OmdA - PFAM28P - GREMLIN Contacts

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OmdA - Bacteriocin-protection, YdeI or OmpD-Associated

PFAM:	PF13376	Sequences: EVEVPADLAAALKANPKAKAFFEALSPSYRREYLEWITSAKRPETRARRIAKAIEMLAEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (59)
Sequences:	83321 (49206)
Seq/√Len:	6406.1
META:	0.96

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_K	23_E	3.191	1.00
15_N	58_A	2.638	1.00
13_K	19_K	2.126	1.00
9_A	13_K	2.046	1.00
52_K	56_M	1.964	1.00
43_P	47_A	1.863	1.00
42_R	45_T	1.792	1.00
26_S	29_Y	1.748	1.00
47_A	51_A	1.681	1.00
32_E	35_E	1.669	1.00
21_F	25_L	1.625	1.00
44_E	48_R	1.555	1.00
48_R	52_K	1.536	1.00
21_F	24_A	1.527	1.00
35_E	39_S	1.335	1.00
40_A	45_T	1.328	1.00
27_P	31_R	1.303	1.00
6_A	10_A	1.302	1.00
21_F	57_L	1.290	1.00
11_A	51_A	1.284	1.00
7_D	46_R	1.265	1.00
11_A	47_A	1.189	1.00
40_A	49_R	1.169	1.00
31_R	35_E	1.161	1.00
55_E	59_E	1.154	1.00
52_K	55_E	1.115	1.00
20_A	24_A	1.089	1.00
4_V	9_A	1.053	1.00
11_A	14_A	1.045	1.00
45_T	48_R	1.038	1.00
8_L	53_A	1.024	1.00
50_I	54_I	1.021	1.00
7_D	50_I	1.012	1.00
29_Y	32_E	1.009	1.00
27_P	30_R	1.006	1.00
9_A	19_K	0.983	1.00
35_E	38_T	0.908	1.00
4_V	22_F	0.906	1.00
53_A	57_L	0.898	1.00
44_E	47_A	0.867	1.00
51_A	55_E	0.859	1.00
4_V	34_L	0.848	1.00
34_L	38_T	0.846	1.00
33_Y	36_W	0.834	1.00
5_P	38_T	0.832	1.00
20_A	23_E	0.828	1.00
37_I	50_I	0.828	1.00
39_S	49_R	0.815	1.00
23_E	30_R	0.813	1.00
25_L	33_Y	0.807	1.00
17_K	20_A	0.802	1.00
56_M	59_E	0.759	1.00
36_W	53_A	0.749	1.00
5_P	8_L	0.749	1.00
36_W	52_K	0.742	1.00
29_Y	33_Y	0.738	1.00
49_R	52_K	0.731	1.00
18_A	54_I	0.726	1.00
16_P	20_A	0.698	1.00
8_L	12_L	0.687	1.00
15_N	54_I	0.686	1.00
28_S	32_E	0.682	1.00
33_Y	53_A	0.679	1.00
33_Y	56_M	0.675	1.00
37_I	53_A	0.666	1.00
28_S	31_R	0.666	1.00
7_D	43_P	0.654	1.00
21_F	60_G	0.652	1.00
36_W	49_R	0.648	1.00
33_Y	57_L	0.639	1.00
16_P	19_K	0.622	1.00
11_A	50_I	0.616	1.00
25_L	29_Y	0.606	1.00
10_A	14_A	0.604	1.00
12_L	19_K	0.586	1.00
2_V	34_L	0.585	1.00
7_D	47_A	0.571	1.00
17_K	21_F	0.568	1.00
43_P	46_R	0.543	1.00
6_A	9_A	0.536	1.00
11_A	15_N	0.535	1.00
48_R	51_A	0.531	1.00
25_L	57_L	0.520	1.00
2_V	31_R	0.511	1.00
30_R	34_L	0.508	1.00
10_A	16_P	0.505	1.00
5_P	34_L	0.501	1.00
42_R	48_R	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
4kreA	1	0.9	30.1	0.791	Contact Map
4ghkA	3	0.9333	28.8	0.792	Contact Map
4qgkA	2	0.8167	17.1	0.813	Contact Map
1o20A	3	0.8833	16.3	0.815	Contact Map
4oe6A	5	0.9667	14.5	0.819	Contact Map
3szaA	2	0.8333	13.2	0.823	Contact Map
4jdcA	5	0.9333	13.1	0.823	Contact Map
3k9dA	2	0.9167	12.9	0.824	Contact Map
3lnsA	2	0.9167	11.8	0.826	Contact Map
4me7E	2	0.8333	11.7	0.827	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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