GREMLIN Database
RPOS - RNA polymerase sigma factor RpoS
UniProt: P13445 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10510
Length: 330 (271)
Sequences: 4549 (2024)
Seq/√Len: 122.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
271_R275_A4.4221.00
75_E93_R3.7981.00
196_E206_V3.6561.00
297_L302_V3.4671.00
82_R87_D3.3951.00
102_V123_G3.3401.00
185_L189_L3.2261.00
191_H197_E3.0321.00
223_D233_A2.9311.00
272_E295_I2.7951.00
101_L143_S2.7611.00
92_R96_E2.7581.00
78_Y82_R2.6091.00
61_Y124_N2.5861.00
301_R304_Q2.5481.00
276_R294_E2.4871.00
300_E303_R2.4511.00
272_E294_E2.4281.00
277_R306_Q2.4241.00
247_E251_Q2.4181.00
270_Q312_R2.3331.00
295_I302_V2.3061.00
65_I103_V2.2701.00
276_R286_A2.2681.00
91_R132_E2.1491.00
289_E293_R2.1261.00
275_A281_L2.0801.00
267_N312_R2.0381.00
72_T75_E2.0011.00
84_L137_E1.9911.00
184_E201_Q1.9341.00
73_A77_V1.9011.00
178_Y202_L1.8971.00
178_Y198_I1.8631.00
188_K201_Q1.8621.00
81_R137_E1.8191.00
129_R133_K1.8151.00
232_K237_I1.8051.00
84_L136_P1.7801.00
264_F271_R1.7751.00
77_V81_R1.7731.00
70_L100_R1.7351.00
198_I209_V1.7251.00
272_E276_R1.6751.00
61_Y76_E1.6741.00
105_I147_T1.6701.00
95_I128_I1.6531.00
101_L144_T1.6411.00
71_L76_E1.6321.00
130_A146_A1.6271.00
135_D138_R1.5931.00
205_P208_D1.5911.00
68_S97_S1.5901.00
300_E304_Q1.5641.00
185_L191_H1.5611.00
301_R305_I1.5191.00
286_A294_E1.5001.00
178_Y181_T1.4861.00
93_R97_S1.4601.00
181_T201_Q1.4481.00
181_T185_L1.4371.00
131_V142_F1.4331.00
256_K260_V1.4321.00
223_D235_L1.4271.00
62_L103_V1.4141.00
195_A210_S1.4081.00
99_L124_N1.4071.00
189_L197_E1.4051.00
288_L300_E1.3861.00
195_A206_V1.3761.00
95_I131_V1.3381.00
273_V309_G1.3371.00
274_L313_L1.3301.00
60_L64_E1.3241.00
88_V92_R1.3221.00
251_Q254_D1.3221.00
199_A209_V1.3221.00
61_Y65_I1.3001.00
58_T120_I1.2961.00
62_L65_I1.2951.00
130_A142_F1.2921.00
250_T254_D1.2871.00
265_E318_Q1.2841.00
122_E157_A1.2751.00
282_G286_A1.2741.00
288_L303_R1.2681.00
315_E318_Q1.2671.00
179_L183_R1.2671.00
193_P197_E1.2541.00
81_R136_P1.2480.99
174_E208_D1.2480.99
103_V120_I1.2460.99
101_L147_T1.2150.99
82_R90_S1.2130.99
181_T202_L1.2040.99
195_A213_L1.2020.99
114_L157_A1.1900.99
94_M131_V1.1870.99
91_R131_V1.1790.99
182_A213_L1.1780.99
268_A271_R1.1770.99
185_L197_E1.1750.99
82_R93_R1.1730.99
178_Y182_A1.1700.99
104_K107_R1.1600.99
185_L198_I1.1540.99
196_E200_E1.1540.99
273_V305_I1.1400.99
62_L66_G1.1280.99
289_E298_T1.1240.99
104_K121_E1.1210.99
288_L306_Q1.1210.99
76_E80_A1.1100.99
270_Q308_E1.0970.99
165_I219_I1.0940.99
133_K145_Y1.0910.99
70_L76_E1.0890.99
267_N270_Q1.0710.98
268_A272_E1.0640.98
288_L292_G1.0610.98
185_L193_P1.0590.98
142_F146_A1.0390.98
289_E299_R1.0300.98
226_L237_I1.0280.98
83_A86_G1.0210.98
204_K209_V1.0200.98
254_D258_S1.0100.98
87_D90_S1.0060.98
184_E188_K1.0040.98
174_E212_M1.0020.98
249_T253_D1.0010.98
253_D257_Q0.9990.98
288_L301_R0.9880.97
288_L304_Q0.9870.97
98_N143_S0.9850.97
289_E292_G0.9830.97
