GREMLIN Database
YBDF - Uncharacterized protein YbdF
UniProt: P0AAT2 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12619
Length: 122 (112)
Sequences: 1248 (859)
Seq/√Len: 81.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
53_N77_M4.6081.00
17_L101_N4.0131.00
74_G84_S3.1561.00
71_I99_L2.8771.00
56_S61_S2.6741.00
13_L101_N2.4831.00
51_F84_S2.3281.00
20_V40_F2.3091.00
65_Q83_I2.1191.00
60_K102_D2.0871.00
81_H106_L2.0711.00
11_K22_L1.9511.00
35_I107_V1.9411.00
41_M54_L1.9201.00
11_K33_F1.8891.00
23_C34_K1.8861.00
72_K86_Y1.7711.00
70_S91_I1.7471.00
70_S89_E1.6761.00
71_I95_L1.6351.00
25_P32_V1.6261.00
24_W31_D1.5551.00
32_V39_I1.5320.99
112_A116_Q1.5160.99
39_I42_L1.4940.99
22_L31_D1.4760.99
14_A41_M1.4140.99
70_S90_E1.4110.99
108_V119_V1.4090.99
115_D118_R1.4000.99
41_M52_I1.4000.99
36_G108_V1.3920.99
21_E37_G1.3710.99
53_N74_G1.2540.98
35_I108_V1.2510.98
45_E48_G1.2400.98
27_G30_F1.2400.98
13_L17_L1.2180.97
95_L98_D1.2070.97
56_S102_D1.2060.97
60_K98_D1.1910.97
34_K39_I1.1820.97
95_L99_L1.1790.97
112_A115_D1.1470.96
26_F76_H1.1120.95
57_D61_S1.1060.95
83_I99_L1.1000.95
108_V111_L1.0990.95
62_L66_Q1.0840.95
70_S88_G1.0810.95
60_K63_L1.0720.94
108_V116_Q1.0500.94
27_G32_V1.0440.94
85_V96_L1.0250.93
63_L67_I1.0230.93
42_L77_M1.0130.93
56_S83_I0.9670.91
19_F36_G0.9640.91
25_P34_K0.9480.90
49_V86_Y0.9230.89
11_K24_W0.9220.89
53_N76_H0.9130.88
93_E97_R0.9040.88
61_S65_Q0.8910.87
103_S106_L0.8850.86
112_A118_R0.8840.86
26_F32_V0.8820.86
36_G119_V0.8780.86
92_S95_L0.8580.85
13_L97_R0.8550.84
28_P32_V0.8390.83
36_G115_D0.8320.83
85_V99_L0.8290.83
61_S102_D0.8270.82
10_A52_I0.8240.82
52_I100_I0.8190.82
39_I77_M0.8180.82
23_C32_V0.8170.82
14_A100_I0.8150.81
37_G115_D0.8140.81
61_S83_I0.8120.81
10_A41_M0.8060.81
56_S60_K0.7980.80
87_P92_S0.7910.80
9_T97_R0.7850.79
10_A43_S0.7650.77
91_I95_L0.7610.77
13_L16_E0.7610.77
27_G39_I0.7580.77
102_D106_L0.7480.76
11_K15_L0.7400.75
53_N73_P0.7390.75
70_S86_Y0.7350.74
58_P81_H0.7350.74
42_L103_S0.7240.73
14_A22_L0.7090.72
53_N84_S0.6950.70
27_G34_K0.6900.70
114_R118_R0.6770.68
23_C37_G0.6760.68
104_W119_V0.6750.68
69_P72_K0.6720.68
60_K105_N0.6680.67
91_I99_L0.6680.67
87_P100_I0.6660.67
106_L109_D0.6650.67
106_L110_G0.6640.67
54_L85_V0.6610.66
98_D102_D0.6550.66
83_I100_I0.6540.65
112_A117_K0.6510.65
15_L22_L0.6470.65
30_F44_S0.6450.64
87_P99_L0.6420.64
46_L49_V0.6400.64
8_E11_K0.6400.64
49_V87_P0.6390.64
74_G77_M0.6340.63
87_P96_L0.6300.63
19_F105_N0.6270.62
54_L65_Q0.6260.62
102_D105_N0.6260.62
25_P28_P0.6220.62
68_Y94_A0.6170.61
69_P89_E0.6120.60
45_E49_V0.6090.60
45_E51_F0.6070.60
45_E50_P0.6070.60
53_N103_S0.6060.60
113_K116_Q0.5980.59
46_L51_F0.5950.58
22_L25_P0.5930.58
101_N105_N0.5920.58
30_F42_L0.5910.58
107_V110_G0.5880.57
51_F86_Y0.5860.57
88_G91_I0.5850.57
96_L114_R0.5830.57
85_V91_I0.5760.56
41_M87_P0.5670.55
63_L80_K0.5670.55
8_E12_R0.5600.54
96_L115_D0.5580.53
74_G80_K0.5570.53
69_P90_E0.5560.53
73_P78_N0.5550.53
111_L115_D0.5530.53
76_H79_K0.5520.53
24_W28_P0.5520.53
50_P87_P0.5460.52
15_L20_V0.5460.52
36_G111_L0.5440.52
44_S53_N0.5440.52
54_L100_I0.5370.51
10_A44_S0.5320.50
57_D83_I0.5270.49
29_E44_S0.5220.49
10_A50_P0.5170.48
14_A33_F0.5130.48
93_E105_N0.5120.47
78_N81_H0.5110.47
94_A98_D0.5080.47
13_L100_I0.5080.47
57_D102_D0.5060.47
17_L104_W0.5060.47
30_F39_I0.5050.47
60_K95_L0.5030.46
68_Y91_I0.5000.46
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  
2fkiA 1 0.9672 100 0.272 Contact Map
2a1vA 1 1 100 0.281 Contact Map
2kfpA 1 0.9098 100 0.337 Contact Map
2od0A 2 0.7869 99 0.752 Contact Map
2kl4A 1 0.8279 93.1 0.886 Contact Map
2i8dA 2 0.8852 92.3 0.889 Contact Map
2oc6A 1 0.8934 91.5 0.891 Contact Map
2bw2A 1 0.7705 25.3 0.937 Contact Map
4lh6A 1 0.5164 21.1 0.939 Contact Map
1tkeA 1 0.9754 20.1 0.94 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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