SPDY - PFAM28P - GREMLIN Contacts

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

SPDY - Domain of unknown function (DUF317)

PFAM:	PF03771	Sequences: TSPDGRARLGFDPEADPGEPAAWTIWARPPGGGPLWHATFTAHTPAELVAAFTAALADPAPV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (60)
Sequences:	1029 (673)
Seq/√Len:	86.9
META:	0.115

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_F	52_F	5.638	1.00
52_F	56_L	2.946	1.00
38_A	52_F	2.790	1.00
25_I	52_F	2.660	1.00
25_I	56_L	2.383	1.00
8_R	26_W	2.206	1.00
23_W	36_W	1.929	1.00
9_L	25_I	1.823	1.00
41_T	54_A	1.650	1.00
23_W	35_L	1.545	1.00
28_R	41_T	1.477	0.99
40_F	44_T	1.430	0.99
7_A	10_G	1.399	0.99
28_R	34_P	1.397	0.99
6_R	29_P	1.343	0.99
29_P	35_L	1.267	0.98
9_L	50_A	1.265	0.98
15_A	21_A	1.222	0.98
51_A	54_A	1.197	0.98
40_F	54_A	1.183	0.97
30_P	33_G	1.133	0.97
28_R	31_G	1.105	0.96
10_G	30_P	1.071	0.95
44_T	58_D	1.069	0.95
5_G	8_R	1.061	0.95
6_R	27_A	1.049	0.95
7_A	44_T	1.045	0.95
3_P	55_A	1.033	0.94
7_A	53_T	1.031	0.94
14_E	22_A	1.025	0.94
19_E	46_A	1.021	0.94
50_A	57_A	1.017	0.94
10_G	42_A	0.979	0.93
36_W	52_F	0.976	0.92
19_E	39_T	0.967	0.92
45_P	48_L	0.956	0.92
37_H	49_V	0.953	0.92
41_T	55_A	0.946	0.91
9_L	56_L	0.921	0.90
8_R	48_L	0.879	0.88
38_A	59_P	0.857	0.87
4_D	55_A	0.810	0.83
17_P	48_L	0.806	0.83
20_P	57_A	0.793	0.82
4_D	59_P	0.775	0.81
4_D	44_T	0.768	0.80
48_L	55_A	0.758	0.79
15_A	42_A	0.742	0.78
47_E	55_A	0.737	0.77
24_T	41_T	0.697	0.73
40_F	49_V	0.696	0.73
30_P	43_H	0.694	0.73
17_P	49_V	0.692	0.73
48_L	53_T	0.691	0.72
19_E	29_P	0.690	0.72
31_G	50_A	0.668	0.70
9_L	53_T	0.662	0.69
50_A	55_A	0.658	0.69
19_E	40_F	0.630	0.65
5_G	57_A	0.629	0.65
10_G	34_P	0.621	0.64
17_P	43_H	0.598	0.61
7_A	57_A	0.597	0.61
47_E	58_D	0.590	0.60
47_E	54_A	0.590	0.60
28_R	32_G	0.588	0.60
28_R	53_T	0.585	0.60
33_G	39_T	0.579	0.59
38_A	55_A	0.578	0.59
13_P	21_A	0.577	0.59
11_F	42_A	0.575	0.58
23_W	56_L	0.570	0.58
22_A	49_V	0.570	0.58
21_A	41_T	0.555	0.56
46_A	53_T	0.551	0.55
38_A	45_P	0.550	0.55
50_A	60_A	0.549	0.55
12_D	24_T	0.546	0.55
48_L	58_D	0.538	0.53
5_G	23_W	0.537	0.53
32_G	39_T	0.532	0.53
38_A	49_V	0.526	0.52
21_A	27_A	0.522	0.51
25_I	57_A	0.511	0.50
24_T	39_T	0.508	0.49
33_G	57_A	0.506	0.49
14_E	17_P	0.504	0.49
31_G	41_T	0.503	0.49
2_S	46_A	0.503	0.49
26_W	34_P	0.500	0.48

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
2d73A	2	0.8387	5.8	0.847	Contact Map
3a24A	1	0.8065	4.5	0.856	Contact Map
2g5xA	1	0.4839	3	0.868	Contact Map
4l4wA	1	0.9032	2.8	0.869	Contact Map
3hvmA	1	0.7903	2.5	0.873	Contact Map
2xn2A	4	0.9516	2.4	0.873	Contact Map
4w4lC	1	0.9032	2.3	0.875	Contact Map
4fnqA	4	0.9516	2.2	0.877	Contact Map
1t9kA	2	0.9355	2.1	0.878	Contact Map
1upkA	1	0.3065	2	0.879	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.