GREMLIN Database
Cyd_oper_YbgE - Cyd operon protein YbgE (Cyd_oper_YbgE)
PFAM: PF09600 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 79 (76)
Sequences: 817 (531)
Seq/√Len: 60.9
META: 0.624

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
59_W63_F5.4811.00
10_L14_L3.8001.00
5_S48_H3.6051.00
35_L39_M2.6211.00
45_G72_L2.3721.00
33_G36_M2.0651.00
9_A45_G1.8761.00
44_A68_A1.8091.00
56_R59_W1.7700.99
47_V63_F1.5740.99
52_F55_R1.5730.99
13_A46_F1.5650.99
19_Y22_L1.4720.98
16_L23_F1.4180.97
17_T46_F1.3550.97
41_A71_L1.3370.96
13_A42_M1.3320.96
41_A72_L1.3180.96
40_W67_A1.3180.96
9_A37_L1.3030.96
25_D28_G1.2710.95
40_W44_A1.2680.95
20_P54_P1.2620.95
32_H36_M1.2560.95
48_H65_P1.2470.94
65_P69_W1.2390.94
12_L15_L1.1220.91
48_H69_W1.1200.91
9_A46_F1.1150.90
2_R48_H1.1140.90
68_A75_G1.0950.90
24_A30_A1.0930.90
44_A47_V1.0900.89
13_A23_F1.0510.88
37_L43_S1.0470.87
56_R61_W1.0160.86
67_A70_L1.0050.85
17_T23_F0.9830.84
68_A71_L0.9780.84
65_P68_A0.9620.83
13_A43_S0.9570.82
23_F46_F0.9420.81
11_A57_W0.9260.80
16_L76_L0.8890.77
33_G72_L0.8840.77
45_G68_A0.8790.76
16_L39_M0.8780.76
8_L73_L0.8700.76
13_A16_L0.8620.75
10_L13_A0.8560.75
32_H60_R0.8360.73
14_L37_L0.8360.73
6_L45_G0.8220.72
2_R5_S0.8180.71
11_A76_L0.8110.70
7_L11_A0.8100.70
18_W43_S0.8080.70
3_A7_L0.8020.70
35_L41_A0.8010.70
41_A75_G0.7910.69
8_L69_W0.7800.67
47_V64_S0.7750.67
13_A35_L0.7750.67
14_L18_W0.7600.65
7_L77_L0.7590.65
54_P60_R0.7490.64
53_V56_R0.7420.64
13_A65_P0.7200.61
10_L38_L0.7200.61
12_L42_M0.6930.58
38_L49_G0.6930.58
6_L47_V0.6870.58
33_G43_S0.6870.58
11_A14_L0.6840.57
5_S69_W0.6840.57
20_P43_S0.6790.57
24_A27_T0.6740.56
39_M52_F0.6620.55
25_D29_G0.6610.55
4_L40_W0.6540.54
39_M43_S0.6500.54
12_L38_L0.6490.53
58_L76_L0.6430.53
74_L77_L0.6420.53
26_A70_L0.6390.52
6_L14_L0.6330.52
16_L21_A0.6290.51
13_A17_T0.6240.51
20_P32_H0.6210.50
26_A29_G0.6130.49
34_L66_L0.6070.49
40_W61_W0.5930.47
40_W71_L0.5810.46
58_L61_W0.5790.46
9_A68_A0.5780.45
7_L30_A0.5770.45
30_A38_L0.5740.45
28_G52_F0.5660.44
60_R67_A0.5600.43
6_L49_G0.5460.42
45_G54_P0.5400.41
19_Y59_W0.5380.41
21_A26_A0.5370.41
32_H43_S0.5270.40
47_V59_W0.5260.40
54_P63_F0.5240.39
12_L36_M0.5240.39
44_A73_L0.5180.39
40_W63_F0.5160.39
5_S9_A0.5090.38
3_A8_L0.5070.38
7_L25_D0.5060.38
15_L39_M0.5030.37
28_G40_W0.5000.37
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  
4ryoA 1 0.962 12.4 0.882 Contact Map
2mgyA 1 0.962 9.7 0.888 Contact Map
4uc1A 3 0.962 3.7 0.908 Contact Map
4g9iA 1 0.5443 2.2 0.918 Contact Map
3tx3A 2 0.519 2 0.92 Contact Map
1m0kA 3 0.5823 2 0.92 Contact Map
4p02A 1 0.8734 1.9 0.921 Contact Map
2qtsA 4 0.2405 1.6 0.924 Contact Map
4xp4A 1 0.9747 1.6 0.924 Contact Map
3wajA 1 1 1.4 0.927 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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