GREMLIN Database
RPSG - RNA polymerase sigma-G factor
UniProt: P19940 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 260 (231)
Sequences: 7453 (4464)
Seq/√Len: 293.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
133_L137_T3.6961.00
40_R81_D3.5111.00
139_K145_D3.2121.00
136_E149_V3.1821.00
51_V72_G3.0011.00
216_K220_R2.9471.00
132_R149_V2.9221.00
144_E154_H2.8331.00
30_Q36_D2.7201.00
238_I243_V2.6701.00
41_E45_N2.5761.00
195_D199_I2.5071.00
129_V149_V2.3741.00
26_K30_Q2.2271.00
221_K235_E2.2271.00
242_Q245_R2.1631.00
143_A158_V2.1551.00
215_E253_Q2.1301.00
210_R257_N2.1261.00
221_K227_K2.1131.00
222_R247_E2.0431.00
217_M235_E1.9891.00
50_L92_S1.9631.00
153_P156_E1.9581.00
230_M234_E1.9241.00
209_R216_K1.9161.00
84_D87_H1.8781.00
171_F183_Y1.8101.00
54_V96_V1.7821.00
227_K235_E1.7741.00
133_L141_P1.7711.00
48_L73_C1.7661.00
217_M221_K1.7431.00
132_R136_E1.7271.00
217_M236_I1.7191.00
71_V106_Y1.6881.00
218_I246_L1.6871.00
241_A244_S1.6801.00
143_A161_L1.6721.00
42_K46_G1.6621.00
212_N253_Q1.6611.00
218_I250_A1.6441.00
90_K93_T1.6151.00
236_I243_V1.6021.00
37_D41_E1.6001.00
144_E148_K1.5961.00
54_V103_I1.5951.00
146_I157_I1.5921.00
55_I103_I1.5621.00
129_V132_R1.5431.00
143_A154_H1.5391.00
129_V133_L1.5381.00
69_F73_C1.5351.00
126_A146_I1.5311.00
82_N94_Y1.5101.00
195_D200_E1.5011.00
52_L69_F1.4781.00
143_A157_I1.4671.00
227_K231_E1.4531.00
126_A160_A1.4511.00
72_G103_I1.4441.00
25_R29_R1.4301.00
44_V77_M1.4301.00
122_I152_V1.4291.00
154_H158_V1.3941.00
130_R161_L1.3871.00
212_N215_E1.3721.00
242_Q246_L1.3671.00
32_Q86_S1.3551.00
133_L139_K1.3251.00
133_L149_V1.3221.00
171_F185_M1.3181.00
80_I91_F1.3161.00
91_F95_A1.3061.00
55_I69_F1.2941.00
111_N120_R1.2771.00
121_D125_K1.2691.00
147_A154_H1.2651.00
129_V150_L1.2601.00
215_E249_A1.2531.00
147_A157_I1.2531.00
32_Q85_L1.2351.00
55_I65_V1.2271.00
219_L254_M1.2141.00
152_V157_I1.2011.00
51_V76_L1.1901.00
196_S200_E1.1901.00
122_I160_A1.1881.00
152_V160_A1.1871.00
126_A150_L1.1561.00
223_F247_E1.1451.00
38_S41_E1.1441.00
142_T145_D1.1271.00
221_K232_V1.1151.00
122_I156_E1.0961.00
246_L250_A1.0951.00
56_Q65_V1.0951.00
141_P145_D1.0941.00
213_D216_K1.0811.00
229_Q233_A1.0791.00
147_A152_V1.0761.00
28_F31_L1.0681.00
44_V80_I1.0611.00
180_D187_Q1.0591.00
134_I141_P1.0541.00
29_R86_S1.0511.00
56_Q59_N1.0461.00
79_S95_A1.0451.00
241_A245_R1.0321.00
217_M220_R1.0311.00
214_R246_L1.0231.00
38_S42_K1.0231.00
28_F32_Q1.0221.00
63_E106_Y1.0211.00
126_A157_I1.0201.00
75_G79_S1.0101.00
