DUF4113 - PFAM28P - GREMLIN Contacts

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DUF4113 - Domain of unknown function (DUF4113)

PFAM:	PF13438	Sequences: ERLMKALDAINRRYGRGTVRLAAQGLKRKWKMRRERLSPRYTTRWDELPVV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	51 (50)
Sequences:	14094 (8970)
Seq/√Len:	1268.6
META:	0.878

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_R	37_L	2.729	1.00
44_R	47_E	2.534	1.00
20_R	24_Q	2.390	1.00
40_R	47_E	2.209	1.00
21_L	24_Q	1.964	1.00
20_R	26_L	1.858	1.00
40_R	44_R	1.800	1.00
45_W	48_L	1.791	1.00
37_L	40_R	1.677	1.00
17_G	24_Q	1.608	1.00
10_I	19_V	1.511	1.00
8_D	11_N	1.457	1.00
28_R	31_K	1.388	1.00
14_Y	18_T	1.358	1.00
2_R	5_K	1.306	1.00
10_I	14_Y	1.300	1.00
7_L	21_L	1.288	1.00
5_K	9_A	1.286	1.00
40_R	43_T	1.285	1.00
15_G	18_T	1.236	1.00
9_A	13_R	1.227	1.00
4_M	7_L	1.200	1.00
11_N	18_T	1.191	1.00
31_K	34_R	1.148	1.00
25_G	28_R	1.116	1.00
23_A	26_L	1.052	1.00
9_A	12_R	1.037	1.00
6_A	10_I	1.009	1.00
20_R	23_A	0.994	1.00
6_A	9_A	0.978	1.00
39_P	50_V	0.963	1.00
20_R	25_G	0.921	1.00
41_Y	49_P	0.916	1.00
26_L	29_K	0.909	1.00
25_G	31_K	0.896	1.00
32_M	37_L	0.844	1.00
6_A	19_V	0.814	1.00
46_D	49_P	0.810	1.00
17_G	20_R	0.808	1.00
42_T	49_P	0.787	1.00
4_M	8_D	0.774	1.00
7_L	19_V	0.768	1.00
41_Y	47_E	0.757	1.00
2_R	6_A	0.744	1.00
5_K	12_R	0.729	1.00
39_P	47_E	0.723	1.00
30_W	33_R	0.720	1.00
45_W	49_P	0.701	1.00
2_R	9_A	0.685	1.00
3_L	6_A	0.680	1.00
6_A	14_Y	0.665	1.00
21_L	45_W	0.643	1.00
17_G	29_K	0.632	1.00
15_G	43_T	0.630	1.00
12_R	15_G	0.628	1.00
11_N	16_R	0.605	1.00
37_L	47_E	0.604	1.00
4_M	21_L	0.584	1.00
30_W	45_W	0.582	1.00
11_N	19_V	0.581	1.00
4_M	9_A	0.578	1.00
28_R	32_M	0.564	1.00
24_Q	28_R	0.557	1.00
25_G	29_K	0.552	1.00
18_T	21_L	0.537	1.00
7_L	11_N	0.535	1.00
14_Y	42_T	0.530	1.00
7_L	10_I	0.528	1.00
12_R	16_R	0.524	1.00
22_A	25_G	0.520	1.00
4_M	22_A	0.519	1.00
4_M	30_W	0.512	1.00
30_W	34_R	0.510	1.00
27_K	31_K	0.502	1.00
2_R	12_R	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
1zkeA	3	0.4314	19	0.833	Contact Map
3hr8A	1	0.8627	12.4	0.846	Contact Map
4udxX	2	1	7.2	0.861	Contact Map
4p8nA	1	0.8627	6.7	0.864	Contact Map
3aafA	1	0.9804	6.3	0.866	Contact Map
2p3pA	1	0.8627	6.3	0.866	Contact Map
1oaoA	2	1	6.2	0.866	Contact Map
1jqkA	3	1	6	0.867	Contact Map
3nb2A	2	1	5.9	0.867	Contact Map
1qe5A	3	1	5.9	0.867	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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