NIKR - HALSA - GREMLIN Contacts

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NIKR - Putative nickel-responsive regulator

UniProt:	Q9HSN7	Sequences: MSVVSVSMPEELLERLDDFADDHGYTGRSEVVREASRNLLGEFEDKKLEGRELMGVVTVVFDYETTTVEEKMMHLRHEHEGLVASNFHSHVGGHHCMELFVLEGSLESISTFVGKIRATKDTLTIDYSVLPVDEFGGLADVS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	142 (128)
Sequences:	695 (485)
Seq/√Len:	42.8

ECOLI - NIKR
HALSA - NIKR
SULSO - NIKR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_G	95_H	3.363	1.00
57_V	102_L	3.147	1.00
63_Y	77_H	2.868	1.00
117_R	125_I	2.778	1.00
77_H	90_H	2.777	1.00
77_H	96_C	2.748	1.00
95_H	123_L	2.724	1.00
88_H	96_C	2.624	1.00
8_M	36_S	2.533	1.00
105_S	108_S	2.531	1.00
30_E	37_R	2.517	1.00
55_G	102_L	2.387	1.00
25_Y	34_E	2.284	1.00
30_E	33_R	2.244	1.00
63_Y	90_H	2.204	1.00
58_T	128_S	2.145	1.00
90_H	96_C	2.080	0.99
50_G	107_E	2.057	0.99
15_R	44_E	1.923	0.99
53_L	109_I	1.917	0.99
78_E	93_G	1.878	0.99
57_V	116_I	1.877	0.99
57_V	127_Y	1.875	0.99
16_L	31_V	1.873	0.99
25_Y	30_E	1.739	0.98
63_Y	96_C	1.737	0.98
13_L	17_D	1.513	0.95
54_M	91_V	1.445	0.93
32_V	99_L	1.407	0.92
84_A	103_E	1.345	0.91
30_E	34_E	1.315	0.90
32_V	67_T	1.261	0.88
63_Y	88_H	1.260	0.88
33_R	37_R	1.257	0.87
61_F	90_H	1.253	0.87
59_V	116_I	1.247	0.87
87_F	101_V	1.225	0.86
51_R	105_S	1.222	0.86
16_L	36_S	1.197	0.85
35_A	39_L	1.174	0.84
72_M	116_I	1.147	0.82
78_E	115_K	1.147	0.82
124_T	130_L	1.144	0.82
73_M	77_H	1.143	0.82
20_A	31_V	1.139	0.82
32_V	78_E	1.138	0.82
56_V	101_V	1.137	0.82
77_H	88_H	1.131	0.81
38_N	126_D	1.126	0.81
44_E	85_S	1.122	0.81
4_V	7_S	1.098	0.79
64_E	93_G	1.098	0.79
73_M	90_H	1.093	0.79
34_E	122_T	1.072	0.78
89_S	97_M	1.070	0.77
16_L	20_A	1.056	0.76
111_T	115_K	1.051	0.76
80_E	112_F	1.039	0.75
79_H	111_T	1.039	0.75
69_E	73_M	1.021	0.74
68_V	93_G	1.011	0.73
8_M	21_D	1.007	0.73
117_R	124_T	0.991	0.72
7_S	16_L	0.965	0.70
5_S	80_E	0.955	0.69
113_V	127_Y	0.955	0.69
6_V	13_L	0.944	0.68
4_V	32_V	0.942	0.68
108_S	111_T	0.938	0.68
59_V	125_I	0.928	0.67
50_G	55_G	0.926	0.67
87_F	131_P	0.914	0.65
11_E	108_S	0.914	0.65
81_G	108_S	0.903	0.65
113_V	125_I	0.900	0.64
15_R	24_G	0.893	0.64
7_S	12_L	0.883	0.63
76_R	100_F	0.881	0.63
56_V	130_L	0.881	0.63
9_P	55_G	0.878	0.62
10_E	14_E	0.876	0.62
83_V	112_F	0.871	0.62
86_N	102_L	0.863	0.61
50_G	106_L	0.860	0.61
14_E	23_H	0.857	0.60
65_T	120_K	0.854	0.60
3_V	17_D	0.852	0.60
117_R	126_D	0.847	0.60
4_V	64_E	0.835	0.58
19_F	40_L	0.834	0.58
13_L	16_L	0.832	0.58
3_V	98_E	0.828	0.58
68_V	119_T	0.819	0.57
39_L	43_F	0.814	0.56
5_S	120_K	0.814	0.56
17_D	28_R	0.808	0.56
12_L	37_R	0.782	0.53
