GREMLIN Database
Q980A3 - DNA-directed RNA polymerase, subunit E' (RpoE1)
UniProt: Q980A3 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 180 (147)
Sequences: 4080 (2269)
Seq/√Len: 187.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
6_K9_S4.3611.00
86_E143_R4.1801.00
113_I136_I3.0371.00
86_E141_K2.7471.00
88_E141_K2.6971.00
41_D44_L2.6161.00
70_V74_M2.3601.00
30_L38_I2.3341.00
131_K134_K2.2741.00
146_V160_I2.2681.00
142_V164_M2.1731.00
84_V145_R2.1041.00
64_G68_H2.0351.00
13_I16_N1.9811.00
99_V108_V1.9771.00
164_M168_Y1.9701.00
90_L100_N1.9201.00
87_G99_V1.9031.00
106_G162_L1.8791.00
80_V83_E1.8651.00
108_V164_M1.8641.00
112_Q166_Q1.8331.00
108_V113_I1.8281.00
148_S161_A1.7981.00
8_R12_R1.7731.00
26_A67_Y1.7691.00
137_Q140_D1.6771.00
29_E56_E1.6751.00
100_N105_D1.6681.00
77_Y83_E1.6551.00
90_L105_D1.6521.00
79_P146_V1.6271.00
71_E74_M1.6161.00
150_A157_L1.5681.00
94_N133_K1.5571.00
70_V73_D1.5311.00
84_V143_R1.5091.00
89_V136_I1.4871.00
112_Q147_I1.4771.00
81_V148_S1.4651.00
52_K56_E1.4591.00
104_M160_I1.4551.00
150_A159_R1.3911.00
92_V138_K1.3851.00
113_I118_L1.3331.00
6_K10_I1.3281.00
63_D66_T1.3281.00
112_Q165_R1.3021.00
115_D167_P1.2901.00
101_L160_I1.2861.00
61_F67_Y1.2511.00
145_R166_Q1.2251.00
147_I161_A1.2161.00
35_Q39_L1.2011.00
65_A68_H1.1881.00
37_K75_I1.1761.00
97_I136_I1.1741.00
61_F66_T1.1591.00
119_K131_K1.1361.00
113_I135_V1.1101.00
43_G46_L1.0861.00
11_V15_P1.0811.00
114_T118_L1.0751.00
41_D45_V1.0591.00
79_P101_L1.0581.00
163_T166_Q1.0541.00
46_L51_V1.0521.00
36_E39_L1.0111.00
95_Y107_L1.0111.00
84_V167_P0.9620.99
48_I71_E0.9600.99
95_Y98_F0.9540.99
108_V136_I0.9460.99
114_T164_M0.9400.99
17_E64_G0.9240.99
113_I132_S0.9240.99
55_E59_L0.9220.99
81_V147_I0.9190.99
18_F22_L0.9160.99
34_Y37_K0.9160.99
143_R167_P0.9120.99
33_Q36_E0.8960.99
92_V132_S0.8830.99
45_V75_I0.8800.99
35_Q38_I0.8770.99
113_I164_M0.8770.99
91_Q138_K0.8750.99
93_D98_F0.8730.99
163_T167_P0.8680.98
116_D134_K0.8680.98
147_I163_T0.8590.98
17_E20_K0.8550.98
149_V160_I0.8530.98
38_I41_D0.8520.98
99_V142_V0.8430.98
34_Y78_V0.8420.98
63_D68_H0.8380.98
14_P18_F0.8260.98
12_R16_N0.8260.98
115_D165_R0.8200.98
61_F64_G0.8160.98
30_L35_Q0.8060.98
19_G22_L0.7990.97
119_K134_K0.7980.97
101_L146_V0.7950.97
91_Q98_F0.7940.97
108_V162_L0.7940.97
88_E100_N0.7840.97
118_L135_V0.7820.97
33_Q39_L0.7800.97
145_R163_T0.7660.97
28_N59_L0.7600.97
84_V166_Q0.7570.96
34_Y38_I0.7570.96
100_N103_P0.7530.96
87_G162_L0.7510.96
