YIBD - ECOLI - GREMLIN Contacts

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YIBD - Uncharacterized glycosyltransferase YibD

UniProt:	P11290	Sequences: MMNSTNKLSVIIPLYNAGDDFRTCMESLITQTWTALEIIIINDGSTDNSVEIAKYYAENYPHVRLLHQANAGASVARNRGIEVATGKYVAFVDADDEVYPTMYETLMTMALEDDLDVAQCNADWCFRETGETWQSIPTDRLRSTGVLTGPDWLRMGLSSRRWTHVVWMGVYRRDVIVKNNIKFIAGLHHQDIVWTTEFMFNALRARYTEQSLYKYYLHNTSVSRLHRQGNKNLNYQRHYIKITRLLEKLNRNYADKIMIYPEFHQQITYEALRVCHAVRKEPDILTRQRMIAEIFTSGMYKRLITNVRSVKVGYQALLWSFRLWQWRDKTRSHHRITRSAFNLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11266
Length:	344 (285)
Sequences:	10510 (9612)
Seq/√Len:	569.4

ECOLI - YIBD WCAA WCAE WBBL ARNC GTRB PGAC YAIP
BACSU - GGAA EPSJ EPSH CGED GGAB EPSE YFNE TUAG SPSA YKCC YWDF TAGF YKOT CSBB YDAM
HALSA - Q9HQP4 Q9HQP8 Q9HSC8 Q9HQQ6 Q9HQP3 Q9HNK3 Q9HR08 Q9HSB1
SULSO - Q7LXF7 Q97TZ0 Q97TY0 Q7LXG6 Q97X05 Q97W52 Q97YG5 Q97YN4 Q7LXY2 Q97WK7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
173_R	177_V	3.819	1.00
17_A	94_A	3.585	1.00
18_G	48_N	3.041	1.00
14_L	49_S	2.996	1.00
23_T	216_Y	2.946	1.00
105_T	210_Q	2.755	1.00
79_R	83_V	2.729	1.00
193_V	197_E	2.665	1.00
32_T	104_E	2.501	1.00
42_N	67_H	2.412	1.00
82_E	182_K	2.378	1.00
71_A	75_V	2.347	1.00
115_L	206_R	2.286	1.00
48_N	51_E	2.267	1.00
22_R	26_E	2.251	1.00
99_Y	214_K	2.239	1.00
9_S	86_G	2.226	1.00
90_A	103_Y	2.147	1.00
16_N	46_T	2.101	1.00
8_L	107_M	2.095	1.00
50_V	54_K	2.087	1.00
40_I	53_A	2.072	1.00
22_R	55_Y	2.071	1.00
75_V	185_A	2.041	1.00
66_L	83_V	2.039	1.00
37_E	64_R	2.019	1.00
123_D	214_K	1.982	1.00
23_T	97_E	1.978	1.00
109_M	206_R	1.936	1.00
98_V	102_M	1.907	1.00
66_L	79_R	1.900	1.00
11_I	80_G	1.889	1.00
50_V	65_L	1.862	1.00
26_E	56_Y	1.858	1.00
12_I	38_I	1.813	1.00
68_Q	71_A	1.805	1.00
116_D	172_R	1.799	1.00
12_I	24_C	1.797	1.00
88_Y	110_A	1.794	1.00
8_L	103_Y	1.789	1.00
41_I	80_G	1.776	1.00
14_L	40_I	1.762	1.00
109_M	208_T	1.752	1.00
90_A	170_V	1.718	1.00
9_S	37_E	1.688	1.00
77_R	93_D	1.678	1.00
90_A	102_M	1.660	1.00
92_V	98_V	1.651	1.00
33_W	107_M	1.651	1.00
7_K	87_K	1.639	1.00
106_L	120_C	1.636	1.00
97_E	214_K	1.622	1.00
106_L	170_V	1.608	1.00
73_A	222_V	1.605	1.00
84_A	173_R	1.601	1.00
37_E	86_G	1.594	1.00
