DUF4129 - PFAM28P - GREMLIN Contacts

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DUF4129 - Domain of unknown function (DUF4129)

PFAM:	PF13559	Sequences: AYRRLLRRLARRGLPRRPSETPREYARRLRALPALAAALRRLTRLYERARYGGRPLDAEELRRLRAALR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (67)
Sequences:	45163 (32936)
Seq/√Len:	4023.8
META:	0.947

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_E	28_R	4.088	1.00
23_R	47_E	3.325	1.00
17_R	20_E	2.149	1.00
57_D	60_E	1.930	1.00
5_L	39_L	1.883	1.00
22_P	47_E	1.841	1.00
16_R	25_Y	1.729	1.00
26_A	43_T	1.687	1.00
26_A	40_R	1.598	1.00
22_P	46_Y	1.562	1.00
43_T	47_E	1.526	1.00
61_L	65_R	1.525	1.00
8_R	12_R	1.497	1.00
41_R	67_A	1.493	1.00
48_R	60_E	1.469	1.00
32_L	35_L	1.425	1.00
21_T	24_E	1.404	1.00
58_A	62_R	1.391	1.00
6_L	16_R	1.380	1.00
48_R	54_R	1.375	1.00
20_E	25_Y	1.371	1.00
38_A	41_R	1.369	1.00
46_Y	50_R	1.366	1.00
23_R	44_R	1.201	1.00
63_R	67_A	1.193	1.00
35_L	38_A	1.145	1.00
26_A	39_L	1.116	1.00
41_R	63_R	1.102	1.00
22_P	43_T	1.082	1.00
5_L	9_L	1.077	1.00
41_R	45_L	1.022	1.00
42_L	64_L	1.003	1.00
45_L	60_E	0.993	1.00
10_A	16_R	0.991	1.00
16_R	20_E	0.990	1.00
56_L	60_E	0.985	1.00
40_R	44_R	0.981	1.00
14_L	28_R	0.979	1.00
45_L	63_R	0.973	1.00
10_A	15_P	0.961	1.00
2_Y	43_T	0.928	1.00
9_L	29_L	0.912	1.00
39_L	43_T	0.897	1.00
9_L	25_Y	0.897	1.00
60_E	63_R	0.895	1.00
7_R	10_A	0.887	1.00
36_A	40_R	0.882	1.00
8_R	11_R	0.855	1.00
25_Y	29_L	0.842	1.00
56_L	61_L	0.836	1.00
14_L	29_L	0.789	1.00
59_E	63_R	0.786	1.00
58_A	61_L	0.783	1.00
62_R	66_A	0.781	1.00
49_A	56_L	0.776	1.00
3_R	7_R	0.772	1.00
23_R	26_A	0.766	1.00
2_Y	6_L	0.750	1.00
3_R	6_L	0.745	1.00
44_R	47_E	0.744	1.00
5_L	8_R	0.739	1.00
33_P	36_A	0.730	1.00
29_L	39_L	0.728	1.00
28_R	31_A	0.724	1.00
7_R	11_R	0.718	1.00
1_A	5_L	0.710	1.00
48_R	52_G	0.698	1.00
59_E	62_R	0.698	1.00
15_P	25_Y	0.687	1.00
21_T	47_E	0.682	1.00
5_L	42_L	0.681	1.00
4_R	8_R	0.676	1.00
2_Y	22_P	0.676	1.00
45_L	48_R	0.661	1.00
38_A	67_A	0.657	1.00
2_Y	25_Y	0.653	1.00
22_P	51_Y	0.653	1.00
27_R	40_R	0.649	1.00
23_R	43_T	0.645	1.00
27_R	30_R	0.643	1.00
44_R	48_R	0.643	1.00
45_L	64_L	0.640	1.00
63_R	66_A	0.640	1.00
6_L	25_Y	0.632	1.00
23_R	40_R	0.630	1.00
45_L	67_A	0.625	1.00
31_A	34_A	0.616	1.00
6_L	9_L	0.594	1.00
42_L	46_Y	0.588	1.00
1_A	61_L	0.581	1.00
62_R	65_R	0.576	1.00
6_L	10_A	0.563	1.00
6_L	51_Y	0.563	1.00
37_A	41_R	0.548	1.00
30_R	33_P	0.542	1.00
6_L	22_P	0.533	1.00
9_L	12_R	0.533	1.00
32_L	36_A	0.528	1.00
4_R	7_R	0.517	1.00
25_Y	51_Y	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
1o3uA	2	0.8986	33.2	0.757	Contact Map
1ufbA	3	0.9855	32.7	0.758	Contact Map
2hsbA	2	0.9855	28	0.766	Contact Map
4nqfA	2	1	26.1	0.769	Contact Map
1wolA	1	0.9565	26	0.769	Contact Map
2g5gX	1	1	12.3	0.802	Contact Map
3o10A	2	0.9855	10.6	0.807	Contact Map
3cuqB	1	0.9855	10.1	0.809	Contact Map
2l6pA	1	0.3913	8.9	0.813	Contact Map
2avuE	2	0.8406	7.1	0.822	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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