GREMLIN Database
YBDD - Uncharacterized protein YbdD
UniProt: P0AAS9 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11107
Length: 65 (61)
Sequences: 268 (141)
Seq/√Len: 18.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
43_T46_E4.8031.00
48_F52_Q3.9931.00
11_Y14_Q2.7850.98
15_A18_L2.4090.95
23_P56_Y2.3230.94
51_R57_G2.0280.89
30_E34_V1.9070.86
14_Q53_D1.6670.77
32_M39_Q1.6650.77
16_A26_D1.6310.75
23_P51_R1.5740.73
44_Y51_R1.4230.65
20_I49_R1.3360.60
46_E60_G1.3060.58
8_A34_V1.1790.50
30_E40_T1.1600.49
12_L57_G1.1510.48
19_M63_R1.1140.46
49_R57_G1.1030.45
54_A59_K1.0810.44
57_G64_C1.0750.44
9_G12_L1.0630.43
48_F65_C1.0620.43
37_P54_A1.0510.42
24_D63_R1.0240.41
24_D33_R1.0240.41
54_A58_G1.0120.40
20_I38_D1.0060.39
15_A22_M0.9890.38
23_P65_C0.9850.38
22_M62_A0.9740.38
30_E60_G0.9690.37
53_D62_A0.9530.36
20_I53_D0.9450.36
12_L26_D0.9270.35
30_E38_D0.9210.35
32_M38_D0.9150.34
26_D35_N0.8930.33
9_G43_T0.8920.33
54_A62_A0.8540.31
18_L47_F0.8500.31
26_D44_Y0.8470.31
11_Y44_Y0.8410.30
29_V41_P0.8350.30
15_A19_M0.8330.30
5_L16_A0.8190.29
35_N45_E0.8170.29
38_D42_M0.8070.29
17_K24_D0.7820.27
10_K61_G0.7770.27
9_G13_G0.7770.27
6_A60_G0.7740.27
22_M56_Y0.7640.26
5_L20_I0.7540.26
23_P48_F0.7510.26
58_G62_A0.7380.25
23_P55_R0.7370.25
46_E53_D0.7310.25
43_T56_Y0.7290.25
16_A51_R0.7280.25
22_M52_Q0.7270.25
10_K44_Y0.7120.24
52_Q57_G0.6900.23
19_M42_M0.6720.22
6_A30_E0.6640.22
42_M49_R0.6630.22
15_A24_D0.6590.22
41_P56_Y0.6520.21
22_M47_F0.6510.21
39_Q50_E0.6480.21
14_Q24_D0.6390.21
41_P63_R0.6300.21
32_M41_P0.6260.20
10_K39_Q0.6250.20
13_G22_M0.6220.20
6_A34_V0.5950.19
16_A24_D0.5940.19
29_V34_V0.5850.19
29_V39_Q0.5780.19
6_A9_G0.5690.18
27_N40_T0.5680.18
33_R53_D0.5470.17
58_G61_G0.5420.17
12_L42_M0.5370.17
42_M51_R0.5340.17
10_K30_E0.5280.17
22_M35_N0.5240.17
57_G65_C0.5210.17
9_G44_Y0.5170.16
32_M54_A0.5100.16
50_E57_G0.5050.16
17_K51_R0.5000.16
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  
4s28A 2 0.9385 10.3 0.921 Contact Map
4tpsB 1 1 9.3 0.923 Contact Map
2im9A 1 0.9231 8.3 0.925 Contact Map
2iw0A 1 0.5385 8 0.925 Contact Map
3epoA 2 0.9385 7.7 0.926 Contact Map
4iaoA 1 0.9846 7 0.927 Contact Map
3qtmA 1 0.5077 6.6 0.928 Contact Map
3msvA 2 0.5077 6.5 0.928 Contact Map
3dr3A 4 0.4462 5.6 0.93 Contact Map
3j0aA 1 0.6615 5.6 0.93 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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