YWKB - BACSU - GREMLIN Contacts

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YWKB - Uncharacterized transporter YwkB

UniProt:	P45869	Sequences: MSILDILILLAPIFFVIVLGWFAGHFGSYDAKSAKGVSTLVTKYALPAHFIAGILTTSRSEFLSQVPLMISLIIGIVGFYIIILLVCRFIFKYDLTNSSVFSLNSAQPTFAFMGIPVLGSLFGANEVAIPIAVTGIVVNAILDPLAIIIATVGESSKKNEESGDSFWKMTGKSILHGLCEPLAAAPLISMILVLVFNFTLPELGVKMLDQLGSTTSGVALFAVGVTVGIRKIKLSMPAIGIALLKVAVQPALMFLIALAIGLPADQTTKAILLVAFPGSAVAAMIATRFEKQEEETATAFVVSAILSLISLPIIIALTA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	319 (293)
Sequences:	6518 (5027)
Seq/√Len:	293.7

ECOLI - YFDV
BACSU - YWKB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_I	192_L	5.364	1.00
175_L	179_C	4.912	1.00
257_A	267_T	4.257	1.00
22_F	26_F	3.321	1.00
45_A	214_T	3.231	1.00
278_G	303_S	2.940	1.00
97_N	292_Q	2.932	1.00
51_I	188_I	2.928	1.00
209_D	213_S	2.842	1.00
15_F	207_M	2.681	1.00
40_L	214_T	2.526	1.00
261_G	264_A	2.511	1.00
246_V	310_S	2.424	1.00
24_G	225_V	2.300	1.00
23_A	44_Y	2.253	1.00
114_G	276_F	2.131	1.00
24_G	228_G	2.079	1.00
40_L	45_A	2.048	1.00
171_G	175_L	2.030	1.00
34_A	225_V	2.030	1.00
52_A	212_G	1.986	1.00
104_N	299_A	1.950	1.00
192_L	198_F	1.932	1.00
45_A	215_T	1.926	1.00
185_A	189_S	1.919	1.00
309_I	312_P	1.912	1.00
52_A	208_L	1.908	1.00
30_D	33_S	1.904	1.00
253_M	274_V	1.894	1.00
264_A	267_T	1.885	1.00
242_A	246_V	1.862	1.00
52_A	205_V	1.854	1.00
184_A	188_I	1.853	1.00
261_G	267_T	1.837	1.00
52_A	209_D	1.799	1.00
290_E	293_E	1.781	1.00
35_K	39_T	1.780	1.00
52_A	56_T	1.752	1.00
30_D	36_G	1.752	1.00
242_A	303_S	1.747	1.00
40_L	221_F	1.740	1.00
39_T	43_K	1.732	1.00
23_A	221_F	1.712	1.00
254_F	271_I	1.600	1.00
119_G	124_A	1.598	1.00
202_E	206_K	1.596	1.00
25_H	228_G	1.592	1.00
50_F	185_A	1.590	1.00
243_L	247_A	1.587	1.00
121_L	315_I	1.587	1.00
275_A	314_I	1.583	1.00
19_L	207_M	1.550	1.00
81_I	85_L	1.550	1.00
94_D	97_N	1.536	1.00
39_T	288_R	1.535	1.00
205_V	209_D	1.525	1.00
206_K	209_D	1.521	1.00
265_D	269_K	1.514	1.00
172_K	175_L	1.507	1.00
254_F	258_L	1.495	1.00
48_A	208_L	1.493	1.00
130_P	266_Q	1.489	1.00
226_T	283_A	1.477	1.00
148_I	152_V	1.476	1.00
192_L	199_T	1.469	1.00
100_V	296_T	1.454	1.00
257_A	262_L	1.446	1.00
283_A	300_F	1.438	1.00
72_L	134_T	1.407	1.00
54_I	189_S	1.405	1.00
