DUF320 - PFAM28P - GREMLIN Contacts

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DUF320 - Small secreted domain (DUF320)

PFAM:	PF03777	Sequences: GAAAAGAGAEGAAAGSPGVLSGNVVQVPVHVPVNVCGNTVNVIGLLNPAFGNTCVN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (55)
Sequences:	3080 (1730)
Seq/√Len:	233.3
META:	0.401

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_C	54_C	8.434	1.00
41_N	44_G	3.194	1.00
18_G	21_S	2.873	1.00
11_G	24_V	2.309	1.00
13_A	24_V	2.118	1.00
39_T	49_A	1.846	1.00
39_T	48_P	1.795	1.00
39_T	46_L	1.733	1.00
5_A	8_G	1.599	1.00
9_A	26_Q	1.539	1.00
23_N	36_C	1.314	1.00
50_F	53_T	1.293	1.00
3_A	6_G	1.287	1.00
25_V	28_P	1.207	1.00
24_V	55_V	1.148	1.00
11_G	26_Q	1.107	1.00
16_S	21_S	1.103	1.00
22_G	38_N	1.093	1.00
41_N	45_L	1.086	1.00
31_V	35_V	1.043	1.00
17_P	45_L	1.006	1.00
17_P	21_S	0.967	1.00
4_A	7_A	0.961	1.00
20_L	24_V	0.944	1.00
25_V	40_V	0.943	1.00
7_A	10_E	0.912	1.00
7_A	32_P	0.911	1.00
15_G	18_G	0.898	0.99
19_V	34_N	0.860	0.99
2_A	5_A	0.848	0.99
23_N	26_Q	0.825	0.99
8_G	12_A	0.818	0.99
34_N	40_V	0.809	0.99
44_G	47_N	0.804	0.99
14_A	24_V	0.803	0.99
2_A	6_G	0.792	0.99
46_L	50_F	0.784	0.99
41_N	46_L	0.773	0.98
39_T	47_N	0.771	0.98
3_A	10_E	0.754	0.98
49_A	53_T	0.742	0.98
10_E	53_T	0.738	0.98
8_G	11_G	0.726	0.98
11_G	16_S	0.719	0.98
24_V	31_V	0.716	0.97
20_L	53_T	0.707	0.97
14_A	55_V	0.702	0.97
34_N	56_N	0.700	0.97
2_A	8_G	0.687	0.97
38_N	51_G	0.675	0.96
11_G	17_P	0.667	0.96
26_Q	30_H	0.660	0.96
35_V	40_V	0.658	0.96
38_N	53_T	0.655	0.96
10_E	24_V	0.651	0.96
19_V	29_V	0.649	0.96
12_A	24_V	0.635	0.95
41_N	47_N	0.635	0.95
48_P	52_N	0.628	0.95
16_S	30_H	0.628	0.95
3_A	55_V	0.604	0.93
23_N	45_L	0.599	0.93
29_V	33_V	0.598	0.93
31_V	36_C	0.592	0.93
20_L	23_N	0.592	0.93
19_V	45_L	0.592	0.93
37_G	49_A	0.591	0.93
13_A	17_P	0.590	0.93
4_A	8_G	0.573	0.92
10_E	15_G	0.557	0.90
44_G	53_T	0.543	0.89
16_S	34_N	0.540	0.89
13_A	16_S	0.536	0.89
27_V	32_P	0.535	0.89
12_A	55_V	0.534	0.89
35_V	38_N	0.512	0.86
17_P	28_P	0.510	0.86
21_S	27_V	0.509	0.86
4_A	12_A	0.507	0.86
2_A	20_L	0.505	0.86
35_V	50_F	0.503	0.85
4_A	53_T	0.500	0.85

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
4uqiB	1	0.3214	1.6	0.883	Contact Map
1e5xA	2	0.4464	0.6	0.91	Contact Map
4pz3A	2	0.9821	0.6	0.91	Contact Map
1o7bT	1	1	0.6	0.911	Contact Map
4hu8A	4	0.75	0.6	0.911	Contact Map
4gysA	2	0.9643	0.6	0.913	Contact Map
1m22A	1	0.9643	0.6	0.913	Contact Map
2gi3A	2	0.9643	0.5	0.914	Contact Map
4wj3A	1	0.9643	0.5	0.915	Contact Map
4nq3A	4	0.6786	0.5	0.916	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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