GREMLIN Database
RPSH - RNA polymerase sigma-H factor
UniProt: P17869 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 218 (191)
Sequences: 8606 (5179)
Seq/√Len: 374.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
35_L76_R3.7491.00
46_V67_G3.0291.00
170_R174_V2.9611.00
175_L188_E2.9111.00
26_K31_D2.8311.00
36_D40_T2.6361.00
175_L180_R2.5441.00
22_Q26_K2.4521.00
164_L210_Y2.4021.00
191_R196_I2.3301.00
176_Y200_L2.3171.00
180_R188_E2.2201.00
169_E206_K2.2141.00
37_Y41_K2.2111.00
195_S198_N2.1661.00
19_E37_Y2.0611.00
171_K175_L2.0451.00
66_E101_A1.9901.00
43_R68_M1.9181.00
49_K91_E1.8941.00
25_E29_V1.8871.00
130_R135_V1.8831.00
171_K188_E1.8791.00
183_Q187_D1.8211.00
79_K82_K1.8191.00
85_S88_A1.8121.00
45_F87_K1.7871.00
171_K189_L1.7821.00
64_V68_M1.7711.00
194_K197_D1.7511.00
166_S206_K1.6831.00
145_E149_I1.6751.00
172_V203_V1.6351.00
21_E25_E1.6231.00
32_S36_D1.6121.00
172_V199_A1.5891.00
50_A98_I1.5651.00
49_K98_I1.5631.00
180_R184_E1.5571.00
74_S90_A1.5431.00
169_E202_R1.4921.00
39_I72_Y1.4871.00
50_A60_R1.4821.00
166_S169_E1.4651.00
195_S199_A1.4651.00
47_R64_V1.4611.00
163_E170_R1.4501.00
175_L185_I1.4201.00
131_T135_V1.4141.00
173_L207_L1.4071.00
189_L196_I1.3681.00
50_A64_V1.3621.00
86_F90_A1.3611.00
138_G141_T1.3601.00
24_I27_V1.3471.00
77_D89_F1.3291.00
130_R134_D1.3291.00
131_T134_D1.3151.00
28_H80_E1.2701.00
75_I86_F1.2531.00
67_G98_I1.2391.00
109_K112_P1.2381.00
28_H81_D1.2331.00
33_D36_D1.2291.00
171_K174_V1.2281.00
177_L200_L1.1971.00
19_E22_Q1.1931.00
23_V37_Y1.1921.00
51_R60_R1.1751.00
26_K29_V1.1711.00
132_L135_V1.1681.00
46_V71_L1.1541.00
168_L199_A1.1531.00
151_Q155_D1.1521.00
49_K95_T1.1501.00
199_A203_V1.1351.00
28_H79_K1.1121.00
194_K198_N1.1001.00
152_E156_D1.0961.00
183_Q193_V1.0941.00
129_D135_V1.0941.00
73_K97_Q1.0901.00
31_D34_A1.0861.00
93_C96_R1.0791.00
122_P126_E1.0711.00
182_Y186_S1.0681.00
58_A101_A1.0671.00
89_F93_C1.0501.00
162_G170_R1.0451.00
51_R54_F1.0391.00
176_Y185_I1.0351.00
24_I28_H1.0341.00
168_L172_V1.0321.00
84_T88_A1.0231.00
154_F158_E1.0211.00
95_T99_I1.0171.00
182_Y197_D1.0161.00
122_P125_D1.0111.00
70_G98_I0.9961.00
149_I152_E0.9861.00
64_V67_G0.9721.00
22_Q25_E0.9681.00
177_L204_K0.9681.00
71_L90_A0.9651.00
73_K77_D0.9551.00
77_D93_C0.9511.00
39_I75_I0.9501.00
47_R60_R0.9481.00
205_R209_K0.9471.00
70_G74_S0.9471.00
167_D171_K0.9441.00
37_Y40_T0.9441.00
129_D132_L0.9391.00
185_I200_L0.9321.00
182_Y194_K0.9301.00
167_D170_R0.9221.00
147_M151_Q0.9211.00
200_L203_V0.9191.00
172_V189_L0.9151.00
26_K34_A0.9071.00
54_F60_R0.9061.00
25_E81_D0.8971.00
160_K163_E0.8961.00
123_I126_E0.8951.00
68_M72_Y0.8911.00
47_R68_M0.8891.00
48_A51_R0.8871.00
38_L75_I0.8871.00
116_Y120_D0.8851.00
169_E199_A0.8771.00
33_D37_Y0.8741.00
143_N146_E0.8701.00
152_E155_D0.8681.00
74_S86_F0.8661.00
121_K125_D0.8641.00
142_L147_M0.8621.00
27_V30_G0.8611.00
25_E80_E0.8611.00
161_M207_L0.8551.00
53_Y98_I0.8471.00
101_A105_A0.8441.00
23_V34_A0.8381.00
142_L150_N0.8281.00
146_E149_I0.8141.00
119_L122_P0.8131.00
182_Y193_V0.8111.00
90_A94_I0.8091.00
168_L191_R0.8041.00
114_N118_S0.8011.00
30_G34_A0.7931.00
174_V178_D0.7901.00
