DUF4351 - PFAM28P - GREMLIN Contacts

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DUF4351 - Domain of unknown function (DUF4351)

PFAM:	PF14261	Sequences: QEGRQEGEAELLLRLLERRFGPLPPEVEERIEALSLEQLEALAEALLDASSLEDLEAWL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (54)
Sequences:	11328 (8650)
Seq/√Len:	1177.1
META:	0.895

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_L	43_A	3.065	1.00
18_R	48_D	2.761	1.00
14_R	44_E	2.557	1.00
18_R	44_E	2.339	1.00
34_L	42_L	2.094	1.00
35_S	38_Q	1.826	1.00
13_L	28_E	1.745	1.00
14_R	40_E	1.561	1.00
15_L	46_L	1.542	1.00
28_E	32_E	1.467	1.00
13_L	31_I	1.413	1.00
24_P	27_V	1.398	1.00
4_R	10_E	1.383	1.00
50_S	54_D	1.349	1.00
13_L	32_E	1.331	1.00
9_A	32_E	1.330	1.00
17_E	28_E	1.281	1.00
2_E	6_E	1.264	1.00
43_A	46_L	1.261	1.00
16_L	23_L	1.242	1.00
8_E	40_E	1.227	1.00
5_Q	9_A	1.215	1.00
45_A	49_A	1.200	1.00
41_A	45_A	1.114	1.00
4_R	7_G	1.084	1.00
16_L	52_L	1.081	1.00
10_E	40_E	1.078	1.00
17_E	22_P	1.049	1.00
13_L	17_E	1.037	1.00
51_S	54_D	1.016	1.00
8_E	11_L	1.013	1.00
12_L	42_L	1.012	1.00
29_E	33_A	0.994	1.00
25_P	29_E	0.992	1.00
44_E	48_D	0.978	1.00
15_L	43_A	0.943	1.00
36_L	40_E	0.942	1.00
20_F	51_S	0.899	1.00
42_L	55_L	0.881	1.00
25_P	28_E	0.871	1.00
14_R	18_R	0.863	1.00
8_E	36_L	0.857	1.00
20_F	52_L	0.854	1.00
49_A	55_L	0.840	1.00
38_Q	41_A	0.822	1.00
15_L	47_L	0.802	1.00
22_P	25_P	0.790	1.00
29_E	32_E	0.767	1.00
17_E	44_E	0.758	1.00
24_P	52_L	0.754	1.00
12_L	43_A	0.746	1.00
19_R	50_S	0.729	1.00
9_A	13_L	0.702	1.00
7_G	43_A	0.694	1.00
11_L	15_L	0.688	1.00
3_G	7_G	0.679	1.00
42_L	49_A	0.673	1.00
34_L	49_A	0.636	1.00
8_E	39_L	0.620	1.00
26_E	29_E	0.606	1.00
34_L	38_Q	0.606	1.00
4_R	8_E	0.593	1.00
7_G	11_L	0.566	1.00
41_A	44_E	0.561	1.00
16_L	46_L	0.557	1.00
45_A	55_L	0.552	1.00
37_E	40_E	0.552	1.00
17_E	23_L	0.551	1.00
5_Q	36_L	0.539	1.00
34_L	45_A	0.536	1.00
9_A	34_L	0.530	1.00
20_F	49_A	0.528	1.00
3_G	6_E	0.526	1.00
19_R	40_E	0.523	1.00
23_L	52_L	0.519	1.00
20_F	50_S	0.517	1.00
16_L	31_I	0.510	1.00
10_E	13_L	0.509	1.00
49_A	52_L	0.506	1.00
27_V	30_R	0.506	1.00
18_R	45_A	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
4x86A	1	0.7119	44.4	0.766	Contact Map
1ywfA	1	0.7627	12.9	0.82	Contact Map
3mjkA	2	0.5763	9.9	0.829	Contact Map
3kyzA	2	0.5763	5.9	0.846	Contact Map
4qkoA	2	0.5593	5.8	0.847	Contact Map
4anoA	1	0.9153	5.7	0.847	Contact Map
2qnlA	2	0.9153	5.7	0.847	Contact Map
3u43A	1	0.5593	5.3	0.849	Contact Map
4xlgB	1	0.8814	5.3	0.849	Contact Map
3mjgA	2	0	5.1	0.85	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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