YVBV - BACSU - GREMLIN Contacts

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YVBV - Uncharacterized transporter YvbV

UniProt:	O32256	Sequences: MKQLPKTRTALLLAFLVIMWGVNWPLSKAALAYSPPLLFAGIRTLIGGLLLVIVALPRIHKLRLKETWPIYLVSALLNITLFYGLQTIGLNYLPAGLFSAIVFFQPVLMGVFSWLWLGESMFVMKVIGLILGFAGVAVISAAGFGGHISVIGVLLALGSAVSWALGTVYMKKTGSRVDSIWMVALQLTIGSVFLLISGFWTESFSAIQWTAPFITSLLFISVFVIALGWLVFFTLVGSGEASKVASYTFLIPLISIVASSIFLHEPLTLSLLAGLLLIVTSICLVNTKSKAQKAAAIGINEKAAQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	305 (275)
Sequences:	39578 (29152)
Seq/√Len:	1757.9

ECOLI - YEDA YICL YHBE YIJE YTFF RARD EAMA RHTA YDDG YIGM
BACSU - YVBV YBFH YDED YDFC YRDR YCXC YWFM YETK YXXF YOJE YCBK YYAM YDEK YOAV
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
89_G	156_A	3.299	1.00
12_L	234_T	2.909	1.00
97_L	153_V	2.881	1.00
234_T	238_S	2.777	1.00
259_S	265_E	2.656	1.00
88_I	155_L	2.524	1.00
41_G	195_L	2.501	1.00
48_G	188_T	2.459	1.00
128_G	281_S	2.369	1.00
85_L	158_G	2.320	1.00
234_T	237_G	2.292	1.00
26_L	219_F	2.267	1.00
108_L	160_A	2.166	1.00
119_E	171_K	2.141	1.00
85_L	155_L	2.132	1.00
99_S	255_S	2.109	1.00
28_K	265_E	2.066	1.00
112_F	168_V	2.063	1.00
27_S	87_T	1.989	1.00
13_L	235_L	1.972	1.00
21_G	254_I	1.924	1.00
46_I	221_S	1.912	1.00
114_W	121_M	1.890	1.00
81_L	162_S	1.884	1.00
45_L	191_S	1.863	1.00
110_G	129_L	1.854	1.00
52_V	184_A	1.824	1.00
122_F	125_K	1.819	1.00
93_L	153_V	1.795	1.00
104_F	108_L	1.785	1.00
113_S	119_E	1.783	1.00
67_T	176_R	1.782	1.00
192_V	196_I	1.742	1.00
92_Y	151_I	1.731	1.00
93_L	152_G	1.727	1.00
109_M	245_A	1.703	1.00
154_L	158_G	1.692	1.00
21_G	258_A	1.684	1.00
178_D	181_W	1.669	1.00
283_C	287_T	1.660	1.00
53_I	56_L	1.653	1.00
240_E	243_K	1.646	1.00
132_G	249_F	1.628	1.00
48_G	191_S	1.613	1.00
268_T	271_L	1.596	1.00
85_L	162_S	1.588	1.00
196_I	199_F	1.579	1.00
221_S	226_A	1.576	1.00
108_L	164_A	1.564	1.00
22_V	219_F	1.561	1.00
18_I	254_I	1.547	1.00
211_A	215_T	1.522	1.00
98_F	156_A	1.500	1.00
88_I	92_Y	1.494	1.00
41_G	191_S	1.490	1.00
128_G	285_V	1.481	1.00
150_V	153_V	1.451	1.00
52_V	56_L	1.433	1.00
70_I	169_Y	1.413	1.00
210_T	213_F	1.407	1.00
108_L	161_V	1.383	1.00
30_A	39_F	1.382	1.00
170_M	233_F	1.381	1.00
135_G	274_G	1.367	1.00
66_E	70_I	1.360	1.00
47_G	187_L	1.358	1.00
16_L	235_L	1.351	1.00
49_L	53_I	1.345	1.00
69_P	73_V	1.344	1.00
65_K	69_P	1.341	1.00
113_S	117_L	1.340	1.00
88_I	91_N	1.340	1.00
112_F	116_W	1.338	1.00
269_L	273_A	1.336	1.00
132_G	281_S	1.330	1.00
258_A	262_F	1.320	1.00
128_G	284_L	1.312	1.00
20_W	228_G	1.308	1.00
94_P	97_L	1.306	1.00
54_V	58_R	1.306	1.00
95_A	259_S	1.304	1.00
29_A	216_S	1.304	1.00
12_L	231_V	1.285	1.00
