GREMLIN Database
RPSK - RNA polymerase sigma-K factor
UniProt: P12254 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 294 (243)
Sequences: 6535 (3850)
Seq/√Len: 247.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
147_V151_F3.6901.00
52_R93_E3.6001.00
153_I159_P3.4891.00
234_K238_V3.4651.00
43_L48_D3.3501.00
63_V84_G3.2341.00
260_I265_V3.0061.00
158_P168_L2.9341.00
53_N57_E2.9241.00
146_K163_M2.7651.00
150_C163_M2.7651.00
36_E54_M2.7541.00
39_K43_L2.4631.00
264_Y267_R2.3851.00
239_G257_E2.3581.00
143_F163_M2.3121.00
233_E275_K2.2571.00
240_R269_E2.2231.00
62_L104_A2.2111.00
235_E257_E2.1761.00
239_G249_K2.1401.00
228_I279_E2.1241.00
184_H197_S1.9921.00
235_E258_L1.9571.00
167_I170_H1.9571.00
249_K257_E1.9401.00
157_M172_R1.9401.00
227_D234_K1.9151.00
263_S266_S1.9091.00
258_L265_V1.8641.00
96_S99_K1.8571.00
252_R256_K1.8551.00
60_L85_T1.8111.00
230_D275_K1.8081.00
235_E239_G1.8071.00
236_V268_I1.7871.00
66_I108_A1.7801.00
42_E46_K1.7641.00
147_V153_I1.7621.00
146_K150_C1.7241.00
56_I89_I1.7201.00
147_V155_K1.7081.00
210_I214_Q1.6931.00
236_V272_A1.6771.00
160_L171_L1.6421.00
94_S106_Y1.6351.00
33_S36_E1.6181.00
143_F147_V1.5991.00
67_V81_I1.5611.00
54_M58_H1.5571.00
184_H199_I1.5551.00
66_I115_I1.5521.00
49_E53_N1.5501.00
45_A98_G1.5401.00
158_P162_V1.5341.00
83_I120_G1.5261.00
38_K42_E1.5171.00
34_S38_K1.4991.00
230_D233_E1.4821.00
157_M171_L1.4791.00
64_A81_I1.4741.00
102_K105_T1.4731.00
157_M168_L1.4481.00
161_F171_L1.4311.00
81_I85_T1.4261.00
168_L172_R1.3961.00
45_A97_A1.3831.00
249_K253_E1.3791.00
166_E171_L1.3701.00
67_V115_I1.3381.00
237_I276_M1.3161.00
155_K159_P1.3111.00
143_F146_K1.2921.00
42_E98_G1.2871.00
233_E271_R1.2671.00
91_G107_A1.2521.00
143_F164_N1.2471.00
217_M221_K1.2441.00
50_H53_N1.2261.00
41_L44_M1.2161.00
56_I92_I1.2081.00
48_D51_A1.2071.00
147_V163_M1.2021.00
84_G115_I1.1941.00
67_V77_A1.1871.00
208_D211_D1.1761.00
43_L54_M1.1591.00
161_F166_E1.1561.00
193_G201_V1.1551.00
136_R140_G1.1481.00
92_I103_L1.1451.00
36_E39_K1.1451.00
264_Y268_I1.1381.00
263_S267_R1.1251.00
103_L107_A1.1251.00
156_S159_P1.1221.00
251_Q255_A1.1111.00
231_D234_K1.1071.00
137_I170_H1.0941.00
251_Q263_S1.0921.00
50_H54_M1.0871.00
278_H281_Y1.0811.00
41_L45_A1.0801.00
119_K123_I1.0781.00
268_I272_A1.0751.00
235_E238_V1.0741.00
75_E120_G1.0551.00
120_G124_H1.0551.00
71_E77_A1.0391.00
63_V88_L1.0371.00
137_I166_E1.0341.00
183_L199_I1.0311.00
209_V213_I1.0291.00
161_F164_N1.0271.00
157_M174_L1.0261.00
147_V159_P1.0261.00
251_Q266_S1.0191.00
90_K94_S1.0191.00
161_F168_L1.0181.00
142_F146_K1.0131.00
214_Q217_M1.0081.00
151_F155_K1.0071.00
216_N220_E1.0071.00
