DUF2387 - PFAM28P - GREMLIN Contacts

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DUF2387 - Probable metal-binding protein (DUF2387)

PFAM:	PF09526	Sequences: TKKRFIAGAVCPRCSEMDKIVMYEDDGVDYRECVACGFSDELPEQGASAPRELETRVNRSAEKEAETEVQVVQFF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (71)
Sequences:	740 (461)
Seq/√Len:	54.7
META:	0.764

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_E	19_K	3.886	1.00
19_K	35_A	3.093	1.00
16_E	35_A	2.354	1.00
24_E	29_D	2.243	1.00
28_V	41_E	2.234	1.00
31_R	40_D	1.981	1.00
31_R	56_R	1.953	1.00
68_E	72_V	1.807	0.99
30_Y	41_E	1.760	0.99
65_A	69_V	1.733	0.99
52_E	58_N	1.673	0.99
22_M	29_D	1.656	0.99
13_R	17_M	1.574	0.98
24_E	27_G	1.559	0.98
15_S	37_G	1.523	0.98
9_A	22_M	1.488	0.97
55_T	58_N	1.473	0.97
53_L	57_V	1.441	0.97
31_R	55_T	1.412	0.96
29_D	42_L	1.393	0.96
3_K	21_V	1.388	0.96
64_E	67_T	1.353	0.95
31_R	38_F	1.325	0.95
52_E	55_T	1.307	0.94
53_L	56_R	1.278	0.94
52_E	56_R	1.268	0.93
63_K	66_E	1.267	0.93
66_E	71_V	1.219	0.92
68_E	73_Q	1.148	0.89
10_V	13_R	1.134	0.89
10_V	15_S	1.132	0.89
67_T	70_Q	1.129	0.88
7_A	56_R	1.103	0.87
25_D	28_V	1.100	0.87
59_R	62_E	1.076	0.86
37_G	40_D	1.065	0.85
23_Y	43_P	1.063	0.85
44_E	48_S	1.054	0.85
21_V	32_E	1.030	0.83
30_Y	44_E	1.026	0.83
6_I	38_F	0.990	0.81
70_Q	73_Q	0.971	0.80
67_T	73_Q	0.970	0.79
23_Y	32_E	0.970	0.79
68_E	71_V	0.965	0.79
60_S	68_E	0.964	0.79
3_K	22_M	0.937	0.77
20_I	34_V	0.887	0.73
4_R	20_I	0.880	0.72
64_E	68_E	0.876	0.72
22_M	40_D	0.824	0.67
67_T	71_V	0.820	0.67
52_E	57_V	0.820	0.67
22_M	42_L	0.776	0.63
38_F	50_P	0.757	0.61
11_C	14_C	0.756	0.61
51_R	54_E	0.745	0.60
60_S	65_A	0.740	0.59
65_A	68_E	0.727	0.58
20_I	42_L	0.703	0.55
30_Y	39_S	0.691	0.54
53_L	58_N	0.690	0.54
41_E	62_E	0.679	0.53
31_R	42_L	0.669	0.52
22_M	32_E	0.667	0.51
22_M	44_E	0.665	0.51
2_K	22_M	0.657	0.50
31_R	53_L	0.651	0.50
60_S	64_E	0.647	0.49
41_E	44_E	0.640	0.48
29_D	41_E	0.631	0.47
19_K	32_E	0.628	0.47
26_D	45_Q	0.625	0.47
23_Y	30_Y	0.624	0.47
32_E	52_E	0.624	0.47
2_K	60_S	0.620	0.46
17_M	21_V	0.614	0.46
19_K	58_N	0.609	0.45
41_E	45_Q	0.606	0.45
29_D	43_P	0.605	0.45
7_A	18_D	0.589	0.43
48_S	51_R	0.587	0.43
5_F	8_G	0.584	0.42
3_K	23_Y	0.584	0.42
61_A	68_E	0.582	0.42
15_S	27_G	0.575	0.42
45_Q	50_P	0.570	0.41
24_E	45_Q	0.569	0.41
63_K	67_T	0.566	0.41
45_Q	48_S	0.563	0.40
7_A	55_T	0.562	0.40
62_E	65_A	0.558	0.40
64_E	71_V	0.557	0.40
33_C	36_C	0.557	0.40
59_R	69_V	0.552	0.39
40_D	56_R	0.551	0.39
59_R	64_E	0.549	0.39
69_V	73_Q	0.540	0.38
10_V	17_M	0.539	0.38
13_R	42_L	0.537	0.38
29_D	44_E	0.533	0.37
69_V	72_V	0.527	0.37
18_D	34_V	0.521	0.36
6_I	30_Y	0.516	0.36
44_E	49_A	0.514	0.35
9_A	13_R	0.500	0.34

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
1neeA	1	0.5867	71.2	0.844	Contact Map
3cw2K	1	0.5867	68.7	0.847	Contact Map
3j81l	1	0	67.5	0.848	Contact Map
3po3S	1	0.5733	66.7	0.849	Contact Map
2k4xA	1	0.5333	65.2	0.85	Contact Map
1pqvS	1	0.5733	63.7	0.852	Contact Map
1nuiA	1	0.8133	62.6	0.853	Contact Map
2e9hA	1	0.8133	60.2	0.855	Contact Map
2g2kA	1	0.7733	57.6	0.858	Contact Map
2d74B	1	0.5733	56.9	0.858	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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