DUF347 - PFAM28P - GREMLIN Contacts

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DUF347 - Repeat of Unknown Function (DUF347)

PFAM:	PF03988	Sequences: LYWLAIILTTTLGTTLGDFLADGLGLGYLGGSLIFAALLAVVLAAWYRTRRY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	52 (50)
Sequences:	31332 (11631)
Seq/√Len:	1644.8
META:	0.901

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_A	48_R	3.164	1.00
7_I	10_T	2.193	1.00
33_L	37_A	2.081	1.00
19_F	23_G	1.962	1.00
30_G	33_L	1.960	1.00
22_D	28_Y	1.955	1.00
2_Y	6_I	1.930	1.00
36_A	40_A	1.651	1.00
40_A	44_A	1.521	1.00
4_L	8_L	1.501	1.00
37_A	41_V	1.456	1.00
38_L	42_V	1.445	1.00
45_A	49_T	1.432	1.00
43_L	47_Y	1.406	1.00
20_L	35_F	1.355	1.00
29_L	33_L	1.300	1.00
21_A	31_G	1.270	1.00
12_L	16_L	1.233	1.00
19_F	24_L	1.222	1.00
6_I	10_T	1.209	1.00
43_L	46_W	1.202	1.00
7_I	11_T	1.182	1.00
28_Y	32_S	1.154	1.00
41_V	45_A	1.152	1.00
20_L	31_G	1.148	1.00
6_I	14_T	1.085	1.00
15_T	18_D	1.075	1.00
29_L	32_S	1.066	1.00
27_G	30_G	1.044	1.00
30_G	34_I	1.025	1.00
17_G	21_A	0.995	1.00
20_L	26_L	0.972	1.00
44_A	47_Y	0.928	1.00
26_L	30_G	0.885	1.00
26_L	34_I	0.857	1.00
2_Y	14_T	0.824	1.00
9_T	15_T	0.816	1.00
14_T	47_Y	0.815	1.00
17_G	31_G	0.804	1.00
20_L	24_L	0.802	1.00
1_L	10_T	0.801	1.00
39_L	46_W	0.792	1.00
28_Y	31_G	0.763	1.00
21_A	28_Y	0.762	1.00
26_L	31_G	0.757	1.00
2_Y	46_W	0.706	1.00
32_S	36_A	0.702	1.00
5_A	14_T	0.696	1.00
11_T	15_T	0.689	1.00
16_L	19_F	0.682	1.00
27_G	31_G	0.681	1.00
9_T	12_L	0.665	1.00
1_L	4_L	0.664	1.00
16_L	20_L	0.652	1.00
5_A	9_T	0.644	1.00
12_L	15_T	0.626	1.00
35_F	38_L	0.624	1.00
38_L	41_V	0.619	1.00
39_L	43_L	0.613	1.00
34_I	37_A	0.605	1.00
1_L	6_I	0.594	1.00
45_A	48_R	0.588	1.00
5_A	15_T	0.580	1.00
9_T	17_G	0.577	1.00
10_T	14_T	0.571	1.00
21_A	27_G	0.554	1.00
33_L	36_A	0.550	1.00
41_V	44_A	0.549	1.00
20_L	34_I	0.548	1.00
46_W	50_R	0.527	1.00
6_I	15_T	0.521	1.00
22_D	25_G	0.513	1.00
20_L	23_G	0.505	1.00
1_L	9_T	0.502	1.00
8_L	12_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
4ev6A	3	0.9808	24.3	0.75	Contact Map
4i0uA	4	0.9615	24.2	0.75	Contact Map
4g1uA	2	0.8654	7.9	0.799	Contact Map
4twkA	2	0.9038	5.9	0.811	Contact Map
2nq2A	2	0.9038	5	0.817	Contact Map
2qksA	4	0.9423	3.5	0.831	Contact Map
4wgvA	2	0.9423	3.1	0.834	Contact Map
1lnqA	6	0.8462	2.7	0.839	Contact Map
2qi9A	2	0.9038	2.6	0.841	Contact Map
1p7bA	3	0.9423	2.5	0.843	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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