DUF350 - PFAM28P - GREMLIN Contacts

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DUF350 - Domain of Unknown Function (DUF350)

PFAM:	PF03994	Sequences: YGVVGLVLLLLAFFIYDKLTPYDLWKEIREGNNVAAAIVLGGVLIGIALIIAAAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (54)
Sequences:	22210 (12615)
Seq/√Len:	1716.7
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
26_K	30_E	3.438	1.00
12_A	47_I	2.617	1.00
27_E	32_N	2.517	1.00
23_D	26_K	2.513	1.00
20_T	24_L	2.094	1.00
25_W	29_R	1.680	1.00
37_A	41_G	1.663	1.00
13_F	25_W	1.663	1.00
14_F	18_K	1.643	1.00
13_F	40_L	1.463	1.00
49_L	52_A	1.437	1.00
27_E	30_E	1.389	1.00
26_K	31_G	1.373	1.00
39_V	42_G	1.352	1.00
13_F	44_L	1.342	1.00
12_A	43_V	1.278	1.00
2_G	6_L	1.260	1.00
14_F	25_W	1.219	1.00
45_I	49_L	1.219	1.00
9_L	44_L	1.196	1.00
33_N	38_I	1.176	1.00
27_E	36_A	1.137	1.00
9_L	48_A	1.131	1.00
32_N	36_A	1.124	1.00
16_Y	43_V	1.118	1.00
30_E	33_N	1.098	1.00
14_F	17_D	1.057	1.00
18_K	23_D	1.054	1.00
48_A	52_A	1.027	1.00
17_D	25_W	1.015	1.00
16_Y	39_V	1.003	1.00
24_L	40_L	0.999	1.00
28_I	36_A	0.983	1.00
27_E	31_G	0.948	1.00
24_L	36_A	0.929	1.00
46_G	50_I	0.908	1.00
10_L	14_F	0.879	1.00
17_D	24_L	0.876	1.00
6_L	10_L	0.871	1.00
11_L	15_I	0.850	1.00
17_D	20_T	0.843	1.00
29_R	32_N	0.839	1.00
26_K	29_R	0.831	1.00
5_G	51_I	0.813	1.00
32_N	35_A	0.811	1.00
11_L	14_F	0.810	1.00
33_N	37_A	0.805	1.00
16_Y	40_L	0.787	1.00
3_V	7_V	0.787	1.00
18_K	21_P	0.751	1.00
45_I	48_A	0.740	1.00
41_G	45_I	0.712	1.00
40_L	44_L	0.698	1.00
42_G	46_G	0.690	1.00
16_Y	20_T	0.686	1.00
44_L	48_A	0.668	1.00
14_F	23_D	0.666	1.00
17_D	23_D	0.641	1.00
8_L	47_I	0.638	1.00
22_Y	36_A	0.625	1.00
2_G	5_G	0.625	1.00
49_L	53_A	0.615	1.00
38_I	41_G	0.609	1.00
47_I	51_I	0.603	1.00
41_G	44_L	0.600	1.00
19_L	39_V	0.595	1.00
44_L	54_A	0.586	1.00
29_R	33_N	0.564	1.00
1_Y	6_L	0.550	1.00
31_G	35_A	0.549	1.00
2_G	8_L	0.544	1.00
39_V	43_V	0.540	1.00
7_V	11_L	0.527	1.00
43_V	47_I	0.522	1.00
5_G	9_L	0.522	1.00
12_A	16_Y	0.521	1.00
37_A	44_L	0.521	1.00
4_V	7_V	0.518	1.00
1_Y	44_L	0.508	1.00
1_Y	53_A	0.504	1.00
1_Y	8_L	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
3aqpA	1	0.9818	2.5	0.83	Contact Map
3mk7C	2	1	1.9	0.84	Contact Map
2wswA	3	1	1.9	0.84	Contact Map
3l1lA	2	0.9455	1.9	0.842	Contact Map
4rp9A	2	0.4909	1.9	0.842	Contact Map
2ww8A	1	0	1.8	0.843	Contact Map
2nq2A	2	1	1.8	0.843	Contact Map
4g1uA	2	1	1.8	0.844	Contact Map
4c7rA	3	1	1.7	0.845	Contact Map
4od4A	1	1	1.6	0.848	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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