30_Q39_A0.9971.00
230_M240_Q0.9841.00
43_L80_I0.9731.00
30_Q34_E0.9701.00
229_Q241_A0.9691.00
229_Q244_S0.9671.00
26_K29_R0.9621.00
196_S199_I0.9601.00
30_Q42_K0.9481.00
130_R146_I0.9321.00
229_Q240_Q0.9291.00
31_L35_G0.9251.00
133_L146_I0.9201.00
51_V73_C0.9101.00
128_Q132_R0.9091.00
78_K82_N0.9051.00
215_E246_L0.9031.00
195_D198_W0.9021.00
252_K256_K0.9001.00
59_N65_V0.8991.00
222_R232_V0.8981.00
69_F72_G0.8931.00
115_V123_A0.8881.00
214_R242_Q0.8861.00
201_E205_K0.8861.00
27_L42_K0.8841.00
100_I104_R0.8831.00
170_L185_M0.8811.00
78_K102_E0.8781.00
29_R85_L0.8731.00
214_R218_I0.8711.00
54_V100_I0.8711.00
134_I140_E0.8701.00
183_Y186_D0.8691.00
129_V146_I0.8631.00
189_S192_R0.8621.00
230_M233_A0.8591.00
47_N92_S0.8591.00
42_K45_N0.8571.00
137_T141_P0.8551.00
213_D217_M0.8511.00
194_T197_Q0.8491.00
31_L43_L0.8481.00
197_Q200_E0.8451.00
208_M220_R0.8381.00
218_I238_I0.8371.00
29_R34_E0.8361.00
52_L73_C0.8361.00
73_C77_M0.8311.00
65_V69_F0.8301.00
98_M101_G0.8301.00
137_T145_D0.8291.00
94_Y98_M0.8271.00
168_V172_E0.8191.00
158_V162_D0.8181.00
239_S242_Q0.8041.00
82_N98_M0.8031.00
35_G39_A0.8010.99
106_Y110_N0.8000.99
52_L65_V0.7980.99
116_S119_L0.7960.99
53_S56_Q0.7950.99
220_R225_Q0.7910.99
156_E159_F0.7830.99
134_I137_T0.7810.99
40_R80_I0.7750.99
218_I236_I0.7740.99
27_L39_A0.7730.99
232_V247_E0.7730.99
126_A161_L0.7720.99
76_L95_A0.7700.99
48_L51_V0.7700.99
105_R109_D0.7590.99
222_R229_Q0.7490.99
25_R88_N0.7490.99
123_A160_A0.7460.99
190_D193_N0.7370.99
223_F251_I0.7360.99
79_S91_F0.7360.99
108_R117_R0.7320.99
247_E250_A0.7320.99
203_A206_E0.7320.99
43_L47_N0.7290.99
58_F103_I0.7280.99
167_P171_F0.7270.99
32_Q84_D0.7240.99
32_Q35_G0.7220.99
219_L251_I0.7180.99
125_K128_Q0.7180.99
89_V93_T0.7150.99
109_D114_R0.7130.99
138_S141_P0.7120.99
137_T149_V0.7120.99
31_L34_E0.7110.99
50_L96_V0.7080.99
231_E234_E0.7030.99
169_S173_P0.7020.99
133_L145_D0.7010.99
36_D39_A0.6990.99
53_S57_R0.6990.99
157_I161_L0.6990.99
207_G254_M0.6940.99
95_A99_I0.6930.99
123_A164_I0.6930.99
93_T96_V0.6880.98
239_S245_R0.6870.98
122_I125_K0.6860.98
120_R124_Y0.6840.98
206_E209_R0.6810.98
229_Q245_R0.6810.98
215_E250_A0.6800.98
183_Y187_Q0.6790.98
122_I150_L0.6780.98
207_G257_N0.6720.98
124_Y127_L0.6720.98
118_S121_D0.6710.98
29_R32_Q0.6680.98
207_G250_A0.6670.98
83_F87_H0.6610.98
67_D70_Q0.6570.98
101_G108_R0.6560.98
229_Q242_Q0.6560.98
119_L123_A0.6550.98
214_R245_R0.6530.98
27_L31_L0.6510.98
74_I77_M0.6500.98
229_Q247_E0.6420.98
63_E107_L0.6410.98
214_R238_I0.6370.97
