GREMLIN Database
YDFD - Uncharacterized HTH-type transcriptional regulator YdfD
UniProt: P96681 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 482 (374)
Sequences: 21397 (14753)
Seq/√Len: 762.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
387_V462_L3.1551.00
245_H284_N3.1061.00
144_G148_Q3.0521.00
386_K390_E2.9861.00
207_T228_K2.9071.00
435_K474_L2.8341.00
272_K276_E2.7301.00
405_T418_K2.6861.00
173_K178_N2.5761.00
187_V193_A2.4911.00
391_L466_Q2.4151.00
235_D274_R2.3711.00
467_K471_E2.3561.00
195_Q199_M2.2941.00
161_Y363_R2.2231.00
202_L227_M2.2151.00
167_A370_T2.1941.00
145_K367_E2.1881.00
286_Q316_H2.1531.00
169_S181_S2.1111.00
467_K470_Y2.0881.00
338_G343_I2.0841.00
282_S289_I2.0661.00
137_A141_E2.0521.00
461_S464_D2.0471.00
431_K434_S2.0001.00
395_A469_I1.9501.00
162_L166_E1.9451.00
473_G477_K1.9181.00
163_P366_A1.9171.00
233_P243_N1.9111.00
394_S398_T1.9041.00
395_A470_Y1.8841.00
393_L408_I1.8791.00
124_L468_G1.8771.00
395_A466_Q1.8451.00
427_L431_K1.8381.00
424_S427_L1.8321.00
391_L462_L1.8291.00
276_E280_A1.8121.00
243_N246_L1.7981.00
290_I320_I1.7961.00
197_I318_L1.7911.00
435_K471_E1.7891.00
393_L397_E1.7881.00
245_H277_E1.7871.00
172_L337_V1.7761.00
240_L243_N1.7601.00
323_L365_A1.7521.00
399_H470_Y1.7461.00
280_A284_N1.7301.00
159_K347_S1.7181.00
271_S274_R1.7161.00
283_E314_N1.7101.00
277_E280_A1.7051.00
167_A170_N1.7001.00
207_T230_T1.7001.00
166_E181_S1.6861.00
397_E406_W1.6791.00
395_A398_T1.6651.00
143_M364_V1.6501.00
392_A469_I1.6431.00
391_L395_A1.6401.00
170_N370_T1.6381.00
336_I346_L1.6341.00
159_K165_R1.6321.00
198_S222_F1.6131.00
241_P281_V1.6131.00
242_E277_E1.6011.00
166_E170_N1.5831.00
243_N247_T1.5821.00
183_S340_E1.5811.00
272_K306_Y1.5801.00
212_Q233_P1.5781.00
393_L415_V1.5761.00
212_Q231_G1.5751.00
384_Q387_V1.5681.00
392_A415_V1.5571.00
294_I322_S1.5551.00
241_P277_E1.5531.00
245_H285_T1.5521.00
358_S361_S1.5511.00
439_I453_I1.5441.00
384_Q462_L1.5331.00
367_E371_S1.5281.00
143_M147_S1.5201.00
141_E145_K1.5171.00
418_K452_Y1.5021.00
301_D410_K1.4961.00
425_M443_S1.4941.00
222_F227_M1.4941.00
190_A320_I1.4831.00
163_P370_T1.4801.00
397_E408_I1.4781.00
282_S287_L1.4691.00
179_V337_V1.4631.00
206_S254_A1.4621.00
140_K144_G1.4421.00
204_R226_G1.4381.00
393_L406_W1.4341.00
395_A473_G1.4221.00
167_A366_A1.4131.00
209_Y232_L1.3981.00
280_A283_E1.3971.00
168_L186_I1.3901.00
142_M367_E1.3771.00
395_A399_H1.3701.00