93_L	97_L	1.278	1.00
123_V	127_I	1.277	1.00
10_A	247_Y	1.256	1.00
96_G	256_I	1.255	1.00
73_V	169_Y	1.253	1.00
254_I	258_A	1.248	1.00
66_E	69_P	1.242	1.00
65_K	68_W	1.237	1.00
53_I	57_P	1.237	1.00
50_L	226_A	1.234	1.00
138_V	277_L	1.232	1.00
92_Y	155_L	1.225	1.00
212_P	215_T	1.224	1.00
35_P	38_L	1.221	1.00
33_Y	213_F	1.221	1.00
172_K	176_R	1.217	1.00
250_L	254_I	1.206	1.00
25_P	258_A	1.205	1.00
72_L	189_I	1.203	1.00
126_V	130_I	1.202	1.00
215_T	219_F	1.196	1.00
150_V	154_L	1.195	1.00
100_A	275_L	1.190	1.00
39_F	220_I	1.189	1.00
272_L	276_L	1.186	1.00
193_F	196_I	1.184	1.00
138_V	270_S	1.184	1.00
276_L	280_T	1.183	1.00
164_A	168_V	1.176	1.00
267_L	272_L	1.173	1.00
124_M	284_L	1.149	1.00
172_K	175_S	1.144	1.00
139_I	274_G	1.138	1.00
151_I	155_L	1.131	1.00
80_T	193_F	1.129	1.00
37_L	197_S	1.128	1.00
90_L	98_F	1.125	1.00
171_K	175_S	1.121	1.00
92_Y	152_G	1.119	1.00
28_K	32_A	1.115	1.00
93_L	156_A	1.115	1.00
171_K	240_E	1.115	1.00
130_I	134_A	1.111	1.00
109_M	241_A	1.108	1.00
112_F	165_L	1.106	1.00
70_I	173_T	1.105	1.00
76_L	193_F	1.096	1.00
11_L	15_F	1.095	1.00
123_V	126_V	1.095	1.00
236_V	244_V	1.092	1.00
92_Y	149_S	1.085	1.00
135_G	278_I	1.082	1.00
34_S	213_F	1.079	1.00
41_G	198_G	1.075	1.00
16_L	231_V	1.073	1.00
80_T	194_L	1.072	1.00
43_R	225_I	1.067	1.00
112_F	164_A	1.060	1.00
95_A	263_L	1.057	1.00
41_G	45_L	1.057	1.00
117_L	168_V	1.057	1.00
86_Q	90_L	1.056	1.00
20_W	232_F	1.056	1.00
115_L	118_G	1.055	1.00
56_L	60_H	1.053	1.00
16_L	20_W	1.052	1.00
15_F	231_V	1.046	1.00
109_M	167_T	1.040	1.00
110_G	121_M	1.039	1.00
48_G	184_A	1.039	1.00
114_W	120_S	1.038	1.00
151_I	154_L	1.029	1.00
75_A	189_I	1.027	1.00
171_K	241_A	1.024	1.00
9_T	235_L	1.024	1.00
121_M	126_V	1.023	1.00
197_S	201_T	1.018	1.00
26_L	216_S	1.016	1.00
22_V	258_A	1.011	1.00
206_A	209_W	1.004	1.00
19_M	231_V	1.003	1.00
124_M	288_K	1.000	1.00
101_I	160_A	0.993	1.00
27_S	90_L	0.992	1.00
119_E	125_K	0.990	1.00
40_A	87_T	0.989	1.00
69_P	72_L	0.988	1.00
19_M	223_F	0.984	1.00
36_P	40_A	0.979	1.00
131_L	281_S	0.976	1.00
60_H	178_D	0.972	1.00
104_F	136_V	0.967	1.00
77_L	165_L	0.966	1.00
50_L	222_V	0.966	1.00
269_L	272_L	0.965	1.00
160_A	164_A	0.964	1.00
45_L	195_L	0.964	1.00
44_T	190_G	0.964	1.00
141_A	268_T	0.963	1.00
68_W	189_I	0.962	1.00
124_M	287_T	0.962	1.00
215_T	218_L	0.961	1.00
137_A	141_A	0.961	1.00
211_A	214_I	0.959	1.00
77_L	162_S	0.956	1.00
196_I	200_W	0.955	1.00
207_I	210_T	0.951	1.00
214_I	218_L	0.948	1.00
9_T	238_S	0.947	1.00
67_T	70_I	0.947	1.00
67_T	177_V	0.931	1.00
37_L	84_G	0.931	1.00
70_I	172_K	0.928	1.00
25_P	262_F	0.922	1.00
109_M	164_A	0.922	1.00
152_G	156_A	0.920	1.00
38_L	198_G	0.919	1.00