54_K	67_H	1.582	1.00
12_I	28_L	1.555	1.00
68_Q	79_R	1.548	1.00
50_V	67_H	1.522	1.00
22_R	56_Y	1.521	1.00
68_Q	75_V	1.520	1.00
102_M	106_L	1.511	1.00
15_Y	70_N	1.509	1.00
73_A	190_Q	1.501	1.00
79_R	82_E	1.494	1.00
8_L	170_V	1.490	1.00
104_E	108_T	1.477	1.00
101_T	105_T	1.476	1.00
174_D	178_K	1.465	1.00
53_A	65_L	1.461	1.00
42_N	50_V	1.444	1.00
116_D	203_L	1.435	1.00
25_M	56_Y	1.429	1.00
7_K	35_A	1.429	1.00
88_Y	170_V	1.424	1.00
42_N	45_S	1.421	1.00
44_G	68_Q	1.401	1.00
36_L	103_Y	1.393	1.00
97_E	216_Y	1.393	1.00
107_M	111_L	1.392	1.00
38_I	63_V	1.392	1.00
184_I	193_V	1.384	1.00
28_L	92_V	1.381	1.00
18_G	52_I	1.362	1.00
24_C	92_V	1.354	1.00
175_V	198_F	1.353	1.00
64_R	83_V	1.350	1.00
120_C	212_L	1.345	1.00
125_C	214_K	1.343	1.00
26_E	30_T	1.332	1.00
123_D	211_S	1.324	1.00
54_K	57_A	1.308	1.00
41_I	76_A	1.304	1.00
14_L	17_A	1.303	1.00
179_N	182_K	1.302	1.00
110_A	118_A	1.292	1.00
102_M	120_C	1.271	1.00
89_V	173_R	1.267	1.00
110_A	170_V	1.262	1.00
122_A	167_W	1.254	1.00
33_W	36_L	1.251	1.00
77_R	91_F	1.249	1.00
55_Y	59_N	1.248	1.00
90_A	98_V	1.234	1.00
109_M	113_D	1.231	1.00
81_I	89_V	1.230	1.00
57_A	65_L	1.228	1.00
101_T	104_E	1.219	1.00
17_A	20_D	1.218	1.00
16_N	45_S	1.217	1.00
176_I	194_W	1.209	1.00
30_T	100_P	1.204	1.00
106_L	118_A	1.203	1.00
22_R	52_I	1.201	1.00
97_E	125_C	1.200	1.00
37_E	85_T	1.192	1.00
81_I	91_F	1.179	1.00
175_V	203_L	1.172	1.00
87_K	172_R	1.169	1.00
25_M	40_I	1.168	1.00
64_R	85_T	1.155	1.00
218_H	221_S	1.154	1.00
74_S	190_Q	1.150	1.00
14_L	53_A	1.142	1.00
73_A	77_R	1.139	1.00
169_G	195_T	1.137	1.00
117_V	205_A	1.129	1.00
221_S	224_R	1.128	1.00
29_I	63_V	1.120	1.00
126_F	130_G	1.119	1.00
105_T	108_T	1.115	1.00
25_M	38_I	1.114	1.00
25_M	29_I	1.108	1.00
9_S	39_I	1.107	1.00
73_A	166_V	1.103	1.00
43_D	70_N	1.099	1.00
108_T	112_E	1.096	1.00
75_V	79_R	1.095	1.00
51_E	54_K	1.092	1.00
43_D	72_G	1.091	1.00
54_K	65_L	1.086	1.00
81_I	84_A	1.074	1.00
8_L	90_A	1.069	1.00
67_H	79_R	1.066	1.00
43_D	76_A	1.065	1.00
77_R	190_Q	1.065	1.00
102_M	212_L	1.063	1.00
117_V	198_F	1.063	1.00
74_S	78_N	1.057	1.00
109_M	112_E	1.056	1.00
171_Y	195_T	1.045	1.00
71_A	76_A	1.042	1.00
105_T	212_L	1.036	1.00
178_K	201_N	1.035	1.00
29_I	60_Y	1.025	1.00
