GREMLIN Database
YBED - UPF0250 protein YbeD
UniProt: P0A8J4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11592
Length: 87 (86)
Sequences: 137 (67)
Seq/√Len: 7.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
5_L67_I2.5070.71
4_K7_E2.4670.70
3_T7_E2.3840.67
39_A69_Q2.3710.67
23_A56_H2.3320.65
35_V60_I2.2540.63
24_L82_I2.0150.54
15_F70_V1.9410.51
30_Q54_N1.9060.49
66_H69_Q1.8670.48
70_V84_R1.7500.43
23_A47_V1.6610.40
6_N67_I1.6590.40
20_M87_L1.5940.38
39_A65_T1.5680.37
19_V77_L1.5670.37
60_I72_T1.5360.35
36_Q40_P1.5250.35
9_L13_T1.5070.34
36_Q51_S1.4310.32
37_R76_E1.4100.31
21_G52_K1.3720.30
58_V73_L1.3700.30
47_V56_H1.3590.29
73_L86_V1.3550.29
28_V40_P1.3490.29
6_N17_Y1.3450.29
15_F34_V1.3330.29
14_P63_N1.3020.28
33_E63_N1.2920.27
5_L64_A1.2870.27
27_L86_V1.2820.27
60_I76_E1.2400.26
46_T57_S1.2370.26
3_T23_A1.2300.25
3_T6_N1.2290.25
8_L56_H1.2200.25
37_R47_V1.2070.25
5_L66_H1.1620.24
42_D45_P1.1310.23
38_H72_T1.1030.22
61_T64_A1.0970.22
49_P66_H1.0950.22
10_E81_D1.0630.21
16_T59_S1.0320.20
20_M42_D1.0310.20
29_D32_V1.0170.20
58_V86_V0.9890.19
31_V39_A0.9770.19
61_T86_V0.9650.18
24_L30_Q0.9460.18
82_I85_M0.9430.18
36_Q41_G0.9230.17
15_F87_L0.9090.17
28_V72_T0.9000.17
8_L69_Q0.8910.17
20_M49_P0.8890.17
59_S79_K0.8840.17
73_L80_I0.8750.16
6_N64_A0.8730.16
44_T64_A0.8570.16
15_F80_I0.8400.16
35_V69_Q0.8260.15
48_K54_N0.8190.15
31_V58_V0.8180.15
4_K13_T0.8140.15
36_Q45_P0.8080.15
56_H77_L0.8020.15
22_Q62_I0.8010.15
2_K73_L0.7930.15
17_Y67_I0.7830.15
46_T61_T0.7830.15
48_K84_R0.7780.14
15_F73_L0.7690.14
2_K61_T0.7680.14
13_T84_R0.7660.14
47_V58_V0.7520.14
13_T49_P0.7490.14
5_L69_Q0.7430.14
78_G86_V0.7400.14
9_L84_R0.7380.14
80_I84_R0.7370.14
17_Y69_Q0.7250.13
10_E60_I0.7250.13
29_D80_I0.7230.13
29_D44_T0.7190.13
21_G80_I0.7170.13
34_V73_L0.7060.13
83_V86_V0.6990.13
9_L67_I0.6890.13
33_E37_R0.6790.13
40_P44_T0.6780.13
23_A48_K0.6700.13
32_V36_Q0.6620.12
19_V32_V0.6620.12
28_V56_H0.6560.12
16_T31_V0.6460.12
9_L56_H0.6460.12
2_K7_E0.6360.12
36_Q39_A0.6310.12
16_T41_G0.6300.12
3_T67_I0.6290.12
16_T30_Q0.6260.12
30_Q33_E0.6230.12
80_I87_L0.6190.12
5_L85_M0.6090.12
7_E30_Q0.6060.11
76_E79_K0.5940.11
26_E81_D0.5920.11
31_V67_I0.5910.11
29_D42_D0.5840.11
58_V78_G0.5830.11
33_E81_D0.5780.11
16_T20_M0.5760.11
37_R54_N0.5750.11
32_V73_L0.5700.11
48_K63_N0.5690.11
5_L17_Y0.5650.11
5_L59_S0.5560.11
26_E59_S0.5540.11
58_V68_E0.5340.10
28_V79_K0.5320.10
22_Q49_P0.5240.10
51_S79_K0.5230.10
57_S85_M0.5220.10
57_S73_L0.5090.10
10_E84_R0.5090.10
6_N69_Q0.5050.10
17_Y25_P0.5000.10
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  
1rwuA 1 0.9885 100 0.364 Contact Map
2h9zA 1 0.9655 99.9 0.483 Contact Map
2ko1A 2 0.8736 82 0.9 Contact Map
2f1fA 4 0.8506 73.7 0.907 Contact Map
2pc6A 2 0.8621 72.5 0.908 Contact Map
2fgcA 2 0.8621 72.3 0.908 Contact Map
2lvwA 2 0.908 55.9 0.918 Contact Map
1y7pA 5 0.8736 55.3 0.918 Contact Map
1zpvA 3 0.8506 38.9 0.926 Contact Map
4n8nA 1 0.8391 35.8 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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