DUF3060 - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

DUF3060 - Protein of unknown function (DUF3060)

PFAM:	PF11259	Sequences: VSGSNNTVTLTGSCDSVTVSGSNNTVTVDSVDTITVSGSNNTVTYKSGDPKVSDSGSG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	58 (56)
Sequences:	3900 (2913)
Seq/√Len:	389.3
META:	0.885

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_N	40_N	2.693	1.00
20_S	37_S	2.556	1.00
22_S	39_S	2.496	1.00
4_S	22_S	2.379	1.00
24_N	41_N	2.238	1.00
25_T	42_T	2.167	1.00
5_N	23_N	2.153	1.00
3_G	6_N	1.955	1.00
2_S	20_S	1.899	1.00
45_Y	50_P	1.881	1.00
37_S	55_S	1.856	1.00
4_S	39_S	1.755	1.00
18_T	35_T	1.666	1.00
6_N	24_N	1.540	1.00
29_D	46_K	1.517	1.00
27_T	44_T	1.507	1.00
7_T	25_T	1.489	1.00
2_S	37_S	1.476	1.00
5_N	40_N	1.377	1.00
19_V	26_V	1.193	1.00
14_C	17_V	1.172	1.00
21_G	24_N	1.168	1.00
28_V	45_Y	1.160	1.00
16_S	35_T	1.105	1.00
31_V	34_I	1.051	1.00
10_L	14_C	1.046	1.00
13_S	30_S	1.042	1.00
9_T	27_T	0.984	1.00
50_P	54_D	0.932	1.00
11_T	29_D	0.923	1.00
19_V	36_V	0.923	1.00
13_S	32_D	0.880	1.00
14_C	31_V	0.877	1.00
34_I	43_V	0.861	1.00
15_D	32_D	0.853	1.00
8_V	26_V	0.837	1.00
10_L	45_Y	0.825	1.00
14_C	32_D	0.807	1.00
30_S	46_K	0.806	1.00
3_G	38_G	0.803	1.00
36_V	43_V	0.790	1.00
35_T	53_S	0.787	1.00
10_L	17_V	0.785	1.00
14_C	29_D	0.775	1.00
11_T	46_K	0.764	1.00
30_S	33_T	0.761	1.00
1_V	8_V	0.732	1.00
26_V	43_V	0.728	1.00
16_S	33_T	0.713	1.00
11_T	14_C	0.707	1.00
32_D	49_D	0.702	1.00
30_S	47_S	0.699	1.00
5_N	16_S	0.665	0.99
28_V	34_I	0.660	0.99
4_S	23_N	0.657	0.99
7_T	42_T	0.651	0.99
51_K	55_S	0.639	0.99
35_T	44_T	0.631	0.99
10_L	28_V	0.628	0.99
28_V	43_V	0.619	0.99
2_S	55_S	0.615	0.99
36_V	55_S	0.600	0.99
15_D	50_P	0.596	0.98
28_V	31_V	0.595	0.98
27_T	48_G	0.592	0.98
30_S	54_D	0.578	0.98
46_K	49_D	0.558	0.98
12_G	45_Y	0.556	0.98
1_V	55_S	0.556	0.98
17_V	31_V	0.554	0.98
36_V	54_D	0.552	0.98
27_T	54_D	0.544	0.97
7_T	27_T	0.541	0.97
8_V	18_T	0.528	0.97
16_S	30_S	0.519	0.96
17_V	28_V	0.516	0.96
15_D	33_T	0.515	0.96
44_T	47_S	0.514	0.96
19_V	24_N	0.513	0.96
7_T	16_S	0.509	0.96
36_V	45_Y	0.507	0.96
4_S	21_G	0.502	0.96
50_P	53_S	0.501	0.96
15_D	18_T	0.500	0.96

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
3ultA	1	0.8793	15.5	0.757	Contact Map
4mtkA	4	0.9828	6.8	0.793	Contact Map
3petA	2	0.9655	5.1	0.805	Contact Map
4opwA	1	0.9828	3.5	0.82	Contact Map
4yguA	3	0.9828	2.9	0.827	Contact Map
3lycA	2	0.9828	2.9	0.827	Contact Map
3jx8A	4	0.9655	1.7	0.848	Contact Map
3h09A	1	0.9828	1.7	0.848	Contact Map
2ks0A	2	0.8448	1.6	0.849	Contact Map
1wthA	3	0.931	1.6	0.849	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.

Page generated in 0.0043 seconds.