DUF1707 - PFAM28P - GREMLIN Contacts

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

DUF1707 - Domain of unknown function (DUF1707)

PFAM:	PF08044	Sequences: LRASDADRERVAERLREAFAEGRLTLDEFDERLDAAYAARTRGELAALTADLP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (53)
Sequences:	21854 (11325)
Seq/√Len:	1555.6
META:	0.904

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_F	26_L	2.493	1.00
12_A	37_Y	2.300	1.00
12_A	33_L	1.970	1.00
11_V	49_T	1.965	1.00
19_F	29_F	1.793	1.00
15_L	29_F	1.731	1.00
3_A	42_R	1.671	1.00
32_R	51_D	1.552	1.00
13_E	16_R	1.522	1.00
18_A	23_R	1.487	1.00
48_L	51_D	1.452	1.00
18_A	21_E	1.410	1.00
30_D	34_D	1.355	1.00
16_R	29_F	1.326	1.00
17_E	21_E	1.316	1.00
26_L	30_D	1.300	1.00
18_A	49_T	1.300	1.00
36_A	48_L	1.290	1.00
35_A	48_L	1.275	1.00
14_R	18_A	1.247	1.00
11_V	45_L	1.228	1.00
4_S	23_R	1.226	1.00
34_D	38_A	1.207	1.00
14_R	49_T	1.194	1.00
42_R	46_A	1.189	1.00
17_E	20_A	1.180	1.00
31_E	35_A	1.176	1.00
23_R	53_P	1.154	1.00
9_E	37_Y	1.102	1.00
9_E	13_E	1.077	1.00
16_R	20_A	1.062	1.00
47_A	50_A	1.061	1.00
15_L	36_A	1.060	1.00
12_A	36_A	1.028	1.00
10_R	14_R	1.020	1.00
11_V	36_A	0.951	1.00
5_D	22_G	0.926	1.00
25_T	28_E	0.891	1.00
28_E	31_E	0.883	1.00
9_E	12_A	0.878	1.00
40_R	44_E	0.878	1.00
7_D	42_R	0.867	1.00
41_T	44_E	0.815	1.00
29_F	33_L	0.796	1.00
2_R	40_R	0.795	1.00
19_F	30_D	0.777	1.00
13_E	17_E	0.773	1.00
9_E	16_R	0.771	1.00
35_A	47_A	0.765	1.00
25_T	40_R	0.762	1.00
6_A	9_E	0.760	1.00
4_S	7_D	0.758	1.00
36_A	45_L	0.746	1.00
3_A	45_L	0.741	1.00
29_F	41_T	0.738	1.00
30_D	33_L	0.728	1.00
6_A	10_R	0.720	1.00
18_A	52_L	0.719	1.00
35_A	50_A	0.718	1.00
1_L	42_R	0.675	1.00
18_A	28_E	0.667	1.00
45_L	48_L	0.651	1.00
27_D	30_D	0.646	1.00
28_E	32_R	0.627	1.00
31_E	40_R	0.603	1.00
4_S	53_P	0.601	1.00
12_A	16_R	0.589	1.00
3_A	41_T	0.587	1.00
10_R	13_E	0.581	1.00
39_A	44_E	0.573	1.00
2_R	51_D	0.571	1.00
31_E	34_D	0.561	1.00
44_E	47_A	0.560	1.00
46_A	50_A	0.539	1.00
15_L	49_T	0.534	1.00
3_A	47_A	0.524	1.00
5_D	8_R	0.513	1.00
7_D	10_R	0.513	1.00
35_A	38_A	0.509	1.00
34_D	37_Y	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
1ug3A	1	0.9057	18.9	0.787	Contact Map
3l6aA	1	0.9057	14.9	0.796	Contact Map
1mliA	5	1	13.1	0.801	Contact Map
3znuA	5	0.9245	12.1	0.804	Contact Map
3eiqC	1	0.9057	10.2	0.81	Contact Map
1qsaA	1	1	9.6	0.813	Contact Map
2ionA	1	0.9057	9.2	0.814	Contact Map
4kisA	2	0.9623	8	0.819	Contact Map
2nszA	1	0.9057	7.6	0.821	Contact Map
3hzsA	3	0.6981	7	0.824	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.