GREMLIN Database
YDCR - Uncharacterized HTH-type transcriptional regulator YdcR
UniProt: P77730 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13761
Length: 468 (363)
Sequences: 28855 (19575)
Seq/√Len: 1027.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
373_E450_G3.4081.00
232_E271_Q3.3851.00
128_A132_K3.3501.00
372_A376_Q3.0831.00
259_P263_A2.8301.00
193_W214_K2.7901.00
421_H462_K2.7371.00
455_Q459_Q2.6471.00
159_A164_T2.6381.00
417_A420_T2.5701.00
391_K404_E2.5411.00
221_D261_K2.4431.00
192_D241_K2.3901.00
121_Q125_R2.3301.00
173_T179_A2.3261.00
377_R454_E2.3051.00
188_T213_L2.2411.00
381_A457_V2.2211.00
455_Q458_K2.1951.00
273_N303_G2.1631.00
160_L361_D2.1421.00
410_D413_E2.1021.00
381_A458_K2.0661.00
149_E352_V2.0651.00
181_N185_Q2.0531.00
269_L276_L2.0091.00
155_A167_P1.9991.00
153_A356_S1.9661.00
108_F456_A1.9441.00
380_Q384_R1.9401.00
129_Q353_D1.9371.00
263_A267_A1.9061.00
449_W452_R1.8621.00
242_A277_I1.8311.00
152_Q156_R1.8251.00
230_A234_A1.8221.00
325_A329_A1.8211.00
156_R356_S1.8131.00
183_S305_L1.8111.00
232_E264_Q1.8041.00
229_Q264_Q1.7971.00
147_N349_L1.7511.00
383_L392_I1.7371.00
148_A152_Q1.7351.00
377_R450_G1.7331.00
417_A463_L1.7111.00
158_Y324_A1.6971.00
267_A271_Q1.6791.00
258_T261_K1.6631.00
219_A230_A1.6511.00
281_V309_S1.6421.00
264_Q267_A1.6401.00
411_A429_K1.6381.00
378_A401_L1.6361.00
208_L213_L1.6311.00
235_L268_L1.6251.00
425_I441_F1.6251.00
378_A457_V1.6251.00
379_W394_H1.6231.00
310_F351_L1.6081.00
277_I307_C1.6021.00
377_R381_A1.5871.00
379_W383_L1.5721.00
230_A233_L1.5671.00
125_R129_Q1.5601.00
149_E356_S1.5331.00
228_L264_Q1.5181.00
232_E272_Y1.5151.00
198_N217_S1.5151.00
193_W216_L1.5131.00
145_P151_R1.5101.00
176_A307_C1.5061.00
376_Q380_Q1.4871.00
129_Q133_T1.4871.00
193_W239_P1.4851.00
227_D230_A1.4701.00
269_L274_V1.4651.00
323_V332_I1.4631.00
370_Q450_G1.4601.00
381_A461_G1.4571.00
267_A270_N1.4501.00
152_Q167_P1.4481.00
259_P293_L1.4471.00
228_L268_L1.4461.00
169_E327_K1.4391.00
418_A460_L1.4271.00
260_Q263_A1.4271.00
421_H459_Q1.4241.00
320_I351_L1.4241.00
165_I324_A1.4151.00
379_W401_L1.4081.00
458_K462_K1.3941.00
156_R160_L1.3801.00
381_A384_R1.3781.00
402_W428_G1.3771.00
127_L350_A1.3651.00
153_A156_R1.3641.00
381_A454_E1.3631.00
154_I172_I1.3631.00
145_P333_Q1.3601.00
268_L274_V1.3511.00
344_S347_M1.3441.00
232_E236_Q1.3421.00
370_Q373_E1.3421.00
385_Y458_K1.3401.00
124_N128_A1.3391.00
379_W392_I1.3361.00
358_R362_A1.3341.00
384_R461_G1.3111.00
266_V300_R1.3111.00
259_P298_W1.3071.00
169_E301_H1.3051.00
336_Q340_T1.3041.00
450_G454_E1.3031.00
268_L272_Y1.3031.00
413_E417_A1.2991.00
195_I240_V1.2951.00
126_S353_D1.2941.00
184_L208_L1.2931.00
103_P422_H1.2931.00
198_N219_A1.2921.00
193_W240_V1.2901.00
305_L325_A1.2881.00
383_L394_H1.2881.00
187_V242_A1.2791.00
183_S277_I1.2781.00
413_E416_L1.2771.00
221_D224_E1.2701.00
415_S425_I1.2641.00
365_R368_R1.2611.00
235_L274_V1.2541.00
288_G396_D1.2541.00