205_K220_R0.6360.97
83_F89_V0.6360.97
204_L207_G0.6340.97
159_F163_A0.6330.97
101_G105_R0.6330.97
169_S172_E0.6320.97
34_E39_A0.6310.97
205_K209_R0.6310.97
25_R32_Q0.6300.97
126_A152_V0.6290.97
159_F162_D0.6270.97
46_G49_R0.6220.97
145_D149_V0.6200.97
148_K151_E0.6190.97
85_L88_N0.6180.97
125_K129_V0.6180.97
40_R44_V0.6140.97
222_R240_Q0.6110.97
49_R52_L0.6100.97
48_L69_F0.6080.97
147_A150_L0.6080.97
233_A240_Q0.6050.97
75_G103_I0.6030.97
130_R140_E0.6030.97
77_M80_I0.6020.96
225_Q235_E0.5990.96
238_I242_Q0.5950.96
37_D40_R0.5950.96
166_D171_F0.5940.96
207_G210_R0.5940.96
98_M244_S0.5930.96
52_L55_I0.5880.96
141_P146_I0.5870.96
98_M241_A0.5860.96
68_L106_Y0.5830.96
104_R117_R0.5810.96
78_K81_D0.5800.96
174_I180_D0.5800.96
50_L93_T0.5800.96
232_V236_I0.5790.96
184_V188_I0.5780.96
127_L130_R0.5770.96
147_A153_P0.5760.95
175_Y187_Q0.5760.95
160_A163_A0.5750.95
48_L52_L0.5740.95
191_E197_Q0.5730.95
212_N250_A0.5730.95
142_T146_I0.5720.95
70_Q74_I0.5710.95
150_L157_I0.5700.95
222_R228_T0.5700.95
173_P179_G0.5680.95
211_L254_M0.5620.95
53_S70_Q0.5600.95
119_L160_A0.5590.95
232_V243_V0.5570.95
32_Q36_D0.5560.95
174_I187_Q0.5550.95
52_L66_D0.5520.94
240_Q245_R0.5520.94
78_K94_Y0.5520.94
130_R141_P0.5490.94
28_F85_L0.5470.94
105_R222_R0.5470.94
168_V171_F0.5460.94
51_V103_I0.5440.94
110_N116_S0.5430.94
98_M105_R0.5380.94
251_I255_N0.5380.94
71_V110_N0.5370.94
175_Y178_G0.5350.93
105_R117_R0.5330.93
31_L36_D0.5320.93
72_G99_I0.5290.93
28_F80_I0.5260.93
52_L56_Q0.5260.93
63_E68_L0.5250.93
47_N50_L0.5220.93
107_L120_R0.5220.93
192_R195_D0.5220.93
234_E237_G0.5220.93
174_I183_Y0.5210.92
233_A241_A0.5200.92
101_G244_S0.5190.92
249_A252_K0.5170.92
51_V99_I0.5160.92
202_L206_E0.5140.92
211_L250_A0.5130.92
123_A126_A0.5120.92
84_D88_N0.5120.92
80_I85_L0.5100.92
184_V187_Q0.5100.92
212_N246_L0.5060.91
185_M188_I0.5060.91
228_T233_A0.5050.91
75_G95_A0.5050.91
208_M212_N0.5030.91
157_I160_A0.5010.91
113_I167_P0.5010.91
162_D165_Q0.5000.91
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  
1l9zH 1 0.9462 100 0.225 Contact Map
2a6hF 1 0.9692 100 0.227 Contact Map
4yfkF 1 0.9885 100 0.32 Contact Map
1l0oC 1 0.2192 100 0.41 Contact Map
1rp3A 1 0.8577 100 0.48 Contact Map
3ugoA 1 0.4192 100 0.519 Contact Map
4nqwA 1 0.5692 99.9 0.615 Contact Map
1or7A 2 0.6962 99.9 0.654 Contact Map
4cxfA 1 0.5846 99.9 0.655 Contact Map
2q1zA 1 0.6731 99.9 0.658 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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