144_P147_M0.7891.00
125_D128_S0.7881.00
46_V68_M0.7871.00
144_P148_I0.7841.00
173_L204_K0.7831.00
27_V38_L0.7811.00
43_R47_R0.7791.00
69_I72_Y0.7781.00
176_Y182_Y0.7741.00
45_F91_E0.7721.00
27_V34_A0.7721.00
151_Q154_F0.7671.00
162_G174_V0.7671.00
168_L195_S0.7651.00
80_E83_L0.7591.00
117_A121_K0.7561.00
20_D41_K0.7521.00
26_K37_Y0.7501.00
148_I151_Q0.7491.00
153_E157_I0.7481.00
192_H195_S0.7441.00
121_K124_F0.7431.00
182_Y198_N0.7391.00
142_L146_E0.7371.00
183_Q186_S0.7361.00
35_L75_I0.7321.00
162_G166_S0.7311.00
133_L136_I0.7301.00
186_S193_V0.7301.00
169_E203_V0.7271.00
149_I153_E0.7241.00
47_R50_A0.7211.00
20_D24_I0.7211.00
123_I127_E0.7161.00
144_P149_I0.7131.00
132_L136_I0.7131.00
23_V27_V0.7101.00
44_N47_R0.7070.99
118_S121_K0.7030.99
161_M164_L0.6990.99
114_N117_A0.6970.99
118_S122_P0.6940.99
154_F157_I0.6930.99
24_I80_E0.6920.99
66_E97_Q0.6920.99
146_E150_N0.6800.99
38_L42_Y0.6760.99
147_M150_N0.6710.99
28_H31_D0.6660.99
106_T113_L0.6630.99
131_T136_I0.6620.99
161_M211_L0.6620.99
141_T150_N0.6590.99
42_Y87_K0.6540.99
27_V31_D0.6530.99
48_A52_S0.6510.99
140_K150_N0.6490.99
132_L137_S0.6480.99
166_S203_V0.6450.99
45_F94_I0.6450.99
43_R46_V0.6430.99
60_R64_V0.6420.99
62_D65_Q0.6400.99
192_H198_N0.6390.99
148_I152_E0.6340.99
78_F82_K0.6240.99
150_N154_F0.6210.99
172_V191_R0.6190.99
100_T104_T0.6180.99
134_D137_S0.6130.99
58_A105_A0.6110.99
96_R100_T0.6100.99
93_C100_T0.6090.99
25_E28_H0.6080.98
182_Y200_L0.6070.98
185_I188_E0.6060.98
129_D133_L0.6030.98
97_Q101_A0.6020.98
185_I196_I0.5980.98
35_L39_I0.5970.98
58_A102_I0.5960.98
19_E41_K0.5960.98
102_I113_L0.5950.98
156_D160_K0.5950.98
143_N147_M0.5930.98
78_F84_T0.5920.98
131_T137_S0.5910.98
137_S140_K0.5890.98
161_M210_Y0.5820.98
46_V50_A0.5810.98
72_Y75_I0.5790.98
124_F128_S0.5760.98
142_L145_E0.5750.98
46_V94_I0.5750.98
115_S118_S0.5640.98
204_K208_E0.5620.97
23_V26_K0.5590.97
21_E24_I0.5580.97
58_A63_I0.5570.97
61_E68_M0.5550.97
88_A91_E0.5550.97
141_T147_M0.5540.97
43_R64_V0.5510.97
47_R51_R0.5510.97
176_Y181_S0.5510.97
153_E156_D0.5500.97
160_K164_L0.5450.97
176_Y193_V0.5440.97
145_E150_N0.5410.97
70_G97_Q0.5400.97
21_E83_L0.5390.97
70_G93_C0.5360.97
46_V75_I0.5350.97
158_E174_V0.5300.96
92_L95_T0.5190.96
186_S194_K0.5190.96
70_G94_I0.5180.96
134_D138_G0.5160.96
120_D123_I0.5130.96
20_D27_V0.5120.96
199_A202_R0.5120.96
130_R133_L0.5110.96
116_Y119_L0.5110.96
117_A125_D0.5110.96
165_L203_V0.5090.96
95_T98_I0.5080.95
42_Y71_L0.5080.95
103_K113_L0.5070.95
140_K147_M0.5060.95
181_S184_E0.5050.95
202_R206_K0.5050.95
143_N148_I0.5020.95
22_Q33_D0.5020.95
107_R116_Y0.5000.95
50_A63_I0.5000.95
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 0.9679 100 0.223 Contact Map
2a6hF 1 0.9725 100 0.224 Contact Map
4yfkF 1 0.9954 100 0.303 Contact Map
3ugoA 1 0.4908 100 0.449 Contact Map
1l0oC 1 0.1055 100 0.455 Contact Map
1rp3A 1 0.8394 99.9 0.506 Contact Map
4nqwA 1 0.6743 99.9 0.53 Contact Map
4cxfA 1 0.7018 99.9 0.57 Contact Map
1or7A 2 0.8394 99.9 0.57 Contact Map
2q1zA 1 0.7982 99.9 0.578 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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