454_E458_K1.2421.00
404_E440_F1.2411.00
194_V208_L1.2371.00
353_D357_T1.2371.00
195_I218_V1.2321.00
194_V242_A1.2291.00
190_P212_R1.2271.00
151_R155_A1.2261.00
369_R372_A1.2241.00
410_D438_S1.2201.00
380_Q454_E1.2121.00
270_N301_H1.2021.00
233_L237_E1.2011.00
375_K379_W1.1971.00
168_D327_K1.1871.00
423_I460_L1.1741.00
155_A170_I1.1711.00
184_L188_T1.1671.00
154_I322_W1.1671.00
365_R369_R1.1651.00
125_R128_A1.1571.00
127_L131_S1.1511.00
276_L295_A1.1481.00
308_S322_W1.1391.00
352_V356_S1.1341.00
243_C274_V1.1261.00
170_I324_A1.1241.00
263_A298_W1.1231.00
375_K445_T1.1171.00
370_Q374_R1.1131.00
205_L209_E1.1121.00
261_K264_Q1.1101.00
353_D356_S1.1091.00
260_Q264_Q1.1031.00
149_E349_L1.1001.00
294_P297_A1.0981.00
193_W236_Q1.0951.00
153_A352_V1.0951.00
299_D302_D1.0941.00
236_Q272_Y1.0931.00
124_N132_K1.0891.00
406_P439_R1.0871.00
108_F453_E1.0851.00
452_R455_Q1.0841.00
113_P371_L1.0811.00
178_E336_Q1.0801.00
188_T194_V1.0801.00
148_A151_R1.0791.00
325_A332_I1.0791.00
146_G151_R1.0761.00
295_A304_V1.0681.00
185_Q211_L1.0671.00
307_C323_V1.0671.00
221_D227_D1.0651.00
148_A167_P1.0631.00
385_Y461_G1.0611.00
378_A453_E1.0531.00
150_L172_I1.0531.00
236_Q240_V1.0531.00
245_L265_L1.0471.00
171_V332_I1.0451.00
126_S130_V1.0441.00
414_L441_F1.0411.00
171_V329_A1.0381.00
208_L215_A1.0351.00
174_A178_E1.0351.00
186_A335_L1.0341.00
163_I296_K1.0241.00
124_N131_S1.0241.00
154_I170_I1.0221.00
179_A307_C1.0181.00
331_K334_R1.0131.00
189_E192_D1.0101.00
286_Y292_P1.0091.00
296_K306_H1.0061.00
224_E261_K1.0041.00
183_S332_I1.0031.00
166_S327_K1.0011.00
270_N303_G0.9981.00
186_A332_I0.9941.00
147_N352_V0.9931.00
226_I261_K0.9911.00
204_A244_W0.9911.00
157_R161_Q0.9891.00
121_Q124_N0.9881.00
286_Y289_R0.9851.00
156_R159_A0.9841.00
229_Q233_L0.9811.00
412_G429_K0.9791.00
178_E340_T0.9751.00
369_R373_E0.9741.00
403_L443_F0.9711.00
376_Q394_H0.9661.00
418_A425_I0.9611.00
381_A385_Y0.9491.00
259_P291_K0.9471.00
149_E152_Q0.9441.00
187_V275_T0.9441.00
451_E454_E0.9421.00
169_E329_A0.9401.00
184_L244_W0.9401.00
138_S349_L0.9391.00
227_D261_K0.9381.00
384_R454_E0.9331.00
226_I243_C0.9321.00
313_C360_Y0.9321.00
157_R284_E0.9311.00
330_R334_R0.9301.00
390_V403_L0.9291.00
336_Q343_T0.9221.00
158_Y322_W0.9211.00
195_I231_L0.9201.00
275_T303_G0.9191.00
270_N302_D0.9171.00
411_A439_R0.9131.00
266_V304_V0.9121.00
117_L370_Q0.9121.00
224_E258_T0.9111.00
266_V276_L0.9091.00
198_N434_G0.9091.00
305_L323_V0.9011.00
195_I234_A0.8931.00
218_V234_A0.8931.00
377_R380_Q0.8901.00
122_Q353_D0.8791.00
288_G375_K0.8751.00
231_L243_C0.8741.00
157_R361_D0.8731.00
176_A309_S0.8731.00
125_R132_K0.8701.00
166_S169_E0.8681.00
232_E268_L0.8681.00
126_S129_Q0.8641.00
404_E439_R0.8641.00
421_H463_L0.8591.00
270_N299_D0.8591.00
378_A443_F0.8541.00
375_K395_N0.8541.00
133_T353_D0.8491.00
153_A355_L0.8491.00
92_Y96_M0.8431.00
179_A323_V0.8391.00
391_K406_P0.8391.00
184_L242_A0.8391.00
282_Y400_F0.8361.00
270_N300_R0.8341.00
