DUF3875 - PFAM28P - GREMLIN Contacts

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

DUF3875 - Domain of unknown function, B. Theta Gene description (DUF3875)

PFAM:	PF12991	Sequences: NIMKAKNLEDIFPILGVEHDCILSKQGDITVAFEVELPEIFTLSDEEYEALHS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (47)
Sequences:	1603 (823)
Seq/√Len:	120.0
META:	0.895

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_I	37_L	3.395	1.00
21_C	31_V	2.619	1.00
45_D	51_L	2.296	1.00
24_S	30_T	2.193	1.00
17_V	22_I	1.847	1.00
6_K	10_D	1.834	1.00
43_L	51_L	1.788	1.00
7_N	10_D	1.721	1.00
8_L	12_F	1.704	1.00
11_I	27_G	1.637	1.00
6_K	11_I	1.589	1.00
24_S	28_D	1.582	1.00
15_L	25_K	1.449	1.00
21_C	29_I	1.429	1.00
20_D	32_A	1.409	1.00
44_S	47_E	1.395	1.00
21_C	35_V	1.325	1.00
16_G	23_L	1.136	0.99
27_G	42_T	1.135	0.99
47_E	51_L	1.132	0.99
32_A	35_V	1.118	0.99
26_Q	41_F	1.112	0.99
35_V	45_D	1.054	0.98
16_G	26_Q	1.038	0.98
12_F	30_T	1.013	0.98
14_I	17_V	0.877	0.94
46_E	51_L	0.862	0.94
12_F	41_F	0.854	0.94
19_H	32_A	0.797	0.91
22_I	25_K	0.794	0.91
45_D	49_E	0.790	0.91
41_F	48_Y	0.766	0.89
33_F	50_A	0.766	0.89
23_L	51_L	0.766	0.89
8_L	39_E	0.761	0.89
35_V	51_L	0.761	0.89
6_K	27_G	0.733	0.87
15_L	22_I	0.728	0.87
14_I	22_I	0.726	0.87
8_L	42_T	0.715	0.86
20_D	46_E	0.698	0.84
44_S	52_H	0.693	0.84
26_Q	36_E	0.690	0.84
8_L	49_E	0.688	0.84
15_L	26_Q	0.681	0.83
7_N	36_E	0.677	0.83
17_V	33_F	0.656	0.81
13_P	38_P	0.656	0.81
16_G	48_Y	0.647	0.80
10_D	36_E	0.641	0.79
23_L	28_D	0.640	0.79
11_I	36_E	0.640	0.79
39_E	42_T	0.638	0.79
7_N	20_D	0.630	0.78
19_H	26_Q	0.630	0.78
15_L	41_F	0.625	0.77
40_I	49_E	0.625	0.77
13_P	37_L	0.618	0.77
21_C	50_A	0.618	0.77
18_E	39_E	0.583	0.72
40_I	52_H	0.574	0.71
19_H	50_A	0.573	0.71
16_G	25_K	0.567	0.70
8_L	22_I	0.548	0.68
26_Q	34_E	0.546	0.67
37_L	47_E	0.538	0.66
16_G	37_L	0.511	0.62
33_F	40_I	0.511	0.62
17_V	50_A	0.509	0.62
7_N	11_I	0.500	0.61

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
4lb8A	2	0.9811	17.7	0.854	Contact Map
2x8kA	5	0.717	14.1	0.86	Contact Map
2iw2A	2	0.8113	5.4	0.884	Contact Map
3cmqA	1	0.9245	5	0.886	Contact Map
1r0vA	2	0.9811	4.7	0.888	Contact Map
1nltA	1	0.6226	4.4	0.889	Contact Map
3mx6A	1	0.8113	4.3	0.89	Contact Map
2rhqB	2	0.8679	4	0.892	Contact Map
4qxzA	2	0.9434	3.7	0.893	Contact Map
3s1sA	1	0.9811	3.7	0.894	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 0.0038 seconds.