DUF3046 - PFAM28P - GREMLIN Contacts

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DUF3046 - Protein of unknown function (DUF3046)

PFAM:	PF11248	Sequences: MRLTEFWERMEEEFGPAYARSLARDHVLAELGGRTVDQALAAGVDPKDVWRAVCAAFDVPAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (61)
Sequences:	3453 (1689)
Seq/√Len:	216.3
META:	0.787

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_R	37_D	3.058	1.00
11_E	20_R	2.605	1.00
34_R	42_A	2.590	1.00
11_E	16_P	2.485	1.00
26_H	56_A	2.439	1.00
37_D	41_A	2.259	1.00
30_E	55_A	2.043	1.00
44_V	48_D	1.873	1.00
21_S	25_D	1.768	1.00
22_L	57_F	1.745	1.00
10_M	19_A	1.664	1.00
40_L	46_P	1.579	1.00
20_R	37_D	1.545	1.00
7_W	23_A	1.472	1.00
26_H	57_F	1.423	1.00
8_E	12_E	1.376	1.00
38_Q	42_A	1.358	1.00
10_M	23_A	1.303	1.00
11_E	19_A	1.293	1.00
51_R	55_A	1.275	1.00
14_F	57_F	1.248	1.00
7_W	37_D	1.245	1.00
30_E	56_A	1.228	1.00
10_M	53_V	1.187	1.00
14_F	22_L	1.102	1.00
34_R	44_V	1.100	1.00
5_E	9_R	1.074	1.00
54_C	59_V	1.059	1.00
6_F	10_M	1.031	1.00
27_V	33_G	1.029	1.00
5_E	8_E	1.026	1.00
22_L	26_H	1.019	1.00
30_E	52_A	1.004	1.00
45_D	48_D	0.992	1.00
3_L	7_W	0.984	1.00
3_L	46_P	0.984	1.00
23_A	36_V	0.961	1.00
48_D	51_R	0.938	1.00
10_M	36_V	0.929	0.99
23_A	37_D	0.916	0.99
27_V	34_R	0.889	0.99
29_A	33_G	0.886	0.99
7_W	20_R	0.880	0.99
13_E	59_V	0.868	0.99
34_R	38_Q	0.849	0.99
13_E	22_L	0.824	0.99
25_D	45_D	0.801	0.98
47_K	51_R	0.796	0.98
46_P	49_V	0.794	0.98
13_E	54_C	0.760	0.98
20_R	24_R	0.753	0.98
36_V	53_V	0.744	0.97
24_R	27_V	0.720	0.97
18_Y	22_L	0.716	0.97
28_L	53_V	0.715	0.97
52_A	55_A	0.711	0.97
3_L	49_V	0.697	0.96
6_F	36_V	0.692	0.96
7_W	11_E	0.689	0.96
40_L	49_V	0.679	0.96
31_L	39_A	0.657	0.95
29_A	56_A	0.656	0.95
7_W	49_V	0.652	0.95
25_D	38_Q	0.642	0.94
32_G	44_V	0.635	0.94
34_R	39_A	0.630	0.94
31_L	44_V	0.605	0.92
55_A	61_A	0.599	0.92
6_F	23_A	0.595	0.92
14_F	59_V	0.595	0.92
21_S	57_F	0.593	0.91
27_V	32_G	0.590	0.91
3_L	6_F	0.586	0.91
9_R	46_P	0.581	0.91
10_M	47_K	0.580	0.90
8_E	11_E	0.566	0.89
28_L	56_A	0.559	0.89
28_L	36_V	0.557	0.89
13_E	61_A	0.555	0.88
19_A	53_V	0.555	0.88
9_R	45_D	0.544	0.87
53_V	59_V	0.544	0.87
18_Y	26_H	0.540	0.87
3_L	40_L	0.535	0.87
22_L	54_C	0.535	0.87
18_Y	28_L	0.533	0.86
39_A	49_V	0.533	0.86
8_E	16_P	0.530	0.86
28_L	31_L	0.523	0.85
7_W	18_Y	0.518	0.85
3_L	14_F	0.507	0.84
6_F	46_P	0.500	0.83

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
1ee8A	2	0.9839	29	0.868	Contact Map
4mb7A	2	0.9677	21.5	0.876	Contact Map
4ls6A	2	0.5806	19.7	0.878	Contact Map
3w0fA	1	1	18.2	0.88	Contact Map
2vz8A	2	0.5645	16.3	0.883	Contact Map
2ix4A	2	0.5484	16.2	0.883	Contact Map
2vbaA	2	0.5645	15.5	0.884	Contact Map
4ewgA	2	0.5806	15	0.885	Contact Map
1j3nA	3	0.5645	14.4	0.885	Contact Map
2iwzA	2	0.6774	13.9	0.886	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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