378_A381_A0.8331.00
419_L424_S0.8321.00
122_Q357_T0.8321.00
177_L203_G0.8321.00
310_F322_W0.8311.00
367_L371_L0.8311.00
415_S427_P0.8291.00
197_E250_Q0.8281.00
161_Q283_S0.8271.00
196_V215_A0.8251.00
361_D365_R0.8251.00
209_E215_A0.8251.00
228_L261_K0.8241.00
231_L268_L0.8231.00
275_T305_L0.8181.00
366_R369_R0.8161.00
300_R303_G0.8151.00
104_S452_R0.8151.00
386_L390_V0.8121.00
195_I243_C0.8101.00
92_Y95_D0.8101.00
104_S422_H0.8081.00
129_Q132_K0.8061.00
240_V274_V0.8041.00
221_D230_A0.8031.00
259_P297_A0.8011.00
114_D374_R0.7981.00
266_V298_W0.7961.00
362_A366_R0.7931.00
220_T250_Q0.7911.00
130_V350_A0.7901.00
320_I343_T0.7841.00
155_A166_S0.7821.00
380_Q383_L0.7811.00
423_I459_Q0.7771.00
197_E218_V0.7741.00
152_Q356_S0.7741.00
411_A427_P0.7731.00
229_Q232_E0.7681.00
300_R304_V0.7641.00
417_A421_H0.7641.00
288_G372_A0.7611.00
276_L300_R0.7611.00
158_Y306_H0.7551.00
357_T361_D0.7541.00
390_V405_L0.7531.00
418_A463_L0.7511.00
218_V226_I0.7501.00
231_L265_L0.7491.00
155_A165_I0.7471.00
174_A344_S0.7461.00
377_R453_E0.7351.00
428_G440_F0.7341.00
198_N432_S0.7341.00
235_L272_Y0.7331.00
204_A208_L0.7331.00
196_V208_L0.7321.00
287_F445_T0.7321.00
174_A343_T0.7321.00
176_A281_V0.7321.00
226_I231_L0.7301.00
111_A400_F0.7291.00
126_S350_A0.7271.00
374_R450_G0.7261.00
414_L463_L0.7241.00
119_P122_Q0.7211.00
225_G261_K0.7171.00
172_I320_I0.7131.00
373_E376_Q0.7121.00
375_K394_H0.7121.00
409_L413_E0.7081.00
183_S307_C0.7071.00
188_T242_A0.7051.00
349_L352_V0.7041.00
455_Q462_K0.7031.00
128_A131_S0.7011.00
405_L441_F0.6981.00
409_L417_A0.6951.00
182_L332_I0.6951.00
157_R283_S0.6931.00
181_N339_S0.6901.00
151_R167_P0.6901.00
402_W440_F0.6891.00
366_R370_Q0.6871.00
257_L262_K0.6861.00
266_V295_A0.6801.00
377_R457_V0.6801.00
182_L336_Q0.6801.00
206_Q209_E0.6791.00
243_C269_L0.6791.00
415_S441_F0.6781.00
119_P123_L0.6761.00
235_L240_V0.6751.00
294_P306_H0.6741.00
184_L213_L0.6731.00
182_L335_L0.6731.00
412_G416_L0.6711.00
102_D422_H0.6711.00
363_H366_R0.6711.00
175_G319_R0.6711.00
94_F97_L0.6691.00
423_I456_A0.6681.00
251_N282_Y0.6641.00
188_T192_D0.6621.00
111_A282_Y0.6621.00
425_I443_F0.6621.00
106_V459_Q0.6591.00
171_V325_A0.6571.00
386_L461_G0.6531.00
122_Q363_H0.6531.00
280_D283_S0.6471.00
184_L211_L0.6461.00
285_L368_R0.6441.00
382_L403_L0.6431.00
287_F372_A0.6421.00
293_L298_W0.6421.00
262_K278_E0.6411.00
248_N280_D0.6401.00
108_F443_F0.6391.00
172_I348_Q0.6361.00
329_A333_Q0.6361.00
142_N342_S0.6361.00
458_K461_G0.6351.00
194_V213_L0.6321.00
284_E313_C0.6301.00
147_N345_S0.6301.00
389_E406_P0.6291.00
104_S455_Q0.6291.00
376_Q379_W0.6281.00
171_V333_Q0.6271.00
249_S397_S0.6251.00
385_Y389_E0.6241.00
378_A445_T0.6231.00
411_A438_S0.6211.00
197_E226_I0.6171.00
299_D303_G0.6161.00
302_D326_G0.6161.00
373_E377_R0.6141.00
435_E438_S0.6141.00
142_N345_S0.6131.00
411_A415_S0.6131.00
320_I347_M0.6111.00
150_L154_I0.6101.00
102_D105_V0.6101.00
142_N147_N0.6091.00
363_H367_L0.6081.00
