DUF2508 - PFAM28P - GREMLIN Contacts

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DUF2508 - Protein of unknown function (DUF2508)

PFAM:	PF10704	Sequences: MFFRKKKGKLKKEEDEELLEEIEKAKEEWENAKSNFENVTDLIDYAIYEIKAAEAKYFYLLKEAKERGIKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	71 (61)
Sequences:	1839 (1377)
Seq/√Len:	176.3
META:	0.697

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_N	46_A	3.493	1.00
26_K	30_E	2.849	1.00
15_D	67_R	2.491	1.00
25_A	53_A	2.018	1.00
63_E	66_E	2.012	1.00
30_E	33_K	1.855	1.00
63_E	67_R	1.789	1.00
23_E	26_K	1.775	1.00
57_Y	61_L	1.731	1.00
42_L	59_Y	1.724	1.00
18_L	60_L	1.559	1.00
29_W	53_A	1.518	1.00
32_A	50_I	1.517	1.00
51_K	54_E	1.512	1.00
33_K	54_E	1.430	1.00
27_E	30_E	1.384	1.00
28_E	53_A	1.375	1.00
30_E	34_S	1.372	1.00
12_K	15_D	1.347	1.00
36_F	47_I	1.300	1.00
32_A	53_A	1.277	1.00
49_E	56_K	1.268	1.00
27_E	31_N	1.258	1.00
25_A	32_A	1.252	1.00
29_W	58_F	1.194	1.00
45_Y	56_K	1.181	1.00
31_N	34_S	1.171	1.00
24_K	28_E	1.114	1.00
33_K	37_E	1.100	1.00
44_D	48_Y	1.023	0.99
20_E	24_K	1.002	0.99
45_Y	49_E	0.982	0.99
17_E	21_E	0.981	0.99
25_A	60_L	0.966	0.99
48_Y	52_A	0.952	0.99
22_I	64_A	0.943	0.99
36_F	43_I	0.909	0.99
14_E	17_E	0.899	0.99
12_K	16_E	0.896	0.99
55_A	58_F	0.889	0.98
51_K	55_A	0.888	0.98
34_S	38_N	0.881	0.98
36_F	46_A	0.875	0.98
36_F	39_V	0.861	0.98
26_K	29_W	0.833	0.98
25_A	57_Y	0.817	0.97
35_N	45_Y	0.813	0.97
10_L	13_E	0.812	0.97
36_F	50_I	0.807	0.97
35_N	49_E	0.800	0.97
45_Y	52_A	0.795	0.97
19_L	64_A	0.789	0.97
16_E	23_E	0.758	0.96
60_L	64_A	0.752	0.96
32_A	36_F	0.751	0.96
13_E	17_E	0.727	0.95
45_Y	53_A	0.718	0.94
22_I	60_L	0.717	0.94
9_K	12_K	0.712	0.94
31_N	35_N	0.711	0.94
39_V	58_F	0.692	0.93
18_L	21_E	0.677	0.92
39_V	43_I	0.673	0.92
58_F	62_K	0.672	0.92
44_D	47_I	0.658	0.91
64_A	68_G	0.657	0.91
36_F	42_L	0.654	0.91
29_W	57_Y	0.652	0.91
15_D	19_L	0.651	0.91
35_N	38_N	0.639	0.90
20_E	23_E	0.632	0.90
28_E	32_A	0.622	0.89
13_E	27_E	0.610	0.88
23_E	27_E	0.605	0.88
36_F	52_A	0.596	0.87
13_E	16_E	0.592	0.86
44_D	52_A	0.591	0.86
39_V	42_L	0.583	0.86
25_A	28_E	0.572	0.84
46_A	51_K	0.555	0.83
22_I	35_N	0.552	0.82
19_L	26_K	0.551	0.82
16_E	20_E	0.544	0.81
61_L	65_K	0.535	0.80
62_K	66_E	0.521	0.79
48_Y	61_L	0.520	0.78
38_N	42_L	0.518	0.78
22_I	57_Y	0.516	0.78
16_E	31_N	0.515	0.78
36_F	44_D	0.513	0.78
14_E	67_R	0.505	0.76
59_Y	63_E	0.500	0.76

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
2kncA	1	0.2535	9.8	0.866	Contact Map
4abxA	2	0.9859	4.9	0.884	Contact Map
4mf9A	1	0.3521	4.8	0.884	Contact Map
1ccwB	2	0.8592	3.7	0.89	Contact Map
3vkgA	2	0.9577	3.5	0.891	Contact Map
4urjA	1	0.7183	3.3	0.893	Contact Map
2inrA	2	0.9155	3.2	0.893	Contact Map
4gelA	2	0.7746	3	0.895	Contact Map
2novA	2	0.9014	3	0.895	Contact Map
4rh7A	1	0.9014	2.9	0.896	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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