YjfB_motility - PFAM28P - GREMLIN Contacts

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YjfB_motility - Putative motility protein

PFAM:	PF14070	Sequences: IAALSTAMSQAQVQQQVGVAVLKKALDTQEQQAAALLQMLPMEASVPPGLGGNIDIT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	57 (55)
Sequences:	4397 (3459)
Seq/√Len:	466.4
META:	0.849

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_A	24_K	2.566	1.00
33_A	39_M	2.067	1.00
13_V	17_V	1.959	1.00
9_S	12_Q	1.918	1.00
29_Q	32_Q	1.909	1.00
10_Q	14_Q	1.905	1.00
8_M	12_Q	1.732	1.00
6_T	9_S	1.712	1.00
5_S	9_S	1.693	1.00
35_A	38_Q	1.672	1.00
49_G	52_G	1.660	1.00
14_Q	18_G	1.603	1.00
47_P	50_L	1.581	1.00
32_Q	35_A	1.435	1.00
17_V	20_A	1.434	1.00
23_K	27_D	1.405	1.00
12_Q	16_Q	1.404	1.00
50_L	53_N	1.314	1.00
23_K	26_L	1.303	1.00
21_V	24_K	1.285	1.00
19_V	23_K	1.224	1.00
43_E	46_V	1.204	1.00
33_A	37_L	1.152	1.00
12_Q	15_Q	1.143	1.00
4_L	8_M	1.118	1.00
28_T	31_Q	1.103	1.00
6_T	10_Q	1.083	1.00
20_A	23_K	1.067	1.00
15_Q	19_V	1.053	1.00
16_Q	20_A	1.009	1.00
47_P	52_G	1.008	1.00
46_V	55_D	1.005	1.00
38_Q	41_P	0.998	1.00
22_L	25_A	0.954	1.00
45_S	48_P	0.949	1.00
44_A	47_P	0.945	1.00
42_M	45_S	0.939	1.00
31_Q	34_A	0.908	1.00
48_P	52_G	0.888	1.00
24_K	28_T	0.887	1.00
30_E	34_A	0.873	1.00
16_Q	19_V	0.863	1.00
35_A	39_M	0.857	1.00
25_A	29_Q	0.834	1.00
46_V	52_G	0.808	1.00
14_Q	17_V	0.802	1.00
36_L	40_L	0.800	1.00
44_A	48_P	0.769	1.00
4_L	7_A	0.740	1.00
13_V	16_Q	0.737	1.00
10_Q	13_V	0.725	1.00
17_V	21_V	0.723	1.00
11_A	14_Q	0.720	1.00
36_L	39_M	0.713	1.00
46_V	49_G	0.696	1.00
33_A	41_P	0.693	1.00
29_Q	33_A	0.689	1.00
45_S	49_G	0.669	1.00
25_A	32_Q	0.669	1.00
34_A	39_M	0.665	1.00
15_Q	26_L	0.662	1.00
23_K	29_Q	0.662	1.00
42_M	46_V	0.646	1.00
33_A	40_L	0.637	1.00
33_A	36_L	0.628	0.99
34_A	38_Q	0.611	0.99
31_Q	35_A	0.603	0.99
28_T	32_Q	0.603	0.99
2_A	5_S	0.602	0.99
22_L	36_L	0.595	0.99
43_E	47_P	0.591	0.99
25_A	28_T	0.589	0.99
24_K	27_D	0.565	0.99
27_D	33_A	0.560	0.99
37_L	41_P	0.557	0.99
2_A	9_S	0.552	0.99
8_M	11_A	0.539	0.98
11_A	15_Q	0.528	0.98
5_S	8_M	0.512	0.98
47_P	55_D	0.508	0.98
3_A	6_T	0.508	0.98
32_Q	39_M	0.500	0.97

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
1ucuA	1	0.6491	4.8	0.839	Contact Map
1e3pA	3	1	2.6	0.859	Contact Map
1oryB	2	0.6491	2.4	0.861	Contact Map
4lg3A	1	0.9474	1.7	0.872	Contact Map
4m4dA	1	0.7895	1.4	0.879	Contact Map
1iedA	2	0.3509	1.2	0.883	Contact Map
1at3A	3	0.2456	1.2	0.883	Contact Map
1ewfA	1	0.7895	1	0.888	Contact Map
2yciX	2	0.3509	1	0.889	Contact Map
3zyqA	1	0.4737	1	0.891	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.

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