GREMLIN Database
DNA_pol3_a_NI - DNA polymerase III polC-type N-terminus I
PFAM: PF14480 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 72 (71)
Sequences: 2432 (1976)
Seq/√Len: 234.6
META: 0.692

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
22_A42_S3.7021.00
25_E41_S3.1791.00
21_D43_D3.0231.00
29_V36_W2.4581.00
19_F54_F2.1871.00
18_L50_V2.0321.00
23_E41_S2.0071.00
57_R60_E1.8561.00
1_K4_E1.8341.00
26_K39_Y1.8311.00
18_L47_P1.6421.00
48_K52_Q1.6141.00
28_V39_Y1.5941.00
47_P50_V1.5571.00
13_D16_K1.5361.00
30_N33_S1.5191.00
11_L54_F1.4641.00
40_I70_V1.4581.00
37_R71_K1.4271.00
19_F22_A1.4151.00
51_I55_E1.4091.00
2_F22_A1.3911.00
12_P53_E1.3471.00
30_N37_R1.2291.00
30_N34_K1.2091.00
55_E70_V1.2041.00
22_A40_I1.1951.00
28_V37_R1.1901.00
59_K63_F1.1561.00
56_K60_E1.1451.00
53_E57_R1.1331.00
13_D17_E1.0841.00
30_N35_K1.0781.00
21_D44_R1.0651.00
17_E44_R1.0481.00
42_S46_I1.0021.00
46_I51_I0.9991.00
9_L57_R0.9951.00
35_K69_S0.9811.00
52_Q55_E0.9681.00
65_I68_V0.9451.00
8_Q62_F0.9351.00
9_L61_Q0.8920.99
12_P15_L0.8840.99
38_F62_F0.8780.99
59_K67_K0.8700.99
22_A46_I0.8390.99
24_V40_I0.8350.99
50_V53_E0.8340.99
22_A37_R0.8080.99
6_F11_L0.7970.99
17_E20_E0.7850.99
3_F16_K0.7840.99
21_D42_S0.7770.99
54_F62_F0.7740.99
24_V38_F0.7640.98
4_E7_P0.7540.98
48_K51_I0.7480.98
35_K67_K0.7400.98
37_R69_S0.7230.98
5_L36_W0.7180.98
37_R48_K0.7070.97
64_H68_V0.7070.97
32_K62_F0.6940.97
3_F7_P0.6900.97
3_F9_L0.6720.96
46_I50_V0.6670.96
49_E56_K0.6620.96
10_K63_F0.6600.96
2_F40_I0.6580.96
11_L57_R0.6580.96
46_I70_V0.6530.96
1_K24_V0.6490.96
9_L58_L0.6490.96
38_F64_H0.6480.96
8_Q38_F0.6470.96
36_W62_F0.6430.95
57_R61_Q0.6390.95
58_L69_S0.6320.95
25_E39_Y0.6280.95
29_V34_K0.6240.95
17_E69_S0.6100.94
16_K20_E0.6100.94
23_E44_R0.5860.93
13_D32_K0.5830.92
8_Q29_V0.5800.92
19_F50_V0.5740.92
31_K54_F0.5550.90
15_L50_V0.5550.90
5_L51_I0.5480.90
3_F12_P0.5430.89
24_V60_E0.5420.89
9_L12_P0.5410.89
5_L8_Q0.5370.89
4_E8_Q0.5330.89
55_E59_K0.5310.88
29_V33_S0.5240.88
49_E52_Q0.5220.88
18_L21_D0.5210.87
7_P16_K0.5180.87
27_V58_L0.5170.87
52_Q56_K0.5140.87
17_E21_D0.5100.86
38_F51_I0.5100.86
61_Q64_H0.5020.85
32_K36_W0.5000.85
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  
2ayaA 1 0.9306 21.4 0.788 Contact Map
4rb5C 1 0.9722 18.1 0.796 Contact Map
3lnoA 1 0.9861 17.8 0.796 Contact Map
4kiyC 1 0.9722 13.8 0.806 Contact Map
4tp8C 1 0.9722 12.5 0.809 Contact Map
3cq1A 2 0.9583 11.6 0.812 Contact Map
3j20C 1 0.9861 11.3 0.813 Contact Map
1uwdA 1 0.9722 9.8 0.819 Contact Map
1mvgA 1 0.9722 8 0.826 Contact Map
3ux2A 2 1 7.9 0.826 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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