101_I	153_V	0.915	1.00
236_V	240_E	0.914	1.00
122_F	126_V	0.912	1.00
212_P	216_S	0.911	1.00
112_F	161_V	0.911	1.00
240_E	244_V	0.909	1.00
30_A	216_S	0.908	1.00
79_I	166_G	0.901	1.00
218_L	222_V	0.898	1.00
218_L	221_S	0.891	1.00
112_F	115_L	0.889	1.00
197_S	200_W	0.884	1.00
120_S	124_M	0.872	1.00
199_F	202_E	0.870	1.00
101_I	156_A	0.867	1.00
239_G	244_V	0.867	1.00
100_A	137_A	0.867	1.00
95_A	265_E	0.866	1.00
17_V	254_I	0.863	1.00
17_V	21_G	0.854	1.00
188_T	192_V	0.852	1.00
149_S	153_V	0.847	1.00
70_I	74_S	0.839	1.00
239_G	243_K	0.839	1.00
84_G	88_I	0.835	1.00
71_Y	177_V	0.811	1.00
56_L	59_I	0.805	1.00
68_W	72_L	0.801	1.00
256_I	267_L	0.801	1.00
235_L	244_V	0.798	1.00
52_V	188_T	0.797	1.00
136_V	140_S	0.794	1.00
156_A	160_A	0.792	1.00
260_S	267_L	0.791	1.00
270_S	273_A	0.789	1.00
77_L	169_Y	0.783	1.00
134_A	138_V	0.780	1.00
114_W	118_G	0.780	1.00
50_L	53_I	0.778	1.00
189_I	192_V	0.778	1.00
165_L	169_Y	0.774	1.00
134_A	277_L	0.772	1.00
275_L	279_V	0.772	1.00
253_L	275_L	0.770	1.00
56_L	61_K	0.765	1.00
48_G	52_V	0.763	1.00
73_V	76_L	0.758	1.00
40_A	194_L	0.756	1.00
107_V	132_G	0.755	1.00
25_P	259_S	0.754	1.00
80_T	84_G	0.754	1.00
184_A	188_T	0.753	1.00
42_I	46_I	0.748	1.00
13_L	247_Y	0.747	1.00
138_V	273_A	0.747	1.00
57_P	61_K	0.745	1.00
260_S	266_P	0.743	1.00
51_L	226_A	0.741	1.00
256_I	275_L	0.738	1.00
217_L	221_S	0.733	1.00
213_F	216_S	0.731	1.00
120_S	123_V	0.729	1.00
110_G	125_K	0.726	1.00
250_L	253_L	0.726	1.00
208_Q	211_A	0.725	1.00
163_W	167_T	0.721	1.00
185_L	189_I	0.721	1.00
216_S	219_F	0.718	1.00
30_A	213_F	0.717	1.00
93_L	98_F	0.712	1.00
273_A	277_L	0.710	1.00
227_L	231_V	0.708	1.00
82_F	162_S	0.701	1.00
198_G	202_E	0.701	1.00
135_G	281_S	0.698	1.00
111_V	115_L	0.698	1.00
267_L	271_L	0.698	1.00
89_G	152_G	0.697	1.00
54_V	180_I	0.697	1.00
246_S	285_V	0.696	1.00
27_S	31_L	0.695	1.00
183_V	186_Q	0.694	1.00
38_L	42_I	0.694	1.00
57_P	60_H	0.692	1.00
79_I	229_W	0.692	1.00
259_S	263_L	0.692	1.00
14_A	254_I	0.687	1.00
121_M	125_K	0.685	1.00
81_L	85_L	0.681	1.00
17_V	250_L	0.681	1.00
24_W	86_Q	0.679	1.00
33_Y	210_T	0.678	1.00
280_T	284_L	0.675	1.00
127_I	131_L	0.675	1.00
70_I	73_V	0.673	1.00
101_I	157_L	0.673	1.00
104_F	107_V	0.670	1.00
25_P	95_A	0.669	1.00
71_Y	182_M	0.668	1.00
13_L	239_G	0.664	1.00
281_S	285_V	0.663	1.00
58_R	61_K	0.662	1.00
82_F	166_G	0.659	1.00
230_L	234_T	0.659	1.00
177_V	182_M	0.658	1.00
24_W	99_S	0.657	1.00
29_A	263_L	0.656	1.00
55_A	184_A	0.656	1.00
189_I	193_F	0.651	1.00
10_A	243_K	0.647	1.00
256_I	260_S	0.646	1.00
109_M	168_V	0.641	1.00
163_W	232_F	0.640	1.00
179_S	183_V	0.638	1.00
89_G	98_F	0.632	1.00
58_R	178_D	0.631	1.00
75_A	80_T	0.631	1.00
