DUF4258 - PFAM28P - GREMLIN Contacts

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DUF4258 - Domain of unknown function (DUF4258)

PFAM:	PF14076	Sequences: FTKHALERMAERGISEEDVEEALLNGEIIEDYPLVLGKTIDGRPLHVVVAIDEDPLVVITVYR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	63 (62)
Sequences:	22772 (17796)
Seq/√Len:	2260.1
META:	0.968

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_R	12_R	3.517	1.00
15_S	18_D	2.665	1.00
5_A	58_V	2.445	1.00
8_R	11_E	2.354	1.00
21_E	25_N	2.266	1.00
6_L	16_E	1.995	1.00
46_H	62_Y	1.820	1.00
1_F	16_E	1.703	1.00
3_K	7_E	1.635	1.00
2_T	57_V	1.600	1.00
52_D	57_V	1.595	1.00
16_E	20_E	1.496	1.00
1_F	19_V	1.473	1.00
22_A	45_L	1.471	1.00
20_E	24_L	1.470	1.00
9_M	61_V	1.451	1.00
7_E	11_E	1.424	1.00
29_I	32_Y	1.406	1.00
1_F	6_L	1.405	1.00
34_L	37_G	1.298	1.00
22_A	47_V	1.217	1.00
1_F	5_A	1.198	1.00
6_L	9_M	1.154	1.00
36_L	44_P	1.126	1.00
53_E	56_L	1.082	1.00
50_A	59_I	1.057	1.00
14_I	45_L	1.041	1.00
50_A	55_P	1.036	1.00
51_I	56_L	1.006	1.00
38_K	44_P	1.001	1.00
36_L	46_H	0.997	1.00
9_M	19_V	0.997	1.00
29_I	33_P	0.996	1.00
3_K	6_L	0.979	1.00
52_D	55_P	0.969	1.00
7_E	10_A	0.956	1.00
28_I	31_D	0.952	1.00
14_I	61_V	0.947	1.00
49_V	58_V	0.938	1.00
49_V	56_L	0.935	1.00
1_F	20_E	0.923	1.00
17_E	21_E	0.918	1.00
6_L	10_A	0.898	1.00
23_L	26_G	0.894	1.00
36_L	49_V	0.892	1.00
52_D	56_L	0.882	1.00
30_E	33_P	0.870	1.00
39_T	43_R	0.812	1.00
18_D	21_E	0.801	1.00
22_A	26_G	0.800	1.00
18_D	40_I	0.799	1.00
5_A	61_V	0.798	1.00
22_A	35_V	0.794	1.00
17_E	20_E	0.785	1.00
23_L	58_V	0.748	1.00
21_E	40_I	0.734	1.00
28_I	32_Y	0.734	1.00
34_L	38_K	0.732	1.00
34_L	39_T	0.710	1.00
40_I	43_R	0.708	1.00
48_V	59_I	0.705	1.00
37_G	46_H	0.700	1.00
1_F	9_M	0.698	1.00
8_R	14_I	0.690	1.00
9_M	16_E	0.673	1.00
50_A	53_E	0.660	1.00
8_R	61_V	0.659	1.00
32_Y	46_H	0.651	1.00
46_H	50_A	0.633	1.00
23_L	47_V	0.626	1.00
47_V	51_I	0.623	1.00
19_V	23_L	0.618	1.00
4_H	60_T	0.612	1.00
8_R	62_Y	0.609	1.00
4_H	8_R	0.605	1.00
47_V	50_A	0.603	1.00
48_V	51_I	0.602	1.00
18_D	37_G	0.599	1.00
34_L	46_H	0.597	1.00
48_V	62_Y	0.594	1.00
19_V	47_V	0.576	1.00
38_K	42_G	0.575	1.00
50_A	57_V	0.553	1.00
3_K	10_A	0.550	1.00
3_K	11_E	0.548	1.00
37_G	40_I	0.548	1.00
26_G	35_V	0.528	1.00
8_R	13_G	0.526	1.00
19_V	61_V	0.524	1.00
21_E	24_L	0.507	1.00
51_I	57_V	0.502	1.00
10_A	16_E	0.501	1.00
49_V	52_D	0.500	1.00

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
3u97A	3	1	36.1	0.769	Contact Map
1rfzA	4	0.9683	13.3	0.812	Contact Map
1tlqA	4	0.9683	12.5	0.814	Contact Map
1y9iA	4	0.9683	11.3	0.818	Contact Map
2fhzB	1	0.9841	10.5	0.82	Contact Map
1y6xA	3	0.3651	9.2	0.825	Contact Map
4muqA	1	0.9841	8.1	0.829	Contact Map
2xvsA	1	1	7.4	0.833	Contact Map
2hx6A	1	0.9841	7.2	0.833	Contact Map
4dn7A	2	0.8571	6.4	0.837	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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