GREMLIN Database
RPSE - RNA polymerase sigma-E factor
UniProt: P06222 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 239 (194)
Sequences: 6653 (4010)
Seq/√Len: 287.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
50_K55_D3.4681.00
59_R100_N3.3561.00
189_K193_E3.1471.00
70_V91_G3.0441.00
194_L212_M2.8351.00
153_L157_L2.6921.00
46_V50_K2.6451.00
60_A64_E2.5641.00
43_E61_I2.5191.00
195_R224_E2.5181.00
194_L204_K2.4851.00
215_I220_I2.3951.00
159_T165_T2.3631.00
173_D176_L2.3181.00
219_Y222_R2.1221.00
156_V169_E2.1041.00
204_K212_M2.0771.00
61_I65_R2.0741.00
69_L111_A2.0561.00
188_E230_R2.0011.00
185_N230_R1.8821.00
190_Q213_M1.8731.00
190_Q212_M1.8571.00
190_Q194_L1.8471.00
207_K211_D1.8131.00
218_S221_S1.8111.00
152_L169_E1.8071.00
98_A114_A1.7451.00
45_Q49_M1.7411.00
183_Q234_E1.7261.00
173_D177_L1.7211.00
63_I96_I1.7111.00
103_N106_K1.6901.00
73_I115_S1.6481.00
182_E189_K1.6301.00
52_P104_P1.6161.00
149_N169_E1.6011.00
41_K45_Q1.5931.00
56_Q60_A1.5921.00
90_I125_Y1.5691.00
185_N188_E1.5441.00
174_K178_K1.5291.00
40_S43_E1.5181.00
67_L92_T1.5121.00
213_M220_I1.4781.00
192_M231_L1.4711.00
74_A122_I1.4491.00
57_A60_A1.4361.00
191_I227_I1.4291.00
175_K178_K1.4191.00
204_K208_D1.3961.00
88_I92_T1.3791.00
191_I223_L1.3761.00
50_K53_N1.3691.00
152_L156_V1.3641.00
74_A88_I1.3561.00
48_L51_L1.3391.00
149_N153_L1.3071.00
164_I174_K1.2901.00
47_L61_I1.2691.00
52_P105_E1.2561.00
71_V88_I1.2511.00
109_K112_T1.2481.00
188_E226_R1.2391.00
74_A84_I1.2381.00
101_T113_Y1.2351.00
52_P103_N1.2291.00
194_L209_V1.2261.00
218_S222_R1.2101.00
158_G161_D1.2001.00
43_E46_V1.1911.00
164_I168_I1.1881.00
55_D58_A1.1551.00
223_L227_I1.1531.00
153_L159_T1.1521.00
219_Y223_L1.1481.00
149_N152_L1.1471.00
78_E84_I1.1351.00
140_E144_I1.1321.00
73_I122_I1.1101.00
190_Q193_E1.1091.00
174_K177_L1.1071.00
176_L179_K1.0901.00
49_M105_E1.0871.00
99_V110_L1.0751.00
175_K179_K1.0741.00
50_K58_A1.0611.00
153_L169_E1.0531.00
72_Y75_R1.0501.00
46_V49_M1.0501.00
70_V95_L1.0421.00
50_K61_I1.0311.00
125_Y129_N1.0301.00
49_M53_N1.0291.00
48_L52_P1.0231.00
97_K121_E1.0191.00
59_R99_V1.0151.00
51_L62_L1.0141.00
135_E138_F1.0061.00
206_Q221_S1.0021.00
98_A110_L1.0001.00
166_K170_A0.9941.00
145_D170_A0.9931.00
54_G58_A0.9901.00
187_R191_I0.9711.00
110_L114_A0.9691.00
173_D178_K0.9671.00
95_L114_A0.9651.00
186_E190_Q0.9531.00
51_L54_G0.9511.00
145_D166_K0.9511.00
141_P172_V0.9411.00
132_I135_E0.9391.00
167_D170_A0.9291.00
57_A61_I0.9241.00
130_N139_D0.9161.00
206_Q218_S0.9161.00
153_L161_D0.9141.00
167_D172_V0.9081.00
191_I213_M0.9021.00
97_K101_T0.8951.00
75_R84_I0.8931.00
142_L145_D0.8901.00
49_M104_P0.8891.00
47_L58_A0.8871.00
51_L58_A0.8851.00
163_I166_K0.8831.00
206_Q222_R0.8811.00
206_Q210_A0.8741.00
161_D165_T0.8691.00
117_C120_N0.8691.00
91_G122_I0.8641.00
42_D46_V0.8621.00
187_R223_L0.8611.00
92_T96_I0.8571.00
180_A183_Q0.8481.00
162_D165_T0.8451.00
195_R209_V0.8421.00
73_I119_E0.8411.00
186_E189_K0.8401.00
63_I99_V0.8391.00
39_L44_E0.8311.00
119_E123_L0.8261.00
75_R78_E0.8161.00
67_L71_V0.8151.00
149_N170_A0.8141.00
161_D166_K0.8101.00
101_T117_C0.8040.99
154_S157_L0.8010.99
168_I171_N0.7990.99
82_I125_Y0.7940.99
229_K233_K0.7930.99
167_D171_N0.7920.99