82_E	180_N	1.018	1.00
121_N	207_Y	1.015	1.00
113_D	206_R	1.012	1.00
114_D	204_R	1.011	1.00
174_D	177_V	1.008	1.00
13_P	76_A	1.003	1.00
92_V	213_Y	1.002	1.00
116_D	204_R	0.996	1.00
14_L	21_F	0.987	1.00
7_K	85_T	0.982	1.00
13_P	94_A	0.982	1.00
14_L	94_A	0.981	1.00
166_V	183_F	0.976	1.00
10_V	28_L	0.970	1.00
10_V	36_L	0.968	1.00
20_D	216_Y	0.968	1.00
29_I	56_Y	0.967	1.00
81_I	176_I	0.964	1.00
9_S	84_A	0.962	1.00
179_N	201_N	0.955	1.00
52_I	56_Y	0.954	1.00
99_Y	123_D	0.940	1.00
125_C	216_Y	0.938	1.00
17_A	218_H	0.938	1.00
33_W	103_Y	0.935	1.00
110_A	115_L	0.930	1.00
237_R	241_K	0.930	1.00
46_T	49_S	0.927	1.00
14_L	42_N	0.920	1.00
10_V	103_Y	0.920	1.00
50_V	53_A	0.918	1.00
109_M	118_A	0.911	1.00
55_Y	58_E	0.905	1.00
245_L	249_L	0.897	1.00
234_N	237_R	0.894	1.00
288_Q	292_A	0.892	1.00
194_W	198_F	0.884	1.00
87_K	111_L	0.877	1.00
84_A	89_V	0.870	1.00
189_H	192_I	0.868	1.00
57_A	63_V	0.867	1.00
73_A	76_A	0.861	1.00
76_A	79_R	0.857	1.00
28_L	98_V	0.856	1.00
148_T	151_D	0.850	1.00
114_D	172_R	0.846	1.00
28_L	38_I	0.841	1.00
217_L	224_R	0.840	1.00
24_C	27_S	0.839	1.00
51_E	55_Y	0.831	1.00
125_C	129_T	0.829	1.00
26_E	59_N	0.828	1.00
7_K	86_G	0.826	1.00
26_E	29_I	0.817	1.00
13_P	77_R	0.816	1.00
67_H	76_A	0.808	1.00
105_T	109_M	0.807	1.00
44_G	70_N	0.806	1.00
32_T	101_T	0.802	1.00
43_D	71_A	0.801	1.00
171_Y	176_I	0.801	1.00
71_A	79_R	0.800	1.00
237_R	240_I	0.798	1.00
119_Q	169_G	0.795	1.00
18_G	47_D	0.793	1.00
106_L	110_A	0.792	1.00
105_T	208_T	0.783	1.00
60_Y	63_V	0.780	1.00
24_C	96_D	0.776	1.00
27_S	98_V	0.773	1.00
99_Y	102_M	0.772	1.00
198_F	202_A	0.763	1.00
40_I	63_V	0.762	1.00
25_M	63_V	0.758	1.00
73_A	93_D	0.757	1.00
179_N	198_F	0.756	1.00
39_I	83_V	0.752	1.00
24_C	28_L	0.751	1.00
48_N	52_I	0.750	1.00
37_E	84_A	0.746	1.00
16_N	49_S	0.743	1.00
167_W	213_Y	0.735	1.00
107_M	170_V	0.735	1.00
99_Y	212_L	0.734	1.00
76_A	80_G	0.726	1.00
118_A	208_T	0.726	1.00
21_F	49_S	0.724	1.00
78_N	183_F	0.723	1.00
126_F	129_T	0.723	1.00
166_V	169_G	0.720	1.00
6_N	33_W	0.719	1.00
53_A	57_A	0.718	1.00
115_L	204_R	0.718	1.00
6_N	87_K	0.714	1.00
91_F	183_F	0.713	1.00
113_D	204_R	0.712	1.00
74_S	186_G	0.707	1.00
124_W	217_L	0.706	1.00
