NIKR - ECOLI - GREMLIN Contacts

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NIKR - Nickel-responsive regulator

UniProt:	P0A6Z6	Sequences: MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKED	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11519
Length:	133 (127)
Sequences:	685 (482)
Seq/√Len:	42.7

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
91_N	94_D	3.316	1.00
56_L	101_L	3.084	1.00
62_H	76_H	2.827	1.00
94_D	122_R	2.799	1.00
116_I	124_G	2.785	1.00
76_H	89_H	2.741	1.00
76_H	95_C	2.730	1.00
87_H	95_C	2.570	1.00
30_E	37_R	2.540	1.00
104_D	107_D	2.476	1.00
8_L	36_L	2.463	1.00
54_A	101_L	2.352	1.00
25_Y	34_D	2.256	1.00
30_E	33_R	2.208	1.00
62_H	89_H	2.108	0.99
57_S	127_Q	2.092	0.99
89_H	95_C	2.045	0.99
52_G	108_V	2.001	0.99
77_H	92_H	1.917	0.99
56_L	126_L	1.879	0.99
16_L	31_A	1.848	0.98
56_L	115_V	1.844	0.98
15_T	44_A	1.829	0.98
49_G	106_G	1.742	0.98
25_Y	30_E	1.734	0.98
62_H	95_C	1.693	0.97
53_F	90_I	1.530	0.95
13_L	17_D	1.492	0.94
83_V	102_K	1.438	0.93
71_I	115_V	1.350	0.91
30_E	34_D	1.338	0.90
32_I	98_I	1.334	0.90
58_Y	115_V	1.329	0.90
33_R	37_R	1.247	0.87
86_L	100_V	1.246	0.87
50_T	104_D	1.228	0.86
77_H	114_D	1.213	0.85
63_E	92_H	1.169	0.83
60_Y	89_H	1.155	0.82
20_S	31_A	1.154	0.82
72_V	76_H	1.151	0.82
76_H	87_H	1.144	0.82
62_H	87_H	1.142	0.82
35_I	39_A	1.129	0.81
72_V	89_H	1.128	0.81
79_H	111_F	1.107	0.80
16_L	36_L	1.102	0.79
44_A	84_A	1.093	0.79
123_H	129_L	1.078	0.78
4_V	7_T	1.078	0.78
47_Q	93_D	1.077	0.78
38_S	125_H	1.076	0.78
32_I	77_H	1.066	0.77
110_H	114_D	1.066	0.77
80_D	107_D	1.052	0.76
68_A	72_V	1.047	0.76
112_A	124_G	1.037	0.75
112_A	126_L	1.035	0.75
8_L	21_Q	1.021	0.74
88_V	96_L	1.019	0.74
34_D	121_V	1.019	0.74
55_V	100_V	1.012	0.73
15_T	24_G	1.008	0.73
78_H	110_H	1.003	0.73
67_L	92_H	0.989	0.72
16_L	20_S	0.984	0.71
7_T	16_L	0.979	0.71
49_G	105_M	0.962	0.69
5_T	79_H	0.961	0.69
18_S	47_Q	0.946	0.68
116_I	123_H	0.943	0.68
32_I	66_D	0.943	0.68
4_V	32_I	0.934	0.67
6_I	13_L	0.929	0.67
67_L	118_Q	0.923	0.66
58_Y	124_G	0.909	0.65
7_T	12_L	0.905	0.65
14_E	23_R	0.904	0.65
82_S	111_F	0.895	0.64
19_L	40_L	0.891	0.63
75_Q	99_A	0.885	0.63
3_R	17_D	0.877	0.62
4_V	63_E	0.860	0.61
94_D	108_V	0.856	0.60
12_L	37_R	0.840	0.59
85_T	101_L	0.839	0.59
10_D	14_E	0.836	0.58
5_T	119_R	0.831	0.58
9_D	54_A	0.830	0.58
17_D	28_R	0.829	0.58
13_L	16_L	0.823	0.57
116_I	125_H	0.818	0.57
26_N	128_C	0.815	0.56
11_D	107_D	0.808	0.56
86_L	98_I	0.793	0.54
87_H	97_E	0.790	0.54
41_A	45_T	0.787	0.54
16_L	63_E	0.778	0.53
