GREMLIN Database
RHAS - HTH-type transcriptional activator RhaS
UniProt: P09377 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10843
Length: 278 (241)
Sequences: 33861 (29000)
Seq/√Len: 1868.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
229_R262_F3.2841.00
214_L222_R3.2821.00
181_E223_L3.0381.00
237_A245_R3.0111.00
225_L262_F2.9731.00
191_D201_L2.8621.00
227_K230_H2.8321.00
179_W183_H2.7981.00
183_H186_D2.6811.00
222_R261_E2.6211.00
258_F269_I2.5431.00
176_L204_L2.3761.00
231_L245_R2.3601.00
228_A254_F2.3301.00
208_L219_Y2.2091.00
231_L246_C2.0951.00
189_N192_A2.0831.00
237_A241_D2.0061.00
184_F223_L1.9681.00
47_I54_P1.9271.00
264_W272_G1.9201.00
217_Q221_N1.8961.00
179_W196_Q1.8901.00
176_L197_F1.8631.00
180_L220_L1.8491.00
231_L237_A1.8421.00
177_L212_T1.8191.00
47_I56_T1.8181.00
173_L212_T1.7801.00
251_S255_S1.7581.00
225_L261_E1.7391.00
238_S241_D1.7361.00
49_V54_P1.7341.00
257_L260_R1.6991.00
229_R269_I1.6891.00
190_W205_H1.6691.00
149_L152_Q1.6621.00
203_T207_Q1.6491.00
193_V216_P1.6481.00
227_K231_L1.6211.00
178_A182_D1.6151.00
58_T61_T1.5951.00
42_E82_T1.5831.00
45_T56_T1.5611.00
223_L227_K1.5561.00
214_L218_R1.5541.00
43_H80_C1.5251.00
240_T251_S1.5231.00
216_P220_L1.5161.00
201_L205_H1.5091.00
232_L239_V1.5071.00
204_L216_P1.5041.00
170_A211_Q1.4951.00
181_E219_Y1.4921.00
264_W268_D1.4851.00
179_W188_V1.4761.00
184_F227_K1.4761.00
241_D244_Y1.4741.00
241_D245_R1.4631.00
230_H234_H1.4591.00
228_A246_C1.4421.00
203_T206_R1.4381.00
125_R129_A1.4331.00
253_H257_L1.4301.00
177_L181_E1.4231.00
248_F257_L1.4111.00
240_T244_Y1.4041.00
45_T58_T1.3971.00
199_L203_T1.3911.00
185_A245_R1.3901.00
180_L223_L1.3861.00
49_V72_L1.3841.00
267_R271_Q1.3801.00
205_H216_P1.3781.00
227_K246_C1.3611.00
36_H67_D1.3561.00
176_L193_V1.3461.00
242_I246_C1.3461.00
47_I74_E1.3381.00
192_A196_Q1.3341.00
148_I152_Q1.3311.00
202_R206_R1.3161.00
222_R226_M1.2981.00
51_N69_D1.2981.00
252_N255_S1.2941.00
152_Q156_L1.2871.00
215_T218_R1.2771.00
221_N257_L1.2471.00
199_L204_L1.2341.00
186_D192_A1.2291.00
148_I151_M1.2271.00
191_D195_D1.2251.00
255_S265_S1.2201.00
126_Q130_Q1.2121.00
223_L226_M1.2121.00
235_S270_R1.2071.00
255_S267_R1.1921.00
200_S203_T1.1911.00
172_R199_L1.1881.00
148_I155_L1.1831.00
42_E80_C1.1661.00
229_R233_R1.1631.00
66_R69_D1.1631.00
256_T260_R1.1301.00
43_H59_G1.1131.00
207_Q210_Q1.1031.00
185_A227_K1.1021.00
237_A242_I1.0911.00
268_D271_Q1.0871.00
207_Q211_Q1.0771.00
190_W216_P1.0741.00
226_M229_R1.0701.00
37_E71_H1.0701.00
145_S152_Q1.0681.00
126_Q129_A1.0601.00
145_S149_L1.0551.00
179_W197_F1.0541.00
31_H71_H1.0491.00
194_A201_L1.0491.00
188_V193_V1.0441.00