218_V230_A0.6071.00
121_Q132_K0.6061.00
106_V455_Q0.6051.00
196_V205_L0.6051.00
391_K407_E0.6041.00
151_R168_D0.6031.00
124_N134_A0.6031.00
262_K298_W0.6021.00
280_D306_H0.6021.00
286_Y291_K0.5991.00
362_A365_R0.5991.00
179_A321_G0.5971.00
385_Y457_V0.5961.00
160_L356_S0.5961.00
416_L420_T0.5951.00
123_L315_V0.5921.00
269_L273_N0.5911.00
165_I296_K0.5911.00
93_I96_M0.5891.00
178_E182_L0.5891.00
280_D294_P0.5891.00
293_L297_A0.5881.00
412_G427_P0.5861.00
327_K330_R0.5841.00
216_L240_V0.5841.00
250_Q253_L0.5831.00
364_L368_R0.5821.00
180_L207_A0.5821.00
122_Q125_R0.5811.00
447_W452_R0.5811.00
173_T321_G0.5791.00
274_V303_G0.5791.00
191_G214_K0.5781.00
311_S319_R0.5781.00
287_F375_K0.5771.00
104_S459_Q0.5751.00
409_L414_L0.5721.00
177_L201_F0.5711.00
345_S349_L0.5701.00
278_E306_H0.5691.00
371_L446_A0.5681.00
224_E260_Q0.5681.00
266_V270_N0.5661.00
269_L300_R0.5661.00
173_T323_V0.5661.00
130_V353_D0.5651.00
371_L399_Y0.5651.00
188_T241_K0.5621.00
237_E240_V0.5611.00
314_L351_L0.5601.00
269_L272_Y0.5601.00
216_L234_A0.5601.00
202_Y430_M0.5591.00
382_L392_I0.5591.00
200_C246_M0.5581.00
205_L217_S0.5581.00
381_A453_E0.5561.00
296_K299_D0.5551.00
129_Q357_T0.5541.00
165_I169_E0.5541.00
382_L457_V0.5521.00
314_L361_D0.5521.00
127_L346_P0.5521.00
243_C268_L0.5491.00
105_V422_H0.5481.00
288_G394_H0.5481.00
192_D239_P0.5481.00
392_I401_L0.5471.00
172_I343_T0.5471.00
330_R333_Q0.5461.00
235_L269_L0.5451.00
415_S419_L0.5441.00
226_I257_L0.5431.00
159_A162_G0.5431.00
181_N207_A0.5431.00
109_A424_S0.5431.00
177_L341_L0.5431.00
152_Q155_A0.5421.00
459_Q462_K0.5421.00
219_A227_D0.5411.00
428_G432_S0.5401.00
402_W442_R0.5401.00
361_D364_L0.5391.00
226_I265_L0.5351.00
255_F261_K0.5351.00
159_A163_I0.5341.00
201_F341_L0.5321.00
248_N256_T0.5291.00
414_L418_A0.5291.00
389_E392_I0.5291.00
283_S308_S0.5281.00
155_A159_A0.5281.00
180_L277_I0.5281.00
257_L261_K0.5271.00
386_L457_V0.5251.00
323_V329_A0.5251.00
216_L236_Q0.5231.00
120_L123_L0.5221.00
200_C205_L0.5191.00
217_S433_T0.5191.00
193_W241_K0.5171.00
287_F395_N0.5171.00
403_L440_F0.5171.00
382_L390_V0.5171.00
107_P110_S0.5161.00
262_K295_A0.5151.00
290_E396_D0.5151.00
410_D429_K0.5141.00
371_L445_T0.5131.00
287_F397_S0.5121.00
301_H304_V0.5121.00
224_E230_A0.5111.00
228_L265_L0.5101.00
169_E326_G0.5081.00
233_L236_Q0.5071.00
386_L389_E0.5071.00
93_I97_L0.5051.00
169_E325_A0.5031.00
346_P350_A0.5011.00
98_Q103_P0.5001.00
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  
4tv7A 2 0.9466 100 0.303 Contact Map
3pplA 2 0.8291 100 0.39 Contact Map
3f6tA 2 0.9017 100 0.404 Contact Map
3qguA 2 0.8269 100 0.423 Contact Map
3ez1A 2 0.8077 100 0.434 Contact Map
2r2nA 2 0.8397 100 0.448 Contact Map
1vp4A 2 0.859 100 0.45 Contact Map
3d6kA 2 0.8141 100 0.452 Contact Map
2x5fA 2 0.8547 100 0.453 Contact Map
3aowA 2 0.844 100 0.454 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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