GREMLIN Database
HOLE - DNA polymerase III subunit theta
UniProt: P0ABS8 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11505
Length: 76 (68)
Sequences: 130 (63)
Seq/√Len: 7.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
41_E53_R4.6940.99
31_Y67_S3.5450.94
39_A43_E2.7930.82
10_Q13_M2.6670.79
10_Q14_D2.5460.75
27_F31_Y2.5260.75
38_E42_R2.4010.71
31_Y69_L2.3640.69
27_F67_S2.2450.65
15_K47_H2.2360.65
38_E43_E1.9940.56
46_E56_L1.9480.54
5_L8_L1.8690.51
58_A62_A1.6370.41
62_A65_N1.5600.38
8_L13_M1.4950.36
20_L24_G1.3270.30
21_A34_P1.2270.27
21_A32_N1.2000.26
23_A59_H1.1980.26
13_M41_E1.1110.23
17_N21_A1.1090.23
26_A58_A1.1060.23
28_K33_M1.0750.22
7_K13_M1.0650.22
61_L64_V1.0640.22
12_E15_K0.9600.19
37_A43_E0.9580.19
45_P54_E0.9550.19
5_L69_L0.9430.19
9_D12_E0.9380.19
50_S53_R0.9370.19
46_E49_R0.9300.18
10_Q47_H0.9240.18
21_A44_Q0.8940.18
21_A33_M0.8870.17
39_A66_L0.8860.17
26_A32_N0.8840.17
25_V35_V0.8830.17
51_W59_H0.8740.17
38_E46_E0.8680.17
6_A49_R0.8670.17
12_E56_L0.8410.16
54_E58_A0.8180.16
7_K11_T0.7980.16
47_H64_V0.7730.15
2_L7_K0.7640.15
5_L27_F0.7600.15
13_M47_H0.7340.14
57_I65_N0.7160.14
17_N57_I0.7070.14
17_N44_Q0.7070.14
15_K43_E0.7010.14
36_I63_S0.6950.13
24_G27_F0.6920.13
16_V38_E0.6870.13
25_V40_V0.6810.13
21_A39_A0.6720.13
16_V49_R0.6700.13
5_L31_Y0.6680.13
3_K57_I0.6610.13
50_S62_A0.6560.13
17_N68_R0.6550.13
28_K58_A0.6520.13
39_A46_E0.6460.13
8_L31_Y0.6400.12
16_V27_F0.6360.12
29_E55_R0.6360.12
54_E67_S0.6350.12
14_D46_E0.6300.12
51_W58_A0.6200.12
5_L13_M0.6150.12
56_L62_A0.6130.12
57_I63_S0.6130.12
13_M51_W0.6100.12
53_R57_I0.6050.12
13_M17_N0.6000.12
3_K26_A0.5990.12
11_T22_A0.5950.12
9_D65_N0.5930.12
3_K15_K0.5900.12
2_L25_V0.5890.12
34_P57_I0.5860.12
44_Q53_R0.5680.11
23_A67_S0.5600.11
39_A54_E0.5580.11
18_V51_W0.5470.11
43_E64_V0.5470.11
6_A9_D0.5460.11
8_L69_L0.5400.11
51_W60_R0.5350.11
7_K34_P0.5320.11
23_A51_W0.5280.11
3_K37_A0.5210.11
51_W65_N0.5200.11
6_A42_R0.5190.10
23_A63_S0.5140.10
50_S68_R0.5100.10
32_N63_S0.5040.10
32_N37_A0.5030.10
7_K40_V0.5020.10
3_K36_I0.5000.10
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  
1du2A 1 1 100 0.258 Contact Map
1se7A 1 0.9868 99.9 0.377 Contact Map
1rrzA 1 0.8553 99.9 0.456 Contact Map
2o70A 2 0.9342 15.5 0.929 Contact Map
3q23A 1 0.7895 15.2 0.93 Contact Map
3o7iA 1 0.7237 14.7 0.93 Contact Map
2o8iA 2 0.8158 11.6 0.933 Contact Map
2dt7B 1 0.7368 10 0.935 Contact Map
1l1lA 1 0.8421 9.7 0.936 Contact Map
3eauA 3 0.3421 7.1 0.939 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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