GREMLIN Database
RPSB - RNA polymerase sigma-B factor
UniProt: P06574 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 262 (231)
Sequences: 7399 (4380)
Seq/√Len: 288.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
125_L129_T3.6701.00
31_Q72_K3.5151.00
128_E141_F3.3231.00
131_R137_E3.2921.00
211_K215_D2.9691.00
124_Q141_F2.9551.00
42_V63_G2.9481.00
136_E146_E2.8281.00
233_I238_V2.7911.00
21_D27_D2.6961.00
32_E36_R2.5531.00
121_A141_F2.3881.00
17_R21_D2.2261.00
216_L230_I2.2131.00
210_E248_K2.1851.00
237_H240_R2.1421.00
135_V150_L2.1271.00
216_L222_K2.0751.00
217_T242_Q2.0471.00
205_V252_A2.0071.00
145_S148_E1.9981.00
212_Q230_I1.9781.00
165_D178_T1.9691.00
225_K229_D1.9611.00
41_L83_E1.9271.00
204_H211_K1.9251.00
75_D78_V1.8091.00
45_L87_I1.7951.00
125_L133_P1.7871.00
222_K230_I1.7811.00
212_Q216_L1.7481.00
213_I241_L1.7431.00
124_Q128_E1.7421.00
39_T64_M1.7281.00
207_S248_K1.7161.00
212_Q231_L1.7141.00
62_V97_F1.6881.00
81_S84_A1.6451.00
213_I245_A1.6421.00
236_M239_S1.6301.00
33_T37_V1.6261.00
231_L238_V1.6111.00
138_I149_V1.6081.00
136_E140_E1.6011.00
135_V153_M1.5891.00
28_E32_E1.5861.00
121_A124_Q1.5691.00
118_I138_I1.5571.00
45_L94_I1.5561.00
73_R85_F1.5291.00
46_A94_I1.5271.00
165_D180_L1.5231.00
135_V146_E1.5151.00
35_V68_L1.5081.00
43_D60_R1.4901.00
222_K226_E1.4901.00
121_A125_L1.4831.00
118_I152_T1.4731.00
60_R64_M1.4671.00
63_G94_I1.4531.00
122_V153_M1.4301.00
125_L131_R1.4171.00
114_L144_V1.4011.00
135_V149_V1.3891.00
207_S210_E1.3771.00
146_E150_L1.3761.00
23_Q77_V1.3611.00
125_L141_F1.3511.00
237_H241_L1.3441.00
71_I82_F1.3311.00
139_A149_V1.3141.00
46_A60_R1.3101.00
210_E244_K1.3081.00
82_F86_A1.2861.00
121_A142_L1.2841.00
113_E117_R1.2761.00
23_Q76_P1.2491.00
139_A146_E1.2421.00
46_A56_H1.2391.00
118_I142_L1.2361.00
214_I249_L1.2321.00
144_V152_T1.2231.00
144_V149_V1.2231.00
22_Y26_Q1.2141.00
194_N198_M1.2011.00
187_E191_E1.1861.00
29_Q32_E1.1781.00
218_Y242_Q1.1651.00
19_I22_Y1.1571.00
42_V67_L1.1531.00
134_K137_E1.1271.00
35_V71_I1.1201.00
114_L152_T1.1091.00
191_E194_N1.0921.00
126_T133_P1.0891.00
118_I149_V1.0851.00
27_D30_A1.0841.00
47_K56_H1.0841.00
208_D211_K1.0811.00
212_Q215_D1.0731.00
241_L245_A1.0731.00
70_A86_A1.0631.00
216_L227_T1.0531.00
20_S77_V1.0531.00
224_Q228_G1.0491.00
196_Q200_Q1.0481.00
133_P137_E1.0481.00
114_L148_E1.0481.00
187_E190_Y1.0341.00
209_R241_L1.0291.00
236_M240_R1.0261.00
19_I23_Q1.0171.00
66_G70_A1.0171.00
54_S97_F1.0101.00
139_A144_V1.0061.00
225_K235_Q0.9971.00
