DUF2188 - PFAM28P - GREMLIN Contacts

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

DUF2188 - Uncharacterized protein conserved in bacteria (DUF2188)

PFAM:	PF09954	Sequences: YHVVPRHDGGWAVKREGASRASSVFDTQAEAIEAAREIARNQGGGELVIHGRDGRIREKDSY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (60)
Sequences:	15528 (11247)
Seq/√Len:	1452.0
META:	0.926

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_F	34_A	2.471	1.00
2_H	50_H	2.456	1.00
35_A	47_L	2.057	1.00
12_A	24_V	2.045	1.00
48_V	59_K	1.998	1.00
51_G	57_R	1.879	1.00
23_S	34_A	1.830	1.00
28_Q	57_R	1.788	1.00
51_G	55_R	1.724	1.00
25_F	31_A	1.632	1.00
32_I	49_I	1.606	1.00
6_R	12_A	1.591	1.00
27_T	30_E	1.510	1.00
3_V	47_L	1.452	1.00
50_H	56_I	1.365	1.00
10_G	24_V	1.357	1.00
36_R	60_D	1.352	1.00
34_A	37_E	1.328	1.00
34_A	38_I	1.280	1.00
12_A	21_A	1.266	1.00
13_V	35_A	1.258	1.00
21_A	24_V	1.224	1.00
4_V	12_A	1.220	1.00
7_H	12_A	1.200	1.00
39_A	45_G	1.173	1.00
4_V	14_K	1.137	1.00
15_R	42_Q	1.136	1.00
18_A	22_S	1.121	1.00
15_R	18_A	1.106	1.00
32_I	47_L	1.097	1.00
5_P	52_R	1.086	1.00
13_V	38_I	1.064	1.00
3_V	13_V	1.050	1.00
49_I	58_E	1.042	1.00
46_E	59_K	1.028	1.00
2_H	16_E	1.024	1.00
10_G	26_D	1.014	1.00
39_A	47_L	1.001	1.00
29_A	33_E	0.983	1.00
4_V	50_H	0.961	1.00
13_V	31_A	0.937	1.00
15_R	22_S	0.925	1.00
2_H	48_V	0.916	1.00
7_H	10_G	0.913	1.00
38_I	41_N	0.907	1.00
7_H	21_A	0.897	1.00
5_P	10_G	0.893	1.00
16_E	48_V	0.879	1.00
7_H	24_V	0.875	1.00
38_I	42_Q	0.849	1.00
13_V	47_L	0.840	1.00
35_A	39_A	0.812	1.00
39_A	62_Y	0.761	1.00
13_V	25_F	0.755	1.00
36_R	40_R	0.745	1.00
36_R	62_Y	0.715	1.00
46_E	61_S	0.713	1.00
32_I	36_R	0.699	1.00
22_S	38_I	0.693	1.00
28_Q	32_I	0.687	1.00
14_K	21_A	0.685	1.00
48_V	56_I	0.678	1.00
6_R	10_G	0.677	1.00
42_Q	45_G	0.674	1.00
36_R	47_L	0.670	1.00
39_A	44_G	0.654	1.00
29_A	32_I	0.653	1.00
26_D	30_E	0.652	1.00
2_H	56_I	0.632	1.00
13_V	22_S	0.631	1.00
25_F	30_E	0.630	1.00
3_V	35_A	0.628	1.00
37_E	40_R	0.604	1.00
6_R	24_V	0.599	1.00
5_P	8_D	0.591	1.00
40_R	62_Y	0.579	1.00
32_I	58_E	0.575	1.00
28_Q	49_I	0.574	1.00
37_E	41_N	0.558	1.00
31_A	35_A	0.548	1.00
15_R	38_I	0.542	1.00
58_E	62_Y	0.539	1.00
13_V	23_S	0.527	1.00
14_K	18_A	0.524	1.00
46_E	60_D	0.517	1.00
32_I	60_D	0.513	1.00
28_Q	51_G	0.510	1.00
13_V	34_A	0.509	1.00
14_K	19_S	0.506	1.00
22_S	34_A	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
2jyaA	1	0.8065	18	0.812	Contact Map
2ljuA	1	0.9194	16.1	0.816	Contact Map
4fypA	2	1	14.8	0.819	Contact Map
2db2A	1	0.9839	10.6	0.831	Contact Map
2dsyA	3	0.9194	10.3	0.832	Contact Map
4bpeW	1	1	8	0.84	Contact Map
1wv8A	2	0.9032	6.8	0.845	Contact Map
3k6qA	2	0.9516	5.9	0.849	Contact Map
1utaA	1	0.7258	5.8	0.849	Contact Map
3vsvA	4	0.7742	5.7	0.85	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.