YccF - PFAM28P - GREMLIN Contacts

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

YccF - Inner membrane component domain

PFAM:	PF03733	Sequences: LGNIIWLVLGGWWLALGHLLAGLLLCITIIGIPFGLQHFKLAGLALWPFGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	51 (51)
Sequences:	16750 (5704)
Seq/√Len:	798.7
META:	0.871

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_T	31_G	3.790	1.00
26_C	35_G	2.831	1.00
37_Q	40_K	2.659	1.00
18_H	38_H	2.414	1.00
19_L	42_A	2.246	1.00
15_A	46_L	1.693	1.00
26_C	32_I	1.686	1.00
10_G	13_W	1.626	1.00
36_L	40_K	1.600	1.00
22_G	39_F	1.577	1.00
9_L	13_W	1.424	1.00
17_G	21_A	1.421	1.00
21_A	25_L	1.318	1.00
15_A	19_L	1.283	1.00
7_L	46_L	1.264	1.00
7_L	47_W	1.229	1.00
14_L	45_A	1.210	1.00
7_L	15_A	1.182	1.00
13_W	17_G	1.163	1.00
24_L	28_T	1.138	1.00
25_L	34_F	1.099	1.00
43_G	51_K	1.042	1.00
22_G	38_H	1.028	1.00
12_W	16_L	1.024	1.00
25_L	38_H	0.999	1.00
21_A	38_H	0.997	1.00
26_C	36_L	0.992	1.00
44_L	49_F	0.985	1.00
22_G	26_C	0.971	1.00
44_L	47_W	0.965	1.00
18_H	41_L	0.962	1.00
10_G	14_L	0.946	1.00
14_L	17_G	0.940	1.00
18_H	45_A	0.920	1.00
20_L	24_L	0.852	1.00
8_V	12_W	0.851	1.00
19_L	39_F	0.836	1.00
37_Q	49_F	0.817	1.00
18_H	21_A	0.803	1.00
34_F	37_Q	0.797	1.00
47_W	51_K	0.794	1.00
24_L	36_L	0.790	1.00
20_L	23_L	0.783	1.00
15_A	42_A	0.767	1.00
32_I	35_G	0.749	1.00
16_L	46_L	0.742	1.00
15_A	43_G	0.737	1.00
14_L	18_H	0.720	1.00
23_L	27_I	0.701	1.00
9_L	12_W	0.663	1.00
29_I	33_P	0.662	1.00
7_L	10_G	0.656	1.00
43_G	47_W	0.646	1.00
13_W	20_L	0.636	1.00
30_I	33_P	0.620	1.00
3_N	50_G	0.618	1.00
2_G	10_G	0.615	1.00
26_C	39_F	0.610	1.00
5_I	9_L	0.601	1.00
42_A	46_L	0.599	1.00
38_H	41_L	0.595	1.00
44_L	51_K	0.590	1.00
29_I	32_I	0.583	1.00
37_Q	41_L	0.580	1.00
38_H	42_A	0.567	1.00
33_P	37_Q	0.553	1.00
13_W	47_W	0.549	1.00
2_G	9_L	0.548	1.00
34_F	40_K	0.532	1.00
40_K	43_G	0.530	1.00
7_L	12_W	0.521	1.00
21_A	24_L	0.518	1.00
28_T	35_G	0.517	1.00
23_L	26_C	0.514	1.00
11_G	45_A	0.511	1.00
4_I	7_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
3j9tb	1	0	1.8	0.87	Contact Map
3x29A	1	0.549	1.5	0.876	Contact Map
1xsqA	2	0.3529	1.2	0.882	Contact Map
3tguG	1	0.3922	0.9	0.891	Contact Map
1pp9G	1	0.3922	0.9	0.892	Contact Map
2mgyA	1	1	0.9	0.893	Contact Map
2bdrA	2	0.3725	0.7	0.898	Contact Map
3bqoB	1	0.1961	0.7	0.899	Contact Map
1yqhA	3	0.3725	0.7	0.901	Contact Map
4geqB	1	0.2157	0.6	0.904	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 0.0041 seconds.