GREMLIN Database
YDEF - Uncharacterized HTH-type transcriptional regulator YdeF
UniProt: P96663 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 462 (354)
Sequences: 25810 (17551)
Seq/√Len: 932.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
370_R444_L3.3811.00
231_E270_K3.3351.00
127_K131_H3.1981.00
369_I373_Q3.1241.00
258_V262_R2.7961.00
413_L456_R2.7181.00
193_R214_Q2.6371.00
383_T396_L2.5711.00
221_E260_N2.4861.00
159_Q164_E2.4771.00
449_Q453_I2.4381.00
173_A179_A2.3971.00
188_C213_V2.3891.00
192_D240_K2.2421.00
374_L448_E2.2311.00
272_N299_Q2.2021.00
120_E124_Y2.1301.00
155_V167_V2.0761.00
449_Q452_M2.0701.00
268_V275_V2.0631.00
378_Y451_L2.0591.00
181_A185_A2.0311.00
378_Y452_M2.0031.00
443_T446_E1.9701.00
153_A353_V1.9621.00
149_W349_A1.9471.00
402_S405_E1.9461.00
405_E409_L1.8881.00
321_V326_K1.8661.00
109_M450_G1.8611.00
262_R266_D1.8571.00
147_S346_E1.8311.00
152_D156_K1.8041.00
156_K353_V1.8001.00
228_E263_M1.7871.00
148_L152_D1.7771.00
124_Y128_N1.7681.00
219_K229_S1.7471.00
183_T301_I1.7391.00
374_L444_L1.7371.00
231_E263_M1.7281.00
241_G276_I1.7201.00
306_L348_T1.6981.00
266_D270_K1.6661.00
375_V451_L1.6531.00
269_K297_P1.6511.00
380_A384_C1.6501.00
229_S232_Y1.6471.00
227_P267_I1.6231.00
376_N386_G1.6201.00
229_S233_A1.6171.00
158_I320_A1.6111.00
374_L378_Y1.6061.00
145_G151_K1.5951.00
169_H323_R1.5891.00
128_N350_R1.5881.00
126_L130_V1.5781.00
226_S229_S1.5751.00
417_V434_V1.5741.00
257_S260_N1.5681.00
409_L412_R1.5661.00
152_D167_V1.5651.00
263_M266_D1.5601.00
208_A213_V1.5541.00
280_S305_S1.5501.00
198_H217_P1.5481.00
376_N380_A1.5471.00
149_W353_V1.5361.00
409_L457_L1.5321.00
276_I303_I1.5311.00
367_Q444_L1.5301.00
258_V290_P1.5271.00
176_G303_I1.5221.00
413_L453_I1.5101.00
227_P263_M1.5031.00
403_G421_E1.4951.00
319_V329_I1.4941.00
266_D269_K1.4901.00
128_N132_E1.4861.00
376_N393_R1.4861.00
231_E271_Y1.4781.00
316_L348_T1.4681.00
375_V393_R1.4681.00
145_G330_S1.4621.00
193_R216_V1.4591.00
373_Q377_R1.4581.00
234_C267_I1.4521.00
355_N359_V1.4511.00
268_V273_L1.4391.00
333_L337_N1.4371.00
452_M456_R1.4301.00
378_Y455_R1.4191.00
402_S431_E1.4191.00
154_A172_F1.4181.00
367_Q370_R1.4171.00
193_R238_N1.4131.00
231_E235_K1.4011.00
394_W420_A1.3911.00
165_T320_A1.3881.00
104_T414_G1.3831.00
341_S344_L1.3801.00
267_I273_L1.3791.00
259_E262_R1.3751.00
198_H219_K1.3691.00
194_I208_A1.3661.00
258_V295_F1.3621.00
123_L131_H1.3581.00
153_A156_K1.3531.00
380_A386_G1.3521.00
125_Q129_M1.3461.00
362_E365_R1.3461.00
160_R358_E1.3261.00
396_L433_A1.3261.00
376_N384_C1.3261.00
183_T276_I1.3201.00
378_Y448_E1.3171.00
123_L127_K1.3101.00
151_K155_V1.3081.00
410_A454_L1.3071.00
168_D323_R1.3021.00
123_L130_V1.2961.00
195_G218_I1.2811.00
406_F409_L1.2781.00
444_L448_E1.2781.00
366_E369_I1.2701.00
195_G239_I1.2691.00
267_I271_Y1.2631.00
122_L125_Q1.2541.00
301_I321_V1.2521.00
187_L241_G1.2491.00