43_L51_A1.0001.00
39_K42_E0.9971.00
161_F167_I0.9961.00
239_G254_I0.9921.00
130_F138_H0.9761.00
197_S200_D0.9751.00
59_N104_A0.9701.00
128_I131_N0.9671.00
42_E97_A0.9631.00
91_G103_L0.9511.00
151_F159_P0.9411.00
38_K100_G0.9391.00
31_P61_R0.9391.00
274_M278_H0.9281.00
85_T89_I0.9261.00
241_F269_E0.9261.00
148_N155_K0.9161.00
126_S130_F0.9141.00
64_A85_T0.9101.00
231_D235_E0.9051.00
221_K224_Q0.9001.00
252_R255_A0.8981.00
44_M55_L0.8981.00
232_R268_I0.8971.00
112_E118_T0.8801.00
252_R262_R0.8680.99
219_L223_K0.8640.99
62_L105_T0.8640.99
87_G91_G0.8620.99
65_H68_K0.8620.99
81_I84_G0.8600.99
148_N151_F0.8580.99
236_V258_L0.8570.99
37_E41_L0.8560.99
162_V165_N0.8540.99
52_R92_I0.8540.99
94_S110_C0.8510.99
232_R236_V0.8460.99
35_S39_K0.8460.99
44_M47_G0.8450.99
123_I128_I0.8440.99
68_K77_A0.8420.99
40_Y54_M0.8420.99
54_M57_E0.8370.99
232_R264_Y0.8290.99
203_K206_N0.8280.99
60_L63_V0.8270.99
211_D214_Q0.8260.99
47_G51_A0.8250.99
144_H160_L0.8240.99
63_V85_T0.8220.99
204_S207_E0.8070.99
68_K71_E0.8070.99
64_A77_A0.8060.99
141_N144_H0.8020.99
147_V160_L0.8020.99
110_C266_S0.8010.99
131_N134_G0.7970.99
240_R254_I0.7970.99
261_S264_Y0.7970.99
251_Q262_R0.7960.99
152_F155_K0.7950.99
226_I238_V0.7920.99
135_V139_N0.7910.99
254_I269_E0.7890.99
181_V185_D0.7890.99
151_F163_M0.7840.99
43_L46_K0.7820.99
40_Y51_A0.7800.99
144_H174_L0.7640.99
120_G126_S0.7590.99
223_K238_V0.7590.99
113_N122_C0.7540.99
224_Q227_D0.7520.98
251_Q267_R0.7510.98
55_L92_I0.7480.98
216_N219_L0.7480.98
225_Y276_M0.7470.98
187_I201_V0.7450.98
212_T216_N0.7430.98
170_H173_A0.7420.98
213_I217_M0.7410.98
97_A100_G0.7410.98
236_V260_I0.7380.98
251_Q264_Y0.7360.98
215_L219_L0.7340.98
90_K114_E0.7330.98
119_K128_I0.7320.98
106_Y110_C0.7310.98
30_Q33_S0.7290.98
77_A81_I0.7250.98
92_I210_I0.7240.98
122_C132_I0.7180.98
269_E272_A0.7180.98
45_A96_S0.7160.98
134_G138_H0.7130.98
119_K240_R0.7080.98
110_C263_S0.7060.98
113_N119_K0.7050.98
230_D272_A0.7040.98
70_F115_I0.7010.98
66_I112_E0.6930.97
223_K227_D0.6910.97
88_L107_A0.6900.97
62_L108_A0.6880.97
110_C113_N0.6830.97
143_F160_L0.6820.97
187_I197_S0.6810.97
40_Y44_M0.6790.97
113_N132_I0.6740.97
120_G123_I0.6740.97
137_I140_G0.6700.97
253_E256_K0.6680.97
86_I89_I0.6670.97
64_A78_E0.6640.97
220_E224_Q0.6570.96
139_N145_D0.6530.96
119_K126_S0.6520.96
240_R250_T0.6510.96
144_H148_N0.6470.96
32_L37_E0.6460.96
187_I200_D0.6460.96
118_T132_I0.6450.96
241_F273_L0.6440.96
226_I230_D0.6380.96
247_K257_E0.6370.96
83_I124_H0.6370.96
157_M161_F0.6340.96
42_E45_A0.6330.96
148_N154_F0.6320.96
60_L81_I0.6310.96
32_L58_H0.6300.96
121_G126_S0.6300.96
133_Y136_R0.6290.95
