DUF2963 - PFAM28P - GREMLIN Contacts

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DUF2963 - Protein of unknown function (DUF2963)

PFAM:	PF11178	Sequences: YNADGKLISYIYEYDSNTGNLIKETYYNADGKTIYYIEEYDSNGNLTKETY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	51 (48)
Sequences:	1150 (1040)
Seq/√Len:	150.2
META:	0.73

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_N	43_N	4.022	1.00
16_S	42_S	3.113	1.00
6_K	32_K	2.422	1.00
13_E	23_K	2.288	1.00
22_I	47_T	2.199	1.00
39_E	48_K	2.055	1.00
15_D	20_N	2.046	1.00
3_A	29_A	1.909	1.00
41_D	45_N	1.767	1.00
7_L	11_I	1.668	1.00
7_L	10_Y	1.477	1.00
23_K	48_K	1.388	1.00
34_I	38_E	1.378	1.00
21_L	24_E	1.240	1.00
11_I	37_I	1.213	1.00
14_Y	40_Y	1.147	1.00
24_E	49_E	1.115	0.99
13_E	39_E	1.096	0.99
33_T	38_E	1.022	0.99
15_D	41_D	1.012	0.99
25_T	33_T	1.006	0.99
42_S	45_N	1.002	0.99
8_I	11_I	1.002	0.99
28_N	31_G	0.966	0.98
10_Y	27_Y	0.951	0.98
7_L	33_T	0.934	0.98
9_S	35_Y	0.864	0.97
19_G	44_G	0.850	0.96
12_Y	38_E	0.832	0.96
46_L	49_E	0.822	0.96
1_Y	27_Y	0.820	0.96
4_D	7_L	0.808	0.95
6_K	9_S	0.805	0.95
8_I	37_I	0.803	0.95
14_Y	21_L	0.800	0.95
14_Y	19_G	0.799	0.95
8_I	34_I	0.792	0.95
3_A	26_Y	0.789	0.95
23_K	39_E	0.727	0.92
17_N	21_L	0.717	0.91
34_I	37_I	0.706	0.91
12_Y	21_L	0.691	0.90
2_N	10_Y	0.684	0.89
7_L	25_T	0.680	0.89
7_L	34_I	0.678	0.89
21_L	46_L	0.672	0.89
16_S	22_I	0.666	0.88
40_Y	46_L	0.663	0.88
35_Y	38_E	0.652	0.87
35_Y	48_K	0.651	0.87
24_E	36_Y	0.650	0.87
9_S	12_Y	0.636	0.86
11_I	33_T	0.629	0.85
12_Y	27_Y	0.626	0.85
4_D	30_D	0.606	0.83
26_Y	36_Y	0.604	0.83
25_T	34_I	0.604	0.83
26_Y	32_K	0.600	0.82
28_N	32_K	0.600	0.82
5_G	20_N	0.599	0.82
6_K	11_I	0.582	0.80
20_N	45_N	0.581	0.80
16_S	26_Y	0.561	0.78
21_L	26_Y	0.558	0.78
2_N	35_Y	0.536	0.75
14_Y	17_N	0.534	0.74
14_Y	20_N	0.526	0.73
5_G	31_G	0.516	0.72
36_Y	41_D	0.515	0.72
2_N	11_I	0.514	0.72
8_I	24_E	0.510	0.71
21_L	38_E	0.500	0.70

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
4iglB	1	0.9804	77.7	0.69	Contact Map
4o9xA	1	0.9804	77.3	0.691	Contact Map
4iglA	1	0.9804	66	0.717	Contact Map
4r03A	1	0.9804	58.2	0.73	Contact Map
4r8oA	2	0.8235	43.6	0.752	Contact Map
3mswA	1	0.9608	42.1	0.754	Contact Map
4x7rA	1	0.902	32.9	0.769	Contact Map
4ld1A	1	0.5098	30.5	0.772	Contact Map
3hiaA	3	0.7647	21.7	0.788	Contact Map
4by2A	1	0.2745	17.4	0.797	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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