GREMLIN Database
RPSD - RNA polymerase sigma-D factor
UniProt: P10726 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 254 (228)
Sequences: 7555 (4531)
Seq/√Len: 300.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
118_L122_Y3.4991.00
24_G68_E3.4651.00
121_R134_E3.3541.00
124_R130_E3.1701.00
35_V59_G2.9651.00
207_Q211_S2.9281.00
129_A139_V2.8821.00
117_K134_E2.7521.00
14_R20_D2.7031.00
25_D29_R2.6471.00
229_L234_I2.6321.00
212_L226_V2.2511.00
114_A134_E2.2351.00
233_R236_Q2.1591.00
201_E248_L2.1531.00
206_E244_K2.1011.00
128_P143_V2.0751.00
212_L218_L2.0651.00
213_F238_H2.0471.00
208_L226_V2.0151.00
34_L79_D1.9501.00
158_D169_N1.9491.00
221_T225_Q1.9191.00
200_H207_Q1.9011.00
71_D74_R1.9001.00
138_T141_D1.8821.00
38_H83_S1.7991.00
232_S235_S1.7851.00
32_M60_M1.7571.00
208_L212_L1.7471.00
118_L126_V1.7441.00
208_L227_L1.7361.00
218_L226_V1.7351.00
58_L93_G1.7241.00
26_D30_R1.6911.00
131_I142_V1.6831.00
117_K121_R1.6771.00
209_V237_I1.6601.00
77_K80_T1.6361.00
209_V241_A1.6331.00
114_A117_K1.6261.00
128_P139_V1.6251.00
227_L234_I1.6211.00
183_E187_M1.6161.00
128_P146_M1.6091.00
111_V131_I1.6021.00
203_S244_K1.5971.00
129_A133_E1.5951.00
176_D179_N1.5591.00
39_V90_I1.5451.00
38_H90_I1.5441.00
28_M64_Y1.5271.00
218_L222_E1.5231.00
158_D171_Q1.5201.00
21_P25_D1.5151.00
111_V145_T1.4921.00
69_K81_Y1.4861.00
56_M60_M1.4801.00
36_T56_M1.4791.00
59_G90_I1.4361.00
203_S206_E1.3991.00
128_P142_V1.3921.00
39_V56_M1.3821.00
118_L134_E1.3771.00
168_E173_M1.3701.00
233_R237_I1.3501.00
139_V143_V1.3421.00
45_G49_S1.3351.00
114_A118_L1.3151.00
67_L78_F1.3091.00
118_L124_R1.3041.00
114_A135_L1.3031.00
78_F82_A1.2951.00
115_I146_M1.2941.00
132_A142_V1.2641.00
206_E240_K1.2461.00
16_K73_S1.2441.00
107_K141_D1.2431.00
35_V63_L1.2341.00
137_M145_T1.2231.00
39_V52_K1.2181.00
210_V245_L1.1971.00
204_E207_Q1.1911.00
137_M142_V1.1911.00
106_E110_K1.1851.00
132_A139_V1.1831.00
127_S130_E1.1741.00
187_M190_E1.1681.00
111_V135_L1.1621.00
22_K25_D1.1601.00
214_Y238_H1.1461.00
107_K145_T1.1391.00
208_L211_S1.1231.00
40_G52_K1.1231.00
126_V130_E1.1221.00
66_A82_A1.1191.00
14_R18_W1.1191.00
190_E194_Q1.0981.00
111_V142_V1.0941.00
28_M67_L1.0861.00
113_A117_K1.0781.00
107_K137_M1.0771.00
205_K237_I1.0751.00
212_L223_I1.0701.00
237_I241_A1.0671.00
15_W19_K1.0571.00
221_T231_T1.0421.00
62_G66_A1.0401.00
232_S236_Q1.0401.00
192_I196_A1.0371.00
220_L224_G1.0301.00
50_V93_G1.0301.00
132_A137_M1.0071.00
119_E126_V1.0011.00
