Bac_export_3 - PFAM28P - GREMLIN Contacts

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Bac_export_3 - Bacterial export proteins, family 3

PFAM:	PF01313	Sequences: QVLDLARQALWTALLLSAPLLLVALVVGLVVSLFQAATQIQEQTLSFVPKLLAVFLVLLLLGPWMLSTLVDFTR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (72)
Sequences:	24204 (12774)
Seq/√Len:	1505.4
META:	0.91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_V	57_V	3.385	1.00
23_V	53_A	3.063	1.00
27_V	53_A	2.547	1.00
4_D	8_Q	2.546	1.00
57_V	61_L	2.488	1.00
33_L	37_A	2.205	1.00
8_Q	11_W	2.122	1.00
11_W	15_L	1.997	1.00
12_T	68_T	1.972	1.00
16_L	65_M	1.828	1.00
24_A	54_V	1.828	1.00
67_S	71_D	1.787	1.00
46_S	49_P	1.749	1.00
66_L	70_V	1.663	1.00
18_A	22_L	1.618	1.00
19_P	23_V	1.568	1.00
7_R	11_W	1.559	1.00
15_L	68_T	1.468	1.00
21_L	48_V	1.449	1.00
4_D	7_R	1.408	1.00
13_A	55_F	1.376	1.00
16_L	69_L	1.326	1.00
12_T	15_L	1.285	1.00
30_V	34_F	1.281	1.00
36_A	43_Q	1.243	1.00
25_L	48_V	1.226	1.00
12_T	16_L	1.210	1.00
37_A	62_G	1.180	1.00
45_L	49_P	1.180	1.00
22_L	26_V	1.164	1.00
69_L	73_T	1.160	1.00
23_V	61_L	1.159	1.00
64_W	68_T	1.062	1.00
56_L	60_L	1.029	1.00
68_T	71_D	0.957	1.00
58_L	62_G	0.937	1.00
23_V	27_V	0.903	1.00
8_Q	12_T	0.866	1.00
14_L	52_L	0.852	1.00
61_L	65_M	0.850	1.00
25_L	28_G	0.849	1.00
32_S	40_I	0.842	1.00
28_G	50_K	0.835	1.00
24_A	46_S	0.834	1.00
14_L	55_F	0.832	1.00
25_L	42_E	0.824	1.00
3_L	6_A	0.813	1.00
20_L	57_V	0.812	1.00
8_Q	72_F	0.805	1.00
52_L	56_L	0.802	1.00
20_L	58_L	0.800	1.00
47_F	50_K	0.790	1.00
6_A	10_L	0.777	1.00
9_A	13_A	0.777	1.00
6_A	9_A	0.772	1.00
29_L	33_L	0.769	1.00
27_V	49_P	0.765	1.00
13_A	16_L	0.750	1.00
26_V	30_V	0.741	1.00
12_T	72_F	0.737	1.00
13_A	17_S	0.736	1.00
63_P	67_S	0.732	1.00
53_A	57_V	0.732	1.00
34_F	40_I	0.727	1.00
33_L	40_I	0.725	1.00
12_T	39_Q	0.720	1.00
9_A	72_F	0.707	1.00
8_Q	15_L	0.697	1.00
20_L	54_V	0.690	1.00
5_L	9_A	0.677	1.00
67_S	70_V	0.672	1.00
20_L	23_V	0.671	1.00
42_E	46_S	0.663	1.00
36_A	41_Q	0.662	1.00
20_L	61_L	0.654	1.00
64_W	70_V	0.651	1.00
9_A	12_T	0.645	1.00
32_S	45_L	0.640	1.00
32_S	36_A	0.639	1.00
46_S	50_K	0.638	1.00
3_L	66_L	0.634	1.00
36_A	39_Q	0.632	1.00
43_Q	46_S	0.625	1.00
31_V	44_T	0.622	1.00
37_A	41_Q	0.615	1.00
70_V	73_T	0.613	1.00
11_W	14_L	0.610	1.00
4_D	11_W	0.604	1.00
7_R	15_L	0.585	1.00
3_L	62_G	0.585	1.00
10_L	14_L	0.580	1.00
39_Q	65_M	0.576	1.00
25_L	49_P	0.571	1.00
10_L	59_L	0.565	1.00
59_L	62_G	0.565	1.00
3_L	7_R	0.557	1.00
58_L	65_M	0.554	1.00
2_V	6_A	0.549	1.00
43_Q	48_V	0.547	1.00
41_Q	45_L	0.546	1.00
20_L	65_M	0.536	1.00
24_A	27_V	0.536	1.00
30_V	53_A	0.533	1.00
65_M	68_T	0.533	1.00
31_V	46_S	0.514	1.00
25_L	47_F	0.508	1.00
46_S	51_L	0.505	1.00
43_Q	50_K	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
4eneA	2	1	1.7	0.901	Contact Map
3nd0A	2	1	1.4	0.906	Contact Map
4pd6A	3	0.4189	1.3	0.907	Contact Map
4u9nA	2	0.9324	1	0.915	Contact Map
4kppA	1	0.3919	0.8	0.918	Contact Map
4wqkA	1	0.4459	0.8	0.919	Contact Map
4pj0R	1	0.3649	0.7	0.923	Contact Map
1xl3C	1	0.3378	0.7	0.923	Contact Map
1oedA	1	0.4595	0.7	0.923	Contact Map
3mktA	1	0.8919	0.6	0.925	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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