YWNA - BACSU - GREMLIN Contacts

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YWNA - Putative HTH-type transcriptional regulator YwnA

UniProt:	P71036	Sequences: MINSRLAVAIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGASLKKDPADISLLEVYRAVQKQEELFAVHENPNPKCPVGKKIQNALDETFESVQRAMENELASKSLKDVMNHLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	133 (127)
Sequences:	1363 (1020)
Seq/√Len:	90.5

ECOLI - ISCR
BACSU - YWNA YWGB NSRR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_S	119_E	4.152	1.00
72_L	121_A	3.602	1.00
70_S	124_S	3.334	1.00
72_L	76_R	3.138	1.00
74_V	125_L	3.034	1.00
126_K	130_N	2.912	1.00
52_T	61_S	2.737	1.00
67_A	126_K	2.734	1.00
113_Q	117_E	2.733	1.00
76_R	117_E	2.533	1.00
31_V	38_V	2.502	1.00
114_R	118_N	2.441	1.00
66_P	129_M	2.310	1.00
37_V	40_R	2.289	1.00
65_D	68_D	2.265	1.00
64_K	69_I	2.035	1.00
52_T	63_K	1.999	1.00
115_A	119_E	1.885	1.00
118_N	121_A	1.783	1.00
8_V	31_V	1.766	1.00
64_K	68_D	1.743	1.00
42_I	51_L	1.684	1.00
62_L	69_I	1.662	1.00
16_I	51_L	1.643	1.00
13_L	50_I	1.634	1.00
104_A	128_V	1.584	1.00
13_L	74_V	1.548	1.00
91_P	98_G	1.487	1.00
15_L	26_I	1.482	1.00
112_V	115_A	1.481	1.00
53_S	60_A	1.470	1.00
108_T	128_V	1.442	0.99
72_L	117_E	1.428	0.99
112_V	120_L	1.408	0.99
17_S	129_M	1.326	0.99
27_I	31_V	1.320	0.99
8_V	30_S	1.310	0.99
64_K	73_E	1.308	0.99
26_I	29_D	1.287	0.99
13_L	125_L	1.225	0.98
112_V	116_M	1.223	0.98
76_R	121_A	1.200	0.98
14_S	128_V	1.193	0.98
62_L	66_P	1.192	0.98
85_F	109_F	1.189	0.98
85_F	88_H	1.179	0.98
99_K	104_A	1.176	0.98
8_V	38_V	1.169	0.98
3_N	79_Q	1.164	0.97
14_S	101_I	1.128	0.97
46_K	60_A	1.115	0.97
13_L	62_L	1.115	0.97
58_P	109_F	1.103	0.97
16_I	60_A	1.092	0.96
119_E	122_S	1.080	0.96
110_E	114_R	1.077	0.96
48_A	77_A	1.031	0.95
18_M	129_M	1.008	0.94
7_A	87_V	0.995	0.94
72_L	85_F	0.995	0.94
120_L	123_K	0.975	0.93
6_L	58_P	0.967	0.93
36_V	40_R	0.955	0.92
92_N	99_K	0.953	0.92
34_N	95_C	0.945	0.92
43_S	51_L	0.934	0.92
25_E	29_D	0.933	0.92
86_A	89_E	0.929	0.91
50_I	64_K	0.926	0.91
74_V	77_A	0.921	0.91
63_K	69_I	0.912	0.91
75_Y	113_Q	0.897	0.90
66_P	125_L	0.896	0.90
44_L	79_Q	0.888	0.89
99_K	103_N	0.878	0.89
106_D	110_E	0.868	0.88
7_A	109_F	0.855	0.88
6_L	45_L	0.851	0.87
43_S	47_K	0.847	0.87
102_Q	106_D	0.801	0.84
30_S	98_G	0.800	0.84
11_H	95_C	0.795	0.83
51_L	60_A	0.790	0.83
94_K	122_S	0.763	0.81
67_A	118_N	0.762	0.81
15_L	27_I	0.759	0.81
21_K	53_S	0.758	0.80
107_E	111_S	0.750	0.80
4_S	89_E	0.746	0.79
19_D	61_S	0.744	0.79
114_R	126_K	0.740	0.79
27_I	30_S	0.735	0.78
50_I	69_I	0.730	0.78
108_T	119_E	0.727	0.78
70_S	73_E	0.718	0.77
