GREMLIN Database
Q9HNL1 - DNA-directed RNA polymerase subunit E
UniProt: Q9HNL1 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 190 (154)
Sequences: 2576 (1498)
Seq/√Len: 120.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
6_R9_D4.9431.00
86_D143_R3.9071.00
30_L38_M3.2291.00
88_E141_S3.2221.00
113_I136_L3.1091.00
41_D44_S2.8431.00
86_D141_S2.7581.00
70_A74_A2.5921.00
90_V100_G2.3801.00
146_I161_I2.3121.00
112_Q167_Q2.2891.00
64_P68_Y2.2391.00
26_V67_Y2.1471.00
13_V16_E2.0791.00
106_G163_L2.0681.00
90_V105_D2.0551.00
108_L113_I2.0431.00
80_E83_E2.0221.00
29_L56_E2.0061.00
142_V165_A2.0051.00
137_G140_D1.9061.00
8_K12_E1.8981.00
2_Y6_R1.8441.00
99_V108_L1.7501.00
94_S122_E1.7461.00
6_R10_T1.7091.00
164_T167_Q1.6441.00
77_F83_E1.6431.00
79_P146_I1.6251.00
55_G61_P1.5981.00
100_G105_D1.5621.00
148_T162_G1.5591.00
70_A73_D1.5271.00
52_H56_E1.5211.00
5_A9_D1.4681.00
65_G68_Y1.4651.00
37_R75_V1.4651.00
101_I161_I1.4181.00
150_S160_K1.3961.00
114_S165_A1.3911.00
79_P101_I1.3601.00
87_G99_V1.3451.00
110_V121_D1.3421.00
50_E55_G1.3251.00
71_E74_A1.3011.00
2_Y5_A1.2841.00
41_D45_I1.2801.00
113_I118_L1.2641.00
108_L165_A1.2631.00
63_R66_V1.2560.99
120_F134_Q1.2540.99
50_E53_D1.2320.99
92_V138_T1.2020.99
108_L136_L1.1940.99
115_D172_K1.1920.99
34_L78_E1.1810.99
11_I15_P1.1780.99
51_V55_G1.1750.99
93_V98_F1.1680.99
64_P67_Y1.1520.99
170_L173_H1.1270.99
92_V121_D1.1100.99
5_A8_K1.1050.99
113_I135_V1.0720.98
65_G69_E1.0650.98
38_M41_D1.0530.98
55_G60_L1.0490.98
28_R59_V1.0430.98
121_D134_Q1.0400.98
81_M148_T1.0380.98
112_Q166_K1.0310.98
87_G163_L1.0250.98
89_V136_L0.9990.97
24_D61_P0.9980.97
113_I121_D0.9980.97
61_P67_Y0.9960.97
95_F107_L0.9920.97
2_Y9_D0.9860.97
95_F98_F0.9690.97
45_I75_V0.9540.97
115_D173_H0.9440.96
62_N67_Y0.9110.96
17_Y64_P0.9090.95
149_K161_I0.9070.95
97_A136_L0.8970.95
140_D165_A0.8940.95
61_P66_V0.8830.95
136_L142_V0.8790.95
50_E60_L0.8770.95
84_V145_R0.8740.94
91_E138_T0.8690.94
34_L37_R0.8650.94
152_D160_K0.8520.94
101_I146_I0.8460.93
91_E160_K0.8440.93
87_G106_G0.8440.93
115_D170_L0.8350.93
50_E61_P0.8330.93
100_G103_P0.8320.93
54_L61_P0.8300.93
112_Q147_V0.8290.93
27_K56_E0.8240.92
51_V54_L0.8180.92
63_R67_Y0.8150.92
33_K36_G0.8140.92
84_V143_R0.8070.92
110_V120_F0.7980.91
118_L134_Q0.7950.91
45_I48_V0.7910.91
1_M8_K0.7900.91
147_V162_G0.7900.91
63_R68_Y0.7880.91
88_E100_G0.7850.91
25_L60_L0.7830.90
4_R8_K0.7820.90
118_L121_D0.7770.90
53_D61_P0.7750.90
38_M45_I0.7740.90
51_V60_L0.7700.90
37_R45_I0.7700.90
93_V138_T0.7670.90
1_M4_R0.7620.89
147_V164_T0.7510.89
