GREMLIN Database
RPOK - DNA-directed RNA polymerase subunit K
UniProt: Q9HQJ0 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 60 (53)
Sequences: 173 (72)
Seq/√Len: 9.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
7_F55_V2.6820.87
16_I50_A2.2650.76
18_A26_G2.1510.72
23_V29_V1.9750.65
18_A21_L1.7680.57
35_Q44_E1.7440.55
33_T41_I1.7120.54
20_A56_R1.6390.51
14_R21_L1.5580.47
26_G40_L1.5210.45
31_V34_D1.4780.43
31_V38_P1.4690.43
30_L55_V1.4120.40
30_L54_T1.3900.40
6_H10_Y1.3850.39
14_R18_A1.3430.38
44_E48_A1.3200.37
24_A34_D1.2870.35
26_G54_T1.2840.35
12_K30_L1.2820.35
10_Y30_L1.2770.35
8_S37_E1.2730.35
18_A54_T1.2110.32
49_D57_R1.2050.32
40_L48_A1.1440.29
12_K53_F1.1240.29
39_I44_E1.1150.28
49_D53_F1.0800.27
7_F56_R1.0720.27
34_D44_E1.0670.27
15_I54_T1.0580.26
20_A46_Y1.0400.26
25_Y39_I1.0340.25
9_R55_V0.9520.23
12_K46_Y0.9470.23
38_P49_D0.9420.22
26_G53_F0.8840.21
13_A18_A0.8750.20
37_E41_I0.8680.20
5_Q24_A0.8630.20
16_I35_Q0.8620.20
25_Y51_L0.8620.20
17_G22_Q0.8540.20
35_Q41_I0.8470.20
12_K50_A0.8250.19
29_V32_D0.8160.19
7_F53_F0.8150.19
8_S46_Y0.8140.19
43_A47_D0.7910.18
16_I43_A0.7730.18
25_Y43_A0.7590.17
15_I55_V0.7540.17
24_A32_D0.7170.16
8_S23_V0.6930.16
23_V46_Y0.6810.15
29_V33_T0.6790.15
27_A44_E0.6540.15
6_H44_E0.6490.14
7_F31_V0.6360.14
40_L51_L0.6300.14
10_Y38_P0.6250.14
14_R29_V0.6220.14
15_I33_T0.6090.14
10_Y39_I0.6080.14
38_P43_A0.5960.13
15_I22_Q0.5960.13
24_A56_R0.5840.13
16_I56_R0.5790.13
35_Q56_R0.5630.13
15_I28_P0.5500.12
32_D40_L0.5490.12
49_D55_V0.5470.12
29_V37_E0.5360.12
32_D53_F0.5300.12
17_G21_L0.5290.12
43_A48_A0.5270.12
5_Q44_E0.5230.12
8_S22_Q0.5180.12
6_H14_R0.5050.12
24_A46_Y0.5000.11
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  
1twfF 1 1 99.5 0.487 Contact Map
3h0gF 1 1 99.4 0.507 Contact Map
1qklA 1 1 99.4 0.52 Contact Map
4qiwK 1 0.9167 99.3 0.532 Contact Map
4aybK 1 1 99.2 0.545 Contact Map
4yfkE 1 0.9667 98.1 0.69 Contact Map
2a6hE 1 0.9667 93.9 0.804 Contact Map
4c2mB 1 0.9 32.6 0.888 Contact Map
4qiwB 1 0.9 16.3 0.903 Contact Map
4aybB 1 0.9 15.7 0.904 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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