YDBK - BACSU - GREMLIN Contacts

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YDBK - Uncharacterized membrane protein YdbK

UniProt:	P96606	Sequences: MKLFNRKVTLVSLILMAVFQFFMALIIKRIVISAGTDENFIGYLSYTPSLNILLQALTIVIAATIVSMEFDKKTIKFLLIRPVKRQKVFWSKLITVVMVSFYLYLAYYILALLFGLLFFGTSVTAESKTLLVNTLALIGSNWLEAVMMGLFGLLCSSLFRNSAVAVVVSFVVLYGASTLVQLMKLFENKWGSFLLFANTDFTQYRSGETALFSGMTPLFSIGILIIHAIFFIVVGWWCFCKRDVRV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	246 (229)
Sequences:	4861 (3899)
Seq/√Len:	257.6

BACSU - YDBK YXLG YHCI
HALSA - Q9HMU9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
78_L	88_V	3.827	1.00
89_F	235_G	3.565	1.00
86_Q	236_W	3.371	1.00
79_L	239_F	3.260	1.00
154_L	235_G	3.078	1.00
238_C	242_R	3.060	1.00
69_E	92_K	2.968	1.00
58_T	100_S	2.843	1.00
195_L	198_N	2.756	1.00
73_K	76_K	2.696	1.00
96_V	149_G	2.678	1.00
59_I	152_G	2.589	1.00
222_G	226_I	2.581	1.00
66_V	157_S	2.564	1.00
97_V	146_V	2.410	1.00
233_V	237_W	2.402	1.00
93_L	150_L	2.376	1.00
218_L	222_G	2.314	1.00
154_L	231_F	2.214	1.00
216_T	219_F	2.181	1.00
154_L	234_V	2.100	1.00
93_L	153_L	2.081	1.00
11_V	15_L	2.077	1.00
198_N	220_S	2.039	1.00
67_S	156_S	2.006	1.00
63_A	165_A	1.986	1.00
65_I	95_T	1.927	1.00
155_C	169_S	1.923	1.00
135_L	139_G	1.908	1.00
90_W	236_W	1.884	1.00
159_F	168_V	1.865	1.00
147_M	228_A	1.822	1.00
155_C	159_F	1.821	1.00
86_Q	240_C	1.809	1.00
101_F	142_W	1.792	1.00
192_S	195_L	1.788	1.00
158_L	238_C	1.764	1.00
116_L	121_T	1.735	1.00
84_K	87_K	1.715	1.00
22_F	26_I	1.702	1.00
93_L	232_I	1.683	1.00
172_V	177_S	1.672	1.00
65_I	96_V	1.642	1.00
8_V	64_T	1.639	1.00
79_L	88_V	1.587	1.00
89_F	236_W	1.581	1.00
223_I	227_H	1.571	1.00
108_Y	142_W	1.558	1.00
197_A	200_D	1.547	1.00
69_E	74_T	1.538	1.00
200_D	203_Q	1.523	1.00
189_K	193_F	1.521	1.00
75_I	79_L	1.521	1.00
59_I	169_S	1.484	1.00
67_S	162_S	1.468	1.00
189_K	192_S	1.466	1.00
105_L	142_W	1.462	1.00
191_G	197_A	1.432	1.00
194_L	199_T	1.424	1.00
144_E	199_T	1.418	1.00
70_F	242_R	1.418	1.00
139_G	143_L	1.417	1.00
154_L	157_S	1.415	1.00
227_H	231_F	1.390	1.00
18_V	22_F	1.371	1.00
164_V	168_V	1.370	1.00
24_A	28_K	1.369	1.00
167_V	171_V	1.351	1.00
225_I	229_I	1.345	1.00
195_L	199_T	1.332	1.00
62_A	96_V	1.303	1.00
