YWGB - BACSU - GREMLIN Contacts

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YWGB - Putative HTH-type transcriptional regulator YwgB

UniProt:	P71047	Sequences: MKMKSGMEQAVSVLLLLSRLPVQASLTSEAISQRLRVSPSYLKKLMRTLVQAGLAESLPGTKGGFTLTKPLADITLYDVYQAVEGRGSMYQGKGLLQSVFEGESHCVLETVMAEIEDKWSNLMREESLQHVMDRVGELYDLEKIDDWVIKQVKGQL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	156 (135)
Sequences:	6243 (4367)
Seq/√Len:	375.8

ECOLI - ISCR NSRR
BACSU - YWGB NSRR CYMR YWNA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_Y	124_R	3.885	1.00
72_A	129_Q	3.191	1.00
56_E	66_T	2.923	1.00
16_L	34_R	2.752	1.00
92_G	106_C	2.712	1.00
10_A	83_V	2.696	1.00
129_Q	133_D	2.649	1.00
14_L	54_L	2.594	1.00
114_E	122_L	2.570	1.00
69_K	78_D	2.505	1.00
52_A	82_A	2.401	1.00
14_L	128_L	2.236	1.00
77_Y	81_Q	2.195	1.00
81_Q	124_R	2.166	1.00
13_V	46_M	2.021	1.00
118_K	122_L	2.002	1.00
25_S	66_T	1.986	1.00
18_S	132_M	1.980	1.00
17_L	55_A	1.856	1.00
29_E	39_P	1.794	1.00
70_P	73_D	1.775	1.00
92_G	100_F	1.750	1.00
118_K	121_N	1.734	1.00
69_K	73_D	1.637	1.00
29_E	33_Q	1.625	1.00
16_L	26_L	1.598	1.00
100_F	106_C	1.594	1.00
114_E	126_E	1.577	1.00
50_V	57_S	1.563	1.00
115_I	119_W	1.551	1.00
20_L	24_A	1.505	1.00
58_L	66_T	1.491	1.00
75_T	127_S	1.448	1.00
47_R	51_Q	1.445	1.00
122_L	125_E	1.434	1.00
7_M	80_Y	1.429	1.00
116_E	120_S	1.418	1.00
81_Q	120_S	1.394	1.00
37_V	42_L	1.393	1.00
13_V	42_L	1.379	1.00
75_T	78_D	1.297	1.00
120_S	124_R	1.289	1.00
69_K	74_I	1.274	1.00
56_E	68_T	1.261	1.00
28_S	46_M	1.250	1.00
13_V	31_I	1.241	1.00
21_P	71_L	1.234	1.00
117_D	121_N	1.192	1.00
111_V	126_E	1.190	1.00
115_I	123_M	1.186	1.00
16_L	20_L	1.157	1.00
114_E	134_R	1.146	1.00
20_L	26_L	1.137	1.00
54_L	74_I	1.131	1.00
16_L	35_L	1.109	1.00
27_T	30_A	1.068	1.00
6_G	44_K	1.066	1.00
7_M	84_E	1.065	1.00
110_T	134_R	1.049	1.00
47_R	50_V	1.044	1.00
121_N	125_E	1.044	1.00
25_S	58_L	1.041	1.00
67_L	71_L	1.019	1.00
9_Q	37_V	1.001	1.00
113_A	117_D	0.975	1.00
54_L	82_A	0.970	1.00
78_D	124_R	0.963	1.00
57_S	65_F	0.961	1.00
33_Q	39_P	0.958	1.00
14_L	79_V	0.945	1.00
46_M	65_F	0.945	1.00
28_S	43_K	0.937	1.00
80_Y	123_M	0.930	1.00
40_S	43_K	0.919	1.00
115_I	118_K	0.915	1.00
8_E	12_S	0.915	1.00
46_M	55_A	0.914	1.00
6_G	48_T	0.912	1.00
11_V	76_L	0.909	1.00
5_S	41_Y	0.905	1.00
47_R	65_F	0.893	1.00
24_A	30_A	0.888	1.00
30_A	33_Q	0.887	1.00
21_P	24_A	0.876	1.00
77_Y	120_S	0.870	1.00
48_T	52_A	0.867	1.00
14_L	49_L	0.849	1.00
76_L	111_V	0.846	1.00
127_S	130_H	0.840	1.00
76_L	131_V	0.840	1.00
89_M	116_E	0.837	1.00
19_R	132_M	0.835	1.00
15_L	132_M	0.831	1.00
122_L	126_E	0.824	1.00
87_G	120_S	0.823	1.00
30_A	34_R	0.808	1.00
6_G	10_A	0.807	1.00
68_T	74_I	0.794	1.00
114_E	125_E	0.789	1.00
6_G	41_Y	0.787	1.00
16_L	30_A	0.785	1.00
