STPA - ECOLI - GREMLIN Contacts

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STPA - DNA-binding protein StpA

UniProt:	P0ACG1	Sequences: MSVMLQSLNNIRTLRAMAREFSIDVLEEMLEKFRVVTKERREEEEQQQRELAERQEKISTWLELMKADGINPEELLGNSSAAAPRAGKKRQPRPAKYKFTDVNGETKTWTGQGRTPKPIAQALAEGKSLDDFLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11554
Length:	134 (132)
Sequences:	379 (251)
Seq/√Len:	21.9

ECOLI - STPA HNS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
120_A	124_A	4.558	1.00
98_K	106_T	4.288	1.00
61_W	64_L	3.308	1.00
115_T	123_L	2.845	0.99
99_F	119_I	2.787	0.99
130_D	133_L	2.725	0.99
30_L	34_R	2.552	0.98
63_E	67_A	2.492	0.98
27_E	41_R	2.469	0.98
93_R	112_Q	2.299	0.97
9_N	25_V	2.242	0.96
38_K	41_R	2.211	0.96
59_S	62_L	2.140	0.95
9_N	13_T	2.039	0.93
127_K	131_D	2.027	0.93
52_A	56_E	1.954	0.92
121_Q	125_E	1.917	0.91
61_W	65_M	1.890	0.90
90_R	112_Q	1.802	0.88
11_I	15_R	1.760	0.87
9_N	29_M	1.684	0.84
56_E	60_T	1.682	0.84
120_A	123_L	1.643	0.83
100_T	106_T	1.631	0.82
30_L	37_T	1.567	0.80
17_M	62_L	1.492	0.76
4_M	17_M	1.482	0.76
108_T	112_Q	1.440	0.73
46_Q	50_E	1.433	0.73
10_N	13_T	1.315	0.66
44_E	47_Q	1.283	0.64
2_S	105_E	1.282	0.64
64_L	68_D	1.282	0.64
18_A	36_V	1.275	0.64
60_T	64_L	1.271	0.64
57_K	71_N	1.267	0.63
21_F	25_V	1.250	0.62
117_K	121_Q	1.248	0.62
94_P	110_T	1.247	0.62
63_E	66_K	1.239	0.62
72_P	78_N	1.233	0.61
44_E	48_Q	1.213	0.60
28_E	32_K	1.207	0.60
7_S	13_T	1.206	0.60
5_L	11_I	1.205	0.59
99_F	107_K	1.204	0.59
61_W	68_D	1.189	0.58
70_I	74_E	1.187	0.58
110_T	129_L	1.178	0.58
27_E	30_L	1.167	0.57
119_I	122_A	1.165	0.57
107_K	119_I	1.152	0.56
65_M	70_I	1.138	0.55
13_T	25_V	1.114	0.53
119_I	129_L	1.091	0.52
77_G	124_A	1.089	0.52
12_R	32_K	1.071	0.50
98_K	108_T	1.069	0.50
110_T	114_R	1.057	0.50
110_T	115_T	1.052	0.49
31_E	63_E	1.038	0.48
30_L	70_I	1.035	0.48
122_A	127_K	1.035	0.48
10_N	16_A	1.010	0.46
4_M	21_F	0.996	0.45
15_R	39_E	0.984	0.45
119_I	128_S	0.965	0.43
13_T	19_R	0.962	0.43
45_E	85_R	0.960	0.43
5_L	29_M	0.955	0.43
10_N	32_K	0.928	0.41
92_P	118_P	0.924	0.41
10_N	15_R	0.924	0.41
3_V	56_E	0.922	0.40
72_P	76_L	0.921	0.40
109_W	113_G	0.915	0.40
105_E	128_S	0.910	0.40
115_T	124_A	0.900	0.39
59_S	63_E	0.880	0.38
9_N	18_A	0.871	0.37
56_E	64_L	0.867	0.37
100_T	105_E	0.865	0.37
21_F	29_M	0.864	0.37
10_N	74_E	0.862	0.37
94_P	112_Q	0.842	0.35
55_Q	117_K	0.841	0.35
16_A	112_Q	0.840	0.35
16_A	19_R	0.839	0.35
6_Q	13_T	0.832	0.35
47_Q	80_S	0.829	0.35
4_M	36_V	0.825	0.34
36_V	55_Q	0.825	0.34
118_P	124_A	0.818	0.34
15_R	19_R	0.818	0.34
119_I	132_F	0.811	0.33
93_R	129_L	0.811	0.33
48_Q	55_Q	0.805	0.33
46_Q	49_R	0.804	0.33
18_A	41_R	0.793	0.32
92_P	112_Q	0.787	0.32
