GREMLIN Database
RPOH - RNA polymerase sigma factor RpoH
UniProt: P0AGB3 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10897
Length: 284 (237)
Sequences: 7240 (4282)
Seq/√Len: 278.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
142_T146_L3.6951.00
50_A91_R3.5571.00
145_R160_E3.5521.00
148_W156_M3.3731.00
61_V82_G3.1191.00
155_E165_S3.0931.00
237_Q241_R3.0291.00
262_V267_V2.9091.00
141_K160_E2.8791.00
40_K46_D2.8681.00
51_K55_L2.7731.00
138_N160_E2.4231.00
33_E52_T2.4041.00
36_A40_K2.3671.00
242_A259_R2.2411.00
236_S277_K2.1981.00
266_R269_Q2.1921.00
154_V169_R2.1151.00
238_D259_R2.0801.00
60_F102_V2.0791.00
242_A251_S2.0641.00
243_R271_E2.0191.00
164_T167_D2.0151.00
231_G281_A2.0061.00
254_Q258_D1.9901.00
230_Q237_Q1.9611.00
251_S259_R1.9551.00
94_N97_V1.9191.00
241_R246_D1.9071.00
58_L83_N1.8511.00
238_D242_A1.8481.00
238_D260_Y1.8121.00
64_I106_V1.8031.00
260_Y267_V1.7521.00
239_I270_L1.7501.00
92_R104_F1.7381.00
155_E159_R1.7311.00
233_D277_K1.7111.00
81_E116_Y1.7061.00
142_T152_D1.6931.00
141_K145_R1.6871.00
265_E268_R1.6671.00
157_V168_V1.6601.00
52_T56_S1.6401.00
239_I274_A1.6271.00
64_I113_I1.6211.00
135_L171_M1.6191.00
154_V165_S1.6131.00
154_V172_E1.5911.00
100_R103_S1.5521.00
62_V79_I1.5511.00
54_I87_M1.5481.00
135_L157_V1.5271.00
138_N141_K1.5261.00
47_L51_K1.4911.00
65_A79_I1.4891.00
154_V168_V1.4631.00
35_R39_E1.4621.00
42_H96_E1.4481.00
251_S255_E1.4451.00
79_I83_N1.4301.00
65_A113_I1.4031.00
165_S169_R1.4011.00
82_G113_I1.3561.00
142_T148_W1.3501.00
233_D236_S1.3491.00
138_N142_T1.3381.00
266_R270_L1.3161.00
163_V171_M1.3051.00
139_L172_E1.3051.00
135_L161_L1.3021.00
236_S273_N1.2981.00
101_L105_A1.2731.00
138_N161_L1.2731.00
142_T160_E1.2551.00
253_L257_A1.2481.00
183_D196_A1.2471.00
158_A165_S1.2451.00
220_Q224_R1.2451.00
65_A75_Q1.2431.00
240_I278_L1.2351.00
90_V101_L1.2331.00
42_H95_P1.2101.00
163_V168_V1.2081.00
152_D156_M1.2061.00
39_E96_E1.1991.00
158_A168_V1.1961.00
153_E156_M1.1871.00
202_Q205_S1.1841.00
174_R177_A1.1811.00
238_D241_R1.1531.00
54_I90_V1.1371.00
38_A42_H1.1341.00
48_E51_K1.1261.00
89_A105_A1.1191.00
38_A41_L1.1161.00
66_R75_Q1.1031.00
33_E36_A1.1021.00
73_L116_Y1.0691.00
213_E217_W1.0611.00
135_L168_V1.0581.00
242_A256_L1.0581.00
183_D193_Q1.0571.00
270_L274_A1.0541.00
219_E223_N1.0531.00
218_E222_A1.0521.00
48_E52_T1.0461.00
265_E269_Q1.0441.00
222_A226_T1.0441.00
234_E237_Q1.0421.00
137_F141_K1.0371.00
192_S200_Y1.0371.00
61_V86_L1.0301.00
36_A39_E1.0201.00
148_W152_D1.0161.00
40_K52_T1.0121.00
253_L265_E1.0111.00
244_W271_E1.0001.00
41_L45_G0.9971.00
