GREMLIN Database
RPOE - ECF RNA polymerase sigma-E factor
UniProt: P0AGB6 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11897
Length: 191 (159)
Sequences: 43365 (31654)
Seq/√Len: 2510.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
56_K81_T3.1851.00
149_R159_I2.6791.00
32_K71_Y2.4671.00
142_L180_A2.3121.00
157_E167_V2.2761.00
137_S184_K2.2311.00
79_V83_K2.2011.00
134_T184_K2.1951.00
37_V78_A2.0381.00
53_A78_A1.9931.00
141_D173_R1.9811.00
154_L162_I1.9801.00
168_G171_R1.9181.00
148_L162_I1.8891.00
165_C173_R1.7071.00
69_A72_T1.7051.00
148_L154_L1.6881.00
139_P142_L1.6721.00
23_N27_V1.6541.00
142_L173_R1.6461.00
166_P169_T1.6461.00
36_L75_Y1.6091.00
81_T84_N1.6071.00
60_A63_S1.6031.00
84_N87_V1.6021.00
156_Y167_V1.6001.00
24_L28_R1.5841.00
150_E178_R1.5761.00
44_G47_P1.5541.00
57_A74_L1.5511.00
40_Y82_A1.5501.00
169_T173_R1.5361.00
45_D85_Y1.5291.00
155_S158_E1.5151.00
32_K75_Y1.5151.00
156_Y174_I1.4891.00
175_F179_E1.4891.00
156_Y171_R1.4681.00
56_K84_N1.4571.00
169_T172_S1.4531.00
143_R147_T1.4491.00
49_V85_Y1.4171.00
180_A184_K1.4111.00
52_E81_T1.4101.00
33_V78_A1.4001.00
29_Y71_Y1.3791.00
165_C170_V1.3481.00
76_R79_V1.3431.00
149_R174_I1.3351.00
37_V82_A1.3341.00
80_N83_K1.3081.00
71_Y75_Y1.3081.00
167_V171_R1.2871.00
56_K60_A1.2861.00
145_A177_A1.2821.00
145_A173_R1.2581.00
145_A174_I1.2381.00
172_S175_F1.2161.00
76_R80_N1.2101.00
55_I59_R1.2031.00
26_V30_Q1.2021.00
142_L177_A1.1641.00
26_V54_F1.1621.00
157_E161_A1.1601.00
33_V50_V1.1471.00
41_V82_A1.1461.00
53_A77_I1.1421.00
36_L79_V1.1421.00
123_L126_E1.1411.00
149_R156_Y1.1331.00
41_V49_V1.1311.00
154_L158_E1.1291.00
64_F67_D1.1291.00
37_V49_V1.1221.00
136_E143_R1.1141.00
150_E174_I1.1111.00
29_Y54_F1.0931.00
172_S176_R1.0911.00
174_I178_R1.0891.00
81_T85_Y1.0781.00
22_F58_Y1.0691.00
34_A38_S1.0671.00
37_V50_V1.0651.00
84_N88_A1.0611.00
85_Y89_Q1.0611.00
168_G172_S1.0551.00
53_A81_T1.0511.00
147_T152_D1.0461.00
134_T137_S1.0441.00
30_Q34_A1.0431.00
38_S46_V1.0421.00
148_L159_I1.0351.00
45_D89_Q1.0331.00
29_Y74_L1.0311.00
159_I170_V1.0291.00
82_A86_L1.0211.00
142_L176_R1.0171.00
49_V81_T1.0161.00
18_D21_A1.0091.00
68_S72_T1.0051.00
156_Y170_V1.0001.00
33_V53_A0.9731.00
83_K86_L0.9691.00
34_A47_P0.9671.00
34_A50_V0.9561.00
144_M147_T0.9501.00
141_D165_C0.9441.00
128_R132_F0.9421.00
29_Y32_K0.9421.00
140_E144_M0.9371.00
147_T151_L0.9361.00
33_V74_L0.9331.00
37_V46_V0.9281.00
34_A46_V0.9271.00
49_V82_A0.9201.00
19_Q23_N0.9191.00
142_L145_A0.9171.00
56_K59_R0.9161.00
25_L70_F0.9041.00
30_Q50_V0.9021.00
119_E123_L0.8851.00
168_G175_F0.8831.00
35_S39_R0.8821.00
88_A91_R0.8801.00
134_T181_I0.8731.00
22_F62_D0.8721.00
