GREMLIN Database
OmdA - Bacteriocin-protection, YdeI or OmpD-Associated
PFAM: PF13376 Sequences:
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_K23_E3.1911.00
15_N58_A2.6381.00
13_K19_K2.1261.00
9_A13_K2.0461.00
52_K56_M1.9641.00
43_P47_A1.8631.00
42_R45_T1.7921.00
26_S29_Y1.7481.00
47_A51_A1.6811.00
32_E35_E1.6691.00
21_F25_L1.6251.00
44_E48_R1.5551.00
48_R52_K1.5361.00
21_F24_A1.5271.00
35_E39_S1.3351.00
40_A45_T1.3281.00
27_P31_R1.3031.00
6_A10_A1.3021.00
21_F57_L1.2901.00
11_A51_A1.2841.00
7_D46_R1.2651.00
11_A47_A1.1891.00
40_A49_R1.1691.00
31_R35_E1.1611.00
55_E59_E1.1541.00
52_K55_E1.1151.00
20_A24_A1.0891.00
4_V9_A1.0531.00
11_A14_A1.0451.00
45_T48_R1.0381.00
8_L53_A1.0241.00
50_I54_I1.0211.00
7_D50_I1.0121.00
29_Y32_E1.0091.00
27_P30_R1.0061.00
9_A19_K0.9831.00
35_E38_T0.9081.00
4_V22_F0.9061.00
53_A57_L0.8981.00
44_E47_A0.8671.00
51_A55_E0.8591.00
4_V34_L0.8481.00
34_L38_T0.8461.00
33_Y36_W0.8341.00
5_P38_T0.8321.00
20_A23_E0.8281.00
37_I50_I0.8281.00
39_S49_R0.8151.00
23_E30_R0.8131.00
25_L33_Y0.8071.00
17_K20_A0.8021.00
56_M59_E0.7591.00
36_W53_A0.7491.00
5_P8_L0.7491.00
36_W52_K0.7421.00
29_Y33_Y0.7381.00
49_R52_K0.7311.00
18_A54_I0.7261.00
16_P20_A0.6981.00
8_L12_L0.6871.00
15_N54_I0.6861.00
28_S32_E0.6821.00
33_Y53_A0.6791.00
33_Y56_M0.6751.00
37_I53_A0.6661.00
28_S31_R0.6661.00
7_D43_P0.6541.00
21_F60_G0.6521.00
36_W49_R0.6481.00
33_Y57_L0.6391.00
16_P19_K0.6221.00
11_A50_I0.6161.00
25_L29_Y0.6061.00
10_A14_A0.6041.00
12_L19_K0.5861.00
2_V34_L0.5851.00
7_D47_A0.5711.00
17_K21_F0.5681.00
43_P46_R0.5431.00
6_A9_A0.5361.00
11_A15_N0.5351.00
48_R51_A0.5311.00
25_L57_L0.5201.00
2_V31_R0.5111.00
30_R34_L0.5081.00
10_A16_P0.5051.00
5_P34_L0.5011.00
42_R48_R0.5001.00
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

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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