DUF4384 - PFAM28P - GREMLIN Contacts

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DUF4384 - Domain of unknown function (DUF4384)

PFAM:	PF14326	Sequences: VYRSGDRLRLRVRSNRDGYLYVFNIDSDGEVTLLFPNRFDGDNRVRAGQTYEIPGPGDGFWFRVDGPPGTETLLAIASREP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	81 (79)
Sequences:	22206 (17205)
Seq/√Len:	1935.7
META:	0.966

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_G	77_A	3.391	1.00
22_V	75_A	2.793	1.00
4_S	68_P	2.737	1.00
14_S	18_G	2.430	1.00
17_D	46_R	2.403	1.00
11_R	50_T	2.385	1.00
13_R	50_T	2.341	1.00
11_R	52_E	2.303	1.00
7_R	61_W	2.297	1.00
3_R	6_D	2.289	1.00
9_R	52_E	2.152	1.00
23_F	33_L	2.015	1.00
16_R	79_R	1.950	1.00
17_D	47_A	1.926	1.00
17_D	44_R	1.738	1.00
7_R	63_R	1.705	1.00
46_R	49_Q	1.674	1.00
25_I	31_V	1.622	1.00
24_N	71_E	1.586	1.00
26_D	30_E	1.552	1.00
26_D	32_T	1.398	1.00
4_S	67_P	1.361	1.00
23_F	76_I	1.311	1.00
24_N	32_T	1.283	1.00
19_Y	43_N	1.256	1.00
21_Y	43_N	1.245	1.00
19_Y	44_R	1.229	1.00
12_V	20_L	1.226	1.00
46_R	51_Y	1.221	1.00
4_S	66_G	1.212	1.00
35_F	43_N	1.184	1.00
21_Y	78_S	1.173	1.00
25_I	74_L	1.171	1.00
55_G	58_D	1.163	1.00
10_L	73_L	1.133	1.00
12_V	51_Y	1.115	1.00
35_F	53_I	1.065	1.00
25_I	72_T	1.059	1.00
20_L	75_A	1.053	1.00
21_Y	33_L	1.040	1.00
23_F	31_V	1.027	1.00
5_G	63_R	0.954	1.00
14_S	45_V	0.950	1.00
57_G	60_F	0.939	1.00
13_R	48_G	0.923	1.00
2_Y	6_D	0.891	1.00
4_S	65_D	0.885	1.00
37_N	41_G	0.876	1.00
34_L	73_L	0.873	1.00
2_Y	64_V	0.850	1.00
27_S	71_E	0.816	1.00
23_F	74_L	0.811	1.00
64_V	71_E	0.801	1.00
27_S	69_G	0.793	1.00
27_S	70_T	0.793	1.00
60_F	63_R	0.789	1.00
41_G	44_R	0.774	1.00
39_F	60_F	0.764	1.00
9_R	61_W	0.760	1.00
20_L	77_A	0.730	1.00
37_N	40_D	0.704	1.00
8_L	64_V	0.699	1.00
15_N	18_G	0.698	1.00
45_V	51_Y	0.695	1.00
55_G	59_G	0.687	1.00
34_L	62_F	0.683	1.00
40_D	55_G	0.678	1.00
60_F	64_V	0.663	1.00
45_V	48_G	0.660	1.00
21_Y	76_I	0.660	1.00
21_Y	25_I	0.658	1.00
20_L	45_V	0.658	1.00
24_N	34_L	0.646	1.00
42_D	46_R	0.645	1.00
52_E	55_G	0.630	1.00
27_S	68_P	0.630	1.00
40_D	58_D	0.624	1.00
31_V	74_L	0.623	1.00
19_Y	78_S	0.609	1.00
8_L	24_N	0.608	1.00
14_S	77_A	0.606	1.00
52_E	56_P	0.591	1.00
69_G	75_A	0.586	1.00
18_G	45_V	0.581	1.00
22_V	53_I	0.578	1.00
58_D	61_W	0.576	1.00
54_P	62_F	0.576	1.00
16_R	47_A	0.571	1.00
28_D	67_P	0.569	1.00
10_L	34_L	0.568	1.00
12_V	45_V	0.566	1.00
20_L	35_F	0.565	1.00
74_L	78_S	0.563	1.00
42_D	45_V	0.558	1.00
26_D	71_E	0.552	1.00
38_R	41_G	0.551	1.00
18_G	79_R	0.547	1.00
40_D	60_F	0.547	1.00
15_N	47_A	0.543	1.00
14_S	20_L	0.540	1.00
10_L	24_N	0.539	1.00
23_F	54_P	0.535	1.00
28_D	31_V	0.533	1.00
27_S	67_P	0.531	1.00
35_F	45_V	0.528	1.00
66_G	69_G	0.524	1.00
39_F	43_N	0.523	1.00
37_N	60_F	0.521	1.00
21_Y	24_N	0.517	1.00
74_L	79_R	0.515	1.00
17_D	48_G	0.514	1.00
2_Y	5_G	0.513	1.00
57_G	61_W	0.510	1.00
10_L	62_F	0.509	1.00
56_P	59_G	0.504	1.00
11_R	14_S	0.502	1.00
41_G	45_V	0.500	1.00
9_R	56_P	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
4eweA	1	0.8765	26.6	0.819	Contact Map
2p17A	1	0.8395	21.5	0.827	Contact Map
3qacA	3	0.9506	19.1	0.831	Contact Map
2vqaA	3	0.963	16.9	0.836	Contact Map
1tq5A	1	0.8025	16.5	0.836	Contact Map
2e9qA	6	0.9506	16.2	0.836	Contact Map
4f7kA	1	0.8889	16	0.837	Contact Map
3kscA	4	0.9506	15.9	0.837	Contact Map
1j58A	5	0.963	14.9	0.839	Contact Map
3hrzA	1	0.9012	14.6	0.84	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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