OPENSEQ.org - STPA - ECOLI GREMLIN

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STPA - DNA-binding protein StpA

UniProt:	P0ACG1	Sequence MSVMLQSLNNIRTLRAMAREFSIDVLEEMLEKFRVVTKERREEEEQQQRELAERQEKISTWLELMKADGINPEELLGNSSAAAPRAGKKRQPRPAKYKFTDVNGETKTWTGQGRTPKPIAQALAEGKSLDDFLI	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11554
Length:	134 (134)
Sequences:	291
Seq/Len:	2.17

STPA
Paralog alert: 0.64 [within 20: 0.01] - ratio of genomes with paralogs
Cluster includes: HNS STPA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
130_D	133_L	2.141	1.00
120_A	124_A	2.099	0.99
98_K	106_T	2.009	0.99
9_N	13_T	1.983	0.99
115_T	123_L	1.982	0.99
61_W	64_L	1.956	0.99
121_Q	125_E	1.911	0.99
30_L	34_R	1.849	0.98
38_K	41_R	1.783	0.98
9_N	25_V	1.774	0.98
27_E	41_R	1.718	0.97
93_R	112_Q	1.716	0.97
119_I	132_F	1.709	0.97
4_M	17_M	1.685	0.97
95_A	134_I	1.635	0.96
119_I	129_L	1.604	0.95
10_N	15_R	1.582	0.95
129_L	132_F	1.579	0.94
114_R	119_I	1.572	0.94
99_F	119_I	1.566	0.94
56_E	64_L	1.537	0.93
120_A	123_L	1.517	0.93
99_F	107_K	1.514	0.93
52_A	56_E	1.478	0.91
63_E	67_A	1.453	0.91
30_L	37_T	1.42	0.89
56_E	60_T	1.418	0.89
13_T	25_V	1.391	0.88
127_K	131_D	1.384	0.87
59_S	62_L	1.346	0.85
60_T	64_L	1.339	0.85
11_I	15_R	1.317	0.84
49_R	58_I	1.298	0.83
119_I	122_A	1.281	0.81
119_I	128_S	1.266	0.80
41_R	103_N	1.243	0.79
44_E	48_Q	1.24	0.78
7_S	13_T	1.227	0.77
10_N	13_T	1.204	0.75
27_E	30_L	1.199	0.75
44_E	47_Q	1.195	0.75
4_M	7_S	1.181	0.73
13_T	19_R	1.173	0.73
57_K	130_D	1.156	0.71
90_R	112_Q	1.147	0.70
18_A	36_V	1.137	0.69
18_A	33_F	1.135	0.69
21_F	25_V	1.129	0.69
98_K	108_T	1.078	0.63
61_W	65_M	1.073	0.63
54_R	114_R	1.069	0.62
18_A	42_E	1.068	0.62
9_N	18_A	1.068	0.62
40_R	94_P	1.062	0.62
20_E	28_E	1.051	0.60
72_P	76_L	1.043	0.60
66_K	83_A	1.041	0.59
13_T	17_M	1.034	0.59
29_M	48_Q	1.029	0.58
117_K	125_E	1.024	0.57
2_S	33_F	1.024	0.57
5_L	11_I	1.015	0.56
46_Q	49_R	1.011	0.56
10_N	19_R	1.01	0.56
34_R	38_K	1.009	0.56

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
3nr7A	2	0.6194	99.8	0.543	Contact Map	0.496
2l93A	1	0.3284	99.7	0.566	Contact Map	0.685
1hnrA	1	0.3284	99.7	0.586	Contact Map	0.431
2l92A	1	0.2612	99.4	0.656	Contact Map	0.664
2jr1A	1	0.5	99.3	0.672	Contact Map	0.108
2levA	1	0.3806	99.3	0.673	Contact Map	0.657
4icgB	2	0.3433	99.2	0.691	Contact Map	0.586
1ov9A	2	0.3731	99.1	0.7	Contact Map	0.603
1x57A	1	0.6269	49.4	0.914	Contact Map	0.35
2jvlA	1	0.5746	39.7	0.919	Contact Map	0.55

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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