40_K44_H0.9881.00
83_N87_M0.9861.00
52_T55_L0.9861.00
146_L152_D0.9821.00
57_H102_V0.9781.00
124_V127_A0.9711.00
276_K280_A0.9701.00
40_K49_A0.9661.00
142_T157_V0.9581.00
139_L157_V0.9581.00
34_E38_A0.9571.00
85_G89_A0.9451.00
143_K152_D0.9431.00
46_D49_A0.9381.00
208_F213_E0.9371.00
62_V83_N0.9361.00
158_A163_V0.9361.00
254_Q257_A0.9331.00
39_E95_P0.9281.00
235_R270_L0.9261.00
254_Q264_A0.9231.00
69_A75_Q0.9081.00
239_I260_Y0.9071.00
143_K146_L0.9051.00
121_W128_T0.8991.00
227_D230_Q0.8971.00
66_R69_A0.8971.00
253_L268_R0.8911.00
110_K114_H0.8891.00
235_R266_R0.8861.00
75_Q79_I0.8801.00
86_L105_A0.8801.00
216_N220_Q0.8791.00
235_R239_I0.8761.00
64_I110_K0.8731.00
146_L156_M0.8681.00
224_R227_D0.8661.00
239_I262_V0.8641.00
37_L52_T0.8641.00
53_L90_V0.8561.00
243_R256_L0.8541.00
68_Y113_I0.8541.00
50_A90_V0.8471.00
41_L53_L0.8461.00
228_A278_L0.8451.00
253_L264_A0.8441.00
79_I82_G0.8441.00
138_N157_V0.8401.00
39_E44_H0.8301.00
37_L49_A0.8301.00
45_G49_A0.8271.00
58_L61_V0.8271.00
88_K92_R0.8271.00
217_W220_Q0.8251.00
92_R108_W0.8241.00
223_N227_D0.8241.00
135_L172_E0.8220.99
168_V172_E0.8140.99
108_W111_A0.8130.99
62_V75_Q0.8080.99
63_H66_R0.8070.99
167_D170_E0.8070.99
35_R98_G0.8050.99
234_E238_D0.7990.99
203_D206_S0.7990.99
236_S270_L0.7950.99
146_L160_E0.7840.99
32_D36_A0.7790.99
263_S266_R0.7750.99
179_D183_D0.7720.99
104_F108_W0.7670.99
41_L44_H0.7610.99
111_A118_L0.7610.99
180_M184_L0.7590.99
118_L128_T0.7560.99
61_V83_N0.7550.99
229_M241_R0.7530.99
133_R136_F0.7490.99
89_A101_L0.7480.99
226_T241_R0.7470.99
60_F103_S0.7450.99
53_L57_H0.7420.99
130_K171_M0.7380.99
105_A109_I0.7380.99
181_T185_S0.7350.99
37_L41_L0.7310.99
242_A246_D0.7310.99
213_E216_N0.7300.99
142_T156_M0.7280.99
42_H45_G0.7270.99
241_R245_L0.7250.99
108_W268_R0.7250.99
220_Q223_N0.7240.99
253_L266_R0.7150.99
138_N146_L0.7110.99
60_F106_V0.7110.99
117_V128_T0.7060.98
178_Q183_D0.7050.98
39_E42_H0.7030.98
88_K112_E0.7010.98
233_D274_A0.6990.98
33_E37_L0.6910.98
263_S269_Q0.6880.98
108_W265_E0.6880.98
148_W153_E0.6870.98
95_P98_G0.6860.98
253_L269_Q0.6860.98
42_H94_N0.6830.98
136_F139_L0.6800.98
139_L143_K0.6790.98
196_A200_Y0.6790.98
271_E274_A0.6760.98
256_L271_E0.6760.98
63_H67_N0.6740.98
255_E258_D0.6670.98
56_S59_R0.6650.98
143_K151_Q0.6630.98
111_A115_E0.6630.98
115_E119_R0.6610.98
158_A161_L0.6570.98
84_I87_M0.6570.98
181_T184_L0.6570.98
116_Y120_N0.6520.97
243_R253_L0.6480.97
61_V113_I0.6480.97
104_F107_H0.6460.97
99_V103_S0.6450.97
88_K104_F0.6430.97
103_S106_V0.6420.97
59_R62_V0.6400.97
159_R162_G0.6380.97
153_E157_V0.6370.97
