GREMLIN Database
YDBB - Uncharacterized protein YdbB
UniProt: P96597 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 113 (101)
Sequences: 774 (489)
Seq/√Len: 48.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
64_K84_V3.7521.00
6_N75_D3.6561.00
36_F95_N3.5001.00
56_E94_V3.4111.00
62_D86_R3.2331.00
24_S78_L3.1011.00
62_D88_R2.3081.00
58_E72_K2.2381.00
59_L93_T2.1921.00
60_L68_T2.1271.00
63_F77_L1.9750.99
40_Y105_T1.8090.99
61_I71_L1.7880.99
62_D68_T1.7720.99
25_E101_K1.7520.99
27_N100_H1.7420.99
11_A94_V1.6730.98
17_K37_T1.6270.98
48_S102_Q1.6260.98
11_A55_L1.6010.97
29_H48_S1.5970.97
58_E70_V1.5450.97
37_T91_V1.5450.97
42_W64_K1.5010.96
16_E19_A1.4990.96
32_R50_E1.4420.95
60_L70_V1.4200.95
17_K92_R1.3770.94
17_K35_V1.3550.93
56_E73_A1.3520.93
4_M69_A1.3340.93
68_T86_R1.3160.92
66_K69_A1.3130.92
87_T97_C1.2560.91
30_C101_K1.2410.90
7_L53_I1.2040.89
36_F59_L1.1790.88
26_V29_H1.1510.86
34_A95_N1.1090.84
29_H100_H1.0960.83
58_E91_V1.0500.81
31_V51_L1.0480.81
22_S30_C1.0370.80
60_L88_R1.0160.78
60_L90_Y1.0140.78
9_A13_E1.0070.78
39_E88_R1.0040.78
10_I23_I0.9840.76
63_F69_A0.9640.75
59_L95_N0.9580.74
28_D101_K0.9510.74
34_A103_A0.9500.74
53_I96_L0.9310.72
51_L96_L0.9280.72
80_P83_T0.9210.71
11_A14_V0.9170.71
50_E85_H0.9160.71
69_A77_L0.9080.70
61_I77_L0.8950.69
33_L97_C0.8790.68
26_V50_E0.8770.68
66_K77_L0.8760.67
4_M70_V0.8640.66
14_V21_F0.8610.66
8_L23_I0.8440.65
17_K95_N0.8420.64
44_H84_V0.8410.64
71_L75_D0.8390.64
42_W84_V0.8390.64
30_C48_S0.8190.62
11_A33_L0.8080.61
83_T91_V0.7940.60
19_A93_T0.7690.57
20_N34_A0.7660.57
12_N81_K0.7620.57
9_A12_N0.7620.57
24_S76_S0.7560.56
18_H89_S0.7440.55
10_I13_E0.7430.55
61_I79_I0.7370.54
56_E91_V0.7310.54
5_Q75_D0.7260.53
53_I76_S0.7210.52
24_S31_V0.7150.52
71_L77_L0.7150.52
10_I14_V0.7110.51
16_E21_F0.7070.51
35_V92_R0.7070.51
63_F66_K0.7000.50
54_V75_D0.6990.50
53_I98_V0.6980.50
66_K72_K0.6960.50
61_I69_A0.6890.49
31_V53_I0.6820.49
4_M77_L0.6780.48
26_V100_H0.6760.48
42_W61_I0.6690.47
37_T81_K0.6680.47
39_E62_D0.6600.46
8_L12_N0.6500.45
39_E70_V0.6470.45
14_V17_K0.6380.44
48_S103_A0.6360.44
7_L96_L0.6320.44
7_L55_L0.6180.42
26_V98_V0.6160.42
8_L73_A0.6130.42
4_M71_L0.6120.42
22_S25_E0.6050.41
31_V98_V0.5940.40
33_L96_L0.5920.40
80_P100_H0.5910.40
68_T90_Y0.5840.39
25_E28_D0.5820.39
28_D81_K0.5820.39
32_R104_E0.5780.38
22_S32_R0.5780.38
44_H61_I0.5730.38
20_N35_V0.5730.38
36_F71_L0.5670.37
22_S51_L0.5650.37
10_I92_R0.5640.37
14_V33_L0.5590.36
34_A50_E0.5570.36
13_E16_E0.5560.36
56_E81_K0.5490.36
62_D70_V0.5480.35
89_S92_R0.5470.35
52_F87_T0.5430.35
10_I21_F0.5380.35
51_L86_R0.5380.35
15_K68_T0.5350.34
36_F66_K0.5350.34
15_K91_V0.5330.34
29_H98_V0.5310.34
46_P72_K0.5290.34
22_S37_T0.5270.34
102_Q105_T0.5260.33
6_N9_A0.5230.33
5_Q23_I0.5230.33
61_I87_T0.5200.33
20_N87_T0.5190.33
12_N39_E0.5160.33
26_V51_L0.5160.33
40_Y104_E0.5140.32
55_L94_V0.5130.32
53_I90_Y0.5110.32
34_A97_C0.5070.32
42_W71_L0.5060.32
93_T97_C0.5040.31
71_L85_H0.5030.31
27_N48_S0.5000.31
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  
2qnkA 1 0.9823 100 0.454 Contact Map
1zvfA 2 0.9912 99.8 0.577 Contact Map
4l2nA 2 0.9912 99.8 0.581 Contact Map
2i45A 2 0.885 99.7 0.636 Contact Map
3d82A 2 0.885 99.6 0.653 Contact Map
3d0jA 2 0.9204 99.6 0.669 Contact Map
2o8qA 3 0.9646 99 0.745 Contact Map
3myxA 1 0.9646 99 0.746 Contact Map
3rnsA 1 0.9027 99 0.753 Contact Map
1zrrA 1 0.9912 98.9 0.756 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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