171_S175_L1.0441.00
151_M155_L1.0321.00
265_S268_D1.0301.00
250_D256_T1.0231.00
174_N178_A1.0211.00
267_R270_R1.0171.00
172_R207_Q1.0151.00
138_N142_S1.0091.00
147_E151_M1.0011.00
30_E70_R0.9951.00
221_N260_R0.9941.00
33_H71_H0.9911.00
187_E249_S0.9821.00
180_L216_P0.9801.00
231_L242_I0.9751.00
193_V196_Q0.9751.00
46_G79_L0.9701.00
175_L196_Q0.9611.00
152_Q155_L0.9571.00
192_A195_D0.9551.00
172_R197_F0.9551.00
202_R205_H0.9511.00
187_E192_A0.9481.00
177_L219_Y0.9441.00
129_A133_Q0.9431.00
61_T115_R0.9401.00
257_L261_E0.9351.00
218_R221_N0.9341.00
255_S259_R0.9281.00
190_W201_L0.9191.00
262_F269_I0.9141.00
130_Q134_Q0.9131.00
239_V242_I0.9111.00
179_W193_V0.9091.00
197_F204_L0.9031.00
229_R258_F0.9021.00
156_L160_S0.8971.00
41_V46_G0.8911.00
218_R222_R0.8851.00
46_G57_I0.8841.00
224_R246_C0.8841.00
268_D272_G0.8841.00
123_Q126_Q0.8791.00
175_L178_A0.8751.00
217_Q253_H0.8671.00
50_F53_Q0.8671.00
87_R90_D0.8561.00
253_H256_T0.8541.00
235_S242_I0.8391.00
225_L257_L0.8321.00
232_L242_I0.8311.00
199_L207_Q0.8301.00
174_N177_L0.8291.00
175_L197_F0.8281.00
155_L159_K0.8251.00
30_E72_L0.8251.00
221_N261_E0.8221.00
173_L176_L0.8141.00
37_E85_L0.8141.00
232_L270_R0.8131.00
173_L207_Q0.8131.00
217_Q220_L0.8121.00
259_R265_S0.8121.00
184_F220_L0.8121.00
144_A147_E0.8121.00
49_V52_G0.8121.00
208_L216_P0.8101.00
89_P93_Q0.8091.00
47_I76_T0.8071.00
122_Q126_Q0.8071.00
49_V74_E0.8021.00
225_L254_F0.7941.00
219_Y223_L0.7941.00
183_H196_Q0.7871.00
184_F188_V0.7871.00
79_L83_N0.7841.00
33_H37_E0.7811.00
233_R269_I0.7801.00
173_L211_Q0.7791.00
183_H192_A0.7751.00
208_L212_T0.7731.00
36_H64_F0.7721.00
206_R210_Q0.7711.00
264_W269_I0.7691.00
130_Q149_L0.7671.00
122_Q125_R0.7671.00
244_Y249_S0.7651.00
218_R261_E0.7611.00
121_L125_R0.7561.00
184_F246_C0.7551.00
39_V83_N0.7531.00
46_G56_T0.7481.00
45_T76_T0.7471.00
228_A231_L0.7411.00
176_L180_L0.7351.00
180_L219_Y0.7261.00
205_H209_K0.7251.00
193_V204_L0.7241.00
205_H217_Q0.7231.00
176_L208_L0.7201.00
177_L208_L0.7201.00
259_R268_D0.7171.00
130_Q152_Q0.7141.00
205_H215_T0.7131.00
243_A251_S0.7121.00
145_S155_L0.7101.00
144_A148_I0.7091.00
48_H63_C0.7081.00
143_T147_E0.7081.00
173_L177_L0.7061.00
188_V192_A0.7031.00
123_Q156_L0.7021.00
249_S253_H0.6981.00
90_D93_Q0.6911.00
169_S172_R0.6911.00
176_L179_W0.6841.00
110_Y113_H0.6831.00
170_A207_Q0.6801.00
123_Q130_Q0.6801.00
176_L216_P0.6781.00
40_I62_V0.6781.00
172_R175_L0.6751.00
145_S148_I0.6691.00
169_S210_Q0.6681.00
209_K215_T0.6671.00
32_H70_R0.6651.00
250_D253_H0.6641.00
35_F85_L0.6631.00
252_N265_S0.6621.00
184_F224_R0.6571.00
238_S242_I0.6571.00
57_I63_C0.6551.00
111_P115_R0.6551.00
251_S254_F0.6541.00