62_V76_A0.6340.97
111_A128_T0.6330.97
87_M90_V0.6320.97
240_I275_M0.6280.97
243_R252_T0.6260.97
236_S274_A0.6250.97
219_E222_A0.6240.97
212_I216_N0.6240.97
139_L151_Q0.6230.97
111_A268_R0.6190.96
262_V266_R0.6130.96
179_D182_F0.6130.96
38_A95_P0.6130.96
228_A281_A0.6100.96
168_V171_M0.6090.96
115_E243_R0.6090.96
244_W275_M0.6060.96
58_L62_V0.6050.96
257_A264_A0.6040.96
235_R262_V0.6030.96
114_H128_T0.6020.96
85_G113_I0.6020.96
180_M183_D0.6010.96
257_A265_E0.6000.96
73_L78_L0.6000.96
158_A164_T0.5990.96
152_D157_V0.5990.96
253_L271_E0.5950.96
78_L116_Y0.5930.96
40_K45_G0.5920.95
229_M233_D0.5900.95
161_L168_V0.5900.95
112_E116_Y0.5890.95
221_A228_A0.5880.95
41_L90_V0.5870.95
215_D219_E0.5860.95
126_V130_K0.5860.95
88_K91_R0.5830.95
195_M205_S0.5820.95
214_D217_W0.5820.95
156_M160_E0.5740.95
243_R264_A0.5730.95
35_R42_H0.5720.95
235_R269_Q0.5690.94
142_T145_R0.5690.94
62_V65_A0.5660.94
147_G152_D0.5630.94
38_A90_V0.5630.94
204_K207_N0.5620.94
202_Q206_S0.5610.94
34_E56_S0.5610.94
137_F140_R0.5600.94
134_K137_F0.5590.94
246_D251_S0.5570.94
58_L79_I0.5530.94
228_A274_A0.5530.94
256_L260_Y0.5500.93
115_E127_A0.5500.93
192_S197_P0.5470.93
216_N219_E0.5470.93
129_T134_K0.5470.93
171_M174_R0.5460.93
233_D270_L0.5440.93
127_A268_R0.5440.93
119_R128_T0.5420.93
90_V95_P0.5400.93
128_T268_R0.5400.93
80_Q84_I0.5400.93
44_H49_A0.5400.93
185_S191_D0.5370.93
115_E124_V0.5360.92
122_R126_V0.5330.92
93_F99_V0.5310.92
187_D190_S0.5290.92
225_L228_A0.5290.92
229_M237_Q0.5280.92
57_H61_V0.5280.92
226_T230_Q0.5260.92
197_P202_Q0.5210.91
257_A268_R0.5180.91
185_S193_Q0.5180.91
47_L50_A0.5180.91
122_R131_A0.5170.91
51_K78_L0.5170.91
264_A269_Q0.5170.91
180_M185_S0.5160.91
200_Y205_S0.5160.91
64_I109_I0.5160.91
154_V161_L0.5140.91
34_E100_R0.5130.91
133_R137_F0.5120.91
65_A74_P0.5120.91
135_L138_N0.5090.90
191_D197_P0.5080.90
106_V263_S0.5070.90
186_S200_Y0.5070.90
118_L132_Q0.5060.90
136_F259_R0.5060.90
179_D185_S0.5060.90
197_P201_L0.5050.90
258_D261_G0.5030.90
41_L46_D0.5030.90
85_G109_I0.5030.90
115_E252_T0.5020.90
129_T132_Q0.5000.90
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 0.8908 100 0.243 Contact Map
2a6hF 1 0.919 100 0.244 Contact Map
4yfkF 1 0.9648 100 0.347 Contact Map
1l0oC 1 0.1937 100 0.49 Contact Map
1rp3A 1 0.8028 100 0.524 Contact Map
3ugoA 1 0.3908 100 0.546 Contact Map
4nqwA 1 0.5211 99.9 0.646 Contact Map
1or7A 2 0.6373 99.9 0.682 Contact Map
4cxfA 1 0.5352 99.8 0.688 Contact Map
2q1zA 1 0.6162 99.8 0.696 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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