310_L	338_W	0.916	1.00
289_G	293_N	0.915	1.00
90_V	93_S	0.912	1.00
213_A	303_G	0.911	1.00
189_R	197_G	0.910	1.00
290_T	294_V	0.907	1.00
337_S	341_F	0.905	1.00
229_G	233_L	0.900	1.00
95_P	99_A	0.898	1.00
284_W	287_V	0.895	1.00
300_I	311_I	0.893	1.00
200_G	204_V	0.887	1.00
129_N	133_M	0.886	1.00
41_A	173_F	0.883	1.00
233_L	244_L	0.877	1.00
77_V	81_P	0.861	1.00
203_A	343_A	0.861	1.00
252_C	258_P	0.860	1.00
143_R	147_G	0.855	1.00
340_L	344_W	0.854	1.00
224_V	228_L	0.852	1.00
131_L	134_G	0.851	1.00
330_G	334_L	0.850	1.00
209_Q	213_A	0.849	1.00
227_V	230_G	0.848	1.00
25_V	28_L	0.846	1.00
183_Q	187_G	0.845	1.00
146_I	149_T	0.842	1.00
55_L	70_M	0.841	1.00
221_T	252_C	0.834	1.00
22_I	25_V	0.834	1.00
199_R	202_A	0.832	1.00
313_S	317_G	0.829	1.00
18_L	21_A	0.828	1.00
306_L	334_L	0.827	1.00
88_S	91_D	0.827	1.00
48_T	70_M	0.824	1.00
53_L	56_Q	0.822	1.00
88_S	92_G	0.821	1.00
132_D	136_T	0.819	1.00
270_Y	275_T	0.817	1.00
136_T	140_A	0.812	1.00
227_V	231_I	0.812	1.00
185_A	189_R	0.808	1.00
115_T	118_V	0.808	1.00
236_S	280_V	0.807	1.00
187_G	191_F	0.805	1.00
248_M	261_V	0.804	1.00
162_R	166_H	0.802	1.00
93_S	97_I	0.802	1.00
58_I	61_G	0.797	1.00
260_P	264_P	0.796	1.00
234_A	237_G	0.795	1.00
234_A	245_T	0.794	1.00
126_G	130_L	0.789	1.00
14_L	17_V	0.787	1.00
119_I	123_L	0.783	1.00
109_D	115_T	0.780	1.00
115_T	119_I	0.777	1.00
244_L	268_W	0.775	1.00
221_T	300_I	0.773	1.00
223_L	227_V	0.772	1.00
17_V	20_L	0.765	1.00
62_R	66_A	0.764	1.00
224_V	295_I	0.761	1.00
266_I	270_Y	0.758	1.00
291_L	296_R	0.758	1.00
55_L	61_G	0.757	1.00
252_C	296_R	0.756	1.00
138_I	141_K	0.755	1.00
174_S	178_Y	0.753	1.00
24_I	27_C	0.751	1.00
225_Q	296_R	0.749	1.00
248_M	252_C	0.748	1.00
222_A	226_A	0.748	1.00
27_C	30_I	0.748	1.00
192_A	196_A	0.747	1.00
267_I	271_W	0.746	1.00
45_V	174_S	0.745	1.00
149_T	153_F	0.744	1.00
222_A	253_L	0.739	1.00
92_G	95_P	0.734	1.00
232_G	287_V	0.734	1.00
127_W	130_L	0.734	1.00
100_I	103_G	0.728	1.00
134_G	137_A	0.724	1.00
318_G	333_L	0.719	1.00
53_L	182_E	0.718	1.00
159_H	163_F	0.715	1.00
212_R	216_L	0.715	1.00
206_L	339_R	0.715	1.00
304_A	331_P	0.708	1.00
98_K	102_S	0.707	1.00
258_P	261_V	0.705	1.00
296_R	300_I	0.704	1.00
199_R	343_A	0.702	1.00
84_L	88_S	0.699	1.00
16_S	20_L	0.699	1.00
152_W	156_Q	0.697	1.00