21_D26_Q0.9961.00
21_D30_A0.9801.00
193_V197_L0.9751.00
47_K50_S0.9741.00
192_R196_Q0.9731.00
120_M124_Q0.9531.00
122_V138_I0.9531.00
102_T112_K0.9511.00
224_Q236_M0.9461.00
125_L138_I0.9441.00
224_Q235_Q0.9431.00
29_Q33_T0.9411.00
162_L166_H0.9401.00
17_R20_S0.9391.00
190_Y194_N0.9391.00
210_E241_L0.9381.00
247_K251_E0.9281.00
164_V180_L0.9251.00
198_M201_S0.9251.00
50_S56_H0.9131.00
34_L71_I0.9071.00
60_R63_G0.9051.00
21_D33_T0.9031.00
21_D25_K0.9011.00
224_Q239_S0.9001.00
38_Y83_E0.8981.00
121_A138_I0.8981.00
209_R237_H0.8981.00
45_L91_I0.8891.00
91_I95_K0.8891.00
126_T132_S0.8861.00
129_T133_P0.8841.00
209_R213_I0.8831.00
174_G182_I0.8831.00
150_L154_E0.8821.00
69_G73_R0.8811.00
42_V64_M0.8811.00
33_T36_R0.8801.00
67_L86_A0.8741.00
20_S76_P0.8741.00
18_L33_T0.8721.00
18_L30_A0.8721.00
43_D64_M0.8681.00
69_G93_E0.8641.00
129_T137_E0.8631.00
85_F89_T0.8621.00
217_T227_T0.8561.00
208_D212_Q0.8511.00
225_K228_G0.8471.00
213_I233_I0.8381.00
64_M68_L0.8301.00
73_R89_T0.8291.00
56_H60_R0.8291.00
22_Y34_L0.8251.00
215_D220_Q0.8231.00
188_D191_E0.8221.00
107_V115_G0.8101.00
43_D56_H0.8070.99
114_L117_R0.7960.99
213_I231_L0.7900.99
89_T92_G0.7880.99
126_T129_T0.7870.99
39_T42_V0.7860.99
148_E151_E0.7860.99
97_F101_K0.7820.99
178_T181_D0.7790.99
44_M47_K0.7770.99
20_S25_K0.7750.99
234_S237_H0.7740.99
227_T242_Q0.7710.99
118_I153_M0.7710.99
96_R100_D0.7700.99
203_L215_D0.7630.99
129_T141_F0.7610.99
49_Y94_I0.7590.99
214_I246_V0.7570.99
108_P111_I0.7560.99
70_A82_F0.7530.99
99_R109_R0.7500.99
149_V153_M0.7390.99
242_Q245_A0.7360.99
201_S204_H0.7340.99
34_L38_Y0.7240.99
31_Q71_I0.7230.99
183_V186_Q0.7220.99
23_Q75_D0.7210.99
179_I182_I0.7200.99
112_K116_P0.7190.99
80_K84_A0.7180.99
65_I68_L0.7170.99
22_Y25_K0.7130.99
84_A87_I0.7060.99
114_L142_L0.7050.99
111_I115_G0.7030.99
224_Q240_R0.7030.99
217_T224_Q0.7010.99
20_S23_Q0.6990.99
202_V249_L0.6980.99
209_R233_I0.6980.99
115_G152_T0.6960.98
86_A90_I0.6940.98
103_W107_V0.6930.98
117_R120_M0.6920.98
179_I183_V0.6910.98
168_I182_I0.6910.98
130_Q133_P0.6900.98
200_Q215_D0.6890.98
44_M48_K0.6850.98
125_L137_E0.6790.98
92_G96_R0.6770.98
41_L87_I0.6700.98
40_N43_D0.6700.98
168_I178_T0.6640.98
37_V40_N0.6640.98
76_P79_G0.6630.98
197_L201_S0.6590.98
92_G99_R0.6540.98
26_Q30_A0.6540.98
116_P119_K0.6530.98
209_R240_R0.6520.98
210_E245_A0.6480.98
189_G193_V0.6480.98
218_Y246_V0.6470.98
224_Q237_H0.6430.97
18_L22_Y0.6420.97
152_T155_M0.6400.97
193_V196_Q0.6400.97
234_S240_R0.6370.97
