YBFH - BACSU - GREMLIN Contacts

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YBFH - Uncharacterized transporter YbhF

UniProt:	O31448	Sequences: MNIQRETSGHIAAIVTILIWGTTFISTKVLLADFSPMEILFYRFLMGFIALILVRPNMIPFRNWRQELLFAGAGLFGVTLYFLLENIALTYTYASNVGMIVSIIPMITAVLAHFLLEGEKLRLTFLIGFISALIGLLLITFNGNVVLRLNPLGDIMAAGAALVFGGYSIFMKKLSAYEYHIIELTQRVFLYGLLFMVPALFLFDFHFDLSRFSSASNILNMLFLGIGASALCFATWNYSVGVLGAVKSSAYIYMVPVITIAASVLILHENMTWIALLGGALTLLGLYISELKPKAKLLENGCKMDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	306 (275)
Sequences:	38720 (28480)
Seq/√Len:	1717.4

ECOLI - YEDA YICL YIJE YHBE YTFF EAMA RARD RHTA YDDG YIGM
BACSU - YBFH YVBV YCXC YDED YDFC YRDR YETK YWFM YXXF YYAM YCBK YOJE YOAV YDEK
HALSA - Q9HHP6 Q9HQ34 Q9HPI0
SULSO - Q97UX3 Q97X73 Q97UE8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
88_A	157_A	3.336	1.00
12_A	238_Y	2.905	1.00
96_N	154_D	2.806	1.00
238_Y	242_V	2.757	1.00
263_S	269_E	2.651	1.00
87_I	156_M	2.550	1.00
41_F	197_V	2.482	1.00
48_F	190_L	2.472	1.00
128_G	285_G	2.363	1.00
84_L	159_G	2.341	1.00
26_S	223_F	2.332	1.00
63_N	66_Q	2.331	1.00
238_Y	241_G	2.255	1.00
107_I	161_A	2.227	1.00
119_E	172_K	2.137	1.00
84_L	156_M	2.107	1.00
215_A	219_L	2.099	1.00
28_K	269_E	2.094	1.00
111_L	169_I	2.088	1.00
98_G	259_T	2.046	1.00
13_A	239_S	2.014	1.00
21_G	258_I	2.009	1.00
46_M	225_G	2.004	1.00
27_T	86_N	1.946	1.00
113_H	121_L	1.908	1.00
80_L	163_V	1.881	1.00
52_I	186_Q	1.857	1.00
45_L	193_L	1.842	1.00
109_A	129_F	1.816	1.00
103_I	107_I	1.811	1.00
155_I	159_G	1.779	1.00
108_T	249_S	1.767	1.00
92_T	153_G	1.761	1.00
112_A	119_E	1.741	1.00
194_L	198_P	1.723	1.00
91_Y	152_L	1.699	1.00
92_T	154_D	1.696	1.00
122_R	125_F	1.673	1.00
287_Y	291_L	1.652	1.00
180_H	183_E	1.638	1.00
244_G	247_K	1.633	1.00
21_G	262_A	1.628	1.00
225_G	230_A	1.612	1.00
22_T	223_F	1.597	1.00
214_S	217_N	1.596	1.00
19_I	227_G	1.583	1.00
84_L	163_V	1.575	1.00
132_A	253_Y	1.574	1.00
66_Q	178_E	1.570	1.00
198_P	201_F	1.568	1.00
48_F	193_L	1.552	1.00
107_I	165_G	1.547	1.00
18_L	258_I	1.545	1.00
272_T	275_A	1.527	1.00
128_G	289_S	1.494	1.00
87_I	91_Y	1.478	1.00
34_F	217_N	1.458	1.00
112_A	116_L	1.453	1.00
97_V	157_A	1.445	1.00
41_F	193_L	1.417	1.00
107_I	162_L	1.405	1.00
151_P	154_D	1.394	1.00
65_R	69_L	1.386	1.00
171_M	237_N	1.381	1.00
16_T	239_S	1.374	1.00
111_L	115_L	1.374	1.00
30_L	39_I	1.370	1.00
273_W	277_L	1.369	1.00
65_R	68_L	1.343	1.00
94_A	263_S	1.342	1.00
33_D	217_N	1.340	1.00
69_L	170_F	1.325	1.00
47_G	189_F	1.320	1.00
262_A	266_I	1.312	1.00
87_I	90_T	1.299	1.00
92_T	96_N	1.296	1.00
20_W	232_C	1.288	1.00
64_W	67_E	1.284	1.00
128_G	288_I	1.274	1.00
123_L	127_I	1.273	1.00
138_L	281_L	1.271	1.00