286_A290_D0.9830.97
171_I212_M0.9780.97
172_V176_N0.9750.97
194_S197_E0.9550.97
278_F310_L0.9520.97
131_V247_E0.9490.97
178_Y212_M0.9490.97
156_R173_K0.9480.97
260_V275_A0.9470.97
265_E316_I0.9430.97
149_W303_R0.9360.96
103_V124_N0.9350.96
246_P250_T0.9350.96
106_A120_I0.9270.96
61_Y70_L0.9260.96
123_G154_I0.9260.96
65_I68_S0.9220.96
89_A92_R0.9220.96
199_A206_V0.9200.96
143_S156_R0.9150.96
167_L171_I0.9120.96
144_T147_T0.9040.96
206_V210_S0.9030.96
79_F90_S0.8890.95
195_A209_V0.8860.95
120_I124_N0.8820.95
56_D76_E0.8810.95
84_L135_D0.8720.95
269_K301_R0.8650.94
167_L175_L0.8610.94
79_F83_A0.8600.94
75_E78_Y0.8580.94
68_S96_E0.8560.94
83_A142_F0.8550.94
89_A93_R0.8530.94
149_W300_E0.8520.94
308_E311_R0.8520.94
51_T54_V0.8480.94
69_P75_E0.8480.94
70_L98_N0.8480.94
288_L299_R0.8460.94
76_E141_R0.8460.94
81_R84_L0.8380.93
110_G116_L0.8330.93
190_D193_P0.8300.93
208_D211_R0.8300.93
287_T298_T0.8280.93
140_F144_T0.8220.93
104_K108_R0.8220.93
171_I175_L0.8210.93
115_A157_A0.8130.92
122_E161_Q0.8090.92
151_R155_E0.8090.92
168_P278_F0.8080.92
259_I262_W0.8080.92
258_S261_K0.8040.92
141_R144_T0.8020.92
147_T151_R0.8020.92
273_V295_I0.8020.92
291_V295_I0.8010.92
105_I154_I0.8010.92
152_Q156_R0.7960.92
305_I308_E0.7920.91
181_T184_E0.7910.91
267_N305_I0.7890.91
82_R85_R0.7860.91
289_E297_L0.7800.91
234_L237_I0.7800.91
86_G90_S0.7790.91
185_L201_Q0.7760.90
291_V306_Q0.7740.90
222_V235_L0.7740.90
173_K177_V0.7720.90
91_R95_I0.7720.90
61_Y66_G0.7710.90
107_R116_L0.7680.90
71_L79_F0.7650.90
198_I201_Q0.7650.90
175_L212_M0.7640.90
125_L128_I0.7630.90
170_H173_K0.7630.90
298_T301_R0.7600.90
245_G249_T0.7600.90
269_K304_Q0.7600.90
61_Y99_L0.7590.89
111_N114_L0.7580.89
50_A53_R0.7560.89
56_D59_Q0.7560.89
263_L271_R0.7560.89
141_R160_N0.7540.89
160_N166_R0.7530.89
269_K300_E0.7520.89
77_V137_E0.7460.89
186_S193_P0.7450.89
245_G250_T0.7390.88
74_E78_Y0.7380.88
202_L209_V0.7280.87
155_E173_K0.7230.87
240_D243_E0.7220.87
263_L275_A0.7210.87
152_Q170_H0.7210.87
259_I278_F0.7100.86
262_W265_E0.7070.86
189_L193_P0.7040.86
121_E298_T0.7020.85
169_I298_T0.7000.85
80_A136_P0.6990.85
83_A131_V0.6990.85
80_A94_M0.6980.85
61_Y80_A0.6970.85
143_S147_T0.6970.85
99_L103_V0.6950.85
174_E177_V0.6930.85
292_G303_R0.6930.85
198_I203_D0.6920.85
157_A161_Q0.6890.84
226_L232_K0.6880.84
260_V281_L0.6870.84
209_V212_M0.6830.84
226_L236_D0.6830.84
197_E201_Q0.6820.84
241_E249_T0.6800.84
225_P231_E0.6770.83
149_W152_Q0.6750.83
61_Y71_L0.6730.83
58_T66_G0.6720.83
148_W151_R0.6710.83
108_R142_F0.6700.83
121_E153_T0.6690.83
114_L158_I0.6680.83
284_E294_E0.6650.82
102_V154_I0.6640.82
107_R110_G0.6640.82
162_T172_V0.6620.82
107_R142_F0.6620.82
79_F93_R0.6610.82
103_V117_L0.6570.82
272_E275_A0.6550.81
159_M169_I0.6550.81
292_G298_T0.6510.81
81_R85_R0.6500.81
113_G162_T0.6490.81
135_D139_G0.6480.81
156_R170_H0.6450.80
156_R160_N0.6440.80
56_D61_Y0.6440.80
148_W153_T0.6410.80
129_R153_T0.6410.80