431_K475_M1.3581.00
398_T473_G1.3431.00
372_G376_Q1.3421.00
208_V222_F1.3371.00
273_K276_E1.3371.00
470_Y474_L1.3271.00
333_I365_A1.3231.00
119_T436_G1.3201.00
366_A370_T1.3131.00
390_E394_S1.3131.00
274_R277_E1.3051.00
462_L466_Q1.3051.00
384_Q388_R1.3001.00
272_K311_I1.2911.00
416_W442_G1.2861.00
307_P310_T1.2851.00
427_L430_T1.2831.00
350_K354_D1.2821.00
254_A290_I1.2691.00
174_T375_Q1.2681.00
197_I290_I1.2641.00
427_L433_L1.2521.00
273_K277_E1.2511.00
168_L184_I1.2501.00
248_R281_V1.2411.00
379_E383_Q1.2371.00
182_S340_E1.2351.00
389_R393_L1.2341.00
394_S466_Q1.2291.00
464_D467_K1.2281.00
198_S202_L1.2261.00
281_V287_L1.2251.00
152_A363_R1.2221.00
192_Q354_D1.2211.00
318_L338_G1.2211.00
188_S192_Q1.2161.00
162_L181_S1.2161.00
281_V285_T1.2141.00
165_R169_S1.2061.00
367_E370_T1.2061.00
379_E382_R1.2031.00
184_I337_V1.1971.00
426_K430_T1.1871.00
399_H473_G1.1811.00
141_E144_G1.1791.00
163_P363_R1.1731.00
428_L431_K1.1671.00
338_G346_L1.1641.00
432_A472_L1.1631.00
169_S184_I1.1601.00
199_M225_A1.1561.00
200_G349_I1.1551.00
180_S340_E1.1541.00
237_E274_R1.1461.00
168_L335_W1.1451.00
428_L433_L1.1411.00
161_Y366_A1.1391.00
219_L223_Q1.1331.00
466_Q470_Y1.1301.00
345_R348_D1.1301.00
276_E311_I1.1131.00
248_R287_L1.1081.00
235_D240_L1.1051.00
209_Y253_R1.1041.00
425_M429_Y1.1011.00
149_H367_E1.1001.00
320_I336_I1.1001.00
200_G346_L1.0971.00
398_T466_Q1.0951.00
192_Q350_K1.0891.00
185_L343_I1.0891.00
164_L186_I1.0831.00
321_G335_W1.0771.00
177_I309_K1.0751.00
142_M146_V1.0711.00
193_A320_I1.0681.00
185_L346_L1.0601.00
383_Q386_K1.0551.00
203_Q206_S1.0501.00
209_Y244_V1.0481.00
299_W305_P1.0421.00
183_S343_I1.0381.00
326_T374_Y1.0361.00
435_K475_M1.0361.00
160_G165_R1.0331.00
429_Y433_L1.0321.00
289_I308_I1.0301.00
344_E348_D1.0301.00
183_S314_N1.0281.00
207_T251_R1.0251.00
350_K357_S1.0181.00
399_H469_I1.0151.00
283_E313_K1.0101.00
391_L394_S1.0081.00
137_A140_K1.0071.00
162_L165_R1.0061.00
163_P166_E1.0041.00
202_L208_V1.0021.00
133_I384_Q1.0011.00
312_D315_G1.0001.00
301_D389_R0.9971.00
222_F229_L0.9941.00
437_I472_L0.9941.00
140_K147_S0.9941.00
343_I347_S0.9831.00
426_K443_S0.9821.00
237_E271_S0.9801.00
383_Q387_V0.9771.00
102_Q105_S0.9751.00
392_A465_L0.9711.00
190_A322_S0.9701.00
430_T434_S0.9681.00
171_Y297_E0.9671.00
212_Q448_E0.9661.00
306_Y311_I0.9641.00
172_L319_Y0.9601.00
140_K148_Q0.9571.00
283_E316_H0.9551.00
389_R457_Y0.9531.00
171_Y375_Q0.9531.00
