YWOH - BACSU - GREMLIN Contacts

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YWOH - Uncharacterized HTH-type transcriptional regulator YwoH

UniProt:	P94578	Sequences: MSYVNRHLIHQINQSARLIAKKANEQLEPFGLYSSQWSVLYCLRTIGPMTQKEIWSYLNVEAPTVTRTIKRLEENGWVQRRQGEDKREKLVVLTKEAEKKYEEINVKMLKFEEELLADFRDEDKEAFSHLFRMFLQQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	137 (127)
Sequences:	21118 (15426)
Seq/√Len:	1368.8

ECOLI - MARR SLYA MPRA
BACSU - YWOH MHQR YETL YUSO YKOM YCGE YSMB YFIV YXAD YWAE YPOP YYBA YWHA OHRR YDCH YDGG YDGJ YHJH YVMB YVNA YBFA
SULSO - Q97Z53 Q97YG9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_P	92_V	3.232	1.00
123_D	133_M	3.105	1.00
81_R	92_V	3.053	1.00
79_Q	92_V	2.569	1.00
50_T	88_E	2.485	1.00
120_R	123_D	2.425	1.00
126_A	129_H	2.352	1.00
126_A	130_L	2.203	1.00
44_R	101_Y	2.131	1.00
82_Q	89_K	2.131	1.00
50_T	53_E	1.979	1.00
36_Q	75_N	1.957	1.00
119_F	130_L	1.942	1.00
123_D	126_A	1.783	1.00
44_R	93_L	1.782	1.00
76_G	96_E	1.652	1.00
36_Q	71_R	1.603	1.00
73_E	80_R	1.585	1.00
51_Q	69_I	1.584	1.00
48_P	90_L	1.555	1.00
96_E	100_K	1.554	1.00
123_D	129_H	1.545	1.00
96_E	99_K	1.530	1.00
11_Q	132_R	1.529	1.00
100_K	103_E	1.523	1.00
69_I	91_V	1.519	1.00
70_K	74_E	1.474	1.00
46_I	57_Y	1.466	1.00
33_Y	36_Q	1.460	1.00
127_F	130_L	1.446	1.00
30_F	107_K	1.435	1.00
39_V	68_T	1.411	1.00
48_P	81_R	1.378	1.00
26_Q	107_K	1.335	1.00
130_L	133_M	1.320	1.00
44_R	98_E	1.320	1.00
42_C	57_Y	1.317	1.00
30_F	103_E	1.301	1.00
11_Q	128_S	1.299	1.00
51_Q	89_K	1.280	1.00
70_K	86_K	1.275	1.00
53_E	56_S	1.265	1.00
52_K	62_A	1.250	1.00
99_K	103_E	1.237	1.00
60_V	64_T	1.187	1.00
129_H	133_M	1.160	1.00
61_E	64_T	1.137	1.00
26_Q	110_K	1.131	1.00
128_S	132_R	1.111	1.00
52_K	56_S	1.106	1.00
39_V	65_V	1.103	1.00
24_N	28_E	1.094	1.00
26_Q	114_E	1.089	1.00
107_K	110_K	1.088	1.00
77_W	100_K	1.079	1.00
66_T	70_K	1.076	1.00
122_E	126_A	1.055	1.00
112_E	115_L	1.049	1.00
51_Q	91_V	1.048	1.00
123_D	130_L	1.038	1.00
124_K	128_S	1.019	1.00
95_K	98_E	1.016	1.00
93_L	97_A	1.013	1.00
75_N	100_K	1.009	1.00
47_G	98_E	1.007	1.00
31_G	75_N	1.002	1.00
75_N	96_E	0.965	1.00
13_N	16_A	0.962	1.00
49_M	57_Y	0.956	1.00
51_Q	65_V	0.955	1.00
30_F	104_I	0.955	1.00
46_I	49_M	0.955	1.00
70_K	73_E	0.955	1.00
80_R	89_K	0.951	1.00
63_P	66_T	0.948	1.00
61_E	67_R	0.941	1.00
49_M	53_E	0.926	1.00
98_E	102_E	0.925	1.00
35_S	68_T	0.923	1.00
16_A	20_A	0.917	1.00
24_N	34_S	0.916	1.00
64_T	67_R	0.916	1.00
95_K	99_K	0.912	1.00
15_S	131_F	0.909	1.00
108_M	112_E	0.887	1.00
69_I	78_V	0.883	1.00
119_F	134_F	0.874	1.00
110_K	114_E	0.872	1.00
44_R	102_E	0.869	1.00
60_V	65_V	0.867	1.00
53_E	57_Y	0.866	1.00
43_L	78_V	0.862	1.00
