GREMLIN Database
RPOZ - DNA-directed RNA polymerase subunit omega
UniProt: O35011 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 67 (63)
Sequences: 301 (186)
Seq/√Len: 23.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
38_I41_T3.4461.00
1_M6_I2.8130.99
30_M36_Q2.3960.98
1_M16_K2.3440.98
37_M58_L2.2770.97
10_M14_D2.1200.96
21_T31_Q2.0730.95
13_L59_L1.6260.84
18_T61_F1.6210.84
2_L20_V1.5940.83
12_K57_G1.5690.82
8_S11_N1.5430.81
44_H49_K1.5390.81
16_K20_V1.5060.79
60_S63_K1.3990.74
2_L48_G1.3670.72
31_Q49_K1.3650.72
1_M20_V1.3150.69
22_V33_K1.2250.64
9_L25_R1.1960.62
6_I21_T1.1950.62
49_K56_A1.1810.61
29_E60_S1.1790.61
29_E63_K1.1700.60
18_T38_I1.1450.58
22_V57_G1.1230.57
11_N34_K1.1050.56
29_E39_E1.1010.55
25_R42_I1.0720.53
13_L39_E1.0450.51
3_D14_D1.0030.48
41_T48_G0.9840.47
49_K57_G0.9670.46
39_E42_I0.9660.46
37_M41_T0.9650.46
23_S47_V0.9520.45
16_K21_T0.9220.43
11_N32_I0.9190.43
11_N30_M0.9190.43
16_K51_L0.9180.42
10_M54_I0.8840.40
39_E59_L0.8770.40
23_S45_K0.8640.39
30_M37_M0.8620.39
6_I19_L0.8560.38
35_D59_L0.8370.37
33_K57_G0.8250.36
29_E36_Q0.8240.36
46_Y49_K0.8230.36
2_L43_S0.8220.36
10_M24_A0.8210.36
3_D13_L0.8180.36
13_L23_S0.8130.35
3_D48_G0.7970.34
39_E60_S0.7840.34
41_T49_K0.7810.33
8_S59_L0.7800.33
27_A47_V0.7690.33
35_D40_H0.7450.31
8_S55_D0.7380.31
24_A44_H0.7360.31
6_I16_K0.7160.30
12_K41_T0.7050.29
10_M22_V0.6960.28
41_T58_L0.6930.28
30_M35_D0.6910.28
3_D45_K0.6870.28
41_T54_I0.6720.27
6_I48_G0.6720.27
6_I10_M0.6660.27
30_M61_F0.6640.27
31_Q46_Y0.6590.26
12_K43_S0.6450.26
3_D42_I0.6350.25
3_D10_M0.6040.23
21_T34_K0.5880.23
58_L63_K0.5810.22
28_R61_F0.5800.22
7_D50_A0.5730.22
22_V54_I0.5700.22
12_K47_V0.5680.22
28_R47_V0.5660.22
25_R38_I0.5610.21
18_T34_K0.5570.21
18_T41_T0.5530.21
48_G52_E0.5420.20
12_K28_R0.5350.20
2_L59_L0.5250.20
18_T28_R0.5250.20
8_S61_F0.5250.20
2_L6_I0.5220.20
21_T33_K0.5010.19
20_V47_V0.5000.19
35_D54_I0.5000.19
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  
2a6hE 1 0.9851 99.8 0.351 Contact Map
4aybK 1 1 99.8 0.356 Contact Map
4yfkE 1 0.9701 99.8 0.361 Contact Map
1qklA 1 1 99.7 0.389 Contact Map
3h0gF 1 1 99.6 0.444 Contact Map
1twfF 1 1 99.5 0.494 Contact Map
4qiwK 1 0.8358 99.4 0.522 Contact Map
3rhzA 4 0.806 9.4 0.914 Contact Map
1snnA 2 0.3433 9.2 0.914 Contact Map
4ffjA 2 0.3582 8.5 0.915 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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