122_Y126_V0.9981.00
22_K26_D0.9881.00
220_L235_S0.9871.00
220_L231_T0.9831.00
186_I190_E0.9771.00
44_V49_S0.9771.00
100_L108_T0.9761.00
40_G43_S0.9731.00
98_D105_R0.9671.00
169_N172_V0.9661.00
205_K233_R0.9641.00
26_D29_R0.9621.00
220_L232_S0.9591.00
189_D193_A0.9491.00
206_E237_I0.9451.00
56_M59_G0.9431.00
16_K72_P0.9411.00
31_Y79_D0.9291.00
194_Q197_E0.9291.00
182_P186_I0.9281.00
119_E122_Y0.9281.00
155_L159_E0.9261.00
20_D23_A0.9221.00
65_D69_K0.9221.00
181_P184_E0.9151.00
188_K192_I0.9101.00
118_L131_I0.9061.00
27_L67_L0.9051.00
115_I131_I0.9041.00
16_K19_K0.8961.00
122_Y130_E0.8941.00
65_D89_A0.8941.00
81_Y85_R0.8921.00
87_R91_I0.8881.00
183_E186_I0.8871.00
101_P104_S0.8821.00
243_F247_N0.8811.00
204_E208_L0.8781.00
114_A131_I0.8771.00
209_V229_L0.8721.00
43_S52_K0.8681.00
19_K23_A0.8681.00
157_I171_Q0.8641.00
38_H87_R0.8641.00
16_K20_D0.8621.00
52_K56_M0.8601.00
36_T52_K0.8551.00
205_K209_V0.8511.00
213_F223_I0.8471.00
35_V60_M0.8441.00
93_G97_E0.8331.00
36_T60_M0.8331.00
14_R23_A0.8331.00
230_S233_R0.8321.00
32_M35_V0.8301.00
107_K110_K0.8291.00
122_Y134_E0.8241.00
143_V147_N0.8191.00
211_S216_E0.8181.00
221_T224_G0.8141.00
85_R88_G0.8131.00
60_M64_Y0.8111.00
69_K85_R0.8101.00
15_W18_W0.8071.00
209_V227_L0.8061.00
63_L82_A0.8061.00
184_E187_M0.7991.00
92_D96_K0.7971.00
223_I238_H0.7951.00
238_H241_A0.7920.99
111_V146_M0.7850.99
199_I211_S0.7810.99
170_I174_I0.7730.99
214_Y242_L0.7720.99
213_F220_L0.7630.99
80_T83_S0.7630.99
172_V175_R0.7600.99
42_I90_I0.7600.99
66_A78_F0.7570.99
141_D144_S0.7520.99
197_E200_H0.7390.99
37_Y40_G0.7370.99
193_A197_E0.7310.99
230_S236_Q0.7280.99
119_E125_N0.7280.99
205_K236_Q0.7250.99
142_V146_M0.7240.99
24_G67_L0.7210.99
220_L236_Q0.7200.99
198_K248_L0.7190.99
61_L64_Y0.7180.99
112_E115_I0.7180.99
118_L130_E0.7170.99
144_S147_N0.7160.99
27_L31_Y0.7150.99
88_G95_R0.7150.99
34_L83_S0.7120.99
76_L80_T0.7120.99
206_E241_A0.7100.99
62_G90_I0.7100.99
185_K189_D0.7080.99
95_R102_R0.7070.99
210_V242_L0.7070.99
196_A211_S0.7040.99
108_T145_T0.6990.99
186_I189_D0.6970.99
220_L233_R0.6940.99
187_M191_L0.6900.99
198_K245_L0.6880.99
161_L169_N0.6860.99
37_Y41_R0.6820.98
104_S108_T0.6770.98
170_I173_M0.6740.98
196_A200_H0.6730.98
72_P75_D0.6720.98
88_G92_D0.6700.98
162_H165_D0.6640.98
105_R109_K0.6620.98
123_L126_V0.6620.98
30_R33_P0.6560.98
82_A86_I0.6560.98
70_F74_R0.6550.98
189_D192_I0.6530.98
222_E225_Q0.6530.98
224_G231_T0.6500.98
198_K241_A0.6420.98
182_P185_K0.6420.98
24_G28_M0.6420.98