16_V	211_L	1.401	1.00
48_A	185_A	1.400	1.00
117_V	276_F	1.400	1.00
241_I	299_A	1.386	1.00
263_P	266_Q	1.385	1.00
66_V	70_I	1.381	1.00
55_L	192_L	1.379	1.00
40_L	218_V	1.371	1.00
77_V	81_I	1.368	1.00
105_S	244_L	1.367	1.00
33_S	36_G	1.367	1.00
189_S	193_V	1.365	1.00
11_A	15_F	1.365	1.00
255_L	258_L	1.361	1.00
131_I	273_L	1.353	1.00
264_A	268_T	1.352	1.00
18_V	22_F	1.350	1.00
58_S	61_E	1.348	1.00
118_L	131_I	1.343	1.00
256_I	259_A	1.341	1.00
245_K	249_Q	1.339	1.00
108_P	276_F	1.331	1.00
19_L	44_Y	1.323	1.00
104_N	278_G	1.322	1.00
177_G	183_A	1.320	1.00
176_H	179_C	1.306	1.00
87_C	98_S	1.303	1.00
187_L	191_I	1.292	1.00
11_A	203_L	1.284	1.00
48_A	211_L	1.276	1.00
251_A	255_L	1.275	1.00
223_V	280_A	1.274	1.00
83_I	105_S	1.269	1.00
286_A	291_K	1.268	1.00
265_D	268_T	1.262	1.00
255_L	259_A	1.253	1.00
122_F	269_K	1.251	1.00
41_V	219_A	1.245	1.00
305_I	309_I	1.218	1.00
313_I	316_A	1.217	1.00
196_F	199_T	1.215	1.00
287_T	293_E	1.214	1.00
16_V	221_F	1.205	1.00
267_T	271_I	1.205	1.00
107_Q	145_L	1.193	1.00
192_L	200_L	1.183	1.00
37_V	218_V	1.183	1.00
238_A	302_V	1.175	1.00
56_T	205_V	1.171	1.00
44_Y	221_F	1.162	1.00
118_L	122_F	1.158	1.00
244_L	248_V	1.151	1.00
101_F	241_I	1.140	1.00
208_L	212_G	1.136	1.00
242_A	302_V	1.130	1.00
278_G	282_A	1.129	1.00
16_V	210_Q	1.122	1.00
125_N	265_D	1.118	1.00
239_I	243_L	1.117	1.00
15_F	19_L	1.114	1.00
122_F	268_T	1.113	1.00
204_G	207_M	1.104	1.00
55_L	205_V	1.102	1.00
191_I	196_F	1.101	1.00
86_V	91_F	1.086	1.00
88_R	92_K	1.081	1.00
271_I	314_I	1.079	1.00
32_K	36_G	1.072	1.00
307_S	311_L	1.072	1.00
59_R	193_V	1.063	1.00
307_S	310_S	1.055	1.00
45_A	218_V	1.051	1.00
19_L	211_L	1.050	1.00
263_P	267_T	1.046	1.00
66_V	69_M	1.044	1.00
99_S	150_A	1.043	1.00
41_V	45_A	1.041	1.00
104_N	282_A	1.041	1.00
275_A	311_L	1.037	1.00
150_A	286_A	1.036	1.00
251_A	314_I	1.032	1.00
84_L	88_R	1.026	1.00
179_C	184_A	1.021	1.00
214_T	217_G	1.019	1.00
104_N	296_T	1.018	1.00
126_E	129_I	1.011	1.00
71_S	75_G	1.000	1.00
242_A	306_L	1.000	1.00
72_L	76_I	0.997	1.00
43_K	288_R	0.996	1.00
108_P	245_K	0.995	1.00
278_G	299_A	0.986	1.00
214_T	218_V	0.981	1.00
21_W	228_G	0.968	1.00
216_S	219_A	0.964	1.00
55_L	189_S	0.953	1.00
118_L	126_E	0.951	1.00
234_L	237_P	0.951	1.00
24_G	229_I	0.946	1.00
