GREMLIN Database
DUF4096 - Putative transposase of IS4/5 family (DUF4096)
PFAM: PF13340 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 75 (74)
Sequences: 55458 (23515)
Seq/√Len: 2733.6
META: 0.94

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
59_Y63_R3.6661.00
41_T47_D3.3911.00
37_Y43_C2.8251.00
41_T44_P2.6801.00
28_L61_R2.2351.00
46_R55_W2.2321.00
56_S60_R2.2231.00
63_R67_R2.2051.00
44_P47_D2.0611.00
40_R44_P1.8431.00
24_R28_L1.7951.00
3_D29_R1.6591.00
48_L58_V1.5511.00
60_R64_R1.5201.00
55_W59_Y1.5161.00
2_T5_Q1.4701.00
56_S59_Y1.4391.00
62_F66_R1.4261.00
38_V43_C1.3731.00
40_R47_D1.3711.00
53_G58_V1.3501.00
54_P57_T1.3401.00
63_R66_R1.3311.00
29_R33_N1.2991.00
34_A58_V1.2951.00
16_P19_R1.2521.00
27_D30_E1.2231.00
64_R68_D1.2101.00
22_R25_K1.1991.00
7_A10_E1.1921.00
1_L5_Q1.1701.00
13_L28_L1.1351.00
32_L71_W1.0441.00
61_R64_R1.0341.00
34_A53_G1.0321.00
57_T60_R1.0191.00
69_G72_E0.9721.00
60_R63_R0.9711.00
9_I32_L0.9441.00
32_L36_L0.9381.00
46_R56_S0.9371.00
26_V57_T0.9311.00
31_V35_I0.9261.00
10_E14_P0.9211.00
26_V31_V0.9041.00
6_W29_R0.8911.00
17_K20_P0.8651.00
3_D7_A0.8561.00
70_V73_R0.8471.00
61_R65_W0.8431.00
8_L11_P0.8371.00
16_P20_P0.8221.00
62_F71_W0.8111.00
37_Y49_P0.7991.00
33_N52_F0.7971.00
26_V54_P0.7931.00
38_V48_L0.7931.00
16_P28_L0.7791.00
54_P60_R0.7671.00
4_E8_L0.7481.00
70_V74_I0.7441.00
7_A11_P0.7321.00
30_E33_N0.7281.00
55_W63_R0.7231.00
34_A52_F0.7221.00
30_E53_G0.7161.00
38_V41_T0.7041.00
66_R71_W0.6941.00
16_P23_P0.6901.00
32_L74_I0.6901.00
9_I74_I0.6841.00
31_V57_T0.6831.00
56_S63_R0.6771.00
1_L32_L0.6751.00
31_V61_R0.6681.00
4_E7_A0.6581.00
5_Q9_I0.6481.00
57_T61_R0.6461.00
20_P23_P0.6381.00
15_P18_P0.6321.00
3_D6_W0.6261.00
50_E53_G0.6231.00
28_L65_W0.6051.00
28_L31_V0.5941.00
47_D50_E0.5851.00
24_R61_R0.5761.00
49_P52_F0.5751.00
18_P24_R0.5711.00
5_Q8_L0.5701.00
20_P24_R0.5671.00
69_G73_R0.5661.00
13_L70_V0.5631.00
10_E28_L0.5601.00
12_L73_R0.5531.00
16_P24_R0.5491.00
8_L12_L0.5471.00
25_K30_E0.5461.00
34_A48_L0.5361.00
66_R72_E0.5351.00
14_P70_V0.5191.00
29_R34_A0.5171.00
25_K31_V0.5151.00
65_W68_D0.5151.00
35_I62_F0.5071.00
37_Y52_F0.5071.00
16_P22_R0.5051.00
14_P17_K0.5041.00
33_N51_D0.5031.00
43_C48_L0.5031.00
55_W58_V0.5031.00
26_V53_G0.5001.00
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  
4bqqA 2 0.52 34.3 0.834 Contact Map
4ch7A 1 0.5733 33.2 0.836 Contact Map
2optA 2 0.6933 31.5 0.838 Contact Map
2fe3A 2 0.9067 24.2 0.847 Contact Map
1jkoC 1 0.6 24.2 0.847 Contact Map
1ji8A 1 0.6933 15.4 0.86 Contact Map
3mwmA 2 0.6933 13.6 0.863 Contact Map
2m8eA 1 0.7467 13.4 0.863 Contact Map
3or1C 1 0.6933 12.7 0.865 Contact Map
2g7gA 2 0.64 12.6 0.865 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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