194_I241_G1.2451.00
184_L208_A1.2441.00
362_E366_E1.2391.00
155_V170_I1.2241.00
125_Q350_R1.2211.00
292_L300_V1.2081.00
372_N376_N1.2031.00
367_Q371_R1.2011.00
408_E412_R1.1951.00
446_E449_Q1.1941.00
153_A349_A1.1931.00
350_R354_S1.1901.00
234_C273_L1.1891.00
291_A294_S1.1861.00
190_P212_S1.1831.00
401_M405_E1.1801.00
259_E263_M1.1781.00
275_V292_L1.1751.00
123_L129_M1.1731.00
403_G407_E1.1731.00
170_I320_A1.1651.00
260_N263_M1.1621.00
146_E151_K1.1611.00
166_S323_R1.1591.00
188_C194_I1.1481.00
193_R239_I1.1341.00
377_R448_E1.1311.00
262_R295_F1.1291.00
149_W346_E1.1251.00
169_H326_K1.1201.00
186_S332_A1.1161.00
154_A318_Y1.1151.00
448_E452_M1.1121.00
304_A318_Y1.1111.00
148_L151_K1.1091.00
148_L167_V1.1081.00
349_A353_V1.1041.00
174_N178_N1.0971.00
178_N333_L1.0931.00
415_V454_L1.0911.00
186_S329_I1.0891.00
242_L273_L1.0891.00
407_E417_V1.0871.00
126_L347_L1.0841.00
150_Q172_F1.0811.00
244_L264_V1.0731.00
225_M260_N1.0721.00
405_E408_E1.0701.00
171_L326_K1.0691.00
204_L243_Y1.0651.00
372_N438_V1.0641.00
125_Q128_N1.0631.00
147_S349_A1.0601.00
350_R353_V1.0591.00
171_L329_I1.0551.00
179_A303_I1.0481.00
223_D260_N1.0451.00
189_K192_D1.0431.00
138_W346_E1.0431.00
184_L188_C1.0401.00
154_A170_I1.0371.00
333_L340_V1.0361.00
178_N337_N1.0361.00
309_S357_F1.0321.00
208_A215_I1.0311.00
185_A211_L1.0291.00
221_E226_S1.0271.00
109_M447_L1.0251.00
403_G406_F1.0241.00
114_P368_T1.0241.00
163_F293_A1.0231.00
235_K271_Y1.0211.00
321_V329_I1.0171.00
269_K299_Q1.0061.00
398_P432_R1.0061.00
395_L436_V1.0041.00
183_T329_I1.0001.00
105_H446_E0.9991.00
327_E331_K0.9971.00
225_M242_L0.9931.00
375_V447_L0.9911.00
269_K298_Q0.9861.00
303_I319_V0.9801.00
404_A421_E0.9761.00
124_Y127_K0.9751.00
195_G230_L0.9751.00
366_E370_R0.9741.00
413_L457_L0.9681.00
410_A417_V0.9631.00
265_A275_V0.9591.00
193_R235_K0.9581.00
121_P350_R0.9571.00
301_I325_Y0.9511.00
124_Y131_H0.9491.00
274_F299_Q0.9471.00
98_L102_K0.9461.00
157_L283_L0.9431.00
265_A300_V0.9431.00
198_H426_G0.9431.00
205_K209_S0.9401.00
223_D257_S0.9361.00
156_K159_Q0.9351.00
328_P331_K0.9341.00
157_L161_G0.9341.00
235_K239_I0.9341.00
373_Q386_G0.9341.00
374_L377_R0.9311.00
410_A457_L0.9311.00
157_L358_E0.9311.00
153_A352_I0.9261.00
293_A302_H0.9191.00
226_S260_N0.9181.00
404_A408_E0.9181.00
326_K330_S0.9171.00
285_N388_E0.9141.00
227_P260_N0.9091.00
401_M406_F0.9061.00
149_W152_D0.9041.00
157_L160_R0.8991.00
195_G233_A0.8981.00
197_D249_H0.8921.00
166_S169_H0.8911.00
420_A433_A0.8861.00
265_A295_F0.8841.00
228_E232_Y0.8831.00
401_M409_L0.8821.00
396_L432_R0.8821.00
301_I319_V0.8811.00
445_E448_E0.8791.00
306_L318_Y0.8701.00
176_G305_S0.8691.00
274_F301_I0.8681.00
285_N372_N0.8641.00
375_V378_Y0.8601.00
179_A319_V0.8601.00
258_V288_P0.8541.00
406_F434_V0.8521.00
187_L274_F0.8491.00
125_Q131_H0.8481.00
375_V436_V0.8421.00
174_N341_S0.8421.00
158_I302_H0.8411.00