103_L	146_A	0.945	1.00
257_A	271_I	0.943	1.00
29_Y	33_S	0.937	1.00
250_P	275_A	0.935	1.00
88_R	98_S	0.931	1.00
103_L	150_A	0.930	1.00
238_A	242_A	0.930	1.00
143_D	147_I	0.928	1.00
209_D	212_G	0.926	1.00
33_S	37_V	0.923	1.00
258_L	267_T	0.923	1.00
190_M	194_L	0.923	1.00
21_W	25_H	0.923	1.00
65_Q	68_L	0.922	1.00
14_F	17_I	0.922	1.00
192_L	196_F	0.919	1.00
32_K	35_K	0.916	1.00
188_I	192_L	0.913	1.00
115_I	128_A	0.912	1.00
38_S	222_A	0.912	1.00
95_L	98_S	0.909	1.00
191_I	194_L	0.909	1.00
139_N	143_D	0.907	1.00
246_V	306_L	0.906	1.00
93_Y	97_N	0.893	1.00
262_L	267_T	0.893	1.00
27_G	30_D	0.890	1.00
203_L	207_M	0.889	1.00
9_L	12_P	0.889	1.00
75_G	253_M	0.887	1.00
98_S	102_S	0.873	1.00
144_P	147_I	0.869	1.00
292_Q	295_E	0.867	1.00
8_I	203_L	0.859	1.00
143_D	146_A	0.848	1.00
49_H	215_T	0.844	1.00
42_T	112_F	0.843	1.00
80_Y	106_A	0.841	1.00
122_F	126_E	0.835	1.00
275_A	310_S	0.835	1.00
83_I	244_L	0.835	1.00
147_I	289_F	0.832	1.00
252_L	256_I	0.831	1.00
24_G	31_A	0.830	1.00
147_I	151_T	0.823	1.00
126_E	265_D	0.817	1.00
55_L	193_V	0.817	1.00
75_G	79_F	0.808	1.00
278_G	300_F	0.806	1.00
35_K	290_E	0.803	1.00
222_A	283_A	0.802	1.00
55_L	200_L	0.802	1.00
107_Q	111_A	0.801	0.99
23_A	28_S	0.801	0.99
309_I	313_I	0.801	0.99
76_I	87_C	0.800	0.99
170_T	174_I	0.786	0.99
111_A	132_A	0.784	0.99
113_M	117_V	0.784	0.99
247_A	250_P	0.780	0.99
14_F	18_V	0.779	0.99
174_I	177_G	0.778	0.99
103_L	107_Q	0.775	0.99
81_I	84_L	0.774	0.99
117_V	272_L	0.767	0.99
78_G	252_L	0.767	0.99
136_I	140_A	0.765	0.99
41_V	215_T	0.765	0.99
243_L	248_V	0.763	0.99
51_I	208_L	0.761	0.99
24_G	27_G	0.760	0.99
182_L	185_A	0.757	0.99
123_G	126_E	0.750	0.99
168_K	171_G	0.747	0.99
252_L	255_L	0.745	0.99
51_I	55_L	0.744	0.99
246_V	303_S	0.743	0.99
202_E	205_V	0.742	0.99
115_I	135_G	0.738	0.99
276_F	282_A	0.737	0.99
282_A	296_T	0.736	0.99
235_S	298_T	0.722	0.99
79_F	249_Q	0.722	0.99
74_I	78_G	0.722	0.99
286_A	293_E	0.721	0.99
86_V	90_I	0.721	0.99
67_P	70_I	0.720	0.99
239_I	242_A	0.720	0.99
87_C	91_F	0.714	0.99
99_S	153_G	0.714	0.99
210_Q	213_S	0.707	0.99
150_A	291_K	0.707	0.99
44_Y	211_L	0.704	0.99
114_G	273_L	0.703	0.99
287_T	290_E	0.700	0.99
180_E	184_A	0.691	0.99
83_I	87_C	0.691	0.99
48_A	212_G	0.689	0.98
87_C	102_S	0.687	0.98
258_L	261_G	0.686	0.98