279_L311_I0.9521.00
245_H281_V0.9501.00
170_N173_K0.9481.00
239_L256_L0.9451.00
272_K304_P0.9401.00
258_T278_I0.9401.00
124_L465_L0.9401.00
180_S183_S0.9351.00
211_D263_H0.9311.00
238_G274_R0.9281.00
293_D296_R0.9261.00
239_L274_R0.9231.00
220_H223_Q0.9201.00
201_L254_A0.9191.00
318_L336_I0.9181.00
312_D316_H0.9171.00
279_L312_D0.9141.00
428_L453_I0.9121.00
197_I346_L0.9091.00
141_E148_Q0.9091.00
145_K148_Q0.9081.00
129_L385_L0.9041.00
418_K451_N0.9021.00
279_L289_I0.9021.00
431_K435_K0.9011.00
120_D436_G0.8991.00
118_N436_G0.8981.00
232_L239_L0.8971.00
394_S397_E0.8971.00
99_S203_Q0.8961.00
288_P318_L0.8951.00
309_K312_D0.8911.00
430_T433_L0.8891.00
432_A475_M0.8881.00
429_Y439_I0.8861.00
218_S257_Y0.8861.00
209_Y247_T0.8841.00
195_Q353_T0.8831.00
111_E114_Q0.8821.00
207_T252_G0.8811.00
404_A417_I0.8781.00
390_E408_I0.8701.00
288_P316_H0.8701.00
146_V364_V0.8691.00
279_L317_V0.8681.00
425_M428_L0.8661.00
437_I471_E0.8581.00
417_I455_L0.8571.00
244_V281_V0.8571.00
193_A336_I0.8551.00
314_N317_V0.8551.00
309_K319_Y0.8541.00
389_R408_I0.8531.00
428_L475_M0.8531.00
239_L244_V0.8451.00
429_Y441_L0.8401.00
242_E246_L0.8351.00
218_S222_F0.8351.00
167_A369_F0.8351.00
318_L342_V0.8331.00
169_S179_V0.8291.00
138_V367_E0.8291.00
380_K383_Q0.8291.00
232_L247_T0.8271.00
442_G452_Y0.8271.00
376_Q380_K0.8201.00
130_S388_R0.8181.00
240_L274_R0.8181.00
172_L335_W0.8171.00
212_Q446_A0.8151.00
425_M441_L0.8141.00
392_A455_L0.8141.00
233_P240_L0.8141.00
299_W302_E0.8131.00
188_S358_S0.8131.00
416_W452_Y0.8121.00
425_M451_N0.8121.00
375_Q379_E0.8111.00
234_M263_H0.8111.00
171_Y174_T0.8091.00
471_E474_L0.8031.00
145_K150_M0.7941.00
377_H380_K0.7891.00
196_L346_L0.7881.00
206_S253_R0.7871.00
396_L406_W0.7871.00
166_E370_T0.7861.00
171_Y296_R0.7861.00
223_Q229_L0.7841.00
171_Y175_I0.7831.00
283_E312_D0.7801.00
120_D464_D0.7791.00
432_A439_I0.7781.00
198_S225_A0.7771.00
323_L335_W0.7741.00
241_P274_R0.7721.00
210_L222_F0.7711.00
392_A395_A0.7701.00
270_M275_R0.7691.00
327_L365_A0.7641.00
433_L438_L0.7621.00
145_K371_S0.7581.00
263_H266_T0.7581.00
114_Q117_S0.7561.00
333_I357_S0.7541.00
191_L217_Y0.7521.00
138_V142_M0.7511.00
136_L140_K0.7451.00
275_R311_I0.7451.00
208_V227_M0.7441.00
387_V391_L0.7421.00
108_I111_E0.7411.00
308_I317_V0.7401.00
188_S357_S0.7401.00
201_L288_P0.7341.00
404_A419_I0.7341.00
389_R409_P0.7341.00
340_E344_E0.7311.00
208_V254_A0.7301.00
156_E161_Y0.7291.00