184_L243_Y0.8331.00
177_Q203_G0.8321.00
265_A292_L0.8321.00
158_I318_Y0.8281.00
407_E419_A0.8261.00
372_N387_V0.8221.00
231_E267_I0.8211.00
121_P124_Y0.8201.00
290_P295_F0.8191.00
220_S249_H0.8141.00
230_L267_I0.8141.00
118_S367_Q0.8111.00
121_P354_S0.8111.00
364_H368_T0.8101.00
120_E123_L0.8061.00
155_V165_T0.8011.00
265_A296_A0.8011.00
218_I225_M0.7961.00
115_D371_R0.7931.00
204_L208_A0.7921.00
408_E411_A0.7911.00
129_M347_L0.7911.00
239_I273_L0.7901.00
181_A336_L0.7881.00
127_K130_V0.7871.00
196_V215_I0.7851.00
403_G419_A0.7841.00
383_T398_P0.7831.00
296_A299_Q0.7811.00
123_L126_L0.7801.00
224_E260_N0.7751.00
206_T209_S0.7731.00
281_Y392_F0.7721.00
316_L340_V0.7691.00
293_A296_A0.7681.00
118_S122_L0.7641.00
415_V453_I0.7611.00
323_R327_E0.7591.00
172_F316_L0.7571.00
382_Y397_L0.7561.00
105_H414_G0.7551.00
196_V208_A0.7541.00
152_D353_V0.7521.00
363_S366_E0.7521.00
195_G242_L0.7451.00
169_H297_P0.7431.00
403_G432_R0.7411.00
184_L241_G0.7371.00
176_G280_S0.7371.00
209_S215_I0.7361.00
359_V363_S0.7361.00
371_R444_L0.7341.00
175_G315_R0.7331.00
415_V450_G0.7331.00
269_K296_A0.7311.00
188_C192_D0.7261.00
107_I453_I0.7251.00
188_C241_G0.7231.00
161_G282_H0.7231.00
198_H424_V0.7211.00
279_A282_H0.7211.00
397_L434_V0.7181.00
354_S358_E0.7181.00
256_M261_R0.7171.00
358_E362_E0.7161.00
377_R380_A0.7161.00
258_V294_S0.7151.00
128_N131_H0.7141.00
230_L242_L0.7141.00
406_F457_L0.7121.00
174_N340_V0.7121.00
121_P360_L0.7121.00
374_L447_L0.7111.00
155_V166_S0.7111.00
394_W433_A0.7091.00
291_A302_H0.7061.00
405_E411_A0.7051.00
298_Q322_P0.7051.00
286_K369_I0.7041.00
151_K167_V0.6981.00
218_I233_A0.6971.00
228_E231_E0.6971.00
360_L363_S0.6951.00
95_A98_L0.6951.00
409_L413_L0.6951.00
360_L364_H0.6941.00
287_N388_E0.6931.00
222_N383_T0.6931.00
234_C271_Y0.6931.00
249_H252_T0.6931.00
182_A333_L0.6931.00
194_I213_V0.6931.00
261_R295_F0.6901.00
171_L321_V0.6871.00
160_R283_L0.6841.00
452_M455_R0.6821.00
248_Y389_T0.6811.00
182_A329_I0.6801.00
221_E229_S0.6801.00
184_L213_V0.6791.00
449_Q456_R0.6741.00
185_A336_L0.6741.00
147_S342_P0.6731.00
370_R373_Q0.6721.00
372_N386_G0.6721.00
363_S367_Q0.6691.00
112_I392_F0.6681.00
142_G339_T0.6621.00
172_F345_A0.6601.00
261_R277_E0.6601.00
225_M230_L0.6591.00
151_K168_D0.6541.00
122_L126_L0.6531.00
157_L282_H0.6531.00
234_C239_I0.6531.00
184_L211_L0.6511.00
142_G342_P0.6471.00
103_P414_G0.6451.00
346_E349_A0.6451.00
343_L347_L0.6441.00
105_H453_I0.6431.00
285_N369_I0.6401.00
122_L131_H0.6391.00
250_N281_Y0.6391.00
109_M436_V0.6391.00
382_Y395_L0.6391.00
242_L268_V0.6371.00
453_I456_R0.6361.00
290_P294_S0.6351.00
379_V395_L0.6351.00
374_L451_L0.6331.00
247_D279_A0.6321.00
165_T293_A0.6321.00
327_E330_S0.6311.00
230_L264_V0.6311.00
183_T303_I0.6271.00
273_L299_Q0.6241.00
417_V436_V0.6221.00
173_A319_V0.6221.00
99_E104_T0.6181.00
193_R237_E0.6181.00
177_Q201_Y0.6171.00