175_V	202_A	0.704	1.00
78_N	182_K	0.704	1.00
21_F	53_A	0.702	1.00
17_A	73_A	0.702	1.00
238_H	242_I	0.699	1.00
7_K	107_M	0.698	1.00
202_A	205_A	0.698	1.00
81_I	182_K	0.694	1.00
7_K	33_W	0.693	1.00
175_V	179_N	0.693	1.00
171_Y	198_F	0.693	1.00
39_I	80_G	0.693	1.00
50_V	57_A	0.689	1.00
119_Q	207_Y	0.688	1.00
8_L	33_W	0.688	1.00
71_A	185_A	0.687	1.00
20_D	218_H	0.685	1.00
41_I	79_R	0.679	1.00
36_L	62_H	0.678	1.00
39_I	64_R	0.677	1.00
21_F	52_I	0.676	1.00
78_N	185_A	0.676	1.00
29_I	38_I	0.673	1.00
39_I	84_A	0.669	1.00
118_A	170_V	0.667	1.00
31_Q	98_V	0.666	1.00
172_R	175_V	0.664	1.00
12_I	94_A	0.664	1.00
6_N	111_L	0.661	1.00
238_H	241_K	0.659	1.00
236_Q	240_I	0.656	1.00
36_L	85_T	0.653	1.00
184_I	187_L	0.653	1.00
109_M	115_L	0.650	1.00
178_K	203_L	0.648	1.00
18_G	21_F	0.648	1.00
88_Y	107_M	0.647	1.00
240_I	244_R	0.647	1.00
24_C	94_A	0.645	1.00
18_G	49_S	0.643	1.00
241_K	244_R	0.643	1.00
177_V	182_K	0.640	1.00
10_V	90_A	0.638	1.00
184_I	197_E	0.636	1.00
89_V	176_I	0.635	1.00
32_T	100_P	0.634	1.00
121_N	209_E	0.634	1.00
93_D	190_Q	0.634	1.00
43_D	93_D	0.632	1.00
7_K	111_L	0.631	1.00
17_A	24_C	0.630	1.00
87_K	174_D	0.628	1.00
18_G	51_E	0.625	1.00
121_N	211_S	0.623	1.00
21_F	94_A	0.622	1.00
8_L	110_A	0.622	1.00
107_M	110_A	0.622	1.00
12_I	92_V	0.622	1.00
54_K	58_E	0.621	1.00
7_K	36_L	0.616	1.00
44_G	69_A	0.616	1.00
80_G	93_D	0.616	1.00
27_S	97_E	0.615	1.00
49_S	52_I	0.615	1.00
13_P	43_D	0.615	1.00
29_I	36_L	0.608	1.00
90_A	120_C	0.604	1.00
24_C	97_E	0.602	1.00
17_A	93_D	0.602	1.00
192_I	196_T	0.601	1.00
208_T	212_L	0.598	1.00
175_V	201_N	0.596	1.00
77_R	166_V	0.595	1.00
90_A	106_L	0.593	1.00
56_Y	59_N	0.592	1.00
115_L	118_A	0.592	1.00
67_H	71_A	0.590	1.00
31_Q	104_E	0.589	1.00
11_I	91_F	0.589	1.00
56_Y	60_Y	0.589	1.00
117_V	202_A	0.587	1.00
117_V	169_G	0.586	1.00
225_L	228_Q	0.584	1.00
98_V	103_Y	0.584	1.00
116_D	119_Q	0.584	1.00
13_P	93_D	0.583	1.00
29_I	62_H	0.582	1.00
45_S	49_S	0.581	1.00
57_A	60_Y	0.581	1.00
88_Y	172_R	0.581	1.00
73_A	91_F	0.578	1.00
78_N	81_I	0.577	1.00
164_H	195_T	0.576	1.00
165_V	168_M	0.575	1.00
11_I	173_R	0.575	1.00
24_C	98_V	0.574	1.00
165_V	192_I	0.573	1.00
80_G	84_A	0.573	1.00
166_V	195_T	0.572	1.00
52_I	55_Y	0.570	0.99
