GREMLIN Database
YdjO - Cold-inducible protein YdjO
PFAM: PF14169 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 59 (58)
Sequences: 532 (360)
Seq/√Len: 47.3
META: 0.457

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
28_G44_L4.4141.00
22_T50_V3.1211.00
2_Y5_K2.4071.00
36_F40_P2.4001.00
43_P48_P2.1511.00
15_E53_T2.1221.00
3_F15_E2.0701.00
4_R7_P1.9810.99
16_T56_L1.8140.99
32_D51_K1.6070.97
17_K32_D1.5670.97
4_R10_E1.5420.97
20_S52_G1.5280.96
8_Q13_E1.4690.95
37_E57_P1.4680.95
20_S54_R1.3980.94
15_E55_M1.3380.93
48_P58_V1.2910.91
34_F40_P1.2450.90
48_P57_P1.2060.88
3_F53_T1.1870.87
3_F43_P1.1200.84
2_Y6_K1.0920.82
13_E55_M1.0830.82
3_F35_S1.0820.82
41_T48_P1.0770.81
19_W40_P1.0260.78
10_E37_E1.0190.78
6_K33_N0.9820.75
22_T47_S0.9700.74
17_K51_K0.9680.74
12_P36_F0.9620.73
3_F7_P0.9060.69
25_D37_E0.8850.67
20_S46_G0.8740.66
13_E34_F0.8690.66
22_T48_P0.8480.64
19_W36_F0.8450.63
27_N32_D0.8360.63
38_E51_K0.8250.62
30_M52_G0.8020.59
5_K30_M0.7980.59
9_E47_S0.7820.57
24_E50_V0.7690.56
32_D54_R0.7390.53
28_G34_F0.7370.53
7_P43_P0.7290.52
30_M36_F0.7190.51
13_E30_M0.7190.51
7_P14_E0.7060.50
19_W49_M0.6990.49
27_N44_L0.6950.49
5_K18_V0.6910.48
5_K8_Q0.6850.48
24_E27_N0.6810.47
53_T57_P0.6780.47
18_V52_G0.6730.47
23_S47_S0.6670.46
25_D54_R0.6640.46
37_E59_L0.6350.43
10_E49_M0.6300.42
20_S57_P0.6280.42
17_K53_T0.6260.42
35_S59_L0.6150.41
23_S56_L0.6140.41
14_E23_S0.6080.40
24_E34_F0.6020.40
31_R57_P0.5850.38
6_K10_E0.5810.38
14_E33_N0.5730.37
8_Q25_D0.5730.37
39_E48_P0.5720.37
17_K49_M0.5680.36
13_E56_L0.5570.35
30_M54_R0.5490.35
41_T44_L0.5460.34
5_K50_V0.5450.34
14_E34_F0.5350.33
36_F55_M0.5310.33
9_E24_E0.5240.33
22_T53_T0.5210.32
2_Y43_P0.5200.32
2_Y15_E0.5100.31
41_T46_G0.5100.31
9_E12_P0.5050.31
16_T31_R0.5030.31
55_M58_V0.5000.30
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  
2kn9A 1 0.8814 38.9 0.859 Contact Map
4aybP 1 0.6441 38.5 0.859 Contact Map
4e2xA 1 0.339 37.7 0.86 Contact Map
1s24A 1 0.6949 36.2 0.861 Contact Map
1lkoA 3 0.9153 34.5 0.863 Contact Map
4d02A 2 0 33.8 0.863 Contact Map
1yk4A 1 0.6271 31.6 0.865 Contact Map
2v3bB 1 0.6441 26.5 0.87 Contact Map
4tpuA 3 0.8814 24.6 0.872 Contact Map
6rxnA 1 0.6271 20.4 0.877 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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