29_Y	225_V	0.684	0.98
79_F	83_I	0.680	0.98
118_L	269_K	0.679	0.98
138_V	141_I	0.679	0.98
107_Q	143_D	0.678	0.98
20_G	225_V	0.678	0.98
271_I	275_A	0.678	0.98
85_L	88_R	0.675	0.98
306_L	310_S	0.674	0.98
84_L	102_S	0.674	0.98
248_V	290_E	0.674	0.98
46_L	219_A	0.674	0.98
126_E	131_I	0.674	0.98
250_P	310_S	0.673	0.98
188_I	191_I	0.672	0.98
103_L	282_A	0.672	0.98
108_P	114_G	0.672	0.98
235_S	239_I	0.672	0.98
19_L	221_F	0.671	0.98
184_A	187_L	0.667	0.98
43_K	112_F	0.666	0.98
38_S	219_A	0.660	0.98
100_V	150_A	0.659	0.98
86_V	240_G	0.658	0.98
150_A	285_I	0.658	0.98
13_I	138_V	0.656	0.98
112_F	216_S	0.656	0.98
306_L	309_I	0.655	0.98
6_I	10_L	0.655	0.98
97_N	295_E	0.653	0.98
204_G	208_L	0.652	0.98
70_I	74_I	0.650	0.98
20_G	221_F	0.648	0.98
109_T	115_I	0.646	0.98
73_I	137_V	0.645	0.98
28_S	43_K	0.645	0.98
23_A	26_F	0.644	0.98
247_A	313_I	0.642	0.98
73_I	77_V	0.640	0.98
73_I	76_I	0.638	0.98
107_Q	289_F	0.638	0.98
13_I	41_V	0.637	0.97
106_A	146_A	0.636	0.97
126_E	130_P	0.635	0.97
59_R	194_L	0.634	0.97
71_S	256_I	0.634	0.97
46_L	182_L	0.634	0.97
262_L	266_Q	0.632	0.97
41_V	218_V	0.632	0.97
174_I	178_L	0.631	0.97
37_V	222_A	0.629	0.97
198_F	201_P	0.629	0.97
236_M	239_I	0.629	0.97
170_T	173_S	0.629	0.97
200_L	205_V	0.628	0.97
68_L	270_A	0.625	0.97
109_T	279_S	0.625	0.97
29_Y	36_G	0.625	0.97
54_I	191_I	0.624	0.97
49_H	217_G	0.624	0.97
119_G	126_E	0.624	0.97
51_I	185_A	0.623	0.97
42_T	281_V	0.622	0.97
128_A	132_A	0.617	0.97
31_A	229_I	0.616	0.97
26_F	30_D	0.615	0.97
140_A	143_D	0.613	0.97
20_G	220_L	0.612	0.97
210_Q	214_T	0.612	0.97
223_V	283_A	0.611	0.97
253_M	271_I	0.609	0.97
65_Q	80_Y	0.608	0.97
206_K	210_Q	0.608	0.97
200_L	204_G	0.607	0.97
314_I	317_L	0.606	0.97
111_A	131_I	0.604	0.97
139_N	142_L	0.604	0.97
286_A	296_T	0.602	0.96
137_V	148_I	0.599	0.96
42_T	180_E	0.599	0.96
114_G	304_A	0.597	0.96
237_P	317_L	0.597	0.96
227_V	301_V	0.596	0.96
65_Q	69_M	0.596	0.96
174_I	179_C	0.589	0.96
110_F	138_V	0.588	0.96
83_I	106_A	0.587	0.96
258_L	263_P	0.585	0.96
115_I	131_I	0.585	0.96
15_F	18_V	0.585	0.96
53_G	132_A	0.584	0.96
140_A	144_P	0.583	0.96
34_A	222_A	0.582	0.96
138_V	279_S	0.581	0.96
74_I	77_V	0.580	0.96
279_S	282_A	0.579	0.96
300_F	304_A	0.578	0.96
75_G	80_Y	0.576	0.95
87_C	101_F	0.576	0.95
230_R	301_V	0.576	0.95