36_L	60_Y	0.569	0.99
91_F	176_I	0.566	0.99
44_G	67_H	0.565	0.99
101_T	210_Q	0.565	0.99
234_N	238_H	0.563	0.99
78_N	197_E	0.560	0.99
151_D	154_R	0.560	0.99
164_H	168_M	0.558	0.99
119_Q	164_H	0.557	0.99
24_C	95_D	0.554	0.99
182_K	194_W	0.554	0.99
120_C	168_M	0.553	0.99
122_A	168_M	0.551	0.99
164_H	169_G	0.549	0.99
98_V	213_Y	0.546	0.99
126_F	217_L	0.545	0.99
96_D	215_Y	0.544	0.99
73_A	189_H	0.543	0.99
200_F	245_L	0.539	0.99
150_P	153_L	0.539	0.99
187_L	193_V	0.539	0.99
33_W	104_E	0.539	0.99
243_T	247_E	0.538	0.99
166_V	190_Q	0.537	0.99
150_P	154_R	0.537	0.99
82_E	177_V	0.536	0.99
28_L	40_I	0.534	0.99
90_A	168_M	0.533	0.99
283_D	287_R	0.532	0.99
29_I	59_N	0.532	0.99
218_H	222_V	0.531	0.99
76_A	93_D	0.531	0.99
78_N	194_W	0.530	0.99
241_K	245_L	0.530	0.99
73_A	188_H	0.529	0.99
15_Y	43_D	0.528	0.99
289_R	293_E	0.528	0.99
195_T	199_M	0.528	0.99
164_H	192_I	0.527	0.99
12_I	40_I	0.526	0.99
41_I	66_L	0.525	0.99
222_V	225_L	0.524	0.99
25_M	53_A	0.524	0.99
208_T	211_S	0.522	0.99
43_D	77_R	0.520	0.99
77_R	183_F	0.520	0.99
122_A	165_V	0.519	0.99
94_A	215_Y	0.519	0.99
96_D	216_Y	0.519	0.99
23_T	26_E	0.519	0.99
41_I	83_V	0.518	0.99
87_K	173_R	0.518	0.99
177_V	180_N	0.516	0.99
11_I	84_A	0.516	0.99
156_G	159_S	0.515	0.99
6_N	35_A	0.515	0.99
68_Q	76_A	0.513	0.99
155_M	158_S	0.512	0.99
106_L	208_T	0.512	0.99
22_R	59_N	0.512	0.99
25_M	52_I	0.512	0.99
8_L	106_L	0.511	0.99
15_Y	72_G	0.511	0.99
244_R	248_K	0.507	0.99
53_A	63_V	0.506	0.99
73_A	94_A	0.506	0.99
88_Y	111_L	0.505	0.99
149_G	156_G	0.503	0.99
179_N	194_W	0.502	0.99
153_L	157_L	0.501	0.99
20_D	24_C	0.501	0.99
131_E	135_S	0.501	0.99
180_N	197_E	0.500	0.99
287_R	290_M	0.500	0.99

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
3bcvA	2	0.532	100	0.324	Contact Map
3l7iA	4	0.0552	100	0.363	Contact Map
1qg8A	1	0.6337	100	0.378	Contact Map
2z86A	2	0.7355	100	0.38	Contact Map
2d7iA	1	0.939	100	0.394	Contact Map
1xhbA	1	0.936	100	0.395	Contact Map
5ajoA	1	0.9535	100	0.414	Contact Map
4fixA	3	0.968	100	0.482	Contact Map
3ckjA	2	0.7529	100	0.491	Contact Map
4p02A	1	0.9186	100	0.495	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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