YCFT - ECOLI - GREMLIN Contacts

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YCFT - Inner membrane protein YcfT

UniProt:	P75955	Sequences: MKQKELWINQIKGLCICLVVIYHSVITFYPHLTTFQHPLSEVLSKCWIYFNLYLAPFRMPVFFFISGYLIRRYIDSVPWGNCLDKRIWNIFWVLALWGVVQWLALSALNQWLAPERDLSNASNAAYADSTGEFLHGMITASTSLWYLYALIVYFVVCKIFSRLALPLFALFVLLSVAVNFVPTPWWGMNSVIRNLPYYSLGAWFGATIMTCVKEVPLRRHLLMASLLTVLAVGAWLFTISLLLSLVSIVVIMKLFYQYEQRFGMRSTSLLNVIGSNTIAIYTTHRILVEIFSLTLLAQMNAARWSPQVELTLLLVYPFVSLFICTVAGLLVRKLSQRAFSDLLFSPPSLPAAVSYSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13438
Length:	357 (305)
Sequences:	15090 (13395)
Seq/√Len:	767.0

ECOLI - YCFT OPGC YIAH
BACSU - YFIQ YRHL YKRP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
272_V	276_N	3.565	1.00
329_L	333_K	3.522	1.00
20_V	280_I	3.360	1.00
15_C	61_V	3.222	1.00
283_T	331_V	3.181	1.00
87_I	91_F	3.112	1.00
71_R	202_A	3.079	1.00
83_L	158_K	2.916	1.00
9_N	275_S	2.721	1.00
272_V	329_L	2.627	1.00
324_C	328_G	2.588	1.00
13_G	274_G	2.568	1.00
276_N	329_L	2.563	1.00
79_W	83_L	2.495	1.00
129_S	132_E	2.454	1.00
333_K	337_R	2.404	1.00
126_Y	129_S	2.371	1.00
146_Y	150_L	2.367	1.00
94_L	144_L	2.298	1.00
80_G	84_D	2.251	1.00
97_W	283_T	2.209	1.00
60_P	197_Y	2.164	1.00
79_W	158_K	2.154	1.00
10_Q	265_R	2.144	1.00
24_S	288_V	2.133	1.00
272_V	333_K	2.112	1.00
131_G	135_H	2.073	1.00
91_F	95_A	2.042	1.00
55_A	58_R	1.978	1.00
123_N	126_Y	1.967	1.00
72_R	205_G	1.939	1.00
132_E	135_H	1.934	1.00
13_G	277_T	1.902	1.00
330_L	334_L	1.834	1.00
69_L	72_R	1.795	1.00
63_F	149_A	1.763	1.00
78_P	81_N	1.751	1.00
9_N	271_N	1.749	1.00
84_D	88_W	1.715	1.00
13_G	273_I	1.704	1.00
219_R	223_M	1.696	1.00
16_I	280_I	1.695	1.00
142_T	285_R	1.653	1.00
279_A	332_R	1.646	1.00
97_W	282_T	1.634	1.00
11_I	61_V	1.633	1.00
251_I	254_L	1.621	1.00
166_P	170_L	1.618	1.00
280_I	324_C	1.606	1.00
64_F	204_F	1.594	1.00
194_N	197_Y	1.586	1.00
130_T	133_F	1.576	1.00
10_Q	266_S	1.575	1.00
71_R	157_C	1.573	1.00
8_I	65_I	1.533	1.00
8_I	69_L	1.523	1.00
22_Y	55_A	1.510	1.00
125_A	129_S	1.475	1.00
249_V	252_M	1.471	1.00
93_V	282_T	1.471	1.00
220_H	224_A	1.462	1.00
136_G	139_T	1.458	1.00
251_I	255_F	1.436	1.00
249_V	253_K	1.427	1.00
68_Y	205_G	1.423	1.00
332_R	337_R	1.422	1.00
126_Y	131_G	1.417	1.00
72_R	76_S	1.417	1.00
77_V	81_N	1.408	1.00
71_R	75_D	1.408	1.00
334_L	338_A	1.406	1.00