420_A424_V0.6161.00
105_H449_Q0.6151.00
283_L309_S0.6131.00
420_A423_F0.6101.00
378_Y447_L0.6101.00
321_V325_Y0.6091.00
370_R374_L0.6081.00
171_L330_S0.6081.00
178_N182_A0.6081.00
172_F340_V0.6071.00
279_A291_A0.6071.00
310_L348_T0.6061.00
242_L267_I0.6051.00
440_A446_E0.6051.00
180_I207_V0.6041.00
185_A332_A0.6031.00
112_I281_Y0.6031.00
279_A302_H0.6031.00
177_Q338_I0.6001.00
379_V384_C0.6001.00
293_A300_V0.6001.00
375_V438_V0.5981.00
324_Q327_E0.5971.00
268_V272_N0.5961.00
277_E302_H0.5951.00
316_L344_L0.5941.00
132_E350_R0.5891.00
173_A317_A0.5881.00
296_A300_V0.5881.00
182_A332_A0.5871.00
307_S315_R0.5851.00
411_A416_Q0.5831.00
122_L129_M0.5821.00
142_G147_S0.5801.00
274_F325_Y0.5771.00
284_L365_R0.5771.00
268_V271_Y0.5761.00
125_Q347_L0.5751.00
197_D218_I0.5731.00
154_A306_L0.5721.00
361_I365_R0.5711.00
223_D259_E0.5711.00
377_R386_G0.5711.00
165_T169_H0.5671.00
400_K458_L0.5651.00
427_N431_E0.5641.00
265_A269_K0.5631.00
385_L396_L0.5621.00
216_V233_A0.5611.00
342_P346_E0.5581.00
227_P231_E0.5581.00
155_V159_Q0.5571.00
227_P264_V0.5571.00
129_M350_R0.5561.00
106_L414_G0.5561.00
219_K226_S0.5551.00
402_S421_E0.5551.00
150_Q154_A0.5551.00
256_M260_N0.5551.00
197_D225_M0.5521.00
216_V239_I0.5511.00
453_I457_L0.5501.00
188_C240_K0.5491.00
407_E411_A0.5481.00
322_P325_Y0.5481.00
202_P422_R0.5461.00
107_I449_Q0.5461.00
373_Q376_N0.5461.00
218_I229_S0.5441.00
356_Q359_V0.5431.00
292_L295_F0.5391.00
222_N385_L0.5391.00
355_N358_E0.5371.00
108_E111_A0.5351.00
180_I276_I0.5331.00
308_K315_R0.5321.00
394_W435_R0.5311.00
200_T205_K0.5311.00
347_L350_R0.5311.00
368_T439_C0.5311.00
147_S345_A0.5291.00
192_D238_N0.5291.00
247_D255_F0.5291.00
159_Q162_G0.5281.00
395_L433_A0.5271.00
179_A317_A0.5271.00
244_L256_M0.5261.00
247_D261_R0.5241.00
397_L400_K0.5231.00
379_V382_Y0.5221.00
108_E416_Q0.5221.00
200_T245_I0.5221.00
196_V205_K0.5211.00
201_Y338_I0.5181.00
379_V451_L0.5181.00
381_G398_P0.5151.00
217_P425_V0.5131.00
189_K240_K0.5121.00
406_F411_A0.5121.00
359_V362_E0.5101.00
97_L100_D0.5101.00
256_M264_V0.5101.00
346_E350_R0.5091.00
110_G416_Q0.5081.00
268_V299_Q0.5081.00
117_A123_L0.5081.00
159_Q163_F0.5071.00
103_P106_L0.5071.00
380_A383_T0.5051.00
310_L358_E0.5041.00
121_P125_Q0.5031.00
222_N260_N0.5021.00
384_C393_R0.5021.00
265_A268_V0.5021.00
403_G434_V0.5011.00
216_V235_K0.5001.00
129_M132_E0.5001.00
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 0.9416 100 0.318 Contact Map
3pplA 2 0.8225 100 0.383 Contact Map
3f6tA 2 0.868 100 0.401 Contact Map
3qguA 2 0.829 100 0.41 Contact Map
3ez1A 2 0.8009 100 0.413 Contact Map
2x5fA 2 0.8485 100 0.427 Contact Map
3d6kA 2 0.8074 100 0.439 Contact Map
2r2nA 2 0.8398 100 0.451 Contact Map
1vp4A 2 0.8506 100 0.46 Contact Map
4je5A 2 0.8463 100 0.466 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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