68_L	72_G	1.267	1.00
91_Y	156_M	1.263	1.00
276_L	280_A	1.260	1.00
12_A	235_T	1.260	1.00
132_A	285_G	1.256	1.00
50_A	230_A	1.255	1.00
49_I	53_L	1.252	1.00
64_W	68_L	1.249	1.00
29_V	220_N	1.246	1.00
135_G	278_G	1.245	1.00
93_Y	96_N	1.245	1.00
95_S	260_I	1.243	1.00
195_F	198_P	1.238	1.00
25_I	262_A	1.234	1.00
216_S	220_N	1.223	1.00
138_L	274_I	1.214	1.00
165_G	169_I	1.212	1.00
258_I	262_A	1.211	1.00
280_A	284_L	1.205	1.00
39_I	224_L	1.201	1.00
99_M	279_G	1.198	1.00
72_G	170_F	1.197	1.00
215_A	218_I	1.191	1.00
10_H	251_Y	1.190	1.00
216_S	219_L	1.186	1.00
28_K	32_A	1.184	1.00
151_P	155_I	1.182	1.00
254_M	258_I	1.182	1.00
35_S	38_E	1.170	1.00
130_I	134_I	1.168	1.00
124_T	288_I	1.166	1.00
126_L	130_I	1.165	1.00
111_L	166_G	1.159	1.00
271_M	276_L	1.145	1.00
172_K	244_G	1.144	1.00
48_F	186_Q	1.136	1.00
135_G	282_T	1.131	1.00
219_L	223_F	1.120	1.00
71_A	191_Y	1.120	1.00
139_I	278_G	1.119	1.00
152_L	156_M	1.117	1.00
55_R	59_I	1.112	1.00
89_L	97_V	1.112	1.00
116_L	169_I	1.102	1.00
37_M	199_A	1.094	1.00
172_K	176_A	1.093	1.00
108_T	245_A	1.091	1.00
79_T	196_M	1.086	1.00
41_F	45_L	1.082	1.00
41_F	200_L	1.075	1.00
11_I	15_V	1.074	1.00
43_R	229_S	1.072	1.00
91_Y	153_G	1.071	1.00
75_L	195_F	1.069	1.00
57_N	60_P	1.068	1.00
91_Y	150_N	1.061	1.00
79_T	195_F	1.059	1.00
15_V	235_T	1.056	1.00
22_T	262_A	1.050	1.00
16_T	20_W	1.049	1.00
240_V	248_S	1.048	1.00
121_L	126_L	1.044	1.00
113_H	120_K	1.042	1.00
172_K	245_A	1.038	1.00
123_L	126_L	1.026	1.00
92_T	157_A	1.023	1.00
16_T	235_T	1.020	1.00
9_G	239_S	1.020	1.00
69_L	174_L	1.020	1.00
124_T	291_L	1.019	1.00
27_T	89_L	1.018	1.00
109_A	121_L	1.017	1.00
20_W	236_W	1.016	1.00
124_T	292_K	1.015	1.00
111_L	165_G	1.011	1.00
85_E	89_L	1.010	1.00
108_T	168_S	1.008	1.00
173_K	176_A	1.005	1.00
94_A	267_L	1.005	1.00
19_I	235_T	1.002	1.00
100_I	161_A	1.001	1.00
152_L	155_I	1.000	1.00
26_S	220_N	0.990	1.00
40_L	86_N	0.989	1.00
199_A	203_F	0.987	1.00
58_M	61_F	0.986	1.00
66_Q	179_Y	0.981	1.00
30_L	217_N	0.977	1.00
119_E	125_F	0.976	1.00
219_L	222_L	0.974	1.00
137_L	141_F	0.972	1.00
74_G	191_Y	0.971	1.00
103_I	136_L	0.969	1.00
161_A	165_G	0.956	1.00
69_L	73_A	0.951	1.00
122_R	126_L	0.945	1.00
227_G	231_L	0.944	1.00
25_I	266_I	0.939	1.00
218_I	222_L	0.937	1.00
153_G	157_A	0.936	1.00
36_P	40_L	0.936	1.00
131_S	285_G	0.935	1.00
198_P	202_L	0.934	1.00
68_L	71_A	0.932	1.00
111_L	162_L	0.930	1.00
222_L	225_G	0.930	1.00
44_F	192_G	0.928	1.00
17_I	21_G	0.928	1.00
221_M	225_G	0.928	1.00
141_F	272_T	0.926	1.00
273_W	276_L	0.923	1.00
100_I	154_D	0.921	1.00
37_M	83_L	0.921	1.00
30_L	220_N	0.916	1.00
111_L	114_F	0.915	1.00
114_F	117_E	0.913	1.00
38_E	200_L	0.907	1.00
9_G	242_V	0.906	1.00
