DUF2619 - PFAM28P - GREMLIN Contacts

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DUF2619 - Protein of unknown function (DUF2619)

PFAM:	PF10942	Sequences: RLLSGSIEITAALLMLKFNRVEKALKINALLALVGPLILITVTTIGLVGLAGKLSLSKLLWILLGVALI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (69)
Sequences:	642 (440)
Seq/√Len:	53.0
META:	0.662

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_F	27_I	2.678	1.00
11_A	27_I	2.657	1.00
61_W	68_L	2.632	1.00
5_G	9_I	2.592	1.00
4_S	8_E	2.566	1.00
37_L	41_T	2.358	1.00
13_L	16_L	2.189	1.00
64_L	68_L	1.936	1.00
32_A	43_T	1.876	0.99
14_L	27_I	1.855	0.99
26_K	29_A	1.780	0.99
26_K	30_L	1.757	0.99
3_L	7_I	1.705	0.99
9_I	13_L	1.696	0.99
6_S	10_T	1.649	0.98
2_L	5_G	1.521	0.97
17_K	53_K	1.508	0.97
8_E	31_L	1.489	0.97
39_L	43_T	1.473	0.97
21_V	55_S	1.403	0.96
25_L	39_L	1.365	0.95
44_T	48_V	1.356	0.95
20_R	23_K	1.349	0.95
26_K	42_V	1.343	0.95
42_V	45_I	1.327	0.94
25_L	58_K	1.285	0.93
11_A	15_M	1.278	0.93
10_T	15_M	1.203	0.91
19_N	32_A	1.197	0.90
22_E	53_K	1.143	0.88
32_A	59_L	0.973	0.79
25_L	50_L	0.971	0.78
2_L	9_I	0.967	0.78
30_L	62_I	0.958	0.77
39_L	49_G	0.950	0.77
6_S	29_A	0.949	0.77
4_S	31_L	0.936	0.76
59_L	63_L	0.923	0.75
5_G	34_V	0.919	0.74
11_A	59_L	0.914	0.74
33_L	40_I	0.908	0.74
23_K	32_A	0.900	0.73
39_L	42_V	0.897	0.73
23_K	42_V	0.885	0.72
29_A	42_V	0.860	0.69
10_T	30_L	0.853	0.69
25_L	63_L	0.841	0.68
14_L	18_F	0.826	0.66
26_K	32_A	0.813	0.65
39_L	69_I	0.802	0.64
14_L	30_L	0.794	0.63
63_L	67_A	0.771	0.61
2_L	13_L	0.766	0.60
23_K	26_K	0.760	0.60
2_L	6_S	0.754	0.59
15_M	42_V	0.751	0.59
46_G	58_K	0.745	0.58
34_V	66_V	0.731	0.57
62_I	66_V	0.723	0.56
24_A	35_G	0.715	0.55
62_I	65_G	0.712	0.55
9_I	41_T	0.711	0.55
4_S	35_G	0.696	0.53
9_I	58_K	0.692	0.53
8_E	39_L	0.676	0.51
58_K	62_I	0.675	0.51
8_E	35_G	0.669	0.50
4_S	32_A	0.666	0.50
24_A	31_L	0.663	0.50
42_V	61_W	0.654	0.49
22_E	49_G	0.652	0.49
56_L	64_L	0.651	0.48
66_V	69_I	0.647	0.48
4_S	34_V	0.640	0.47
58_K	61_W	0.639	0.47
4_S	11_A	0.635	0.47
5_G	48_V	0.616	0.45
51_A	58_K	0.615	0.45
7_I	34_V	0.602	0.43
6_S	67_A	0.597	0.43
21_V	50_L	0.594	0.42
40_I	63_L	0.592	0.42
9_I	24_A	0.590	0.42
13_L	37_L	0.588	0.42
5_G	12_A	0.582	0.41
17_K	49_G	0.580	0.41
35_G	42_V	0.576	0.41
47_L	62_I	0.565	0.40
7_I	10_T	0.564	0.39
12_A	57_S	0.561	0.39
3_L	6_S	0.557	0.39
21_V	42_V	0.556	0.39
29_A	68_L	0.546	0.38
34_V	48_V	0.544	0.37
25_L	46_G	0.542	0.37
47_L	67_A	0.532	0.36
65_G	69_I	0.532	0.36
14_L	69_I	0.522	0.35
40_I	56_L	0.522	0.35
32_A	39_L	0.519	0.35
30_L	54_L	0.507	0.34
15_M	18_F	0.502	0.33
7_I	23_K	0.502	0.33
27_I	68_L	0.500	0.33

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
4pypA	1	1	5.8	0.901	Contact Map
2i68A	2	0.7681	4.1	0.907	Contact Map
2m67A	1	0.7536	2.6	0.916	Contact Map
4zw9A	1	0.9565	2.2	0.919	Contact Map
4dx5A	3	0.913	2	0.921	Contact Map
2nwlA	3	0.971	1.8	0.923	Contact Map
4ev6A	3	0.913	1.8	0.923	Contact Map
2h3oA	1	0.4638	1.7	0.924	Contact Map
1wazA	1	0.5072	1.6	0.926	Contact Map
4mt1A	3	0.913	1.6	0.926	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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