207_M	210_Q	0.574	0.95
49_H	245_K	0.574	0.95
80_Y	84_L	0.573	0.95
14_F	305_I	0.572	0.95
240_G	243_L	0.569	0.95
172_K	176_H	0.569	0.95
247_A	310_S	0.568	0.95
80_Y	102_S	0.567	0.95
146_A	150_A	0.567	0.95
78_G	82_I	0.564	0.95
243_L	246_V	0.562	0.95
75_G	252_L	0.562	0.95
86_V	244_L	0.561	0.95
10_L	308_L	0.560	0.95
237_P	295_E	0.560	0.95
310_S	314_I	0.559	0.95
141_I	144_P	0.558	0.95
23_A	211_L	0.558	0.95
74_I	256_I	0.557	0.95
57_T	193_V	0.552	0.94
132_A	135_G	0.552	0.94
222_A	225_V	0.550	0.94
41_V	112_F	0.548	0.94
24_G	29_Y	0.547	0.94
136_I	139_N	0.546	0.94
220_L	278_G	0.546	0.94
283_A	287_T	0.543	0.94
112_F	280_A	0.543	0.94
247_A	251_A	0.541	0.94
33_S	225_V	0.541	0.94
223_V	301_V	0.540	0.94
26_F	29_Y	0.540	0.94
37_V	273_L	0.536	0.93
137_V	141_I	0.536	0.93
212_G	215_T	0.536	0.93
102_S	106_A	0.534	0.93
273_L	301_V	0.534	0.93
38_S	283_A	0.534	0.93
101_F	295_E	0.530	0.93
99_S	152_V	0.529	0.93
135_G	279_S	0.527	0.93
171_G	174_I	0.524	0.93
199_T	203_L	0.524	0.93
9_L	111_A	0.523	0.93
180_E	185_A	0.522	0.93
169_M	172_K	0.520	0.92
241_I	278_G	0.520	0.92
138_V	142_L	0.519	0.92
67_P	71_S	0.518	0.92
65_Q	266_Q	0.515	0.92
48_A	188_I	0.515	0.92
199_T	202_E	0.515	0.92
173_S	177_G	0.514	0.92
282_A	300_F	0.511	0.92
46_L	49_H	0.510	0.92
70_I	96_T	0.510	0.92
246_V	275_A	0.508	0.92
233_K	294_E	0.508	0.92
111_A	139_N	0.507	0.91
240_G	244_L	0.507	0.91
234_L	294_E	0.505	0.91
12_P	223_V	0.504	0.91
119_G	128_A	0.504	0.91
143_D	289_F	0.504	0.91
7_L	11_A	0.503	0.91
29_Y	40_L	0.503	0.91
286_A	290_E	0.503	0.91
88_R	91_F	0.502	0.91
223_V	300_F	0.502	0.91
68_L	72_L	0.501	0.91
7_L	10_L	0.500	0.91

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
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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
3zuxA	1	0.4577	99.7	0.686	Contact Map
4n7wA	2	0.442	99.7	0.693	Contact Map
2cfqA	1	0.9592	89.3	0.913	Contact Map
4czbA	2	0.5204	81.5	0.922	Contact Map
3o7qA	1	0.931	81.3	0.922	Contact Map
4cz8A	2	0.5172	79.2	0.924	Contact Map
4bwzA	2	0.4765	61.7	0.933	Contact Map
4m64A	1	0.953	50.5	0.937	Contact Map
2gfpA	2	0.9279	48.8	0.938	Contact Map
3wdoA	1	0.9216	46.8	0.938	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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