182_A185_L0.6400.80
155_E169_I0.6390.80
133_K173_K0.6380.80
220_T223_D0.6380.80
141_R159_M0.6370.80
159_M173_K0.6330.79
63_G68_S0.6310.79
109_Y154_I0.6300.79
135_D221_S0.6280.79
109_Y151_R0.6260.78
136_P139_G0.6230.78
277_R291_V0.6220.78
71_L97_S0.6220.78
58_T116_L0.6200.78
178_Y213_L0.6190.78
254_D257_Q0.6170.77
102_V150_I0.6160.77
100_R103_V0.6140.77
152_Q168_P0.6090.76
289_E302_V0.6080.76
215_L291_V0.6060.76
171_I178_Y0.6050.76
284_E290_D0.6030.76
80_A83_A0.6020.76
288_L298_T0.6000.75
58_T117_L0.6000.75
147_T298_T0.5990.75
280_L283_Y0.5990.75
156_R287_T0.5980.75
261_K264_F0.5960.75
156_R169_I0.5940.75
292_G300_E0.5930.75
50_A198_I0.5920.74
275_A280_L0.5910.74
57_A60_L0.5900.74
108_R170_H0.5870.74
94_M169_I0.5850.74
129_R132_E0.5820.73
199_A204_K0.5820.73
101_L156_R0.5790.73
78_Y81_R0.5780.73
187_H190_D0.5770.73
177_V180_R0.5760.72
245_G248_D0.5760.72
155_E170_H0.5750.72
298_T304_Q0.5740.72
277_R288_L0.5730.72
125_L153_T0.5720.72
83_A136_P0.5700.72
103_V116_L0.5690.71
287_T299_R0.5650.71
225_P236_D0.5650.71
259_I280_L0.5630.71
65_I87_D0.5620.71
274_L309_G0.5610.70
157_A279_G0.5600.70
114_L122_E0.5590.70
99_L115_A0.5560.70
315_E319_T0.5550.70
178_Y209_V0.5530.69
144_T156_R0.5510.69
166_R170_H0.5510.69
179_L185_L0.5510.69
220_T224_T0.5500.69
115_A259_I0.5470.68
178_Y185_L0.5430.68
100_R104_K0.5420.68
155_E158_I0.5390.67
233_A236_D0.5380.67
292_G301_R0.5380.67
80_A131_V0.5370.67
112_R163_R0.5370.67
125_L129_R0.5360.67
109_Y113_G0.5340.67
108_R314_R0.5340.67
77_V139_G0.5330.67
168_P279_G0.5320.66
78_Y85_R0.5310.66
73_A80_A0.5310.66
73_A76_E0.5290.66
276_R295_I0.5290.66
185_L194_S0.5250.65
69_P320_Q0.5250.65
106_A122_E0.5240.65
122_E163_R0.5240.65
314_R318_Q0.5240.65
156_R299_R0.5210.65
110_G115_A0.5200.65
263_L269_K0.5190.64
307_V311_R0.5190.64
238_L252_D0.5190.64
142_F168_P0.5180.64
112_R176_N0.5170.64
204_K212_M0.5170.64
293_R296_G0.5160.64
64_E67_Y0.5150.64
292_G304_Q0.5150.64
182_A193_P0.5150.64
224_T234_L0.5150.64
54_V57_A0.5140.64
302_V317_L0.5140.64
56_D60_L0.5130.64
70_L80_A0.5130.64
260_V264_F0.5130.64
99_L122_E0.5120.63
172_V211_R0.5120.63
56_D117_L0.5110.63
95_I125_L0.5110.63
232_K252_D0.5100.63
229_D233_A0.5090.63
172_V175_L0.5090.63
263_L267_N0.5070.63
61_Y64_E0.5060.63
266_L274_L0.5050.62
143_S170_H0.5040.62
94_M147_T0.5040.62
65_I99_L0.5030.62
186_S206_V0.5030.62
79_F198_I0.5020.62
148_W155_E0.5010.62
65_I124_N0.5000.62
179_L182_A0.5000.62
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 0.8242 100 0.306 Contact Map
1l9zH 1 0.8 100 0.306 Contact Map
4yfkF 1 0.8333 100 0.365 Contact Map
3ugoA 1 0.3333 100 0.592 Contact Map
1l0oC 1 0.1727 100 0.592 Contact Map
1rp3A 1 0.6939 100 0.622 Contact Map
4nqwA 1 0.4485 99.9 0.736 Contact Map
1sigA 1 0.4879 99.9 0.743 Contact Map
4x8kA 1 0.2758 99.9 0.755 Contact Map
1or7A 2 0.5576 99.8 0.77 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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