91_S	94_I	1.300	1.00
70_F	160_R	1.285	1.00
60_V	167_V	1.285	1.00
147_M	231_F	1.259	1.00
230_F	233_V	1.248	1.00
95_T	98_M	1.246	1.00
136_A	139_G	1.243	1.00
62_A	152_G	1.240	1.00
39_N	42_G	1.234	1.00
155_C	168_V	1.230	1.00
222_G	225_I	1.224	1.00
226_I	230_F	1.207	1.00
46_Y	49_S	1.198	1.00
152_G	165_A	1.195	1.00
100_S	149_G	1.185	1.00
112_L	116_L	1.175	1.00
89_F	157_S	1.174	1.00
64_T	68_M	1.174	1.00
129_T	132_V	1.159	1.00
68_M	72_K	1.153	1.00
96_V	100_S	1.147	1.00
41_I	44_L	1.140	1.00
6_R	9_T	1.139	1.00
119_F	122_S	1.132	1.00
96_V	153_L	1.117	1.00
194_L	197_A	1.107	1.00
98_M	102_Y	1.095	1.00
193_F	196_F	1.093	1.00
109_I	113_L	1.087	1.00
113_L	117_L	1.068	1.00
91_S	95_T	1.058	1.00
58_T	62_A	1.055	1.00
154_L	238_C	1.053	1.00
10_L	14_I	1.051	1.00
223_I	226_I	1.049	1.00
70_F	75_I	1.048	1.00
78_L	81_R	1.045	1.00
23_M	27_I	1.039	1.00
189_K	194_L	1.033	1.00
163_A	167_V	1.027	1.00
28_K	118_F	1.024	1.00
40_F	47_T	1.021	1.00
20_Q	24_A	1.019	1.00
161_N	164_V	1.015	1.00
67_S	157_S	1.013	1.00
34_A	42_G	1.007	1.00
201_F	204_Y	1.003	1.00
158_L	234_V	0.999	1.00
200_D	204_Y	0.996	1.00
67_S	165_A	0.996	1.00
7_K	10_L	0.976	1.00
148_M	173_L	0.973	1.00
152_G	169_S	0.972	1.00
113_L	116_L	0.967	1.00
229_I	233_V	0.961	1.00
61_I	99_V	0.960	1.00
58_T	149_G	0.943	1.00
86_Q	90_W	0.937	1.00
200_D	206_S	0.932	1.00
65_I	77_F	0.932	1.00
166_V	169_S	0.927	1.00
221_I	225_I	0.923	1.00
37_D	40_F	0.923	1.00
35_G	45_S	0.916	1.00
159_F	165_A	0.903	1.00
237_W	241_K	0.900	1.00
238_C	241_K	0.895	1.00
55_Q	148_M	0.892	1.00
58_T	169_S	0.875	1.00
77_F	80_I	0.872	1.00
37_D	42_G	0.864	1.00
164_V	167_V	0.860	1.00
62_A	149_G	0.857	1.00
97_V	153_L	0.850	0.99
63_A	152_G	0.848	0.99
104_Y	146_V	0.845	0.99
147_M	150_L	0.835	0.99
12_S	57_L	0.833	0.99
16_M	103_L	0.831	0.99
14_I	18_V	0.825	0.99
218_L	221_I	0.823	0.99
85_R	243_D	0.819	0.99
128_K	131_L	0.814	0.99
36_T	40_F	0.810	0.99
29_R	32_I	0.808	0.99
215_M	223_I	0.801	0.99
89_F	239_F	0.801	0.99
16_M	57_L	0.801	0.99
150_L	154_L	0.799	0.99
58_T	152_G	0.798	0.99
156_S	165_A	0.798	0.99
132_V	136_A	0.797	0.99
21_F	28_K	0.794	0.99
43_Y	47_T	0.793	0.99
142_W	146_V	0.792	0.99
176_A	180_V	0.790	0.99
191_G	194_L	0.790	0.99
234_V	237_W	0.789	0.99
