GREMLIN Database
DNA_pol_alpha_N - DNA polymerase alpha subunit p180 N terminal
PFAM: PF12254 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 66 (65)
Sequences: 613 (435)
Seq/√Len: 54.0
META: 0.409

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
37_K41_K3.6581.00
38_I42_R3.5841.00
30_V38_I3.1211.00
2_E6_A2.1911.00
39_V42_R2.0121.00
51_D54_G1.9791.00
14_R17_Q1.8260.99
31_D34_E1.8230.99
41_K45_D1.6280.98
17_Q29_E1.5820.98
5_K9_A1.5600.98
25_D28_D1.5020.97
59_D62_R1.3630.95
35_Y42_R1.3570.95
34_E38_I1.3490.95
40_R43_L1.2830.93
32_E55_E1.2820.93
38_I63_E1.1810.90
2_E42_R1.1720.90
48_F65_W1.1660.90
13_K18_Y1.1590.89
43_L62_R1.1570.89
50_V54_G1.1500.89
34_E37_K1.1320.88
21_E25_D1.1230.88
57_Y61_G1.1210.88
12_K15_L1.1090.87
7_A10_G1.0980.87
19_E22_E1.0950.86
2_E5_K1.0840.86
48_F60_D1.0730.85
7_A14_R1.0500.84
60_D63_E1.0440.84
25_D29_E1.0440.84
30_V42_R1.0390.83
4_L36_K1.0370.83
27_Y64_D1.0330.83
4_L58_V1.0310.83
49_V58_V1.0290.83
11_G35_Y0.9910.80
33_E49_V0.9870.80
13_K49_V0.9550.78
45_D50_V0.9510.78
40_R46_D0.9400.77
3_E7_A0.9230.75
48_F59_D0.9210.75
43_L47_D0.9160.75
35_Y59_D0.9120.75
27_Y40_R0.8890.73
36_K48_F0.8810.72
9_A12_K0.8040.65
39_V44_D0.8020.65
32_E39_V0.7990.64
22_E25_D0.7800.63
14_R23_E0.7800.63
7_A11_G0.7700.62
44_D47_D0.7650.61
13_K16_D0.7610.61
6_A9_A0.7610.61
49_V59_D0.7600.61
48_F64_D0.7450.59
58_V64_D0.7290.57
3_E19_E0.7280.57
39_V49_V0.7220.57
3_E12_K0.7050.55
4_L26_I0.6920.53
34_E41_K0.6740.52
7_A37_K0.6740.52
26_I29_E0.6660.51
10_G13_K0.6630.50
26_I39_V0.6380.48
40_R50_V0.6340.47
17_Q24_E0.6300.47
47_D51_D0.6290.47
40_R58_V0.6150.45
12_K31_D0.6050.44
6_A10_G0.5980.43
3_E6_A0.5940.43
38_I41_K0.5890.43
29_E37_K0.5720.41
17_Q22_E0.5680.40
31_D56_G0.5680.40
32_E65_W0.5640.40
4_L47_D0.5610.40
6_A12_K0.5510.39
7_A13_K0.5430.38
5_K20_V0.5400.38
49_V55_E0.5390.37
32_E40_R0.5370.37
10_G47_D0.5350.37
3_E17_Q0.5290.36
27_Y39_V0.5280.36
52_D56_G0.5160.35
58_V65_W0.5150.35
8_R59_D0.5110.35
24_E37_K0.5110.35
15_L31_D0.5080.34
28_D55_E0.5000.34
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  
2pi2A 1 0 6 0.889 Contact Map
3bo6A 1 0.4394 4.4 0.895 Contact Map
3i0uA 1 0.303 4.4 0.895 Contact Map
2p1wA 1 0.3182 4.4 0.896 Contact Map
1b5eA 4 0.5758 3.5 0.901 Contact Map
4d10B 1 0 3.2 0.903 Contact Map
4kqtA 1 0.9545 2.5 0.908 Contact Map
4az1A 2 0.5303 2.4 0.908 Contact Map
1xg4A 4 0.6364 2.3 0.91 Contact Map
1l1lA 1 0.803 2.2 0.911 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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