92_D106_E0.6410.98
213_F231_T0.6350.98
169_N173_M0.6340.98
14_R26_D0.6340.98
33_P36_T0.6330.98
85_R235_S0.6330.98
70_F76_L0.6310.98
109_K112_E0.6300.97
220_L238_H0.6290.97
135_L142_V0.6270.97
205_K229_L0.6270.97
18_W23_A0.6230.97
203_S241_A0.6200.97
132_A135_L0.6200.97
32_M36_T0.6190.97
161_L173_M0.6180.97
229_L233_R0.6180.97
188_K196_A0.6150.97
216_E226_V0.6140.97
161_L172_V0.6130.97
14_R19_K0.6100.97
54_D57_S0.6100.97
50_V55_L0.6060.97
108_T149_G0.6050.97
65_D68_E0.6040.97
115_I125_N0.6030.97
133_E136_G0.6030.97
85_R232_S0.6010.97
32_M56_M0.5990.97
50_V94_L0.5980.97
198_K201_E0.5980.97
231_T236_Q0.5970.97
94_L105_R0.5940.96
195_L198_K0.5930.96
85_R92_D0.5900.96
64_Y67_L0.5890.96
16_K71_D0.5860.96
198_K249_L0.5860.96
34_L80_T0.5860.96
67_L72_P0.5820.96
36_T53_D0.5810.96
223_I227_L0.5780.96
115_I119_E0.5760.96
144_S148_E0.5760.96
36_T39_V0.5760.96
130_E134_E0.5740.96
213_F219_T0.5720.96
199_I203_S0.5710.96
36_T40_G0.5670.95
180_V185_K0.5660.95
114_A122_Y0.5660.95
18_W21_P0.5620.95
91_I102_R0.5610.95
55_L93_G0.5580.95
160_K167_G0.5510.95
242_L246_K0.5500.95
88_G235_S0.5490.95
35_V90_I0.5460.94
203_S237_I0.5430.94
89_A93_G0.5410.94
57_S61_L0.5410.94
18_W22_K0.5410.94
118_L121_R0.5390.94
132_A138_T0.5380.94
62_G82_A0.5360.94
111_V137_M0.5350.94
127_S131_I0.5350.94
15_W23_A0.5330.94
59_G86_I0.5310.94
104_S145_T0.5300.93
128_P135_L0.5290.93
126_V131_I0.5290.93
108_T111_V0.5280.93
21_P24_G0.5260.93
107_K135_L0.5260.93
231_T235_S0.5240.93
58_L97_E0.5220.93
62_G86_I0.5220.93
130_E133_E0.5220.93
156_S161_L0.5190.93
191_L198_K0.5170.93
99_W105_R0.5160.93
223_I234_I0.5160.93
155_L158_D0.5150.92
37_Y57_S0.5140.92
65_D81_Y0.5120.92
142_V148_E0.5120.92
92_D213_F0.5100.92
219_T224_G0.5100.92
168_E172_V0.5070.92
110_K114_A0.5060.92
145_T148_E0.5060.92
103_T106_E0.5030.92
202_L245_L0.5020.91
162_H173_M0.5020.91
183_E191_L0.5010.91
38_H86_I0.5010.91
81_Y84_F0.5010.91
171_Q174_I0.5000.91
225_Q228_N0.5000.91
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  
2a6hF 1 0.9528 100 0.231 Contact Map
1l9zH 1 0.937 100 0.231 Contact Map
4yfkF 1 0.9724 100 0.284 Contact Map
1rp3A 1 0.9213 100 0.42 Contact Map
1l0oC 1 0.2165 100 0.422 Contact Map
3ugoA 1 0.374 99.9 0.562 Contact Map
4nqwA 1 0.5827 99.9 0.589 Contact Map
1or7A 2 0.7205 99.9 0.627 Contact Map
4cxfA 1 0.6063 99.9 0.627 Contact Map
2q1zA 1 0.689 99.9 0.634 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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