ARSD - HALSA - GREMLIN Contacts

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ARSD - Putative arsenical resistance operon repressor ArsD

UniProt:	O52028	Sequences: MTQLTLYEEAMCCSTGVCGPDPDDELVEVSAALDQLENEFDVDVSRANMQHNIEQFLETQQIADLVEEHGPSILPITVVNDEIVARETYLSYDELASTFEDSPDPQEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	108 (101)
Sequences:	353 (246)
Seq/√Len:	24.5

HALSA - ARSD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_E	30_S	5.332	1.00
2_T	80_N	3.531	1.00
69_H	86_R	3.252	1.00
65_L	76_I	2.770	0.99
5_T	47_A	2.576	0.99
73_I	87_E	2.388	0.98
85_A	94_E	2.317	0.98
88_T	94_E	2.307	0.98
32_A	92_Y	2.294	0.98
33_L	44_V	1.926	0.93
29_V	95_L	1.838	0.92
17_V	22_P	1.786	0.90
62_I	76_I	1.778	0.90
16_G	19_G	1.776	0.90
11_M	14_S	1.746	0.89
85_A	88_T	1.707	0.88
60_Q	63_A	1.690	0.88
11_M	19_G	1.673	0.87
64_D	68_E	1.601	0.85
65_L	73_I	1.568	0.83
24_D	28_E	1.537	0.82
32_A	95_L	1.528	0.82
14_S	17_V	1.517	0.81
26_L	89_Y	1.504	0.81
32_A	35_Q	1.419	0.77
61_Q	82_E	1.418	0.77
28_E	92_Y	1.410	0.76
54_E	58_E	1.383	0.75
16_G	26_L	1.332	0.72
66_V	78_V	1.308	0.71
76_I	83_I	1.299	0.70
8_E	52_N	1.284	0.69
16_G	89_Y	1.275	0.69
5_T	81_D	1.254	0.67
19_G	26_L	1.253	0.67
78_V	83_I	1.182	0.63
12_C	19_G	1.178	0.62
8_E	51_H	1.174	0.62
18_C	26_L	1.162	0.61
45_S	52_N	1.156	0.61
35_Q	92_Y	1.106	0.57
6_L	29_V	1.104	0.57
4_L	62_I	1.092	0.56
95_L	100_E	1.088	0.56
55_Q	58_E	1.051	0.53
11_M	16_G	1.041	0.53
7_Y	62_I	1.035	0.52
18_C	89_Y	0.978	0.48
4_L	99_F	0.977	0.48
79_V	84_V	0.956	0.47
10_A	15_T	0.942	0.46
55_Q	59_T	0.936	0.45
30_S	54_E	0.935	0.45
79_V	83_I	0.932	0.45
25_E	91_S	0.923	0.44
22_P	53_I	0.906	0.43
11_M	26_L	0.897	0.42
4_L	79_V	0.885	0.42
49_M	66_V	0.885	0.42
5_T	45_S	0.877	0.41
7_Y	68_E	0.865	0.40
7_Y	87_E	0.858	0.40
61_Q	64_D	0.842	0.39
34_D	38_N	0.837	0.38
9_E	22_P	0.835	0.38
34_D	37_E	0.832	0.38
30_S	44_V	0.830	0.38
69_H	73_I	0.827	0.38
8_E	14_S	0.822	0.37
11_M	25_E	0.819	0.37
41_D	59_T	0.808	0.36
36_L	42_V	0.802	0.36
83_I	96_A	0.792	0.35
57_L	95_L	0.779	0.34
57_L	60_Q	0.778	0.34
47_A	52_N	0.775	0.34
65_L	85_A	0.774	0.34
6_L	44_V	0.772	0.34
73_I	76_I	0.769	0.34
11_M	18_C	0.758	0.33
17_V	20_P	0.757	0.33
20_P	99_F	0.744	0.32
38_N	81_D	0.741	0.32
38_N	102_S	0.737	0.32
57_L	66_V	0.733	0.32
29_V	92_Y	0.728	0.31
62_I	87_E	0.726	0.31
19_G	89_Y	0.719	0.31
65_L	69_H	0.712	0.30
65_L	88_T	0.707	0.30
60_Q	64_D	0.702	0.30
70_G	76_I	0.696	0.29
2_T	77_T	0.695	0.29
60_Q	95_L	0.694	0.29
77_T	102_S	0.686	0.29
4_L	98_T	0.675	0.28
5_T	43_D	0.673	0.28
90_L	98_T	0.668	0.28
76_I	93_D	0.658	0.27
11_M	93_D	0.657	0.27
33_L	42_V	0.653	0.27
47_A	98_T	0.651	0.27
72_S	79_V	0.650	0.27
76_I	86_R	0.646	0.26
8_E	66_V	0.640	0.26
48_N	55_Q	0.638	0.26
19_G	23_D	0.638	0.26
73_I	98_T	0.635	0.26
86_R	97_S	0.635	0.26
33_L	85_A	0.635	0.26
63_A	67_E	0.630	0.26
58_E	79_V	0.627	0.25
48_N	84_V	0.620	0.25
7_Y	90_L	0.616	0.25
14_S	29_V	0.613	0.25
64_D	95_L	0.613	0.25
32_A	57_L	0.607	0.24
21_D	56_F	0.606	0.24
15_T	67_E	0.600	0.24
18_C	48_N	0.582	0.23
29_V	32_A	0.577	0.23
50_Q	56_F	0.573	0.23
39_E	44_V	0.569	0.22
20_P	47_A	0.569	0.22
35_Q	96_A	0.566	0.22
13_C	19_G	0.562	0.22
11_M	17_V	0.562	0.22
30_S	41_D	0.555	0.22
84_V	98_T	0.553	0.22
21_D	27_V	0.553	0.22
47_A	96_A	0.548	0.21
8_E	27_V	0.546	0.21
37_E	59_T	0.543	0.21
34_D	79_V	0.539	0.21
68_E	84_V	0.539	0.21
42_V	64_D	0.538	0.21
73_I	85_A	0.536	0.21
65_L	82_E	0.535	0.21
6_L	92_Y	0.532	0.21
54_E	57_L	0.531	0.21
3_Q	91_S	0.529	0.20
51_H	56_F	0.529	0.20
62_I	100_E	0.529	0.20
25_E	29_V	0.526	0.20
7_Y	71_P	0.523	0.20
88_T	91_S	0.519	0.20
68_E	86_R	0.509	0.20
13_C	18_C	0.507	0.19
20_P	39_E	0.504	0.19
29_V	88_T	0.504	0.19
62_I	78_V	0.501	0.19
50_Q	57_L	0.500	0.19

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
3kgkA	2	0.8889	100	0.309	Contact Map
3ktbA	5	0.9537	100	0.325	Contact Map
1iloA	1	0.713	96.5	0.859	Contact Map
3zitA	2	0.7222	96.5	0.859	Contact Map
1fo5A	1	0.7685	93.7	0.882	Contact Map
1t1vA	2	0.787	92.6	0.886	Contact Map
4k8mA	2	0.75	91	0.891	Contact Map
2fgxA	1	0.713	90.5	0.892	Contact Map
1nhoA	1	0.7778	90.3	0.893	Contact Map
3ic4A	1	0.7593	89.4	0.895	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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