145_A165_C0.8711.00
165_C169_T0.8621.00
179_E183_N0.8511.00
144_M148_L0.8451.00
146_I150_E0.8411.00
57_A73_W0.8391.00
31_H35_S0.8351.00
52_E85_Y0.8351.00
144_M163_M0.8261.00
73_W77_I0.8151.00
160_A167_V0.8091.00
146_I177_A0.8051.00
76_R83_K0.8021.00
134_T185_V0.7941.00
50_V54_F0.7821.00
20_K23_N0.7771.00
89_Q92_R0.7621.00
52_E55_I0.7551.00
148_L152_D0.7531.00
24_L27_V0.7531.00
157_E171_R0.7521.00
32_K36_L0.7501.00
46_V50_V0.7451.00
51_Q55_I0.7431.00
65_R68_S0.7381.00
36_L40_Y0.7251.00
88_A92_R0.7201.00
30_Q54_F0.7191.00
145_A163_M0.7151.00
159_I163_M0.7141.00
38_S42_P0.7061.00
97_D101_I0.7031.00
148_L163_M0.7021.00
155_S159_I0.7011.00
75_Y79_V0.6991.00
126_E130_I0.6891.00
129_Q133_R0.6841.00
158_E161_A0.6831.00
127_L130_I0.6821.00
130_I133_R0.6801.00
132_F136_E0.6761.00
83_K87_V0.6751.00
97_D100_A0.6691.00
27_V30_Q0.6591.00
141_D144_M0.6561.00
122_M126_E0.6501.00
176_R179_E0.6481.00
40_Y83_K0.6441.00
41_V46_V0.6421.00
40_Y79_V0.6361.00
118_P121_L0.6361.00
86_L90_G0.6331.00
176_R180_A0.6311.00
85_Y88_A0.6311.00
32_K35_S0.6261.00
48_D51_Q0.6241.00
126_E129_Q0.6201.00
58_Y61_L0.6201.00
67_D70_F0.6151.00
178_R182_D0.6131.00
36_L82_A0.6131.00
99_D102_E0.6121.00
64_F68_S0.6051.00
78_A82_A0.6011.00
173_R177_A0.5971.00
82_A85_Y0.5921.00
53_A57_A0.5871.00
122_M125_E0.5841.00
125_E128_R0.5831.00
121_L125_E0.5811.00
90_G94_P0.5791.00
57_A77_I0.5731.00
61_L70_F0.5711.00
66_G69_A0.5681.00
160_A163_M0.5671.00
146_I181_I0.5621.00
140_E143_R0.5601.00
138_L177_A0.5601.00
144_M162_I0.5581.00
20_K24_L0.5561.00
86_L89_Q0.5551.00
139_P180_A0.5521.00
180_A183_N0.5521.00
171_R175_F0.5511.00
160_A170_V0.5501.00
156_Y159_I0.5501.00
120_N124_S0.5471.00
57_A70_F0.5461.00
43_S47_P0.5411.00
33_V54_F0.5361.00
124_S127_L0.5341.00
41_V85_Y0.5331.00
72_T75_Y0.5311.00
117_N120_N0.5291.00
159_I174_I0.5291.00
132_F151_L0.5281.00
98_V101_I0.5261.00
49_V78_A0.5251.00
64_F72_T0.5241.00
41_V45_D0.5211.00
130_I134_T0.5191.00
112_L115_I0.5181.00
89_Q93_P0.5161.00
37_V40_Y0.5151.00
54_F58_Y0.5121.00
135_I146_I0.5111.00
22_F26_V0.5081.00
133_R137_S0.5061.00
173_R176_R0.5031.00
123_L127_L0.5021.00
135_I147_T0.5001.00
163_M170_V0.5001.00
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  
1or7A 2 0.9529 100 0.141 Contact Map
4cxfA 1 0.801 100 0.165 Contact Map
4nqwA 1 0.7644 100 0.224 Contact Map
4yfkF 1 1 100 0.226 Contact Map
2q1zA 1 0.9005 100 0.226 Contact Map
1rp3A 1 0.9215 100 0.268 Contact Map
1l0oC 1 0.0785 100 0.269 Contact Map
2a6hF 1 0.9686 100 0.283 Contact Map
1l9zH 1 0.9529 100 0.288 Contact Map
2lfwA 1 0.7644 100 0.315 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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