94_G	97_I	0.696	1.00
13_I	16_S	0.695	1.00
301_R	311_I	0.694	1.00
201_D	205_L	0.694	1.00
302_M	305_D	0.694	1.00
269_L	274_D	0.693	1.00
40_W	44_V	0.692	1.00
186_Q	201_D	0.691	1.00
144_P	148_T	0.689	1.00
308_L	312_L	0.688	1.00
222_A	225_Q	0.688	1.00
159_H	162_R	0.688	1.00
225_Q	288_V	0.688	1.00
149_T	152_W	0.680	1.00
150_T	154_V	0.679	1.00
38_F	177_L	0.678	1.00
113_L	116_I	0.676	1.00
296_R	299_L	0.672	1.00
55_L	66_A	0.672	1.00
198_V	202_A	0.671	1.00
203_A	207_A	0.671	1.00
207_A	339_R	0.671	1.00
104_D	108_P	0.670	1.00
288_V	291_L	0.669	1.00
22_I	29_W	0.669	1.00
195_L	198_V	0.667	1.00
226_A	242_T	0.666	1.00
218_V	222_A	0.662	1.00
45_V	49_W	0.661	1.00
154_V	158_A	0.661	1.00
148_T	152_W	0.661	1.00
119_I	122_K	0.659	1.00
191_F	341_F	0.658	1.00
77_V	80_I	0.652	1.00
141_K	145_Y	0.650	1.00
187_G	310_L	0.649	1.00
80_I	84_L	0.649	1.00
85_L	89_I	0.648	1.00
311_I	331_P	0.648	1.00
49_W	178_Y	0.646	1.00
21_A	24_I	0.645	1.00
121_A	125_A	0.644	1.00
73_L	76_M	0.644	1.00
210_A	213_A	0.640	1.00
20_L	27_C	0.639	1.00
63_R	67_V	0.638	1.00
197_G	200_G	0.636	1.00
134_G	138_I	0.636	1.00
334_L	338_W	0.635	1.00
226_A	246_V	0.635	1.00
71_T	175_A	0.635	1.00
55_L	69_V	0.635	1.00
48_T	174_S	0.630	1.00
221_T	299_L	0.630	1.00
206_L	210_A	0.629	1.00
124_Y	127_W	0.627	1.00
147_G	151_T	0.626	0.99
229_G	245_T	0.624	0.99
89_I	93_S	0.620	0.99
123_L	126_G	0.620	0.99
145_Y	148_T	0.618	0.99
322_F	326_G	0.617	0.99
289_G	292_D	0.616	0.99
218_V	221_T	0.614	0.99
108_P	114_N	0.613	0.99
27_C	31_V	0.612	0.99
176_L	180_R	0.612	0.99
291_L	295_I	0.611	0.99
19_F	23_M	0.611	0.99
272_T	277_W	0.610	0.99
184_V	187_G	0.608	0.99
165_V	169_L	0.607	0.99
148_T	151_T	0.607	0.99
218_V	252_C	0.607	0.99
220_V	299_L	0.606	0.99
247_L	264_P	0.603	0.99
48_T	51_V	0.602	0.99
78_F	82_I	0.602	0.99
220_V	223_L	0.598	0.99
306_L	311_I	0.598	0.99
315_V	331_P	0.596	0.99
298_M	301_R	0.595	0.99
261_V	265_A	0.595	0.99
37_G	166_H	0.594	0.99
91_D	94_G	0.594	0.99
205_L	209_Q	0.594	0.99
100_I	104_D	0.593	0.99
150_T	153_F	0.591	0.99
36_L	39_A	0.590	0.99
221_T	258_P	0.586	0.99
269_L	277_W	0.586	0.99
216_L	303_G	0.586	0.99
177_L	309_I	0.586	0.99
114_N	118_V	0.585	0.99
30_I	33_P	0.584	0.99
76_M	79_I	0.584	0.99
163_F	166_H	0.582	0.99
252_C	291_L	0.582	0.99
213_A	216_L	0.582	0.99