71_L	128_L	0.784	1.00
16_L	31_I	0.783	1.00
121_N	124_R	0.783	1.00
28_S	39_P	0.781	1.00
109_E	113_A	0.778	1.00
17_L	26_L	0.776	1.00
70_P	129_Q	0.764	1.00
114_E	118_K	0.761	1.00
43_K	65_F	0.756	1.00
50_V	55_A	0.744	1.00
48_T	51_Q	0.741	1.00
47_R	57_S	0.738	1.00
3_M	112_M	0.736	1.00
54_L	78_D	0.731	1.00
7_M	83_V	0.726	1.00
10_A	45_L	0.721	1.00
78_D	81_Q	0.720	1.00
71_L	132_M	0.718	1.00
53_G	68_T	0.711	1.00
130_H	133_D	0.702	0.99
9_Q	45_L	0.702	0.99
113_A	116_E	0.701	0.99
43_K	50_V	0.700	0.99
78_D	82_A	0.687	0.99
74_I	79_V	0.682	0.99
91_Q	94_G	0.682	0.99
3_M	80_Y	0.681	0.99
9_Q	35_L	0.678	0.99
39_P	43_K	0.675	0.99
41_Y	45_L	0.674	0.99
81_Q	86_R	0.669	0.99
40_S	44_K	0.668	0.99
36_R	101_E	0.668	0.99
79_V	128_L	0.664	0.99
4_K	84_E	0.662	0.99
15_L	131_V	0.647	0.99
112_M	119_W	0.645	0.99
102_G	105_H	0.643	0.99
32_S	37_V	0.640	0.99
38_S	41_Y	0.636	0.99
9_Q	41_Y	0.631	0.99
111_V	122_L	0.623	0.99
3_M	7_M	0.621	0.99
75_T	124_R	0.621	0.99
115_I	122_L	0.616	0.99
80_Y	84_E	0.615	0.99
79_V	82_A	0.611	0.99
92_G	109_E	0.608	0.99
98_S	103_E	0.605	0.98
4_K	7_M	0.602	0.98
111_V	114_E	0.591	0.98
54_L	69_K	0.586	0.98
31_I	46_M	0.586	0.98
71_L	74_I	0.584	0.98
20_L	30_A	0.577	0.98
114_E	117_D	0.572	0.98
55_A	65_F	0.571	0.98
27_T	59_P	0.569	0.98
31_I	35_L	0.569	0.98
59_P	112_M	0.568	0.98
17_L	63_G	0.568	0.98
12_S	35_L	0.565	0.98
103_E	109_E	0.565	0.98
106_C	109_E	0.562	0.98
27_T	62_K	0.555	0.97
94_G	97_Q	0.553	0.97
133_D	136_G	0.551	0.97
52_A	78_D	0.551	0.97
129_Q	132_M	0.551	0.97
5_S	91_Q	0.549	0.97
101_E	105_H	0.543	0.97
50_V	65_F	0.541	0.97
20_L	34_R	0.541	0.97
41_Y	44_K	0.539	0.97
74_I	128_L	0.539	0.97
86_R	89_M	0.538	0.97
35_L	42_L	0.537	0.97
19_R	135_V	0.535	0.97
76_L	126_E	0.535	0.97
17_L	31_I	0.535	0.97
98_S	101_E	0.534	0.97
118_K	123_M	0.534	0.97
53_G	56_E	0.533	0.97
108_L	112_M	0.532	0.97
69_K	72_A	0.528	0.96
75_T	125_E	0.526	0.96
52_A	69_K	0.522	0.96
22_V	136_G	0.519	0.96
110_T	113_A	0.518	0.96
8_E	108_L	0.517	0.96
95_L	105_H	0.515	0.96
117_D	120_S	0.514	0.96
68_T	71_L	0.514	0.96
17_L	65_F	0.513	0.96
6_G	50_V	0.513	0.96
22_V	70_P	0.511	0.96
41_Y	59_P	0.510	0.96
21_P	70_P	0.507	0.95
6_G	43_K	0.504	0.95
111_V	115_I	0.500	0.95
44_K	47_R	0.500	0.95

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
4hf1A	2	0.9103	100	0.249	Contact Map
1xd7A	2	0.7308	100	0.276	Contact Map
4hf0A	3	0.7821	100	0.304	Contact Map
1ylfA	5	0.7692	100	0.314	Contact Map
4cicA	2	0.859	100	0.319	Contact Map
3lwfA	5	0.8974	100	0.32	Contact Map
3k69A	2	0.9038	100	0.325	Contact Map
3t8rA	2	0.7756	100	0.36	Contact Map
2y75A	5	0.8205	99.9	0.397	Contact Map
2jscA	2	0.5641	98.3	0.772	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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