61_I64_E0.7920.99
71_V92_T0.7920.99
166_K171_N0.7920.99
207_K217_Q0.7900.99
209_V224_E0.7850.99
180_A231_L0.7820.99
168_I172_V0.7800.99
38_P68_R0.7750.99
196_F228_I0.7630.99
48_L104_P0.7610.99
71_V84_I0.7590.99
39_L65_R0.7540.99
94_G122_I0.7520.99
207_K210_A0.7500.99
224_E227_I0.7440.99
71_V74_A0.7350.99
53_N58_A0.7350.99
144_I147_D0.7350.99
69_L112_T0.7350.99
149_N166_K0.7260.99
108_I112_T0.7250.99
153_L156_V0.7170.99
180_A235_F0.7170.99
141_P144_I0.7100.99
137_S141_P0.7070.99
66_N111_A0.7050.99
172_V176_L0.7040.99
56_Q59_R0.7040.99
196_F224_E0.7020.99
52_P55_D0.6940.98
165_T169_E0.6930.98
143_N146_W0.6880.98
47_L51_L0.6870.98
90_I121_E0.6850.98
88_I91_G0.6840.98
216_S219_Y0.6800.98
113_Y117_C0.6800.98
139_D143_N0.6800.98
67_L70_V0.6780.98
147_D152_L0.6670.98
69_L115_S0.6670.98
70_V92_T0.6660.98
59_R63_I0.6660.98
77_F122_I0.6620.98
210_A217_Q0.6600.98
93_I96_I0.6590.98
45_Q107_K0.6580.98
184_L227_I0.6570.98
44_E65_R0.6530.98
157_L169_E0.6480.98
159_T166_K0.6480.98
181_L193_E0.6470.98
206_Q217_Q0.6460.98
48_L99_V0.6420.97
94_G117_C0.6410.97
195_R206_Q0.6350.97
150_E154_S0.6350.97
104_P107_K0.6320.97
209_V220_I0.6310.97
206_Q224_E0.6310.97
157_L165_T0.6310.97
62_L99_V0.6290.97
187_R215_I0.6230.97
138_F145_D0.6200.97
163_I167_D0.6180.97
121_E125_Y0.6170.97
143_N147_D0.6170.97
154_S160_D0.6160.97
67_L88_I0.6120.97
139_D145_D0.6090.97
180_A234_E0.6080.96
72_Y76_K0.6080.96
66_N197_G0.6050.96
94_G98_A0.6010.96
137_S140_E0.6010.96
164_I167_D0.6000.96
149_N157_L0.6000.96
206_Q219_Y0.5940.96
157_L161_D0.5940.96
209_V213_M0.5910.96
159_T167_D0.5880.96
152_L155_D0.5860.96
174_K179_K0.5810.95
117_C124_M0.5800.95
159_T162_D0.5800.95
185_N223_L0.5790.95
44_E48_L0.5780.95
166_K177_L0.5770.95
48_L62_L0.5770.95
124_M128_R0.5730.95
44_E109_K0.5720.95
181_L189_K0.5710.95
51_L110_L0.5700.95
120_N124_M0.5690.95
141_P145_D0.5610.95
41_K44_E0.5600.94
82_I126_L0.5600.94
39_L47_L0.5600.94
114_A118_I0.5570.94
124_M195_R0.5550.94
163_I170_A0.5540.94
117_C218_S0.5530.94
150_E153_L0.5530.94
226_R229_K0.5520.94
187_R219_Y0.5520.94
170_A173_D0.5490.94
65_R68_R0.5490.94
117_C221_S0.5450.94
120_N216_S0.5390.93
162_D166_K0.5380.93
173_D179_K0.5380.93
37_P40_S0.5370.93
86_D89_S0.5370.93
68_R71_V0.5340.93
82_I129_N0.5300.93
192_M228_I0.5280.93
161_D170_A0.5280.93
69_L118_I0.5270.93
134_S138_F0.5260.92
164_I171_N0.5260.92
191_I209_V0.5260.92
170_A177_L0.5250.92
181_L185_N0.5240.92
153_L165_T0.5240.92
205_T208_D0.5210.92
53_N56_Q0.5190.92
133_R137_S0.5190.92
58_A62_L0.5190.92
129_N132_I0.5180.92
136_V140_E0.5150.92
89_S121_E0.5080.91
164_I170_A0.5070.91
127_R136_V0.5060.91
138_F144_I0.5060.91
90_I221_S0.5040.91
54_G100_N0.5020.91
120_N136_V0.5010.91
116_R119_E0.5000.90
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 0.9038 100 0.256 Contact Map
2a6hF 1 0.8996 100 0.26 Contact Map
4yfkF 1 0.9958 100 0.366 Contact Map
1l0oC 1 0.1632 100 0.464 Contact Map
3ugoA 1 0.4561 100 0.482 Contact Map
1rp3A 1 0.7615 100 0.533 Contact Map
4nqwA 1 0.6192 99.9 0.577 Contact Map
1or7A 2 0.7657 99.9 0.601 Contact Map
4cxfA 1 0.6444 99.9 0.614 Contact Map
2q1zA 1 0.7322 99.9 0.619 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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