463_E466_Q0.7281.00
306_Y310_T0.7271.00
380_K384_Q0.7231.00
192_Q196_L0.7211.00
137_A148_Q0.7201.00
437_I468_G0.7181.00
467_K474_L0.7131.00
161_Y359_S0.7131.00
279_L308_I0.7101.00
156_E359_S0.7061.00
419_I453_I0.7041.00
186_I333_I0.7031.00
99_S102_Q0.7031.00
202_L206_S0.7011.00
190_A294_I0.7011.00
249_G252_G0.7011.00
299_W304_P0.7001.00
242_E245_H0.6991.00
169_S180_S0.6991.00
231_G447_Q0.6981.00
471_E475_M0.6981.00
388_R462_L0.6971.00
246_L250_E0.6941.00
405_T420_L0.6921.00
423_I428_L0.6881.00
138_V373_H0.6881.00
256_L287_L0.6871.00
301_D386_K0.6871.00
460_A464_D0.6871.00
391_L465_L0.6861.00
138_V377_H0.6861.00
376_Q379_E0.6821.00
189_G332_R0.6821.00
423_I431_K0.6821.00
377_H381_V0.6801.00
124_L455_L0.6791.00
122_I467_K0.6781.00
196_L350_K0.6731.00
235_D243_N0.6731.00
381_V385_L0.6691.00
142_M145_K0.6671.00
199_M353_T0.6671.00
470_Y473_G0.6661.00
104_P108_I0.6661.00
145_K149_H0.6651.00
197_I320_I0.6651.00
219_L231_G0.6641.00
396_L417_I0.6631.00
194_L290_I0.6601.00
146_V367_E0.6591.00
194_L221_V0.6581.00
474_L477_K0.6581.00
186_I362_Q0.6561.00
127_G414_F0.6561.00
241_P278_I0.6551.00
439_I455_L0.6541.00
138_V141_E0.6541.00
255_I290_I0.6501.00
288_P342_V0.6501.00
248_R252_G0.6501.00
144_G147_S0.6491.00
198_S227_M0.6481.00
122_I468_G0.6461.00
196_L349_I0.6441.00
272_K310_T0.6421.00
193_A334_G0.6411.00
210_L229_L0.6401.00
101_I105_S0.6391.00
270_M274_R0.6381.00
165_R181_S0.6371.00
363_R366_A0.6371.00
168_L323_L0.6351.00
399_H466_Q0.6341.00
179_V183_S0.6331.00
363_R367_E0.6331.00
185_L347_S0.6321.00
291_E308_I0.6311.00
446_A452_Y0.6301.00
101_I104_P0.6291.00
378_V382_R0.6281.00
248_R251_R0.6271.00
382_R386_K0.6271.00
395_A465_L0.6251.00
344_E347_S0.6211.00
307_P319_Y0.6191.00
208_V255_I0.6191.00
211_D239_L0.6181.00
186_I357_S0.6181.00
396_L469_I0.6161.00
161_Y362_Q0.6151.00
123_Q438_L0.6141.00
360_L364_V0.6141.00
136_L139_M0.6141.00
199_M349_I0.6131.00
214_S219_L0.6131.00
207_T249_G0.6121.00
270_M278_I0.6111.00
156_E356_G0.6101.00
138_V371_S0.6101.00
373_H376_Q0.6101.00
392_A457_Y0.6101.00
187_V334_G0.6091.00
244_V278_I0.6091.00
230_T247_T0.6091.00
361_S364_V0.6081.00
375_Q378_V0.6061.00
235_D238_G0.6051.00
122_I460_A0.6011.00
185_L338_G0.6011.00
142_M364_V0.5991.00
237_E273_K0.5971.00
309_K317_V0.5971.00
241_P245_H0.5971.00
303_I410_K0.5961.00
106_R109_V0.5961.00
387_V390_E0.5941.00
166_E169_S0.5921.00
325_K332_R0.5911.00
359_S363_R0.5911.00
104_P107_K0.5911.00