123_Q127_L0.6521.00
65_V71_H0.6521.00
242_I270_R0.6451.00
254_F258_F0.6431.00
158_R162_L0.6431.00
193_V197_F0.6411.00
41_V81_L0.6401.00
156_L159_K0.6391.00
221_N253_H0.6391.00
214_L219_Y0.6361.00
236_E242_I0.6331.00
41_V44_G0.6331.00
112_S115_R0.6271.00
90_D94_F0.6251.00
170_A174_N0.6211.00
139_D142_S0.6211.00
234_H237_A0.6191.00
181_E227_K0.6171.00
225_L248_F0.6151.00
228_A242_I0.6141.00
144_A151_M0.6141.00
258_F264_W0.6131.00
169_S211_Q0.6111.00
190_W217_Q0.6111.00
118_H121_L0.6081.00
226_M262_F0.6031.00
39_V65_V0.6021.00
51_N70_R0.6021.00
130_Q133_Q0.6021.00
41_V57_I0.6001.00
252_N256_T0.5951.00
220_L224_R0.5921.00
43_H78_N0.5921.00
39_V63_C0.5891.00
194_A197_F0.5861.00
226_M261_E0.5851.00
221_N225_L0.5851.00
108_G111_P0.5841.00
113_H116_V0.5801.00
179_W192_A0.5791.00
195_D198_S0.5771.00
126_Q133_Q0.5751.00
39_V48_H0.5741.00
176_L196_Q0.5711.00
188_V224_R0.5711.00
204_L212_T0.5701.00
129_A132_E0.5691.00
178_A181_E0.5691.00
127_L130_Q0.5691.00
38_I62_V0.5681.00
127_L149_L0.5681.00
188_V220_L0.5601.00
101_L104_Q0.5591.00
36_H39_V0.5581.00
173_L204_L0.5571.00
220_L223_L0.5571.00
117_N120_V0.5561.00
254_F266_P0.5561.00
142_S146_R0.5561.00
149_L156_L0.5551.00
190_W202_R0.5531.00
145_S159_K0.5531.00
132_E136_G0.5501.00
78_N81_L0.5501.00
212_T219_Y0.5501.00
180_L188_V0.5491.00
109_Q112_S0.5451.00
42_E129_A0.5441.00
39_V81_L0.5421.00
34_D87_R0.5411.00
134_Q159_K0.5411.00
80_C83_N0.5361.00
221_N248_F0.5361.00
231_L234_H0.5361.00
77_D80_C0.5361.00
232_L269_I0.5361.00
50_F65_V0.5361.00
229_R264_W0.5361.00
41_V79_L0.5361.00
142_S145_S0.5351.00
45_T77_D0.5331.00
230_H233_R0.5301.00
73_Y81_L0.5281.00
40_I121_L0.5271.00
171_S211_Q0.5261.00
239_V267_R0.5251.00
159_K163_Q0.5231.00
132_E135_E0.5211.00
174_N211_Q0.5211.00
135_E138_N0.5211.00
114_W117_N0.5211.00
157_L161_S0.5191.00
141_P145_S0.5191.00
46_G73_Y0.5191.00
133_Q137_E0.5181.00
209_K212_T0.5141.00
248_F253_H0.5131.00
108_G112_S0.5131.00
204_L207_Q0.5111.00
38_I64_F0.5111.00
239_V251_S0.5101.00
37_E65_V0.5091.00
82_T85_L0.5071.00
99_N103_P0.5041.00
250_D260_R0.5041.00
258_F262_F0.5031.00
257_L262_F0.5021.00
173_L197_F0.5001.00
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  
3gbgA 1 0.8993 100 0.213 Contact Map
3oouA 1 0.3777 100 0.468 Contact Map
1bl0A 1 0.3957 100 0.47 Contact Map
3oioA 1 0.4029 100 0.475 Contact Map
3mn2A 1 0.3813 100 0.476 Contact Map
3mklA 1 0.3993 100 0.477 Contact Map
3w6vA 1 0.3921 100 0.483 Contact Map
2k9sA 1 0.3813 100 0.484 Contact Map
3lsgA 2 0.3669 100 0.49 Contact Map
1d5yA 1 0.3957 99.9 0.498 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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