267_T	270_L	1.403	1.00
337_R	340_S	1.399	1.00
19_V	59_M	1.398	1.00
132_E	136_G	1.386	1.00
162_R	165_L	1.363	1.00
74_I	157_C	1.358	1.00
86_R	154_F	1.356	1.00
96_L	335_S	1.355	1.00
129_S	135_H	1.347	1.00
192_I	196_P	1.340	1.00
69_L	73_Y	1.338	1.00
279_A	331_V	1.338	1.00
126_Y	130_T	1.329	1.00
276_N	280_I	1.326	1.00
272_V	275_S	1.325	1.00
128_D	132_E	1.317	1.00
230_L	233_G	1.308	1.00
276_N	328_G	1.300	1.00
77_V	85_K	1.299	1.00
172_V	175_S	1.298	1.00
332_R	336_Q	1.296	1.00
280_I	328_G	1.285	1.00
153_Y	198_Y	1.281	1.00
100_V	283_T	1.279	1.00
93_V	331_V	1.279	1.00
148_Y	152_V	1.277	1.00
101_Q	286_I	1.276	1.00
130_T	134_L	1.275	1.00
337_R	341_D	1.272	1.00
71_R	206_A	1.266	1.00
157_C	198_Y	1.262	1.00
5_E	68_Y	1.248	1.00
81_N	85_K	1.243	1.00
269_L	273_I	1.226	1.00
70_I	157_C	1.225	1.00
66_S	150_L	1.222	1.00
208_I	212_V	1.220	1.00
293_L	297_A	1.216	1.00
123_N	129_S	1.213	1.00
230_L	234_A	1.208	1.00
314_L	318_F	1.200	1.00
271_N	275_S	1.200	1.00
252_M	256_Y	1.199	1.00
70_I	154_F	1.199	1.00
126_Y	132_E	1.194	1.00
15_C	58_R	1.191	1.00
136_G	140_A	1.180	1.00
326_V	330_L	1.176	1.00
276_N	279_A	1.176	1.00
320_S	324_C	1.175	1.00
13_G	17_C	1.175	1.00
143_S	285_R	1.173	1.00
135_H	139_T	1.173	1.00
150_L	154_F	1.162	1.00
126_Y	135_H	1.142	1.00
73_Y	77_V	1.139	1.00
13_G	270_L	1.138	1.00
222_L	226_L	1.137	1.00
175_S	178_V	1.136	1.00
123_N	128_D	1.135	1.00
18_L	58_R	1.126	1.00
155_V	158_K	1.125	1.00
10_Q	270_L	1.123	1.00
284_H	288_V	1.122	1.00
221_L	225_S	1.113	1.00
268_S	272_V	1.109	1.00
322_F	326_V	1.103	1.00
129_S	133_F	1.098	1.00
71_R	205_G	1.098	1.00
60_P	194_N	1.081	1.00
247_S	251_I	1.075	1.00
339_F	342_L	1.074	1.00
91_F	151_I	1.072	1.00
97_W	144_L	1.069	1.00
97_W	101_Q	1.063	1.00
243_L	247_S	1.061	1.00
248_I	251_I	1.050	1.00
170_L	174_L	1.035	1.00
127_A	131_G	1.033	1.00
318_F	322_F	1.029	1.00
145_W	149_A	1.026	1.00
224_A	228_T	1.026	1.00
257_Q	260_Q	1.025	1.00
123_N	132_E	1.024	1.00
83_L	151_I	1.021	1.00
125_A	128_D	1.020	1.00
94_L	278_I	1.012	1.00
63_F	150_L	1.011	1.00
291_F	295_L	1.005	1.00
328_G	332_R	1.000	1.00
291_F	320_S	0.997	1.00
208_I	211_C	0.991	1.00
210_T	213_K	0.988	1.00
92_W	96_L	0.986	1.00
87_I	151_I	0.981	1.00
250_V	253_K	0.980	1.00
157_C	202_A	0.978	1.00
279_A	336_Q	0.978	1.00
129_S	136_G	0.975	1.00
138_I	141_S	0.975	1.00
70_I	73_Y	0.974	1.00
82_C	154_F	0.973	1.00
331_V	335_S	0.973	1.00