229_G	284_W	0.582	0.99
90_V	94_G	0.579	0.99
225_Q	291_L	0.579	0.99
67_V	179_W	0.578	0.99
92_G	96_L	0.578	0.99
207_A	211_I	0.576	0.99
82_I	86_V	0.576	0.99
197_G	201_D	0.576	0.99
258_P	288_V	0.574	0.99
185_A	205_L	0.573	0.99
207_A	210_A	0.573	0.99
45_V	178_Y	0.572	0.99
211_I	214_V	0.571	0.99
132_D	135_G	0.570	0.99
261_V	288_V	0.570	0.99
228_L	232_G	0.568	0.99
42_G	181_G	0.567	0.99
66_A	69_V	0.567	0.99
56_Q	62_R	0.566	0.99
16_S	19_F	0.563	0.99
189_R	192_A	0.562	0.99
222_A	249_I	0.553	0.99
324_M	327_L	0.553	0.99
224_V	291_L	0.553	0.99
233_L	285_S	0.550	0.99
238_V	241_A	0.549	0.99
238_V	265_A	0.548	0.99
139_M	142_V	0.547	0.99
130_L	133_M	0.547	0.99
210_A	339_R	0.547	0.99
339_R	343_A	0.545	0.99
218_V	253_L	0.544	0.99
262_L	286_G	0.543	0.99
248_M	258_P	0.541	0.99
206_L	209_Q	0.540	0.99
295_I	298_M	0.540	0.99
225_Q	249_I	0.540	0.99
217_G	303_G	0.539	0.98
23_M	27_C	0.538	0.98
98_K	101_S	0.536	0.98
128_H	134_G	0.535	0.98
167_C	171_L	0.534	0.98
252_C	292_D	0.534	0.98
56_Q	60_F	0.534	0.98
169_L	316_I	0.533	0.98
37_G	301_R	0.533	0.98
135_G	141_K	0.533	0.98
252_C	259_L	0.532	0.98
176_L	308_L	0.532	0.98
248_M	285_S	0.528	0.98
225_Q	228_L	0.528	0.98
146_I	150_T	0.528	0.98
27_C	337_S	0.526	0.98
217_G	335_A	0.524	0.98
173_F	312_L	0.522	0.98
315_V	318_G	0.521	0.98
285_S	300_I	0.521	0.98
172_L	293_N	0.519	0.98
154_V	157_A	0.519	0.98
186_Q	189_R	0.518	0.98
325_I	330_G	0.517	0.98
161_G	165_V	0.517	0.98
141_K	146_I	0.515	0.98
19_F	22_I	0.514	0.98
263_I	267_I	0.514	0.98
162_R	293_N	0.512	0.98
173_F	316_I	0.512	0.98
24_I	28_L	0.508	0.98
318_G	330_G	0.507	0.98
293_N	316_I	0.505	0.98
172_L	308_L	0.503	0.98
261_V	331_P	0.503	0.98
279_T	282_L	0.503	0.98
160_I	164_M	0.502	0.98
252_C	327_L	0.500	0.98
222_A	285_S	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
3wdoA	1	0.9297	65.3	0.941	Contact Map
3mktA	1	0.9486	61.2	0.943	Contact Map
4tphA	2	0.8243	46.8	0.948	Contact Map
3w4tA	1	0.8595	38.6	0.95	Contact Map
2l16A	1	0.1405	19.7	0.957	Contact Map
4ltoA	3	0.3216	17.7	0.958	Contact Map
4pypA	1	0.8622	14	0.96	Contact Map
2kluA	1	0.1568	13.6	0.96	Contact Map
2kv5A	1	0.0892	13.1	0.96	Contact Map
4r0cA	3	0.6135	11	0.961	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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