GREMLIN Database
RHAR - HTH-type transcriptional activator RhaR
UniProt: P09378 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10842
Length: 282 (240)
Sequences: 35067 (29677)
Seq/√Len: 1915.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
219_M227_Q3.2131.00
234_Q267_T3.2121.00
186_A228_V3.0361.00
230_V267_T3.0321.00
242_L250_E2.9861.00
232_H235_Y2.9051.00
196_D206_E2.8151.00
184_R188_S2.7811.00
227_Q266_E2.6271.00
188_S191_S2.6161.00
263_F274_W2.4411.00
233_A259_F2.2921.00
236_L250_E2.2761.00
213_F224_Y2.1861.00
181_L209_L2.1741.00
194_A197_K2.0751.00
236_L251_C2.0391.00
242_L246_D2.0131.00
269_M277_L1.9741.00
189_L228_V1.9461.00
50_L57_P1.9301.00
185_L225_L1.8831.00
184_R201_E1.8611.00
230_V266_E1.8371.00
236_L242_L1.8201.00
222_N226_R1.8031.00
178_L217_T1.7751.00
181_L202_A1.7711.00
50_L59_R1.7681.00
182_I217_T1.7521.00
243_L246_D1.7481.00
256_S260_S1.7461.00
183_T187_A1.7191.00
198_F221_I1.7001.00
46_R83_V1.6601.00
52_V57_P1.6531.00
235_Y239_H1.6511.00
195_L210_R1.6211.00
151_L154_Q1.6201.00
208_V212_Q1.6101.00
262_V265_R1.6021.00
232_H236_L1.5941.00
234_Q274_W1.5861.00
48_N59_R1.5741.00
219_M223_Q1.5691.00
127_R131_G1.5591.00
184_R193_F1.5411.00
258_Y262_V1.5391.00
221_I225_L1.5361.00
228_V232_H1.5351.00
209_L221_I1.5311.00
237_L244_I1.5301.00
61_T64_D1.5101.00
245_S256_S1.5031.00
186_A224_Y1.4981.00
175_E216_Q1.4731.00
208_V211_Q1.4701.00
206_E210_R1.4701.00
45_W85_Q1.4631.00
246_D250_E1.4611.00
39_C70_A1.4491.00
48_N61_T1.4481.00
246_D249_T1.4411.00
245_S249_T1.4401.00
269_M273_Q1.4381.00
189_L232_H1.4331.00
182_I186_A1.4191.00
190_K250_E1.4151.00
253_F262_V1.4131.00
204_C208_V1.4071.00
233_A251_C1.4071.00
52_V75_S1.4031.00
272_S276_H1.3941.00
247_I251_C1.3761.00
185_L228_V1.3531.00
220_T223_Q1.3501.00
232_H251_C1.3471.00
150_L154_Q1.3411.00
197_K201_E1.3371.00
210_R221_I1.3351.00
196_D200_D1.3331.00
207_R211_Q1.3231.00
181_L198_F1.3201.00
227_Q231_C1.3141.00
191_S197_K1.2911.00
150_L157_M1.2861.00
54_N72_D1.2841.00
257_N260_S1.2821.00
226_R262_V1.2631.00
154_Q158_L1.2561.00
260_S270_T1.2521.00
69_H72_D1.2421.00
260_S272_S1.2181.00
240_S275_R1.2151.00
228_V231_C1.2131.00
150_L153_G1.2111.00
234_Q238_Q1.2051.00
205_S208_V1.2021.00
204_C209_L1.2001.00
177_L204_C1.1851.00
46_R62_R1.1671.00
140_H144_A1.1511.00
261_V265_R1.1441.00
40_E74_H1.1191.00
36_H74_H1.1181.00
193_F198_F1.1081.00
242_L247_I1.1061.00
192_P254_E1.1031.00
128_Q132_Q1.1031.00
231_C234_Q1.0981.00
190_K232_H1.0911.00
184_R202_A1.0881.00
34_H74_H1.0841.00
149_E153_G1.0801.00
195_L221_I1.0761.00
128_Q131_G1.0691.00
273_Q276_H1.0661.00
45_W83_V1.0631.00
179_D183_T1.0621.00
270_T273_Q1.0591.00