3_R	97_E	0.756	0.51
22_R	47_Q	0.754	0.51
18_S	22_R	0.749	0.50
20_S	25_Y	0.739	0.49
104_D	108_V	0.737	0.49
63_E	86_L	0.732	0.49
97_E	103_G	0.731	0.49
41_A	129_L	0.726	0.48
16_L	99_A	0.721	0.48
24_G	99_A	0.719	0.47
3_R	34_D	0.710	0.47
32_I	44_A	0.703	0.46
17_D	113_D	0.702	0.46
65_R	114_D	0.697	0.45
31_A	39_A	0.696	0.45
58_Y	72_V	0.693	0.45
42_Q	46_Q	0.692	0.45
39_A	43_E	0.692	0.45
119_R	129_L	0.690	0.45
108_V	112_A	0.689	0.45
49_G	54_A	0.684	0.44
72_V	95_C	0.676	0.43
107_D	110_H	0.674	0.43
45_T	128_C	0.671	0.43
77_H	107_D	0.669	0.43
66_D	70_R	0.663	0.42
45_T	108_V	0.662	0.42
60_Y	87_H	0.656	0.42
26_N	118_Q	0.652	0.41
58_Y	67_L	0.651	0.41
7_T	25_Y	0.651	0.41
50_T	105_M	0.645	0.41
22_R	49_G	0.645	0.41
58_Y	99_A	0.644	0.40
40_L	125_H	0.639	0.40
9_D	43_E	0.636	0.40
7_T	57_S	0.632	0.39
59_V	113_D	0.631	0.39
78_H	112_A	0.627	0.39
27_N	123_H	0.626	0.39
78_H	124_G	0.616	0.38
3_R	33_R	0.614	0.38
88_V	91_N	0.610	0.37
5_T	68_A	0.610	0.37
27_N	35_I	0.606	0.37
63_E	87_H	0.604	0.37
26_N	113_D	0.601	0.37
64_K	119_R	0.594	0.36
34_D	37_R	0.592	0.36
35_I	124_G	0.592	0.36
27_N	121_V	0.590	0.36
78_H	104_D	0.589	0.36
33_R	95_C	0.588	0.35
11_D	64_K	0.584	0.35
69_S	73_S	0.581	0.35
17_D	33_R	0.577	0.34
22_R	73_S	0.577	0.34
6_I	37_R	0.577	0.34
27_N	124_G	0.575	0.34
15_T	18_S	0.575	0.34
85_T	111_F	0.571	0.34
3_R	31_A	0.566	0.34
32_I	47_Q	0.563	0.33
16_L	35_I	0.561	0.33
91_N	108_V	0.554	0.33
59_V	129_L	0.554	0.33
41_A	94_D	0.552	0.32
15_T	125_H	0.551	0.32
4_V	35_I	0.551	0.32
12_L	28_R	0.551	0.32
75_Q	89_H	0.550	0.32
10_D	81_L	0.547	0.32
27_N	118_Q	0.544	0.32
73_S	82_S	0.544	0.32
62_H	97_E	0.539	0.31
109_Q	113_D	0.533	0.31
47_Q	96_L	0.532	0.31
52_G	58_Y	0.532	0.31
22_R	43_E	0.532	0.31
5_T	31_A	0.527	0.30
35_I	52_G	0.526	0.30
21_Q	73_S	0.525	0.30
20_S	91_N	0.523	0.30
3_R	27_N	0.518	0.30
34_D	91_N	0.514	0.29
27_N	64_K	0.511	0.29
60_Y	85_T	0.510	0.29
55_V	98_I	0.508	0.29
28_R	97_E	0.507	0.29
55_V	129_L	0.504	0.29
53_F	123_H	0.500	0.28
3_R	35_I	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	1	100	0.144	Contact Map
2hzaA	3	0.985	100	0.153	Contact Map
2bj7A	3	1	100	0.196	Contact Map
1q5yA	4	0.6316	99.9	0.486	Contact Map
2nzcA	3	0.6015	99.8	0.563	Contact Map
4me7E	2	0.594	98.9	0.754	Contact Map
3kxeC	2	0.5188	98.9	0.756	Contact Map
2k5jA	2	0.5414	98.7	0.767	Contact Map
2cpgA	2	0.3308	98.4	0.788	Contact Map
2mdvA	2	0.2857	98	0.81	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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