GREMLIN Database
YBII - Uncharacterized protein YbiI
UniProt: P41039 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12421
Length: 88 (88)
Sequences: 372 (198)
Seq/√Len: 21.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
48_Q52_E4.2321.00
12_N16_N3.8211.00
36_L58_R3.3041.00
36_L40_E2.6310.98
40_E58_R2.6180.98
3_S7_N2.5190.98
3_S6_A2.3210.96
18_T22_A2.0560.93
17_S68_D1.9950.92
25_R29_E1.9580.91
38_E43_G1.8590.89
5_W53_A1.7720.86
7_N72_P1.6830.83
35_S48_Q1.5980.80
22_A25_R1.5940.79
35_S57_V1.4740.74
8_D14_Q1.4710.74
66_E69_L1.4430.72
3_S18_T1.4100.70
43_G66_E1.4070.70
59_L67_K1.4040.70
77_Y81_G1.3880.69
49_A52_E1.3500.67
25_R59_L1.2600.61
5_W10_A1.2490.61
3_S68_D1.2460.61
17_S26_A1.2190.59
67_K70_Q1.2150.59
6_A10_A1.2030.58
54_I61_I1.1960.57
48_Q51_R1.1910.57
27_R64_Q1.1760.56
9_D13_E1.1570.55
32_R65_Q1.1560.55
26_A30_I1.1550.55
3_S34_E1.1280.53
20_E28_G1.1190.52
6_A14_Q1.1130.52
16_N22_A1.1120.52
38_E61_I1.0890.50
72_P77_Y1.0860.50
7_N23_I1.0780.49
3_S75_T1.0600.48
17_S55_P1.0360.47
68_D75_T1.0260.46
36_L45_P1.0190.46
27_R30_I1.0120.45
20_E61_I1.0000.44
13_E88_R0.9880.44
6_A16_N0.9820.43
38_E45_P0.9730.43
11_V23_I0.9720.42
12_N15_I0.9520.41
61_I65_Q0.9450.41
8_D49_A0.9380.40
31_P59_L0.9280.40
12_N64_Q0.9240.39
3_S8_D0.9090.38
11_V15_I0.8910.37
12_N19_I0.8910.37
9_D14_Q0.8640.36
45_P48_Q0.8220.33
43_G88_R0.8060.32
31_P67_K0.8020.32
13_E16_N0.7970.32
34_E81_G0.7810.31
76_G82_S0.7800.31
5_W33_G0.7660.30
22_A55_P0.7620.30
23_I26_A0.7600.30
44_A49_A0.7520.29
16_N26_A0.7500.29
5_W21_D0.7430.29
24_A44_A0.7420.29
22_A26_A0.7340.28
14_Q21_D0.7240.28
26_A88_R0.7190.27
48_Q82_S0.7040.27
29_E70_Q0.7000.26
24_A38_E0.7000.26
81_G86_Q0.7000.26
35_S59_L0.6980.26
40_E73_A0.6950.26
10_A23_I0.6920.26
38_E62_H0.6860.26
30_I64_Q0.6860.26
29_E67_K0.6550.24
36_L59_L0.6360.23
10_A56_G0.6280.23
20_E24_A0.6240.23
65_Q72_P0.6230.23
21_D24_A0.6210.22
10_A36_L0.6190.22
11_V14_Q0.6190.22
19_I22_A0.6150.22
12_N30_I0.6000.22
5_W14_Q0.5960.21
52_E69_L0.5930.21
30_I49_A0.5860.21
24_A65_Q0.5850.21
65_Q71_K0.5820.21
44_A88_R0.5800.21
27_R49_A0.5750.20
7_N13_E0.5730.20
52_E72_P0.5620.20
20_E26_A0.5600.20
66_E72_P0.5580.20
11_V16_N0.5560.20
5_W8_D0.5550.20
17_S58_R0.5540.20
10_A14_Q0.5500.19
33_G58_R0.5500.19
41_E67_K0.5500.19
65_Q69_L0.5490.19
1_M15_I0.5380.19
2_A15_I0.5380.19
35_S58_R0.5340.19
3_S9_D0.5280.18
58_R69_L0.5270.18
72_P76_G0.5220.18
23_I67_K0.5190.18
35_S61_I0.5160.18
38_E82_S0.5140.18
28_G70_Q0.5100.18
25_R70_Q0.5090.18
35_S69_L0.5070.18
13_E17_S0.5060.18
23_I72_P0.5050.18
13_E72_P0.5030.17
9_D16_N0.5020.17
24_A35_S0.5010.17
32_R74_Y0.5000.17
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  
2kgoA 1 0.9886 100 0.318 Contact Map
1tjlA 2 0.8409 99.2 0.712 Contact Map
4ijjA 1 0.8182 99.1 0.729 Contact Map
2kq9A 1 0.75 99.1 0.73 Contact Map
2gviA 3 0.7386 87.2 0.892 Contact Map
3lvqE 1 0.7614 51.4 0.919 Contact Map
5a3dA 1 0.6023 42.1 0.923 Contact Map
1dcqA 1 0.7159 38.5 0.925 Contact Map
2owaA 1 0.8182 37.3 0.925 Contact Map
3d00A 2 0.7159 35.6 0.926 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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