34_A	38_E	0.789	0.99
176_A	196_F	0.787	0.99
42_G	48_P	0.783	0.99
35_G	40_F	0.780	0.99
146_V	228_A	0.778	0.99
135_L	138_I	0.777	0.99
198_N	223_I	0.776	0.99
66_V	156_S	0.776	0.99
217_P	220_S	0.775	0.99
4_F	10_L	0.773	0.99
35_G	38_E	0.772	0.99
44_L	49_S	0.768	0.99
192_S	198_N	0.761	0.99
108_Y	138_I	0.758	0.99
77_F	81_R	0.754	0.99
151_F	172_V	0.753	0.99
160_R	242_R	0.751	0.99
157_S	239_F	0.745	0.99
57_L	227_H	0.737	0.98
90_W	232_I	0.732	0.98
99_V	103_L	0.728	0.98
29_R	33_S	0.722	0.98
29_R	35_G	0.719	0.98
71_D	161_N	0.717	0.98
71_D	162_S	0.713	0.98
215_M	218_L	0.712	0.98
33_S	41_I	0.710	0.98
235_G	239_F	0.709	0.98
44_L	47_T	0.709	0.98
219_F	223_I	0.703	0.98
29_R	34_A	0.699	0.98
64_T	162_S	0.696	0.98
56_A	170_F	0.693	0.98
52_I	174_Y	0.693	0.98
21_F	113_L	0.688	0.98
34_A	41_I	0.685	0.98
62_A	154_L	0.685	0.98
220_S	223_I	0.684	0.98
226_I	229_I	0.684	0.98
180_V	194_L	0.684	0.98
163_A	166_V	0.682	0.98
114_F	118_F	0.680	0.97
175_G	178_T	0.676	0.97
6_R	78_L	0.676	0.97
40_F	43_Y	0.676	0.97
116_L	120_G	0.673	0.97
9_T	72_K	0.669	0.97
228_A	232_I	0.668	0.97
36_T	39_N	0.667	0.97
13_L	103_L	0.666	0.97
162_S	165_A	0.663	0.97
101_F	139_G	0.660	0.97
104_Y	108_Y	0.651	0.97
213_S	216_T	0.647	0.97
71_D	80_I	0.646	0.97
78_L	82_P	0.644	0.96
138_I	142_W	0.644	0.96
17_A	110_L	0.644	0.96
34_A	40_F	0.636	0.96
180_V	183_M	0.636	0.96
94_I	97_V	0.635	0.96
56_A	173_L	0.633	0.96
42_G	46_Y	0.631	0.96
97_V	150_L	0.630	0.96
69_E	75_I	0.628	0.96
23_M	28_K	0.627	0.96
15_L	181_Q	0.627	0.96
202_T	206_S	0.627	0.96
85_R	160_R	0.625	0.96
87_K	91_S	0.625	0.96
197_A	203_Q	0.624	0.96
215_M	229_I	0.624	0.96
6_R	159_F	0.623	0.96
45_S	49_S	0.623	0.96
236_W	240_C	0.621	0.96
64_T	83_V	0.621	0.96
110_L	113_L	0.617	0.96
134_T	138_I	0.614	0.95
37_D	43_Y	0.611	0.95
53_L	91_S	0.610	0.95
38_E	49_S	0.608	0.95
172_V	176_A	0.608	0.95
161_N	174_Y	0.605	0.95
38_E	41_I	0.603	0.95
191_G	196_F	0.602	0.95
64_T	156_S	0.601	0.95
169_S	173_L	0.599	0.95
159_F	164_V	0.595	0.95
204_Y	207_G	0.594	0.95
35_G	39_N	0.593	0.94
215_M	220_S	0.592	0.94
141_N	199_T	0.590	0.94
74_T	77_F	0.586	0.94
78_L	97_V	0.585	0.94
42_G	45_S	0.585	0.94
44_L	48_P	0.584	0.94
24_A	27_I	0.584	0.94
132_V	137_L	0.582	0.94
35_G	49_S	0.582	0.94
29_R	36_T	0.579	0.94
