GREMLIN Database
RPON - DNA-directed RNA polymerase subunit N
UniProt: Q9HQJ1 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 66 (62)
Sequences: 305 (148)
Seq/√Len: 18.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
24_R37_V2.9970.99
3_V52_L2.6480.98
18_W61_V2.5040.97
21_F25_A2.1820.93
24_R40_D2.1370.92
24_R32_E2.0520.91
25_A37_V1.8670.86
38_L53_I1.6590.78
32_E40_D1.6320.77
14_V51_M1.5650.74
2_M55_H1.5630.74
13_V58_L1.5280.72
32_E37_V1.4650.69
35_A39_D1.4270.67
12_T16_E1.3940.65
43_V53_I1.3130.60
14_V52_L1.2360.55
19_E35_A1.2280.55
21_F29_D1.2240.54
21_F33_D1.1740.51
45_R50_R1.1650.51
31_D34_P1.1490.50
9_S54_A1.0900.46
3_V55_H1.0870.46
3_V14_V1.0840.46
6_R45_R1.0600.44
32_E36_D1.0590.44
13_V50_R1.0520.44
15_G21_F1.0450.43
13_V54_A1.0360.43
37_V63_S1.0080.41
7_C10_C1.0040.41
22_K57_D0.9970.40
9_S20_A0.9910.40
15_G43_V0.9900.40
3_V12_T0.9900.40
12_T43_V0.9850.40
32_E52_L0.9620.38
23_A30_G0.9360.37
1_M63_S0.9310.36
55_H65_Y0.9240.36
1_M57_D0.9130.35
33_D36_D0.9060.35
23_A40_D0.9000.35
15_G59_V0.8690.33
15_G37_V0.8680.33
39_D49_R0.8600.32
7_C49_R0.8580.32
39_D64_P0.8500.32
19_E64_P0.8500.32
13_V46_H0.8490.32
55_H58_L0.8410.31
53_I63_S0.8400.31
2_M18_W0.8300.31
45_R65_Y0.8260.31
9_S45_R0.8230.30
6_R50_R0.8130.30
54_A65_Y0.8120.30
10_C49_R0.8090.30
13_V16_E0.7990.29
11_G38_L0.7800.28
20_A23_A0.7750.28
23_A29_D0.7550.27
46_H59_V0.7450.26
11_G39_D0.7380.26
24_R33_D0.7340.26
37_V62_V0.7270.26
18_W53_I0.6900.24
60_D65_Y0.6830.23
43_V54_A0.6740.23
16_E62_V0.6630.23
12_T61_V0.6560.22
42_G56_Q0.6450.22
46_H60_D0.6400.22
5_V64_P0.6340.21
21_F51_M0.6100.20
44_D61_V0.6090.20
5_V50_R0.6000.20
14_V61_V0.5860.19
57_D62_V0.5680.19
23_A44_D0.5600.18
8_F54_A0.5590.18
25_A63_S0.5560.18
20_A29_D0.5540.18
30_G36_D0.5530.18
58_L63_S0.5500.18
30_G43_V0.5500.18
45_R64_P0.5420.18
36_D40_D0.5380.18
46_H61_V0.5370.18
13_V51_M0.5250.17
44_D63_S0.5060.16
15_G45_R0.5000.16
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  
1twfJ 1 0.9545 100 0.099 Contact Map
4qiwN 1 0.9545 100 0.099 Contact Map
4aybN 1 0.9545 100 0.102 Contact Map
1ef4A 1 0.8333 100 0.203 Contact Map
4ex5A 2 0.8636 26 0.911 Contact Map
4xbaA 2 0.4545 18.6 0.917 Contact Map
3a5yA 2 0.803 17.9 0.917 Contact Map
3a74A 4 0.8636 17.6 0.918 Contact Map
4up7A 2 0.8636 16.9 0.918 Contact Map
4ycuA 3 0.9545 16.5 0.919 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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