176_T180_K1.0571.00
199_C206_E1.0481.00
226_R265_R1.0461.00
212_Q215_Q1.0451.00
244_I247_I1.0321.00
50_L77_A1.0271.00
131_G135_H0.9961.00
223_Q226_R0.9931.00
212_Q216_Q0.9871.00
272_S275_R0.9841.00
255_D261_V0.9831.00
198_F201_E0.9801.00
49_G82_L0.9801.00
180_K201_E0.9731.00
147_M151_L0.9721.00
157_M161_R0.9701.00
177_L202_A0.9701.00
262_V266_E0.9541.00
236_L247_I0.9511.00
147_M154_Q0.9501.00
182_I224_Y0.9501.00
33_E73_K0.9481.00
267_T274_W0.9471.00
64_D117_R0.9471.00
197_K200_D0.9451.00
177_L212_Q0.9381.00
260_S264_T0.9361.00
202_A209_L0.9291.00
185_L221_I0.9271.00
207_R210_R0.9131.00
230_V262_V0.9091.00
154_Q157_M0.9081.00
195_L206_E0.9061.00
184_R198_F0.9031.00
44_V49_G0.8991.00
132_Q136_E0.8941.00
222_N258_Y0.8891.00
153_G157_M0.8851.00
180_K183_T0.8821.00
53_L56_R0.8821.00
273_Q277_L0.8741.00
91_P95_K0.8731.00
234_Q263_F0.8671.00
229_R251_C0.8581.00
178_L181_L0.8581.00
258_Y261_V0.8581.00
264_T270_T0.8571.00
52_V55_D0.8501.00
226_R266_E0.8491.00
223_Q227_Q0.8471.00
204_C212_Q0.8401.00
178_L212_Q0.8401.00
49_G60_I0.8381.00
213_F221_I0.8341.00
192_P197_K0.8321.00
124_A128_Q0.8291.00
49_G59_R0.8281.00
180_K202_A0.8261.00
237_L247_I0.8231.00
222_N225_L0.8221.00
125_Q158_L0.8211.00
240_S247_I0.8211.00
230_V259_F0.8181.00
125_Q128_Q0.8181.00
188_S201_E0.8101.00
189_L225_L0.7971.00
233_A236_L0.7971.00
39_C67_Y0.7961.00
224_Y228_V0.7911.00
158_L162_H0.7901.00
174_S215_Q0.7861.00
237_L275_R0.7861.00
213_F217_T0.7851.00
189_L193_F0.7841.00
178_L216_Q0.7781.00
249_T254_E0.7781.00
179_D182_I0.7771.00
42_V86_N0.7691.00
223_Q266_E0.7671.00
181_L213_F0.7651.00
40_E88_I0.7641.00
182_I213_F0.7621.00
43_I65_L0.7581.00
185_L224_Y0.7581.00
269_M274_W0.7571.00
51_H66_F0.7551.00
145_N149_E0.7541.00
33_E75_S0.7511.00
189_L251_C0.7491.00
248_S256_S0.7361.00
238_Q274_W0.7321.00
210_R214_R0.7301.00
146_E149_E0.7291.00
36_H40_E0.7291.00
188_S197_K0.7261.00
46_R81_D0.7251.00
181_L184_R0.7251.00
134_E138_S0.7241.00
198_F209_L0.7201.00
177_L180_K0.7191.00
68_I74_H0.7131.00
210_R220_T0.7101.00
264_T273_Q0.7081.00
255_D258_Y0.7081.00
124_A127_R0.7071.00
211_Q215_Q0.7001.00
141_V144_A0.6961.00
193_F197_K0.6951.00
178_L182_I0.6941.00
147_M157_M0.6941.00
175_E212_Q0.6871.00
175_E179_D0.6851.00
186_A232_H0.6801.00
189_L229_R0.6801.00
123_M127_R0.6771.00
254_E258_Y0.6761.00
44_V84_L0.6761.00
60_I66_F0.6751.00
132_Q151_L0.6721.00
181_L221_I0.6721.00
82_L86_N0.6721.00
44_V47_G0.6711.00
210_R222_N0.6621.00
225_L229_R0.6611.00
135_H139_Q0.6611.00
214_R220_T0.6611.00
230_V253_F0.6611.00
132_Q135_H0.6581.00
243_L247_I0.6571.00
38_F88_I0.6561.00
132_Q154_Q0.6551.00
257_N270_T0.6531.00