112_Q163_T0.7500.96
60_V66_T0.7430.96
57_G60_V0.7370.96
64_G67_Y0.7360.96
118_L134_K0.7330.96
40_K43_G0.7310.96
92_V136_I0.7300.96
110_I132_S0.7220.95
143_R164_M0.7200.95
14_P17_E0.7200.95
50_N54_S0.7180.95
91_Q159_R0.7160.95
50_N55_E0.7120.95
115_D168_Y0.7120.95
73_D77_Y0.7060.95
148_S156_R0.7030.95
50_N58_I0.7020.95
24_E61_F0.6990.94
60_V64_G0.6890.94
16_N20_K0.6850.94
22_L25_I0.6850.94
45_V48_I0.6840.94
25_I29_E0.6750.93
27_L56_E0.6740.93
34_Y39_L0.6730.93
63_D67_Y0.6710.93
15_P18_F0.6710.93
98_F107_L0.6680.93
107_L110_I0.6660.93
44_L48_I0.6630.93
114_T135_V0.6540.92
144_A164_M0.6500.92
48_I52_K0.6480.92
40_K44_L0.6430.92
110_I117_T0.6420.92
93_D138_K0.6420.92
96_G107_L0.6410.92
75_I103_P0.6390.91
108_V167_P0.6370.91
66_T69_E0.6350.91
116_D135_V0.6290.91
57_G72_F0.6270.91
62_G67_Y0.6230.90
29_E32_Q0.6210.90
25_I58_I0.6190.90
81_V149_V0.6190.90
103_P158_P0.6180.90
87_G106_G0.6170.90
65_A69_E0.6160.90
60_V67_Y0.6160.90
36_E42_L0.6150.90
106_G109_H0.6140.90
77_Y103_P0.6090.89
26_A68_H0.6080.89
101_L162_L0.6080.89
40_K55_E0.6070.89
101_L104_M0.6030.89
60_V65_A0.5990.89
97_I108_V0.5930.88
89_V108_V0.5930.88
136_I142_V0.5830.87
15_P20_K0.5810.87
140_D164_M0.5800.87
96_G109_H0.5790.87
98_F150_A0.5730.86
51_V55_E0.5720.86
77_Y101_L0.5720.86
31_R78_V0.5710.86
47_A50_N0.5670.86
43_G51_V0.5670.86
76_T160_I0.5670.86
147_I165_R0.5620.85
53_T66_T0.5590.85
24_E30_L0.5520.84
91_Q161_A0.5500.84
31_R37_K0.5490.84
17_E21_P0.5450.83
95_Y105_D0.5450.83
41_D49_L0.5400.83
14_P20_K0.5400.83
16_N19_G0.5380.83
38_I45_V0.5370.83
108_V144_A0.5330.82
58_I61_F0.5320.82
14_P21_P0.5320.82
43_G49_L0.5300.82
92_V110_I0.5270.81
85_V144_A0.5260.81
94_N148_S0.5170.80
29_E33_Q0.5140.80
62_G69_E0.5120.80
51_V57_G0.5110.79
22_L34_Y0.5100.79
62_G65_A0.5100.79
92_V139_G0.5090.79
44_L47_A0.5090.79
25_I60_V0.5080.79
159_R162_L0.5080.79
114_T117_T0.5060.79
95_Y111_S0.5030.78
98_F111_S0.5020.78
52_K58_I0.5010.78
12_R15_P0.5010.78
116_D119_K0.5000.78
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  
3ayhB 1 0.9667 100 0.208 Contact Map
4aybE 1 0.95 100 0.222 Contact Map
1go3E 1 0.9778 100 0.229 Contact Map
4qjfA 1 1 100 0.24 Contact Map
2ckzB 1 1 100 0.257 Contact Map
2b8kG 1 0.9222 100 0.289 Contact Map
3h0gG 1 0.9111 100 0.302 Contact Map
1y14B 2 0.8667 100 0.317 Contact Map
2c35B 1 0.9222 99.9 0.343 Contact Map
3cdiA 3 0.0667 99.9 0.427 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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