164_N171_L0.6240.95
214_Q218_E0.6240.95
113_N266_S0.6230.95
251_Q269_E0.6220.95
119_K250_T0.6220.95
34_S37_E0.6210.95
63_V115_I0.6200.95
108_A261_S0.6200.95
125_P128_I0.6190.95
36_E40_Y0.6170.95
82_S114_E0.6170.95
233_E268_I0.6160.95
222_V225_Y0.6140.95
41_L92_I0.6120.95
60_L64_A0.6070.95
228_I281_Y0.6070.95
123_I129_R0.6050.94
41_L97_A0.6010.94
105_T108_A0.6000.94
121_G125_P0.5990.94
261_S267_R0.5980.94
230_D268_I0.5980.94
156_S161_F0.5980.94
52_R56_I0.5970.94
80_L120_G0.5970.94
65_H69_K0.5960.94
30_Q36_E0.5940.94
114_E120_G0.5920.94
225_Y279_E0.5920.94
217_M220_E0.5900.94
101_T105_T0.5880.94
119_K129_R0.5880.94
162_V166_E0.5870.93
61_R64_A0.5820.93
255_A263_S0.5800.93
229_L276_M0.5750.93
58_H61_R0.5750.93
239_G258_L0.5720.93
233_E272_A0.5710.93
90_K106_Y0.5700.92
64_A67_V0.5670.92
262_R267_R0.5660.92
197_S201_V0.5650.92
49_E52_R0.5640.92
130_F134_G0.5640.92
44_M51_A0.5620.92
240_R262_R0.5600.92
121_G128_I0.5590.92
187_I193_G0.5570.92
144_H147_V0.5560.92
113_N242_G0.5520.91
153_I156_S0.5500.91
255_A262_R0.5490.91
159_P162_V0.5490.91
82_S119_K0.5490.91
260_I264_Y0.5480.91
92_I97_A0.5470.91
46_K98_G0.5450.91
126_S129_R0.5450.91
254_I258_L0.5440.91
72_N75_E0.5440.91
70_F112_E0.5430.91
110_C269_E0.5430.91
146_K149_N0.5400.90
146_K228_I0.5400.90
237_I273_L0.5390.90
232_R267_R0.5390.90
225_Y228_I0.5380.90
34_S41_L0.5370.90
131_N135_V0.5370.90
66_I111_I0.5340.90
182_S186_P0.5320.90
188_G201_V0.5320.90
123_I126_S0.5320.90
37_E58_H0.5300.90
43_L47_G0.5270.89
240_R251_Q0.5260.89
119_K124_H0.5260.89
120_G127_L0.5260.89
67_V76_D0.5250.89
256_K259_G0.5240.89
132_I262_R0.5230.89
169_M172_R0.5230.89
44_M92_I0.5200.89
160_L163_M0.5200.89
160_L164_N0.5170.88
75_E80_L0.5170.88
131_N136_R0.5160.88
222_V280_F0.5160.88
226_I242_G0.5160.88
113_N267_R0.5150.88
118_T121_G0.5150.88
121_G129_R0.5140.88
65_H82_S0.5140.88
238_V247_K0.5140.88
75_E121_G0.5120.88
213_I216_N0.5110.88
37_E44_M0.5110.88
61_R65_H0.5100.88
183_L202_L0.5100.88
95_Y101_T0.5050.87
198_L201_V0.5030.87
62_L65_H0.5030.87
128_I180_D0.5030.87
121_G254_I0.5020.87
118_T123_I0.5010.87
186_P204_S0.5000.87
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  
1l9zH 1 0.8878 100 0.285 Contact Map
2a6hF 1 0.915 100 0.285 Contact Map
4yfkF 1 0.9728 100 0.372 Contact Map
1l0oC 1 0.1871 100 0.533 Contact Map
1rp3A 1 0.7721 100 0.565 Contact Map
3ugoA 1 0.3741 100 0.584 Contact Map
4nqwA 1 0.5034 99.9 0.665 Contact Map
4cxfA 1 0.5238 99.9 0.699 Contact Map
1or7A 2 0.6259 99.9 0.7 Contact Map
2q1zA 1 0.5952 99.9 0.706 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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