25_L58_A0.7430.88
38_M57_G0.7430.88
114_S118_L0.7410.88
113_I165_A0.7410.88
53_D60_L0.7340.87
145_R167_Q0.7250.87
19_G22_G0.7180.86
115_D171_G0.7150.86
99_V142_V0.7130.86
36_G41_D0.7100.86
108_L142_V0.7090.86
53_D57_G0.7060.85
167_Q170_L0.7060.85
116_E119_A0.7060.85
92_V136_L0.7030.85
66_V69_E0.6860.84
143_R165_A0.6800.83
52_H58_A0.6770.83
35_E51_V0.6760.83
36_G42_V0.6750.83
48_V71_E0.6730.82
50_E54_L0.6700.82
91_E98_F0.6700.82
116_E135_V0.6660.82
112_Q164_T0.6650.82
50_E58_A0.6620.81
95_F105_D0.6620.81
94_S148_T0.6580.81
108_L163_L0.6570.81
98_F150_S0.6550.81
91_E162_G0.6540.81
167_Q171_G0.6530.81
63_R69_E0.6520.80
85_V144_A0.6510.80
101_I104_V0.6500.80
14_P18_L0.6500.80
145_R166_K0.6500.80
62_N68_Y0.6380.79
122_E137_G0.6370.79
96_G107_L0.6370.79
50_E57_G0.6370.79
23_P43_G0.6350.79
74_A77_F0.6350.79
77_F101_I0.6330.78
43_G46_V0.6240.77
28_R76_T0.6210.77
118_L136_L0.6200.77
55_G63_R0.6180.77
87_G105_D0.6180.77
98_F107_L0.6170.77
18_L24_D0.6160.77
114_S135_V0.6150.76
112_Q148_T0.6130.76
39_D43_G0.6110.76
148_T151_I0.6100.76
107_L111_S0.6090.76
112_Q162_G0.6060.75
79_P104_V0.6050.75
54_L58_A0.6010.75
40_E43_G0.5960.74
80_E85_V0.5950.74
55_G68_Y0.5930.74
73_D77_F0.5810.72
122_E138_T0.5770.72
31_Q78_E0.5720.71
146_I163_L0.5710.71
26_V68_Y0.5670.70
23_P39_D0.5670.70
97_A121_D0.5620.70
30_L35_E0.5590.69
18_L22_G0.5590.69
12_E16_E0.5540.69
118_L135_V0.5530.69
1_M135_V0.5510.68
11_I14_P0.5490.68
68_Y73_D0.5450.67
152_D159_S0.5450.67
93_V107_L0.5440.67
90_V98_F0.5420.67
68_Y74_A0.5410.67
81_M147_V0.5410.67
49_T71_E0.5370.66
29_L54_L0.5360.66
49_T69_E0.5360.66
23_P40_E0.5340.66
97_A108_L0.5330.66
97_A134_Q0.5320.66
77_F85_V0.5300.65
84_V166_K0.5270.65
51_V61_P0.5260.65
98_F109_H0.5240.64
136_L165_A0.5230.64
1_M5_A0.5210.64
35_E46_V0.5200.64
40_E46_V0.5180.64
24_D66_V0.5160.63
146_I149_K0.5160.63
83_E143_R0.5130.63
92_V95_F0.5120.63
7_L47_T0.5090.62
108_L144_A0.5090.62
1_M172_K0.5080.62
57_G61_P0.5080.62
26_V59_V0.5080.62
11_I89_V0.5060.62
93_V162_G0.5060.62
57_G72_F0.5050.62
17_Y24_D0.5000.61
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  
3cdiA 3 0.0632 99.9 0.365 Contact Map
4nbqA 3 0.7316 99.9 0.387 Contact Map
4aidA 3 0.1895 99.9 0.39 Contact Map
1e3pA 3 0.4263 99.9 0.439 Contact Map
2b8kG 1 0.8737 99.9 0.453 Contact Map
3h0gG 1 0.8789 99.9 0.457 Contact Map
1go3E 1 0.9421 99.9 0.46 Contact Map
1y14B 2 0.8368 99.8 0.478 Contact Map
2c35B 1 0.8789 99.8 0.487 Contact Map
4qjfA 1 0.9789 99.8 0.493 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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