385_L458_A0.5901.00
301_D408_I0.5881.00
239_L270_M0.5871.00
234_M268_I0.5871.00
428_L439_I0.5861.00
315_G339_P0.5861.00
333_I361_S0.5851.00
245_H249_G0.5831.00
105_S108_I0.5821.00
121_L436_G0.5811.00
122_I471_E0.5811.00
195_Q225_A0.5771.00
146_V149_H0.5741.00
201_L318_L0.5741.00
175_I296_R0.5721.00
135_P138_V0.5691.00
155_Y325_K0.5681.00
341_P344_E0.5661.00
109_V113_N0.5641.00
371_S375_Q0.5631.00
423_I427_L0.5631.00
394_S408_I0.5621.00
107_K110_Q0.5611.00
396_L404_A0.5611.00
177_I307_P0.5591.00
174_T297_E0.5591.00
100_G103_M0.5591.00
279_L283_E0.5581.00
125_S438_L0.5581.00
364_V367_E0.5571.00
282_S286_Q0.5561.00
446_A450_G0.5561.00
406_W415_V0.5531.00
407_N418_K0.5521.00
236_N405_T0.5521.00
210_L219_L0.5491.00
108_I112_I0.5471.00
426_K429_Y0.5471.00
240_L277_E0.5461.00
164_L168_L0.5461.00
100_G104_P0.5461.00
248_R285_T0.5441.00
187_V336_I0.5441.00
295_Y414_F0.5441.00
300_I386_K0.5421.00
198_S256_L0.5411.00
169_S173_K0.5411.00
399_H403_V0.5411.00
191_L215_Y0.5381.00
246_L249_G0.5381.00
275_R308_I0.5381.00
425_M433_L0.5381.00
300_I457_Y0.5371.00
279_L313_K0.5361.00
293_D319_Y0.5361.00
248_R253_R0.5351.00
106_R110_Q0.5351.00
141_E371_S0.5331.00
308_I311_I0.5321.00
297_E326_T0.5291.00
236_N407_N0.5281.00
102_Q106_R0.5261.00
442_G446_A0.5261.00
233_P247_T0.5221.00
403_V406_W0.5211.00
140_K143_M0.5201.00
425_M453_I0.5191.00
338_G342_V0.5181.00
123_Q126_K0.5181.00
399_H477_K0.5181.00
437_I475_M0.5161.00
406_W417_I0.5161.00
291_E319_Y0.5161.00
422_S451_N0.5151.00
120_D467_K0.5141.00
277_E281_V0.5141.00
429_Y432_A0.5121.00
269_L299_W0.5121.00
216_L444_I0.5111.00
239_L278_I0.5091.00
287_L316_H0.5081.00
129_L329_P0.5081.00
312_D317_V0.5061.00
173_K177_I0.5061.00
210_L231_G0.5061.00
372_G375_Q0.5051.00
103_M106_R0.5041.00
105_S109_V0.5031.00
272_K275_R0.5031.00
220_H352_Q0.5031.00
159_K185_L0.5021.00
199_M224_S0.5021.00
386_K389_R0.5011.00
255_I287_L0.5001.00
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 0.9378 100 0.305 Contact Map
3pplA 2 0.8029 100 0.389 Contact Map
3f6tA 2 0.8838 100 0.408 Contact Map
3qguA 2 0.7988 100 0.416 Contact Map
3ez1A 2 0.7842 100 0.427 Contact Map
2r2nA 2 0.8091 100 0.437 Contact Map
4je5A 2 0.8237 100 0.439 Contact Map
2x5fA 2 0.8216 100 0.44 Contact Map
1vp4A 2 0.832 100 0.442 Contact Map
3aowA 2 0.8174 100 0.449 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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