9_T	15_L	0.579	0.94
196_F	199_T	0.578	0.94
191_G	195_L	0.575	0.94
68_M	107_Y	0.574	0.93
44_L	181_Q	0.574	0.93
10_L	234_V	0.573	0.93
228_A	231_F	0.571	0.93
13_L	102_Y	0.570	0.93
196_F	200_D	0.569	0.93
60_V	166_V	0.567	0.93
88_V	239_F	0.567	0.93
104_Y	142_W	0.565	0.93
193_F	223_I	0.564	0.93
194_L	198_N	0.563	0.93
51_N	141_N	0.559	0.93
194_L	200_D	0.559	0.93
237_W	240_C	0.558	0.93
47_T	116_L	0.558	0.93
8_V	13_L	0.556	0.92
72_K	162_S	0.555	0.92
16_M	22_F	0.554	0.92
9_T	25_L	0.554	0.92
178_T	181_Q	0.553	0.92
24_A	121_T	0.552	0.92
75_I	239_F	0.550	0.92
55_Q	145_A	0.550	0.92
236_W	241_K	0.549	0.92
150_L	153_L	0.548	0.92
155_C	165_A	0.547	0.92
11_V	14_I	0.547	0.92
158_L	235_G	0.546	0.92
153_L	156_S	0.546	0.92
67_S	80_I	0.545	0.92
20_Q	107_Y	0.544	0.92
68_M	162_S	0.544	0.92
101_F	104_Y	0.542	0.91
32_I	38_E	0.537	0.91
59_I	173_L	0.537	0.91
55_Q	174_Y	0.537	0.91
104_Y	110_L	0.535	0.91
143_L	168_V	0.532	0.91
150_L	228_A	0.532	0.91
56_A	181_Q	0.532	0.91
203_Q	206_S	0.531	0.91
63_A	156_S	0.531	0.91
45_S	51_N	0.530	0.90
32_I	35_G	0.528	0.90
54_L	145_A	0.528	0.90
63_A	67_S	0.525	0.90
201_F	205_R	0.524	0.90
88_V	175_G	0.521	0.90
15_L	233_V	0.519	0.90
215_M	219_F	0.519	0.90
180_V	186_F	0.517	0.89
23_M	153_L	0.516	0.89
220_S	224_L	0.516	0.89
57_L	76_K	0.515	0.89
9_T	99_V	0.514	0.89
95_T	175_G	0.514	0.89
147_M	227_H	0.514	0.89
189_K	195_L	0.512	0.89
146_V	150_L	0.509	0.89
7_K	14_I	0.508	0.89
40_F	49_S	0.507	0.88
34_A	37_D	0.507	0.88
177_S	183_M	0.507	0.88
13_L	106_A	0.505	0.88
83_V	91_S	0.504	0.88
36_T	45_S	0.503	0.88
115_G	220_S	0.502	0.88
21_F	25_L	0.501	0.88
120_G	123_V	0.501	0.88
12_S	171_V	0.500	0.88
42_G	47_T	0.500	0.88
69_E	78_L	0.500	0.88

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
4us3A	1	0.4309	10.2	0.93	Contact Map
1qleD	1	0.1748	4.6	0.941	Contact Map
1iijA	1	0.1423	4.1	0.942	Contact Map
3j2wE	1	0.187	4	0.942	Contact Map
2l2tA	2	0.1667	3.7	0.943	Contact Map
2mmuA	1	0.2033	3.4	0.944	Contact Map
2llmA	1	0.1748	2.9	0.947	Contact Map
3ar4A	1	0.2846	2.6	0.948	Contact Map
4c7rA	3	0.5813	2.3	0.949	Contact Map
2wswA	3	0.6423	2.2	0.95	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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