158_L161_R0.6511.00
174_S177_L0.6501.00
125_Q132_Q0.6421.00
181_L201_E0.6401.00
193_F229_R0.6381.00
181_L185_L0.6341.00
219_M224_Y0.6331.00
44_V60_I0.6271.00
263_F269_M0.6261.00
42_V68_I0.6241.00
256_S259_F0.6241.00
129_V132_Q0.6221.00
48_N80_N0.6211.00
195_L222_N0.6191.00
114_P117_R0.6191.00
247_I275_R0.6161.00
199_C202_A0.6131.00
200_D203_S0.6131.00
146_E150_L0.6121.00
217_T224_Y0.6111.00
95_K99_D0.6101.00
172_T175_E0.6091.00
128_Q135_H0.6081.00
136_E139_Q0.6071.00
259_F263_F0.6071.00
44_V82_L0.6051.00
116_W119_G0.6051.00
35_T73_K0.6011.00
49_G76_Y0.6011.00
231_C266_E0.6001.00
42_V51_H0.6001.00
39_C42_V0.5981.00
174_S216_Q0.5981.00
231_C267_T0.5971.00
119_G122_G0.5971.00
198_F202_A0.5961.00
226_R258_Y0.5941.00
148_A151_L0.5941.00
42_V84_L0.5941.00
122_G125_Q0.5911.00
236_L239_H0.5881.00
183_T186_A0.5861.00
225_L228_V0.5821.00
184_R197_K0.5821.00
147_M150_L0.5801.00
41_L65_L0.5801.00
257_N261_V0.5801.00
178_L209_L0.5791.00
233_A247_I0.5791.00
54_N73_K0.5781.00
125_Q129_V0.5771.00
226_R230_V0.5751.00
43_I123_M0.5731.00
45_W131_G0.5721.00
259_F271_P0.5721.00
235_Y238_Q0.5711.00
146_E153_G0.5701.00
255_D265_R0.5681.00
129_V151_L0.5621.00
112_G115_H0.5621.00
151_L158_L0.5611.00
253_F258_Y0.5571.00
192_P229_R0.5561.00
193_F225_L0.5541.00
214_R217_T0.5521.00
114_P118_L0.5501.00
42_V66_F0.5481.00
244_I272_S0.5481.00
120_S123_M0.5471.00
93_R96_L0.5461.00
237_L274_W0.5461.00
92_E95_K0.5461.00
185_L193_F0.5451.00
234_Q269_M0.5441.00
176_T216_Q0.5441.00
43_I130_I0.5431.00
195_L207_R0.5421.00
91_P94_L0.5381.00
96_L100_W0.5371.00
115_H118_L0.5331.00
198_F229_R0.5321.00
232_H250_E0.5281.00
209_L217_T0.5261.00
41_L67_Y0.5261.00
76_Y86_N0.5261.00
244_I256_S0.5251.00
248_S253_F0.5221.00
76_Y84_L0.5221.00
263_F267_T0.5211.00
53_L68_I0.5201.00
92_E96_L0.5171.00
223_Q265_R0.5171.00
51_H76_Y0.5141.00
226_R253_F0.5101.00
147_M161_R0.5101.00
51_H68_I0.5091.00
188_S193_F0.5091.00
163_R166_S0.5081.00
249_T256_S0.5081.00
202_A206_E0.5071.00
155_L159_L0.5071.00
134_E137_S0.5061.00
231_C235_Y0.5031.00
65_L68_I0.5031.00
144_A148_A0.5031.00
160_N164_Y0.5021.00
44_V62_R0.5021.00
143_F147_M0.5001.00
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 0.8936 100 0.219 Contact Map
3oioA 1 0.3972 100 0.463 Contact Map
1bl0A 1 0.3865 100 0.463 Contact Map
3oouA 1 0.3723 100 0.465 Contact Map
3mn2A 1 0.3759 100 0.47 Contact Map
3w6vA 1 0.383 100 0.476 Contact Map
3mklA 1 0.3936 100 0.477 Contact Map
2k9sA 1 0.3759 100 0.478 Contact Map
3lsgA 2 0.3617 100 0.487 Contact Map
1d5yA 1 0.3865 99.9 0.492 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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