25_E	46_K	0.708	0.76
10_I	71_L	0.705	0.75
98_G	105_L	0.704	0.75
18_M	27_I	0.701	0.75
4_S	116_M	0.700	0.75
20_E	26_I	0.697	0.75
47_K	68_D	0.695	0.74
36_V	59_G	0.692	0.74
42_I	60_A	0.692	0.74
4_S	37_V	0.691	0.74
40_R	86_A	0.680	0.73
61_S	67_A	0.678	0.73
73_E	110_E	0.677	0.72
43_S	60_A	0.672	0.72
75_Y	80_K	0.669	0.72
33_T	41_M	0.667	0.71
110_E	118_N	0.657	0.70
83_E	87_V	0.656	0.70
17_S	66_P	0.654	0.70
15_L	23_S	0.652	0.70
22_T	27_I	0.652	0.70
70_S	117_E	0.651	0.70
111_S	123_K	0.650	0.69
65_D	69_I	0.649	0.69
105_L	128_V	0.644	0.69
32_N	40_R	0.643	0.69
6_L	16_I	0.640	0.68
22_T	71_L	0.640	0.68
8_V	41_M	0.636	0.68
4_S	8_V	0.635	0.68
22_T	26_I	0.635	0.68
28_A	33_T	0.632	0.67
10_I	105_L	0.632	0.67
29_D	94_K	0.625	0.66
21_K	61_S	0.615	0.65
8_V	88_H	0.613	0.65
83_E	89_E	0.612	0.65
74_V	109_F	0.612	0.65
38_V	53_S	0.611	0.65
46_K	53_S	0.611	0.65
93_P	130_N	0.610	0.65
3_N	6_L	0.597	0.63
66_P	126_K	0.592	0.62
55_A	58_P	0.592	0.62
78_V	98_G	0.592	0.62
33_T	37_V	0.590	0.62
127_D	130_N	0.588	0.62
73_E	76_R	0.587	0.62
73_E	123_K	0.587	0.62
75_Y	82_E	0.586	0.61
46_K	113_Q	0.579	0.61
12_I	16_I	0.578	0.60
108_T	126_K	0.577	0.60
5_R	78_V	0.575	0.60
3_N	55_A	0.574	0.60
26_I	67_A	0.574	0.60
15_L	29_D	0.573	0.60
33_T	59_G	0.573	0.60
78_V	92_N	0.572	0.60
28_A	45_L	0.571	0.59
4_S	7_A	0.570	0.59
38_V	46_K	0.566	0.59
44_L	109_F	0.563	0.58
33_T	40_R	0.559	0.58
3_N	8_V	0.556	0.57
66_P	73_E	0.552	0.57
32_N	41_M	0.550	0.57
88_H	120_L	0.549	0.57
7_A	88_H	0.548	0.56
15_L	97_V	0.546	0.56
103_N	130_N	0.541	0.55
38_V	106_D	0.540	0.55
112_V	119_E	0.540	0.55
98_G	101_I	0.538	0.55
11_H	128_V	0.536	0.55
42_I	59_G	0.533	0.54
47_K	52_T	0.526	0.53
26_I	103_N	0.522	0.53
34_N	78_V	0.522	0.53
28_A	40_R	0.518	0.52
75_Y	84_L	0.517	0.52
30_S	50_I	0.517	0.52
23_S	123_K	0.516	0.52
33_T	87_V	0.516	0.52
49_D	63_K	0.515	0.52
5_R	37_V	0.515	0.52
59_G	120_L	0.512	0.51
64_K	94_K	0.510	0.51
12_I	30_S	0.508	0.51
28_A	128_V	0.508	0.51
31_V	41_M	0.507	0.51
34_N	88_H	0.503	0.50
51_L	59_G	0.501	0.50
40_R	55_A	0.501	0.50
42_I	46_K	0.500	0.50

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
1xd7A	2	0.8722	100	0.408	Contact Map
1ylfA	5	0.8872	99.9	0.446	Contact Map
3k69A	2	0.9624	99.9	0.451	Contact Map
4hf1A	2	0.9549	99.9	0.452	Contact Map
4hf0A	3	0.8722	99.9	0.49	Contact Map
3lwfA	5	0.9248	99.9	0.493	Contact Map
4cicA	2	0.8797	99.9	0.509	Contact Map
3t8rA	2	0.8722	99.9	0.529	Contact Map
2y75A	5	0.9248	99.8	0.566	Contact Map
2jscA	2	0.609	97.7	0.826	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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