OPENSEQ.org - NIKR - ECOLI GREMLIN

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NIKR - Nickel-responsive regulator

UniProt:	P0A6Z6	Sequence MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKED	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11519
Length:	133 (132)
Sequences:	410
Seq/Len:	3.11

NIKR
Paralog alert: 0.05 [within 20: 0.00] - ratio of genomes with paralogs

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
87_H	95_C	2.427	1.00
56_L	101_L	2.402	1.00
62_H	89_H	2.224	1.00
62_H	76_H	2.036	1.00
30_E	33_R	2.03	1.00
89_H	95_C	2.005	1.00
94_D	122_R	1.977	1.00
76_H	89_H	1.914	0.99
116_I	124_G	1.881	0.99
91_N	94_D	1.875	0.99
76_H	95_C	1.832	0.99
30_E	37_R	1.81	0.99
25_Y	34_D	1.761	0.99
15_T	44_A	1.755	0.99
54_A	101_L	1.719	0.99
8_L	36_L	1.672	0.98
63_E	92_H	1.509	0.96
104_D	107_D	1.488	0.96
77_H	107_D	1.426	0.94
16_L	31_A	1.424	0.94
13_L	17_D	1.387	0.93
62_H	95_C	1.378	0.93
83_V	102_K	1.36	0.92
35_I	39_A	1.345	0.92
12_L	37_R	1.34	0.91
78_H	110_H	1.326	0.91
85_T	111_F	1.316	0.90
77_H	114_D	1.311	0.90
57_S	127_Q	1.281	0.89
25_Y	30_E	1.279	0.89
33_R	37_R	1.246	0.87
40_L	46_Q	1.237	0.86
49_G	106_G	1.218	0.85
44_A	84_A	1.209	0.85
76_H	87_H	1.207	0.84
34_D	121_V	1.192	0.83
87_H	97_E	1.149	0.80
16_L	20_S	1.146	0.80
56_L	115_V	1.146	0.80
58_Y	115_V	1.145	0.80
107_D	110_H	1.135	0.79
5_T	65_R	1.131	0.79
27_N	124_G	1.13	0.79
16_L	36_L	1.125	0.78
80_D	107_D	1.116	0.77
58_Y	99_A	1.109	0.77
123_H	129_L	1.096	0.76
30_E	34_D	1.093	0.75
76_H	97_E	1.083	0.74
53_F	90_I	1.073	0.73
9_D	54_A	1.073	0.73
62_H	87_H	1.065	0.73
56_L	126_L	1.063	0.72
110_H	114_D	1.062	0.72
27_N	39_A	1.05	0.71
10_D	108_V	1.037	0.70
18_S	21_Q	1.036	0.70
41_A	130_P	1.034	0.69
55_V	129_L	1.025	0.69
94_D	100_V	1.024	0.68
3_R	33_R	1.02	0.68
54_A	59_V	1.014	0.67
45_T	108_V	1.013	0.67
35_I	43_E	1.01	0.67
14_E	107_D	1.008	0.67

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
2wvfA	2	1	100	0.101	Contact Map	0.607
2hzaA	2	1	100	0.113	Contact Map	0.555
2bj7A	2	1	100	0.157	Contact Map	0.615
1q5yA	4	0.6391	99.9	0.466	Contact Map	0.725
2nzcA	4	0.6391	99.8	0.54	Contact Map	0.566
4me7E	2	0.6541	98.8	0.74	Contact Map	0.474
3kxeC	2	0.6015	98.8	0.741	Contact Map	0.669
2k5jA	2	0.5414	98.7	0.753	Contact Map	0.423
2cpgA	3	0.3308	98.4	0.77	Contact Map	0.64
2k9iA	2	0.3534	98.1	0.789	Contact Map	0.653

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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