240_V	244_G	0.898	1.00
223_F	227_G	0.897	1.00
58_M	180_H	0.897	1.00
117_E	120_K	0.895	1.00
66_Q	69_L	0.893	1.00
100_I	157_A	0.891	1.00
244_G	248_S	0.886	1.00
45_L	197_V	0.881	1.00
76_F	163_V	0.879	1.00
17_I	258_I	0.879	1.00
120_K	124_T	0.872	1.00
199_A	202_L	0.870	1.00
83_L	87_I	0.866	1.00
76_F	166_G	0.866	1.00
63_N	67_E	0.855	1.00
33_D	214_S	0.848	1.00
243_L	248_S	0.848	1.00
108_T	165_G	0.847	1.00
99_M	137_L	0.843	1.00
201_F	204_D	0.841	1.00
67_E	191_Y	0.840	1.00
94_A	269_E	0.834	1.00
190_L	194_L	0.824	1.00
50_A	226_I	0.823	1.00
56_P	60_P	0.820	1.00
78_V	167_Y	0.819	1.00
264_V	271_M	0.819	1.00
56_P	59_I	0.819	1.00
69_L	173_K	0.811	1.00
202_L	205_F	0.810	1.00
134_I	138_L	0.808	1.00
243_L	247_K	0.807	1.00
52_I	190_L	0.805	1.00
25_I	263_S	0.803	1.00
239_S	248_S	0.801	1.00
55_R	58_M	0.799	1.00
120_K	123_L	0.792	1.00
166_G	170_F	0.791	1.00
260_I	271_M	0.784	1.00
70_F	179_Y	0.779	1.00
113_H	117_E	0.778	1.00
134_I	281_L	0.770	1.00
138_L	277_L	0.768	1.00
150_N	154_D	0.767	1.00
222_L	226_I	0.766	1.00
186_Q	190_L	0.766	1.00
116_L	119_E	0.763	1.00
257_V	279_G	0.762	1.00
40_L	196_M	0.759	1.00
191_Y	194_L	0.756	1.00
254_M	257_V	0.755	1.00
157_A	161_A	0.752	1.00
50_A	53_L	0.751	1.00
136_L	140_T	0.751	1.00
213_S	218_I	0.749	1.00
79_T	83_L	0.744	1.00
279_G	283_L	0.744	1.00
274_I	277_L	0.743	1.00
48_F	52_I	0.743	1.00
106_M	132_A	0.740	1.00
164_F	168_S	0.740	1.00
42_Y	46_M	0.740	1.00
214_S	218_I	0.738	1.00
260_I	279_G	0.736	1.00
14_I	258_I	0.734	1.00
277_L	281_L	0.731	1.00
72_G	75_L	0.731	1.00
67_E	71_A	0.719	1.00
110_V	114_F	0.717	1.00
179_Y	184_L	0.713	1.00
213_S	217_N	0.712	1.00
191_Y	195_F	0.712	1.00
81_Y	163_V	0.711	1.00
264_V	270_N	0.710	1.00
231_L	235_T	0.709	1.00
51_L	230_A	0.709	1.00
121_L	125_F	0.706	1.00
80_L	84_L	0.704	1.00
38_E	42_Y	0.704	1.00
45_L	49_I	0.703	1.00
27_T	31_L	0.703	1.00
263_S	267_L	0.703	1.00
108_T	169_I	0.702	1.00
187_R	191_Y	0.701	1.00
127_I	131_S	0.700	1.00
13_A	251_Y	0.698	1.00
10_H	247_K	0.697	1.00
183_E	187_R	0.695	1.00
59_I	62_R	0.689	1.00
103_I	106_M	0.688	1.00
109_A	125_F	0.688	1.00
34_F	39_I	0.688	1.00
74_G	79_T	0.688	1.00
78_V	233_F	0.687	1.00
17_I	254_M	0.685	1.00
100_I	158_A	0.685	1.00
29_V	267_L	0.684	1.00
25_I	94_A	0.681	1.00
201_F	205_F	0.674	1.00
69_L	72_G	0.672	1.00
164_F	236_W	0.669	1.00
13_A	243_L	0.668	1.00
92_T	97_V	0.668	1.00
54_V	182_I	0.667	1.00
271_M	275_A	0.666	1.00
284_L	288_I	0.666	1.00
141_F	144_N	0.665	1.00
193_L	197_V	0.665	1.00
81_Y	167_Y	0.661	1.00
220_N	223_F	0.660	1.00
217_N	220_N	0.658	1.00
135_G	285_G	0.657	1.00
88_A	97_V	0.655	1.00
24_F	98_G	0.653	1.00
107_I	158_A	0.653	1.00
214_S	219_L	0.652	1.00
63_N	68_L	0.651	1.00
194_L	197_V	0.650	1.00
