DUF4160 - PFAM28P - GREMLIN Contacts

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

DUF4160 - Domain of unknown function (DUF4160)

PFAM:	PF13711	Sequences: GIRIFFYSNDKDHEPPHFHVEYGGYEAKFWIEPVELAEGGLPRRELRLVLEWAEEHRDELLEAWN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	65 (64)
Sequences:	38708 (25684)
Seq/√Len:	3210.5
META:	0.971

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_F	46_L	2.477	1.00
18_F	53_A	2.336	1.00
5_F	21_E	2.145	1.00
57_R	61_L	2.065	1.00
30_W	33_P	1.981	1.00
28_K	37_A	1.948	1.00
56_H	59_E	1.909	1.00
30_W	37_A	1.898	1.00
34_V	53_A	1.731	1.00
9_N	12_D	1.728	1.00
59_E	63_A	1.611	1.00
32_E	61_L	1.602	1.00
16_P	61_L	1.588	1.00
28_K	38_E	1.583	1.00
42_P	45_E	1.508	1.00
29_F	36_L	1.506	1.00
21_E	26_E	1.484	1.00
36_L	46_L	1.448	1.00
22_Y	25_Y	1.437	1.00
30_W	35_E	1.356	1.00
46_L	50_L	1.346	1.00
29_F	50_L	1.294	1.00
2_I	20_V	1.218	1.00
27_A	41_L	1.197	1.00
25_Y	42_P	1.185	1.00
12_D	15_P	1.182	1.00
22_Y	45_E	1.179	1.00
50_L	53_A	1.143	1.00
58_D	62_E	1.129	1.00
16_P	60_L	1.098	1.00
15_P	30_W	1.094	1.00
41_L	49_V	1.020	1.00
53_A	60_L	1.013	1.00
27_A	36_L	1.005	1.00
43_R	47_R	0.980	1.00
48_L	51_E	0.962	1.00
27_A	46_L	0.952	1.00
53_A	57_R	0.950	1.00
19_H	28_K	0.943	1.00
62_E	65_N	0.940	1.00
41_L	45_E	0.898	1.00
14_E	28_K	0.893	1.00
32_E	57_R	0.862	1.00
52_W	56_H	0.848	1.00
50_L	54_E	0.847	1.00
45_E	48_L	0.838	1.00
61_L	65_N	0.830	1.00
31_I	60_L	0.821	1.00
36_L	39_G	0.818	1.00
34_V	50_L	0.811	1.00
25_Y	41_L	0.809	1.00
5_F	8_S	0.799	1.00
34_V	57_R	0.789	1.00
20_V	49_V	0.789	1.00
20_V	29_F	0.789	1.00
52_W	55_E	0.785	1.00
5_F	26_E	0.762	1.00
21_E	24_G	0.761	1.00
4_I	60_L	0.732	1.00
7_Y	10_D	0.732	1.00
39_G	46_L	0.730	1.00
58_D	61_L	0.729	1.00
25_Y	40_G	0.727	1.00
47_R	50_L	0.726	1.00
44_R	48_L	0.717	1.00
4_I	52_W	0.715	1.00
2_I	22_Y	0.705	1.00
4_I	18_F	0.704	1.00
1_G	22_Y	0.690	1.00
59_E	62_E	0.690	1.00
3_R	21_E	0.684	1.00
2_I	49_V	0.674	1.00
51_E	55_E	0.657	1.00
26_E	38_E	0.656	1.00
29_F	53_A	0.654	1.00
2_I	45_E	0.651	1.00
48_L	52_W	0.647	1.00
54_E	57_R	0.643	1.00
51_E	54_E	0.637	1.00
2_I	41_L	0.637	1.00
47_R	51_E	0.629	1.00
45_E	51_E	0.609	1.00
16_P	65_N	0.607	1.00
30_W	34_V	0.603	1.00
31_I	61_L	0.591	1.00
55_E	59_E	0.584	1.00
15_P	32_E	0.580	1.00
52_W	60_L	0.554	1.00
8_S	12_D	0.547	1.00
44_R	47_R	0.538	1.00
9_N	13_H	0.538	1.00
15_P	35_E	0.523	1.00
33_P	57_R	0.522	1.00
4_I	49_V	0.516	1.00
3_R	7_Y	0.503	1.00
20_V	41_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
4akgA	2	0.8615	10.9	0.845	Contact Map
3pmcA	2	0.3077	10.3	0.847	Contact Map
3pmdA	2	0.4154	10.2	0.847	Contact Map
3dljA	2	0.3846	9.6	0.849	Contact Map
2bnlA	2	0.3231	9.5	0.849	Contact Map
3vkgA	2	0.8615	9	0.851	Contact Map
2l4hA	1	0.3846	9	0.851	Contact Map
4rh7A	1	0.8615	8.4	0.853	Contact Map
2kglA	1	0.5077	6.3	0.861	Contact Map
4bj6A	1	1	5.5	0.865	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 0.0044 seconds.