100_D106_H0.6370.97
200_Q204_H0.6360.97
202_V252_A0.6360.97
202_V245_A0.6340.97
169_E182_I0.6330.97
66_G94_I0.6330.97
220_Q230_I0.6320.97
194_N197_L0.6310.97
74_Y78_V0.6290.97
151_E155_M0.6290.97
226_E229_D0.6290.97
118_I144_V0.6290.97
89_T236_M0.6280.97
89_T239_S0.6270.97
169_E172_S0.6240.97
217_T235_Q0.6220.97
119_K122_V0.6210.97
142_L149_V0.6200.97
195_Q202_V0.6190.97
68_L71_I0.6150.97
151_E154_E0.6130.97
207_S245_A0.6130.97
139_A142_L0.6120.97
115_G156_G0.6120.97
69_G72_K0.6110.97
190_Y193_V0.6100.97
41_L84_A0.6070.96
110_R113_E0.6060.96
228_G235_Q0.6050.96
43_D46_A0.6050.96
169_E173_D0.6020.96
180_L183_V0.6020.96
74_Y80_K0.6010.96
39_T43_D0.6010.96
31_Q35_V0.6010.96
39_T60_R0.6000.96
111_I152_T0.5980.96
137_E141_F0.5980.96
28_E31_Q0.5960.96
69_G85_F0.5950.96
233_I237_H0.5940.96
54_S98_L0.5940.96
59_L97_F0.5930.96
217_T223_S0.5930.96
42_V94_I0.5930.96
58_D61_Q0.5910.96
246_V250_R0.5890.96
224_Q242_Q0.5890.96
103_W112_K0.5870.96
63_G90_I0.5870.96
23_Q26_Q0.5860.96
227_T231_L0.5840.96
134_K138_I0.5820.96
122_V132_S0.5810.95
207_S241_L0.5800.95
43_D57_E0.5780.95
163_S166_H0.5780.95
46_A59_L0.5740.95
22_Y30_A0.5710.95
181_D184_G0.5700.95
19_I76_P0.5670.95
168_I181_D0.5670.95
96_R217_T0.5620.95
103_W108_P0.5610.95
22_Y27_D0.5590.94
105_V161_A0.5590.94
89_T96_R0.5540.94
235_Q240_R0.5530.94
139_A145_S0.5490.94
115_G118_I0.5470.94
244_K247_K0.5430.94
44_M61_Q0.5430.94
117_R121_A0.5350.93
202_V205_V0.5340.93
154_E157_K0.5340.93
206_L249_L0.5330.93
54_S59_L0.5330.93
133_P138_I0.5280.93
228_G236_M0.5280.93
135_V142_L0.5260.92
162_L165_D0.5260.92
121_A129_T0.5260.92
92_G239_S0.5250.92
71_I76_P0.5250.92
140_E143_D0.5250.92
199_L202_V0.5240.92
43_D47_K0.5240.92
149_V152_T0.5230.92
62_V101_K0.5220.92
164_V183_V0.5210.92
149_V155_M0.5170.92
178_T182_I0.5170.92
229_D232_G0.5150.92
19_I71_I0.5100.91
42_V71_I0.5100.91
66_G86_A0.5080.91
61_Q65_I0.5080.91
137_E140_E0.5040.91
42_V90_I0.5030.91
168_I174_G0.5030.91
227_T238_V0.5010.91
98_L112_K0.5000.90
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  
2a6hF 1 0.9618 100 0.228 Contact Map
1l9zH 1 0.9466 100 0.228 Contact Map
4yfkF 1 0.9771 100 0.287 Contact Map
1l0oC 1 0.2176 100 0.425 Contact Map
1rp3A 1 0.8702 100 0.477 Contact Map
3ugoA 1 0.3931 100 0.536 Contact Map
4nqwA 1 0.5649 99.9 0.618 Contact Map
4cxfA 1 0.5878 99.9 0.657 Contact Map
1or7A 2 0.7023 99.9 0.658 Contact Map
2q1zA 1 0.6679 99.9 0.661 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.

Page generated in 0.0088 seconds.