GREMLIN Database
RPOH - DNA-directed RNA polymerase subunit H
UniProt: P0CX06 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 75 (72)
Sequences: 390 (218)
Seq/√Len: 25.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
14_T56_E5.1011.00
21_L54_V4.2461.00
14_T58_V3.4291.00
10_V13_H2.0980.96
49_A53_D1.9930.95
3_D47_D1.9390.94
61_S64_T1.9270.94
10_V59_R1.7100.90
18_E22_D1.6650.88
45_L49_A1.5740.85
10_V57_I1.5160.83
6_Q40_Y1.4790.81
31_D57_I1.4240.79
40_Y50_E1.3990.78
59_R63_T1.3970.77
45_L48_N1.3740.76
43_P61_S1.3520.75
18_E31_D1.3240.73
10_V43_P1.3160.73
38_I55_V1.2830.71
6_Q23_G1.2760.71
38_I73_V1.2420.68
16_L70_Y1.2220.67
45_L69_V1.2200.67
38_I59_R1.2110.66
16_L69_V1.1990.66
30_I34_E1.1350.61
20_T23_G1.1340.61
30_I37_K1.1220.60
3_D17_D1.1120.60
57_I69_V1.1060.59
17_D30_I1.0870.58
21_L32_R1.0870.58
16_L24_V1.0550.56
5_S47_D1.0380.54
27_D56_E1.0120.52
38_I72_L1.0090.52
48_N55_V0.9820.50
13_H61_S0.9790.50
10_V61_S0.9290.46
23_G27_D0.9230.46
6_Q47_D0.9150.45
35_L71_R0.9130.45
12_E41_K0.9080.45
24_V30_I0.8830.43
25_L52_G0.8830.43
49_A55_V0.8500.41
15_V53_D0.8410.40
24_V54_V0.8400.40
37_K51_I0.8330.40
35_L70_Y0.8260.39
37_K67_A0.8240.39
27_D66_E0.8200.39
4_V44_A0.8170.38
31_D41_K0.8110.38
32_R53_D0.7980.37
43_P59_R0.7890.36
33_T39_K0.7870.36
44_A55_V0.7860.36
9_L16_L0.7840.36
56_E72_L0.7840.36
34_E45_L0.7710.35
37_K56_E0.7690.35
38_I45_L0.7690.35
16_L21_L0.7570.34
59_R72_L0.7570.34
31_D34_E0.7530.34
57_I68_V0.7290.32
4_V27_D0.7260.32
4_V12_E0.7240.32
40_Y73_V0.7140.32
18_E54_V0.6960.30
44_A47_D0.6770.29
5_S12_E0.6730.29
9_L24_V0.6700.29
13_H43_P0.6660.29
52_G70_Y0.6580.28
34_E54_V0.6350.27
15_V26_A0.6270.26
3_D6_Q0.6250.26
45_L51_I0.6110.25
38_I44_A0.6010.25
24_V27_D0.5940.24
61_S65_D0.5890.24
25_L64_T0.5780.24
18_E30_I0.5700.23
23_G56_E0.5700.23
9_L68_V0.5660.23
12_E58_V0.5630.23
59_R65_D0.5600.23
28_Y56_E0.5590.23
14_T20_T0.5580.23
21_L24_V0.5470.22
28_Y54_V0.5460.22
5_S44_A0.5380.22
15_V33_T0.5360.21
21_L39_K0.5320.21
8_E12_E0.5290.21
30_I33_T0.5280.21
10_V17_D0.5280.21
8_E60_D0.5250.21
28_Y33_T0.5150.20
47_D53_D0.5150.20
4_V34_E0.5120.20
33_T53_D0.5060.20
18_E58_V0.5050.20
11_P70_Y0.5050.20
28_Y67_A0.5000.20
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  
4qiwH 1 1 100 0.087 Contact Map
1eikA 1 1 100 0.089 Contact Map
3h0gE 1 0.9867 100 0.101 Contact Map
1dzfA 1 0.9867 100 0.101 Contact Map
1hmjA 1 0.8667 100 0.102 Contact Map
4aybH 1 1 100 0.173 Contact Map
2mgvA 1 0.7333 45 0.897 Contact Map
2gu1A 1 0.88 34.9 0.903 Contact Map
4rnzA 1 0.84 31 0.905 Contact Map
2ekdA 5 0.48 23.2 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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