DUF2497 - PFAM28P - GREMLIN Contacts

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DUF2497 - Protein of unknown function (DUF2497)

PFAM:	PF10691	Sequences: EALLSEATAAAAASAFAALAAAVAAPRAPQGGGGRTLEDLVREMLRPMLKEWLDENLPGLVERLVRAEIERIAR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (70)
Sequences:	4459 (2506)
Seq/√Len:	299.5
META:	0.939

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_L	69_I	3.852	1.00
51_E	55_E	3.799	1.00
35_R	39_D	2.719	1.00
66_R	70_E	2.231	1.00
50_K	54_D	2.125	1.00
62_E	66_R	2.057	1.00
60_L	64_L	1.971	1.00
44_M	48_M	1.915	1.00
64_L	67_A	1.778	1.00
41_V	44_M	1.754	1.00
45_L	49_L	1.742	1.00
16_F	73_A	1.735	1.00
6_E	10_A	1.699	1.00
41_V	45_L	1.528	1.00
4_L	8_T	1.512	1.00
16_F	20_A	1.480	1.00
43_E	46_R	1.450	1.00
38_E	42_R	1.439	1.00
2_A	6_E	1.397	1.00
39_D	42_R	1.384	1.00
68_E	71_R	1.335	1.00
18_A	66_R	1.274	1.00
36_T	40_L	1.248	1.00
37_L	40_L	1.245	1.00
22_A	25_A	1.213	1.00
9_A	12_A	1.205	1.00
6_E	9_A	1.204	1.00
36_T	39_D	1.186	1.00
34_G	37_L	1.154	1.00
5_S	8_T	1.115	1.00
8_T	12_A	1.067	1.00
38_E	41_V	1.065	1.00
12_A	15_A	1.044	1.00
7_A	10_A	1.010	1.00
10_A	14_S	0.992	1.00
56_N	59_G	0.986	1.00
8_T	11_A	0.982	1.00
18_A	21_A	0.980	1.00
31_G	34_G	0.972	1.00
53_L	57_L	0.947	1.00
65_V	69_I	0.935	1.00
2_A	9_A	0.919	1.00
5_S	50_K	0.916	1.00
12_A	16_F	0.880	1.00
31_G	35_R	0.861	1.00
58_P	62_E	0.853	1.00
18_A	25_A	0.831	1.00
66_R	72_I	0.814	1.00
52_W	56_N	0.804	1.00
21_A	25_A	0.800	1.00
11_A	18_A	0.788	0.99
15_A	19_L	0.774	0.99
55_E	59_G	0.770	0.99
53_L	71_R	0.754	0.99
62_E	68_E	0.754	0.99
4_L	72_I	0.753	0.99
23_V	26_P	0.741	0.99
35_R	43_E	0.734	0.99
13_A	17_A	0.728	0.99
40_L	44_M	0.727	0.99
60_L	63_R	0.719	0.99
24_A	27_R	0.716	0.99
59_G	63_R	0.713	0.99
15_A	18_A	0.708	0.99
67_A	72_I	0.693	0.99
27_R	34_G	0.678	0.98
25_A	40_L	0.671	0.98
2_A	7_A	0.666	0.98
7_A	11_A	0.659	0.98
44_M	58_P	0.656	0.98
35_R	42_R	0.655	0.98
4_L	9_A	0.652	0.98
11_A	15_A	0.651	0.98
39_D	43_E	0.638	0.98
46_R	58_P	0.635	0.98
69_I	73_A	0.627	0.97
5_S	49_L	0.619	0.97
34_G	39_D	0.611	0.97
70_E	73_A	0.607	0.97
21_A	28_A	0.607	0.97
3_L	10_A	0.607	0.97
57_L	65_V	0.606	0.97
4_L	53_L	0.603	0.97
13_A	72_I	0.600	0.97
18_A	23_V	0.597	0.97
17_A	21_A	0.595	0.96
64_L	70_E	0.594	0.96
17_A	23_V	0.591	0.96
11_A	17_A	0.580	0.96
16_F	69_I	0.576	0.96
23_V	37_L	0.568	0.95
28_A	33_G	0.564	0.95
8_T	58_P	0.562	0.95
12_A	17_A	0.556	0.95
61_V	65_V	0.553	0.95
37_L	41_V	0.546	0.94
19_L	48_M	0.520	0.93
50_K	64_L	0.520	0.93
38_E	45_L	0.518	0.93
5_S	14_S	0.512	0.92
5_S	55_E	0.510	0.92
60_L	69_I	0.506	0.92
67_A	73_A	0.505	0.92
14_S	21_A	0.501	0.91
25_A	28_A	0.500	0.91

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
4hy1A	1	0.9865	38.6	0.818	Contact Map
3lnuA	1	0.973	32.4	0.826	Contact Map
4wubA	2	0.973	30.4	0.828	Contact Map
3zkbA	5	0.9865	27.8	0.831	Contact Map
4urlA	1	0.9459	27.1	0.832	Contact Map
1kijA	2	0.973	24.1	0.836	Contact Map
1s16A	2	0.9595	21.1	0.841	Contact Map
4i3hA	2	0.9595	15.3	0.851	Contact Map
3i1iA	3	0.7838	14.1	0.853	Contact Map
3ewtE	1	0.1892	12.4	0.857	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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