171_F	175_S	0.966	1.00
288_V	320_S	0.964	1.00
137_M	141_S	0.952	1.00
128_D	131_G	0.950	1.00
335_S	339_F	0.943	1.00
16_I	146_Y	0.937	1.00
149_A	194_N	0.930	1.00
287_L	291_F	0.930	1.00
81_N	84_D	0.928	1.00
127_A	130_T	0.923	1.00
198_Y	202_A	0.923	1.00
287_L	327_A	0.922	1.00
123_N	130_T	0.921	1.00
186_W	190_S	0.921	1.00
9_N	12_K	0.919	1.00
280_I	325_T	0.919	1.00
99_V	103_L	0.917	1.00
227_L	231_A	0.910	1.00
172_V	176_V	0.909	1.00
124_A	128_D	0.907	1.00
247_S	250_V	0.904	1.00
18_L	57_F	0.899	1.00
231_A	234_A	0.893	1.00
144_L	282_T	0.892	1.00
173_L	177_A	0.888	1.00
16_I	62_F	0.888	1.00
88_W	91_F	0.886	1.00
250_V	254_L	0.884	1.00
218_R	222_L	0.879	1.00
181_V	185_W	0.878	1.00
283_T	286_I	0.876	1.00
199_S	202_A	0.874	1.00
216_P	219_R	0.871	1.00
136_G	141_S	0.870	1.00
250_V	257_Q	0.869	1.00
179_N	184_P	0.867	1.00
20_V	284_H	0.867	1.00
333_K	338_A	0.865	1.00
229_V	233_G	0.864	1.00
210_T	214_E	0.862	1.00
126_Y	133_F	0.861	1.00
125_A	130_T	0.859	1.00
315_V	318_F	0.858	1.00
90_I	154_F	0.855	1.00
179_N	183_T	0.855	1.00
135_H	141_S	0.854	1.00
278_I	282_T	0.854	1.00
168_F	175_S	0.852	1.00
147_L	282_T	0.852	1.00
19_V	58_R	0.846	1.00
190_S	193_R	0.846	1.00
137_M	140_A	0.838	1.00
93_V	279_A	0.834	1.00
256_Y	260_Q	0.830	1.00
246_V	249_V	0.828	1.00
131_G	134_L	0.827	1.00
12_K	65_I	0.826	1.00
223_M	227_L	0.825	1.00
143_S	281_Y	0.820	1.00
276_N	333_K	0.820	1.00
241_L	244_S	0.819	1.00
13_G	16_I	0.817	1.00
317_P	320_S	0.814	1.00
98_G	102_W	0.809	1.00
268_S	271_N	0.800	1.00
233_G	237_F	0.797	1.00
266_S	271_N	0.786	1.00
103_L	107_A	0.785	1.00
240_S	244_S	0.785	1.00
327_A	331_V	0.783	1.00
103_L	106_S	0.780	1.00
88_W	339_F	0.777	1.00
265_R	268_S	0.777	1.00
266_S	269_L	0.775	1.00
235_W	239_I	0.775	1.00
250_V	258_Y	0.774	1.00
290_I	293_L	0.773	1.00
225_S	229_V	0.766	1.00
188_M	191_V	0.765	1.00
317_P	321_L	0.764	1.00
246_V	250_V	0.764	1.00
64_F	197_Y	0.764	1.00
22_Y	58_R	0.762	1.00
20_V	321_L	0.761	1.00
9_N	274_G	0.759	1.00
188_M	194_N	0.759	1.00
22_Y	56_P	0.757	1.00
244_S	247_S	0.755	1.00
196_P	199_S	0.755	1.00
17_C	21_I	0.754	1.00
240_S	243_L	0.750	1.00
67_G	202_A	0.748	1.00
143_S	284_H	0.747	1.00
129_S	139_T	0.745	1.00
68_Y	208_I	0.744	1.00
242_L	245_L	0.744	1.00
82_C	86_R	0.742	1.00
267_T	271_N	0.742	1.00
209_M	212_V	0.737	1.00
125_A	132_E	0.737	1.00
70_I	198_Y	0.737	1.00
104_A	108_L	0.735	1.00