105_S	109_I	0.780	0.53
88_H	98_E	0.769	0.52
18_D	22_D	0.759	0.51
41_G	131_P	0.755	0.51
32_V	44_E	0.746	0.50
92_G	109_I	0.746	0.50
26_T	129_V	0.742	0.50
87_F	99_L	0.736	0.49
89_S	92_G	0.735	0.49
78_E	108_S	0.734	0.49
31_V	39_L	0.721	0.48
42_E	46_K	0.719	0.48
51_R	106_L	0.715	0.47
16_L	100_F	0.709	0.47
98_E	104_G	0.704	0.46
73_M	96_C	0.702	0.46
95_H	109_I	0.700	0.46
3_V	34_E	0.693	0.45
64_E	88_H	0.690	0.45
41_G	45_D	0.687	0.44
17_D	114_G	0.682	0.44
5_S	69_E	0.679	0.44
79_H	105_S	0.679	0.44
59_V	73_M	0.675	0.43
22_D	50_G	0.674	0.43
59_V	100_F	0.671	0.43
66_T	115_K	0.670	0.43
45_D	109_I	0.661	0.42
22_D	43_F	0.657	0.42
61_F	88_H	0.656	0.42
3_V	33_R	0.651	0.41
41_G	130_L	0.651	0.41
27_G	35_A	0.649	0.41
6_V	37_R	0.645	0.41
51_R	82_L	0.645	0.41
53_L	130_L	0.642	0.40
7_S	25_Y	0.635	0.40
20_A	25_Y	0.633	0.39
16_L	35_A	0.631	0.39
40_L	126_D	0.628	0.39
10_E	131_P	0.626	0.39
109_I	113_V	0.623	0.39
63_Y	98_E	0.621	0.38
33_R	96_C	0.614	0.38
35_A	125_I	0.608	0.37
3_V	27_G	0.606	0.37
49_E	52_E	0.605	0.37
3_V	31_V	0.598	0.36
24_G	100_F	0.597	0.36
55_G	58_T	0.594	0.36
27_G	124_T	0.591	0.36
15_R	18_D	0.591	0.36
26_T	119_T	0.590	0.36
16_L	64_E	0.587	0.35
23_H	117_R	0.586	0.35
27_G	119_T	0.585	0.35
60_V	114_G	0.581	0.35
110_S	114_G	0.579	0.35
64_E	87_F	0.578	0.35
119_T	131_P	0.574	0.34
76_R	90_H	0.571	0.34
79_H	113_V	0.569	0.34
20_A	92_G	0.567	0.34
34_E	37_R	0.562	0.33
3_V	35_A	0.554	0.33
26_T	114_G	0.553	0.33
18_D	107_E	0.551	0.32
7_S	58_T	0.551	0.32
64_E	90_H	0.548	0.32
74_H	106_L	0.546	0.32
7_S	130_L	0.545	0.32
34_E	92_G	0.543	0.32
17_D	33_R	0.540	0.31
12_L	28_R	0.540	0.31
11_E	65_T	0.539	0.31
52_E	58_T	0.537	0.31
18_D	21_D	0.534	0.31
50_G	75_L	0.530	0.31
90_H	93_G	0.526	0.30
24_G	32_V	0.525	0.30
5_S	31_V	0.524	0.30
28_R	98_E	0.519	0.30
74_H	129_V	0.519	0.30
86_N	112_F	0.517	0.30
27_G	122_T	0.516	0.30
67_T	75_L	0.516	0.30
70_E	74_H	0.514	0.29
24_G	82_L	0.509	0.29
9_P	43_F	0.507	0.29
12_L	40_L	0.507	0.29
83_V	123_L	0.506	0.29
21_D	74_H	0.505	0.29
82_L	108_S	0.504	0.29
54_M	124_T	0.504	0.29
75_L	115_K	0.500	0.28

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
2wvfA	2	0.9577	100	0.196	Contact Map
2hzaA	3	0.9225	100	0.216	Contact Map
2bj7A	3	0.9577	100	0.261	Contact Map
1q5yA	4	0.5915	99.9	0.523	Contact Map
2nzcA	3	0.5634	99.8	0.586	Contact Map
3kxeC	2	0.5211	98.9	0.769	Contact Map
4me7E	2	0.5563	98.8	0.775	Contact Map
2k5jA	2	0.507	98.7	0.788	Contact Map
2cpgA	2	0.3099	98.4	0.805	Contact Map
2mdvA	2	0.2676	98	0.825	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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