DUF4236 - PFAM28P - GREMLIN Contacts

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DUF4236 - Protein of unknown function (DUF4236)

PFAM:	PF14020	Sequences: FRFRKSIKLGPGVRLNLSKSGVSLSVGVRGARVTVGPRGGTYVTVGIPGTGLSYR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (54)
Sequences:	7061 (4637)
Seq/√Len:	631.0
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_S	14_R	3.322	1.00
25_S	32_R	2.435	1.00
42_Y	55_R	2.198	1.00
28_V	32_R	2.078	1.00
33_V	41_T	1.977	1.00
36_G	40_G	1.946	1.00
2_R	53_S	1.878	1.00
23_S	34_T	1.790	1.00
47_I	50_T	1.746	1.00
15_L	24_L	1.555	1.00
1_F	54_Y	1.551	1.00
32_R	44_T	1.541	1.00
7_I	17_L	1.529	1.00
8_K	14_R	1.477	1.00
37_P	40_G	1.459	1.00
18_S	21_G	1.444	1.00
17_L	22_V	1.358	1.00
14_R	32_R	1.325	1.00
33_V	43_V	1.322	1.00
10_G	13_V	1.274	1.00
35_V	41_T	1.273	1.00
44_T	55_R	1.235	1.00
13_V	26_V	1.164	1.00
15_L	22_V	1.158	1.00
4_R	53_S	1.151	1.00
31_A	45_V	1.145	1.00
45_V	54_Y	1.094	1.00
28_V	31_A	1.009	1.00
3_F	52_L	0.994	1.00
8_K	11_P	0.963	1.00
20_S	38_R	0.960	1.00
4_R	14_R	0.932	1.00
4_R	18_S	0.906	1.00
46_G	50_T	0.896	1.00
9_L	13_V	0.892	1.00
27_G	32_R	0.886	1.00
30_G	46_G	0.845	1.00
34_T	42_Y	0.840	1.00
27_G	30_G	0.830	1.00
16_N	23_S	0.820	1.00
23_S	37_P	0.817	1.00
1_F	19_K	0.810	1.00
46_G	49_G	0.802	1.00
43_V	54_Y	0.796	1.00
21_G	37_P	0.784	1.00
11_P	26_V	0.749	1.00
1_F	52_L	0.745	1.00
44_T	53_S	0.735	1.00
37_P	41_T	0.728	1.00
2_R	44_T	0.700	1.00
31_A	43_V	0.689	1.00
25_S	34_T	0.679	1.00
44_T	54_Y	0.668	1.00
41_T	45_V	0.660	1.00
29_R	46_G	0.656	1.00
8_K	12_G	0.646	1.00
35_V	40_G	0.643	1.00
31_A	35_V	0.631	1.00
34_T	44_T	0.630	1.00
7_I	22_V	0.624	1.00
22_V	26_V	0.623	1.00
9_L	12_G	0.620	1.00
16_N	25_S	0.606	1.00
9_L	15_L	0.604	1.00
23_S	36_G	0.599	1.00
6_S	16_N	0.598	1.00
46_G	53_S	0.571	1.00
13_V	24_L	0.559	1.00
7_I	12_G	0.554	1.00
17_L	30_G	0.551	1.00
44_T	47_I	0.547	1.00
12_G	26_V	0.538	0.99
22_V	37_P	0.531	0.99
16_N	34_T	0.526	0.99
25_S	44_T	0.525	0.99
21_G	36_G	0.525	0.99
3_F	44_T	0.517	0.99
4_R	34_T	0.511	0.99
3_F	7_I	0.507	0.99
25_S	53_S	0.501	0.99
5_K	29_R	0.500	0.99

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
2digA	1	0.5636	2.2	0.881	Contact Map
4xc5A	3	0.7455	2.2	0.881	Contact Map
1whsA	2	0.9818	1.7	0.889	Contact Map
4ci9A	2	0.9273	1.6	0.89	Contact Map
2wjrA	1	0.8182	1.5	0.891	Contact Map
4fqeA	1	0.8182	1.3	0.895	Contact Map
4n1iA	1	0.2	1.3	0.896	Contact Map
1dbdA	2	0.9273	1.3	0.896	Contact Map
4bvwA	1	0.2	1.3	0.896	Contact Map
1c7sA	2	0.8727	1.3	0.897	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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