63_F	146_Y	0.733	1.00
89_N	336_Q	0.733	1.00
55_A	59_M	0.732	1.00
143_S	286_I	0.729	1.00
275_S	337_R	0.728	1.00
12_K	146_Y	0.725	1.00
125_A	131_G	0.724	1.00
283_T	327_A	0.724	1.00
276_N	332_R	0.721	1.00
16_I	273_I	0.720	1.00
125_A	135_H	0.719	1.00
10_Q	267_T	0.719	1.00
226_L	230_L	0.718	1.00
82_C	158_K	0.718	1.00
248_I	252_M	0.716	1.00
273_I	325_T	0.714	1.00
127_A	134_L	0.714	1.00
219_R	226_L	0.713	1.00
209_M	213_K	0.713	1.00
168_F	172_V	0.712	1.00
124_A	133_F	0.707	1.00
18_L	22_Y	0.707	1.00
88_W	342_L	0.706	1.00
124_A	127_A	0.704	1.00
260_Q	263_G	0.698	1.00
228_T	232_V	0.695	1.00
74_I	161_S	0.695	1.00
20_V	324_C	0.694	1.00
218_R	221_L	0.693	1.00
287_L	290_I	0.690	1.00
100_V	104_A	0.689	1.00
170_L	173_L	0.688	1.00
24_S	320_S	0.687	1.00
153_Y	194_N	0.687	1.00
243_L	246_V	0.685	1.00
218_R	223_M	0.685	1.00
316_Y	320_S	0.684	1.00
262_F	266_S	0.683	1.00
6_L	9_N	0.682	1.00
66_S	70_I	0.680	1.00
149_A	153_Y	0.678	1.00
63_F	194_N	0.675	1.00
331_V	334_L	0.673	1.00
11_I	65_I	0.673	1.00
24_S	317_P	0.672	1.00
245_L	249_V	0.669	1.00
166_P	175_S	0.668	1.00
96_L	100_V	0.668	1.00
75_D	206_A	0.666	1.00
94_L	98_G	0.663	1.00
129_S	134_L	0.663	1.00
60_P	193_R	0.663	1.00
153_Y	158_K	0.663	1.00
66_S	198_Y	0.661	1.00
124_A	130_T	0.660	1.00
7_W	10_Q	0.657	1.00
132_E	137_M	0.656	1.00
149_A	191_V	0.655	1.00
271_N	274_G	0.652	1.00
243_L	251_I	0.651	1.00
130_T	135_H	0.651	1.00
287_L	323_I	0.651	1.00
270_L	274_G	0.650	1.00
179_N	185_W	0.649	1.00
59_M	62_F	0.648	1.00
202_A	206_A	0.641	1.00
268_S	275_S	0.640	1.00
180_F	184_P	0.640	1.00
167_L	170_L	0.638	1.00
251_I	257_Q	0.636	1.00
5_E	72_R	0.630	1.00
101_Q	105_L	0.629	1.00
66_S	146_Y	0.628	1.00
199_S	203_W	0.623	1.00
251_I	258_Y	0.620	1.00
218_R	224_A	0.617	1.00
244_S	248_I	0.616	1.00
246_V	257_Q	0.615	1.00
8_I	68_Y	0.615	1.00
22_Y	60_P	0.613	1.00
125_A	134_L	0.613	1.00
261_R	264_M	0.611	1.00
217_L	220_H	0.611	1.00
12_K	150_L	0.609	1.00
111_W	114_P	0.609	1.00
179_N	182_P	0.608	1.00
240_S	247_S	0.606	1.00
129_S	138_I	0.606	1.00
287_L	320_S	0.604	1.00
291_F	294_T	0.603	1.00
187_G	191_V	0.602	1.00
124_A	131_G	0.599	1.00
123_N	135_H	0.599	1.00
16_I	20_V	0.598	1.00
191_V	194_N	0.597	1.00
291_F	316_Y	0.597	1.00
58_R	153_Y	0.597	1.00
14_L	18_L	0.596	1.00
203_W	207_T	0.595	1.00
168_F	171_F	0.594	1.00
248_I	256_Y	0.593	1.00
80_G	83_L	0.592	1.00
