GREMLIN Database
GH-E - HNH/ENDO VII superfamily nuclease with conserved GHE residues
PFAM: PF14410 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 70 (68)
Sequences: 1359 (1117)
Seq/√Len: 135.5
META: 0.861

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
20_D65_R4.9451.00
43_R47_L2.5431.00
29_Y46_F2.2581.00
5_K14_P2.1031.00
63_S69_A2.0931.00
67_H70_E2.0861.00
28_E31_N1.9981.00
22_G59_E1.8201.00
61_P65_R1.8201.00
42_T45_E1.8021.00
19_W58_L1.7451.00
34_G38_E1.5881.00
32_L50_Y1.5781.00
33_R37_E1.5521.00
29_Y33_R1.4941.00
48_D51_N1.4881.00
59_E67_H1.4681.00
44_K48_D1.4661.00
20_D61_P1.3961.00
35_R40_G1.3161.00
22_G57_R1.2791.00
24_K27_V1.2651.00
60_D63_S1.2521.00
8_D11_T1.2311.00
3_D7_I1.2191.00
22_G67_H1.1961.00
62_S65_R1.1931.00
10_N69_A1.1870.99
21_M56_Y1.1840.99
49_W55_N1.1050.99
32_L49_W1.0700.99
52_D55_N1.0690.99
34_G37_E1.0540.99
11_T63_S1.0360.99
20_D62_S1.0090.98
41_I49_W0.9750.98
6_V19_W0.9730.98
63_S67_H0.9650.98
50_Y56_Y0.9610.98
24_K57_R0.9550.98
57_R67_H0.9420.97
7_I14_P0.9250.97
13_K60_D0.9230.97
32_L35_R0.9170.97
21_M58_L0.9030.97
10_N59_E0.8710.96
8_D63_S0.8590.96
6_V58_L0.8510.95
9_P13_K0.8410.95
29_Y36_A0.8230.94
27_V49_W0.8180.94
20_D64_N0.7830.93
31_N35_R0.7730.92
26_G31_N0.7670.92
3_D14_P0.7650.92
47_L51_N0.7640.92
52_D56_Y0.7600.92
43_R51_N0.7390.91
35_R49_W0.7340.90
41_I46_F0.7300.90
59_E63_S0.7190.89
27_V55_N0.7080.89
32_L46_F0.7020.88
30_W34_G0.6870.87
19_W61_P0.6850.87
5_K16_D0.6780.86
35_R39_G0.6760.86
41_I45_E0.6730.86
43_R46_F0.6610.85
22_G56_Y0.6450.83
33_R36_A0.6400.83
39_G49_W0.6270.82
50_Y55_N0.6260.82
27_V30_W0.6230.81
27_V32_L0.6160.81
63_S68_G0.6120.80
25_P57_R0.6010.79
7_I15_I0.5960.78
45_E48_D0.5880.77
10_N57_R0.5810.77
42_T51_N0.5650.75
19_W60_D0.5640.75
6_V9_P0.5640.75
31_N34_G0.5610.74
6_V21_M0.5580.74
14_P17_G0.5580.74
24_K54_D0.5560.73
10_N63_S0.5530.73
39_G45_E0.5450.72
10_N13_K0.5430.72
56_Y59_E0.5360.71
23_H64_N0.5340.71
32_L41_I0.5330.70
46_F50_Y0.5310.70
47_L50_Y0.5290.70
18_Q21_M0.5230.69
3_D16_D0.5230.69
27_V35_R0.5210.69
40_G43_R0.5150.68
49_W52_D0.5150.68
27_V36_A0.5010.66
28_E67_H0.5000.66
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  
4un4B 1 0.7286 88.1 0.774 Contact Map
4ogeA 1 0.7429 62.8 0.821 Contact Map
4h9dA 3 0.7286 56.6 0.827 Contact Map
3m7kA 2 0.9429 11.6 0.879 Contact Map
5aj3Q 1 0.3571 8.1 0.887 Contact Map
4iloA 3 0.2571 6.9 0.891 Contact Map
2pu3A 1 1 6.6 0.892 Contact Map
3mhsE 1 0.3571 6.1 0.894 Contact Map
2v0cA 1 0.9286 6 0.894 Contact Map
3ephA 2 0.6571 6 0.894 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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