51_L	55_Q	0.778	0.32
45_E	53_E	0.775	0.31
11_I	19_R	0.775	0.31
48_Q	88_K	0.767	0.31
129_L	132_F	0.753	0.30
11_I	32_K	0.751	0.30
20_E	40_R	0.747	0.30
19_R	110_T	0.744	0.30
11_I	99_F	0.744	0.30
48_Q	81_A	0.737	0.29
43_E	51_L	0.729	0.29
16_A	110_T	0.729	0.29
5_L	65_M	0.725	0.29
42_E	46_Q	0.723	0.28
99_F	118_P	0.722	0.28
47_Q	50_E	0.722	0.28
2_S	101_D	0.718	0.28
123_L	129_L	0.708	0.28
64_L	70_I	0.700	0.27
13_T	39_E	0.694	0.27
40_R	71_N	0.688	0.26
6_Q	15_R	0.685	0.26
72_P	98_K	0.683	0.26
8_L	11_I	0.681	0.26
57_K	93_R	0.680	0.26
29_M	36_V	0.679	0.26
14_L	36_V	0.677	0.26
118_P	122_A	0.672	0.26
16_A	90_R	0.670	0.26
16_A	28_E	0.669	0.26
40_R	120_A	0.668	0.25
55_Q	59_S	0.664	0.25
9_N	41_R	0.656	0.25
115_T	119_I	0.655	0.25
22_S	25_V	0.655	0.25
35_V	107_K	0.655	0.25
2_S	33_F	0.655	0.25
6_Q	11_I	0.652	0.25
42_E	84_P	0.650	0.25
3_V	62_L	0.649	0.24
42_E	45_E	0.649	0.24
108_T	119_I	0.646	0.24
20_E	24_D	0.644	0.24
3_V	7_S	0.643	0.24
9_N	28_E	0.642	0.24
42_E	50_E	0.641	0.24
52_A	73_E	0.633	0.24
16_A	32_K	0.628	0.23
10_N	19_R	0.625	0.23
1_M	14_L	0.624	0.23
109_W	116_P	0.621	0.23
111_G	116_P	0.621	0.23
6_Q	29_M	0.619	0.23
4_M	18_A	0.617	0.23
4_M	9_N	0.614	0.23
28_E	78_N	0.604	0.22
58_I	64_L	0.599	0.22
67_A	76_L	0.596	0.22
65_M	74_E	0.596	0.22
113_G	116_P	0.594	0.22
73_E	99_F	0.594	0.22
10_N	94_P	0.592	0.22
117_K	120_A	0.590	0.22
5_L	9_N	0.588	0.22
3_V	88_K	0.576	0.21
26_L	43_E	0.573	0.21
77_G	88_K	0.570	0.21
105_E	133_L	0.569	0.21
58_I	70_I	0.569	0.21
12_R	16_A	0.567	0.21
57_K	130_D	0.566	0.21
58_I	61_W	0.564	0.20
11_I	29_M	0.564	0.20
22_S	121_Q	0.559	0.20
11_I	18_A	0.558	0.20
60_T	63_E	0.554	0.20
17_M	115_T	0.544	0.20
53_E	102_V	0.535	0.19
40_R	44_E	0.533	0.19
34_R	38_K	0.531	0.19
33_F	101_D	0.530	0.19
15_R	18_A	0.527	0.19
38_K	117_K	0.523	0.19
1_M	5_L	0.521	0.19
56_E	61_W	0.517	0.18
23_I	45_E	0.516	0.18
58_I	87_G	0.515	0.18
61_W	70_I	0.514	0.18
40_R	43_E	0.514	0.18
63_E	73_E	0.513	0.18
73_E	84_P	0.511	0.18
5_L	120_A	0.510	0.18
59_S	67_A	0.509	0.18
50_E	53_E	0.508	0.18
15_R	95_A	0.508	0.18
3_V	80_S	0.505	0.18
3_V	53_E	0.500	0.18
10_N	99_F	0.500	0.18

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
3nr7A	2	0.6045	99.9	0.547	Contact Map
2l93A	1	0.3284	99.7	0.639	Contact Map
1hnrA	1	0.3284	99.7	0.652	Contact Map
4icgB	2	0.3284	99.5	0.701	Contact Map
1ov9A	2	0.3582	99.4	0.708	Contact Map
2l92A	1	0.2612	99.3	0.731	Contact Map
2levA	1	0.3806	99.1	0.744	Contact Map
2jr1A	1	0.5075	99.1	0.748	Contact Map
3bpjA	2	0.306	47.6	0.928	Contact Map
1z56A	2	0.5224	25.1	0.938	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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