82_Q	86_K	0.861	1.00
37_W	104_I	0.858	1.00
83_G	90_L	0.857	1.00
51_Q	62_A	0.855	1.00
67_R	71_R	0.851	1.00
121_D	125_E	0.848	1.00
22_K	111_F	0.848	1.00
40_L	101_Y	0.834	1.00
79_Q	94_T	0.828	1.00
81_R	90_L	0.823	1.00
85_D	88_E	0.818	1.00
110_K	113_E	0.817	1.00
29_P	107_K	0.808	1.00
15_S	134_F	0.805	1.00
77_W	96_E	0.803	1.00
93_L	98_E	0.793	1.00
69_I	73_E	0.791	1.00
12_I	16_A	0.784	1.00
42_C	58_L	0.781	1.00
103_E	107_K	0.779	1.00
22_K	114_E	0.766	1.00
42_C	49_M	0.763	1.00
37_W	108_M	0.761	1.00
46_I	53_E	0.757	1.00
72_L	77_W	0.751	1.00
73_E	79_Q	0.750	1.00
44_R	105_N	0.746	1.00
106_V	109_L	0.744	1.00
106_V	110_K	0.743	1.00
38_S	58_L	0.738	1.00
35_S	64_T	0.730	1.00
116_L	124_K	0.729	1.00
122_E	125_E	0.728	1.00
67_R	70_K	0.723	1.00
114_E	117_A	0.723	1.00
12_I	15_S	0.723	1.00
125_E	128_S	0.721	1.00
17_R	21_K	0.718	1.00
26_Q	111_F	0.718	1.00
55_W	62_A	0.714	1.00
109_L	113_E	0.713	1.00
43_L	93_L	0.710	1.00
13_N	17_R	0.707	1.00
126_A	133_M	0.706	1.00
51_Q	66_T	0.700	1.00
99_K	102_E	0.688	1.00
20_A	24_N	0.684	1.00
8_L	128_S	0.684	1.00
70_K	80_R	0.683	1.00
120_R	124_K	0.681	1.00
125_E	129_H	0.671	1.00
71_R	74_E	0.671	1.00
65_V	69_I	0.666	1.00
39_V	58_L	0.661	1.00
37_W	101_Y	0.660	1.00
41_Y	45_T	0.659	1.00
42_C	54_I	0.656	1.00
43_L	49_M	0.655	1.00
47_G	92_V	0.654	1.00
42_C	46_I	0.651	1.00
39_V	54_I	0.631	1.00
36_Q	68_T	0.628	1.00
26_Q	29_P	0.627	1.00
55_W	65_V	0.626	1.00
41_Y	105_N	0.614	1.00
23_A	108_M	0.598	1.00
119_F	133_M	0.597	1.00
120_R	133_M	0.597	1.00
11_Q	14_Q	0.594	1.00
103_E	106_V	0.586	1.00
111_F	114_E	0.580	1.00
71_R	75_N	0.577	1.00
38_S	42_C	0.566	1.00
25_E	29_P	0.566	1.00
14_Q	18_L	0.560	1.00
54_I	91_V	0.559	1.00
105_N	109_L	0.558	1.00
25_E	28_E	0.558	1.00
22_K	25_E	0.555	1.00
119_F	124_K	0.555	1.00
73_E	78_V	0.553	1.00
40_L	44_R	0.550	1.00
23_A	26_Q	0.543	1.00
102_E	106_V	0.541	1.00
18_L	22_K	0.538	1.00
52_K	55_W	0.537	1.00
35_S	60_V	0.530	1.00
116_L	120_R	0.530	1.00
12_I	131_F	0.527	1.00
51_Q	88_E	0.525	1.00
32_L	100_K	0.521	1.00
12_I	19_I	0.518	1.00
41_Y	101_Y	0.517	1.00
102_E	105_N	0.514	1.00
8_L	127_F	0.505	1.00
101_Y	105_N	0.504	1.00
13_N	34_S	0.503	1.00
76_G	79_Q	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
4yifA	2	0.9854	99.9	0.244	Contact Map
3oopA	2	0.9781	99.9	0.245	Contact Map
3deuA	2	0.927	99.9	0.246	Contact Map
3cjnA	2	0.9854	99.9	0.247	Contact Map
3zplA	2	1	99.9	0.248	Contact Map
3u2rA	4	0.9562	99.9	0.25	Contact Map
4rguA	4	0.9927	99.9	0.253	Contact Map
2fbkA	2	0.9416	99.9	0.255	Contact Map
3cdhA	4	0.9562	99.9	0.258	Contact Map
3e6mA	2	1	99.9	0.258	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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