Lipoprotein_19 - PFAM28P - GREMLIN Contacts

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Lipoprotein_19 - YnbE-like lipoprotein

PFAM:	PF13617	Sequences: LLLLLLLALLLAACTPTVKVEAPDKPITINLNVKIEHEVRVKVDKDLDDLISENPD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (55)
Sequences:	3849 (2148)
Seq/√Len:	289.6
META:	0.895

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_E	42_K	3.826	1.00
45_K	48_D	3.000	1.00
36_E	40_R	2.629	1.00
47_L	50_L	2.212	1.00
17_T	21_E	2.164	1.00
47_L	51_I	2.012	1.00
15_T	19_K	1.947	1.00
25_K	28_T	1.791	1.00
28_T	32_N	1.492	1.00
21_E	24_D	1.481	1.00
19_K	24_D	1.462	1.00
52_S	55_P	1.436	1.00
3_L	10_L	1.417	1.00
7_L	10_L	1.304	1.00
47_L	54_N	1.285	1.00
6_L	10_L	1.252	1.00
4_L	7_L	1.224	1.00
46_D	49_D	1.199	1.00
49_D	52_S	1.159	1.00
44_D	50_L	1.145	1.00
8_A	11_L	1.143	1.00
43_V	47_L	1.139	1.00
41_V	45_K	1.137	1.00
4_L	8_A	1.098	1.00
52_S	56_D	1.073	1.00
21_E	25_K	1.069	1.00
4_L	10_L	1.042	1.00
43_V	51_I	1.008	1.00
7_L	12_A	0.995	1.00
6_L	9_L	0.979	1.00
37_H	41_V	0.967	1.00
46_D	50_L	0.953	1.00
6_L	11_L	0.913	1.00
5_L	8_A	0.907	1.00
3_L	7_L	0.906	1.00
20_V	23_P	0.896	1.00
49_D	53_E	0.892	1.00
40_R	44_D	0.891	1.00
11_L	15_T	0.861	1.00
44_D	47_L	0.847	1.00
51_I	54_N	0.841	1.00
3_L	6_L	0.817	1.00
29_I	37_H	0.762	0.99
5_L	9_L	0.761	0.99
2_L	5_L	0.759	0.99
29_I	47_L	0.734	0.99
36_E	41_V	0.734	0.99
34_K	38_E	0.715	0.99
16_P	19_K	0.714	0.99
23_P	29_I	0.713	0.99
19_K	25_K	0.710	0.99
4_L	9_L	0.708	0.99
5_L	10_L	0.688	0.98
35_I	56_D	0.684	0.98
38_E	43_V	0.682	0.98
9_L	12_A	0.679	0.98
35_I	41_V	0.670	0.98
33_V	48_D	0.668	0.98
17_T	20_V	0.662	0.98
42_K	46_D	0.661	0.98
16_P	23_P	0.653	0.98
6_L	12_A	0.652	0.98
45_K	55_P	0.637	0.97
31_L	37_H	0.622	0.97
7_L	11_L	0.616	0.97
2_L	6_L	0.608	0.97
29_I	40_R	0.608	0.97
3_L	11_L	0.586	0.96
10_L	13_A	0.575	0.95
37_H	47_L	0.568	0.95
37_H	46_D	0.565	0.95
42_K	48_D	0.565	0.95
43_V	48_D	0.550	0.94
40_R	56_D	0.547	0.94
5_L	11_L	0.539	0.93
29_I	32_N	0.530	0.93
22_A	28_T	0.525	0.92
6_L	56_D	0.523	0.92
19_K	22_A	0.511	0.91
30_N	34_K	0.501	0.91
15_T	18_V	0.501	0.91
11_L	54_N	0.500	0.91

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
3tlkA	1	0.5179	52.9	0.808	Contact Map
4r9fA	1	0.5714	44.6	0.817	Contact Map
3ombA	1	0.5893	40.6	0.822	Contact Map
4mfiA	1	0.6429	36.6	0.826	Contact Map
4kysA	1	0.5357	33.1	0.83	Contact Map
4r2fA	1	0.5357	31.7	0.832	Contact Map
4r6hA	1	0.625	27.4	0.837	Contact Map
4r6kA	1	0.5714	25.1	0.84	Contact Map
4utoA	1	0.5536	23.8	0.842	Contact Map
4n01A	1	0.5	22.9	0.843	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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