219_F	223_F	0.631	1.00
103_F	106_P	0.630	1.00
68_W	185_L	0.629	1.00
50_L	221_S	0.627	1.00
45_L	49_L	0.627	1.00
103_F	136_V	0.626	1.00
119_E	242_S	0.625	1.00
117_L	172_K	0.618	1.00
144_F	148_I	0.615	1.00
108_L	157_L	0.614	1.00
34_S	39_F	0.613	1.00
19_M	228_G	0.613	1.00
110_G	114_W	0.611	1.00
58_R	180_I	0.609	1.00
86_Q	159_S	0.609	1.00
46_I	50_L	0.605	1.00
181_W	185_L	0.605	1.00
191_S	195_L	0.604	1.00
47_G	226_A	0.604	1.00
271_L	275_L	0.602	1.00
266_P	270_S	0.600	1.00
106_P	249_F	0.598	1.00
72_L	76_L	0.597	1.00
70_I	176_R	0.596	1.00
257_V	261_I	0.588	1.00
79_I	186_Q	0.587	1.00
15_F	19_M	0.587	1.00
79_I	190_G	0.587	1.00
23_N	224_V	0.587	1.00
34_S	38_L	0.586	1.00
104_F	160_A	0.584	1.00
9_T	239_G	0.582	1.00
166_G	233_F	0.579	1.00
183_V	233_F	0.578	1.00
86_Q	98_F	0.576	1.00
125_K	240_E	0.575	1.00
282_I	285_V	0.575	1.00
40_A	84_G	0.574	1.00
131_L	284_L	0.570	1.00
209_W	214_I	0.570	1.00
87_T	91_N	0.569	1.00
155_L	158_G	0.569	1.00
192_V	195_L	0.567	1.00
140_S	153_V	0.560	1.00
68_W	71_Y	0.560	1.00
258_A	261_I	0.559	1.00
167_T	232_F	0.559	1.00
135_G	277_L	0.558	1.00
190_G	194_L	0.558	1.00
17_V	251_I	0.558	1.00
268_T	272_L	0.557	1.00
188_T	191_S	0.556	1.00
49_L	52_V	0.556	1.00
249_F	282_I	0.556	1.00
223_F	227_L	0.555	1.00
185_L	188_T	0.552	1.00
24_W	28_K	0.551	1.00
37_L	201_T	0.547	1.00
10_A	14_A	0.546	1.00
193_F	197_S	0.544	1.00
80_T	197_S	0.544	1.00
35_P	202_E	0.539	1.00
210_T	214_I	0.538	1.00
82_F	86_Q	0.532	1.00
100_A	139_I	0.532	1.00
55_A	181_W	0.531	1.00
248_T	251_I	0.531	1.00
55_A	59_I	0.528	1.00
142_A	270_S	0.528	1.00
113_S	242_S	0.525	1.00
167_T	245_A	0.523	1.00
117_L	171_K	0.523	1.00
266_P	271_L	0.521	1.00
166_G	170_M	0.520	1.00
284_L	288_K	0.518	1.00
19_M	227_L	0.518	1.00
79_I	83_Y	0.516	1.00
71_Y	75_A	0.515	1.00
72_L	193_F	0.515	1.00
116_W	165_L	0.515	1.00
183_V	187_L	0.514	1.00
100_A	140_S	0.513	1.00
14_A	17_V	0.513	1.00
31_L	91_N	0.512	1.00
54_V	57_P	0.511	1.00
13_L	232_F	0.509	1.00
85_L	159_S	0.507	1.00
31_L	90_L	0.506	1.00
42_I	217_L	0.504	1.00
235_L	239_G	0.503	1.00
153_V	157_L	0.503	1.00
84_G	194_L	0.503	1.00
203_S	208_Q	0.502	1.00
103_F	160_A	0.501	1.00
67_T	71_Y	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	0.2525	98.8	0.771	Contact Map
3b5dA	2	0.3311	98.2	0.804	Contact Map
1pw4A	1	0.9705	66.4	0.916	Contact Map
4he8J	1	0.5049	64.1	0.917	Contact Map
4j05A	3	0.9508	60.2	0.919	Contact Map
4pypA	1	0.9311	54.6	0.922	Contact Map
2cfqA	1	0.6	47.2	0.925	Contact Map
3wdoA	1	0.9508	42.9	0.927	Contact Map
3l1lA	2	0.8754	37.5	0.929	Contact Map
4zw9A	1	0.9672	28.3	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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