109_A	113_H	0.647	1.00
88_A	153_G	0.643	1.00
185_T	188_V	0.642	1.00
76_F	170_F	0.640	1.00
102_S	136_L	0.638	1.00
270_N	274_I	0.637	1.00
24_F	85_E	0.635	1.00
190_L	193_L	0.634	1.00
250_A	289_S	0.631	1.00
70_F	184_L	0.629	1.00
200_L	204_D	0.625	1.00
131_S	288_I	0.623	1.00
285_G	289_S	0.621	1.00
234_A	238_Y	0.621	1.00
47_G	230_A	0.616	1.00
19_I	228_A	0.614	1.00
119_E	246_V	0.612	1.00
260_I	264_V	0.612	1.00
50_A	225_G	0.612	1.00
85_E	160_A	0.612	1.00
181_I	185_T	0.607	1.00
105_P	253_Y	0.605	1.00
67_E	70_F	0.603	1.00
19_I	232_C	0.603	1.00
275_A	279_G	0.601	1.00
35_S	204_D	0.596	1.00
46_M	50_A	0.596	1.00
34_F	38_E	0.594	1.00
71_A	75_L	0.591	1.00
185_T	237_N	0.589	1.00
167_Y	237_N	0.584	1.00
86_N	90_T	0.581	1.00
140_T	154_D	0.580	1.00
15_V	19_I	0.579	1.00
85_E	97_V	0.579	1.00
103_I	161_A	0.578	1.00
79_T	199_A	0.577	1.00
102_S	105_P	0.574	1.00
192_G	196_M	0.572	1.00
67_E	187_R	0.568	1.00
31_L	89_L	0.568	1.00
125_F	244_G	0.567	1.00
116_L	172_K	0.567	1.00
262_A	265_L	0.566	1.00
272_T	276_L	0.566	1.00
261_A	265_L	0.562	1.00
156_M	159_G	0.562	1.00
187_R	190_L	0.560	1.00
78_V	188_V	0.559	1.00
10_H	14_I	0.559	1.00
23_T	228_A	0.558	1.00
71_A	74_G	0.557	1.00
49_I	52_I	0.553	1.00
99_M	139_I	0.553	1.00
24_F	28_K	0.552	1.00
168_S	236_W	0.551	1.00
9_G	243_L	0.550	1.00
70_F	74_G	0.549	1.00
115_L	166_G	0.547	1.00
84_L	160_A	0.545	1.00
78_V	192_G	0.542	1.00
37_M	203_F	0.540	1.00
253_Y	286_L	0.539	1.00
149_L	152_L	0.538	1.00
270_N	275_A	0.537	1.00
252_I	255_V	0.535	1.00
116_L	173_K	0.531	1.00
14_I	17_I	0.529	1.00
162_L	166_G	0.529	1.00
81_Y	85_E	0.528	1.00
102_S	161_A	0.527	1.00
168_S	249_S	0.527	1.00
73_A	76_F	0.526	1.00
57_N	61_F	0.526	1.00
110_V	129_F	0.526	1.00
17_I	255_V	0.524	1.00
288_I	292_K	0.523	1.00
99_M	140_T	0.519	1.00
103_I	132_A	0.517	1.00
286_L	289_S	0.517	1.00
42_Y	221_M	0.516	1.00
71_A	195_F	0.515	1.00
264_V	276_L	0.515	1.00
261_A	264_V	0.515	1.00
276_L	279_G	0.513	1.00
38_E	204_D	0.508	1.00
112_A	246_V	0.507	1.00
223_F	226_I	0.505	1.00
167_Y	171_M	0.505	1.00
171_M	175_S	0.505	1.00
179_Y	183_E	0.504	1.00
235_T	238_Y	0.503	1.00
142_N	274_I	0.502	1.00
19_I	231_L	0.500	1.00
88_A	92_T	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
2i68A	2	0.2516	98.8	0.758	Contact Map
3b5dA	2	0.3301	98.3	0.798	Contact Map
4he8J	1	0.5033	53.7	0.92	Contact Map
4pypA	1	0.915	49.9	0.922	Contact Map
1pw4A	1	0.9608	49.7	0.922	Contact Map
3wdoA	1	0.9346	36.7	0.928	Contact Map
2cfqA	1	0.5948	28.2	0.932	Contact Map
4j05A	3	0.9216	25.5	0.933	Contact Map
4zw9A	1	0.951	23.8	0.934	Contact Map
2kluA	1	0.1503	23	0.934	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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