63_F	153_Y	0.590	1.00
214_E	218_R	0.590	1.00
283_T	324_C	0.590	1.00
289_E	293_L	0.590	1.00
110_Q	113_A	0.585	1.00
236_L	239_I	0.585	1.00
6_L	266_S	0.585	1.00
284_H	324_C	0.585	1.00
180_F	185_W	0.584	1.00
166_P	169_A	0.583	1.00
89_N	150_L	0.582	1.00
90_I	278_I	0.578	1.00
50_F	54_L	0.573	1.00
123_N	133_F	0.571	1.00
316_Y	319_V	0.571	1.00
131_G	140_A	0.566	1.00
186_W	192_I	0.562	1.00
126_Y	137_M	0.560	1.00
102_W	105_L	0.559	1.00
24_S	324_C	0.559	1.00
166_P	176_V	0.558	1.00
193_R	197_Y	0.558	1.00
174_L	178_V	0.556	1.00
63_F	145_W	0.556	1.00
227_L	230_L	0.553	1.00
134_L	137_M	0.550	1.00
228_T	231_A	0.550	1.00
256_Y	259_E	0.550	1.00
54_L	58_R	0.549	1.00
233_G	236_L	0.549	1.00
224_A	227_L	0.549	1.00
254_L	258_Y	0.547	1.00
311_T	314_L	0.547	1.00
153_Y	157_C	0.547	1.00
56_P	60_P	0.545	1.00
232_V	236_L	0.542	1.00
99_V	102_W	0.542	1.00
215_V	218_R	0.541	1.00
151_I	155_V	0.541	1.00
70_I	74_I	0.541	1.00
253_K	257_Q	0.541	1.00
132_E	138_I	0.540	1.00
269_L	272_V	0.539	1.00
70_I	82_C	0.538	1.00
10_Q	13_G	0.537	1.00
102_W	106_S	0.536	1.00
294_T	297_A	0.536	1.00
95_A	151_I	0.536	1.00
96_L	331_V	0.536	1.00
101_Q	143_S	0.531	1.00
203_W	206_A	0.530	1.00
243_L	258_Y	0.529	1.00
106_S	110_Q	0.528	1.00
242_L	247_S	0.527	1.00
182_P	185_W	0.525	1.00
275_S	285_R	0.525	1.00
126_Y	136_G	0.523	1.00
290_I	294_T	0.520	1.00
123_N	131_G	0.519	1.00
134_L	138_I	0.519	1.00
57_F	61_V	0.518	1.00
149_A	152_V	0.518	1.00
16_I	277_T	0.516	1.00
90_I	151_I	0.514	1.00
109_N	113_A	0.513	1.00
10_Q	14_L	0.513	1.00
204_F	207_T	0.511	1.00
242_L	246_V	0.510	1.00
129_S	140_A	0.510	1.00
255_F	259_E	0.508	1.00
259_E	262_F	0.507	1.00
88_W	340_S	0.506	1.00
90_I	150_L	0.505	1.00
91_F	94_L	0.505	1.00
95_A	99_V	0.504	1.00
213_K	217_L	0.504	1.00
166_P	178_V	0.504	1.00
151_I	198_Y	0.503	1.00
212_V	216_P	0.500	1.00
220_H	223_M	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
4j72A	2	0.1036	7.4	0.954	Contact Map
2kluA	1	0.1457	4.7	0.958	Contact Map
3udcA	3	0.1345	4.6	0.958	Contact Map
2kv5A	1	0.0924	4.1	0.959	Contact Map
3ffvA	1	0.1681	3.1	0.962	Contact Map
2dgcA	2	0.042	3.1	0.962	Contact Map
4p02A	1	0.3529	2.7	0.963	Contact Map
5ajiA	3	0.1457	2.6	0.963	Contact Map
4pj0R	1	0.0952	2.6	0.963	Contact Map
4px7A	1	0.6471	2.2	0.965	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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