GREMLIN Database
YHDI - Uncharacterized HTH-type transcriptional regulator YhdI
UniProt: O07578 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 469 (361)
Sequences: 23659 (16036)
Seq/√Len: 844.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
130_V134_D3.2541.00
371_K448_E3.2511.00
370_R374_A2.9421.00
195_K216_D2.8801.00
233_Y268_E2.8561.00
256_I260_Q2.6561.00
161_R167_N2.6031.00
389_E402_R2.5561.00
419_H460_T2.5561.00
375_V452_R2.4711.00
190_L215_M2.3971.00
176_G182_L2.3051.00
453_L457_K2.2841.00
194_T238_Y2.2811.00
151_E350_A2.1841.00
155_M354_E2.1731.00
123_N127_K2.1441.00
415_A418_D2.1441.00
157_A170_P2.1141.00
223_D258_R2.0371.00
270_N300_R2.0261.00
266_A273_I2.0151.00
149_E347_L2.0111.00
447_S450_D1.9811.00
415_A461_A1.9461.00
379_A452_R1.9371.00
131_K351_D1.9221.00
377_L392_G1.9191.00
379_A455_I1.9151.00
379_A456_Q1.9041.00
459_K463_A1.9031.00
375_V448_E1.8971.00
322_V327_M1.8911.00
150_Y154_H1.8881.00
186_L302_I1.8831.00
110_F454_G1.8721.00
453_L456_Q1.8331.00
200_E219_P1.8171.00
221_C231_E1.8151.00
158_R354_E1.8071.00
231_E234_R1.7941.00
147_Q331_Q1.7881.00
154_H170_P1.7731.00
408_S411_E1.7671.00
172_Q324_P1.7461.00
377_L381_R1.7381.00
229_P261_E1.7261.00
307_F349_L1.7211.00
228_L231_E1.7111.00
378_E382_S1.7081.00
260_Q264_A1.7041.00
419_H457_K1.7001.00
274_I304_L1.7001.00
195_K218_T1.7001.00
162_L359_Q1.6971.00
256_I290_P1.6911.00
126_R130_V1.6741.00
255_T258_R1.6691.00
376_L455_I1.6511.00
261_E264_A1.6501.00
129_I348_A1.6321.00
320_M330_I1.6251.00
233_Y261_E1.6181.00
267_A298_N1.6081.00
155_M158_R1.6061.00
264_A268_E1.6051.00
154_H158_R1.6021.00
192_P214_H1.5961.00
368_L448_E1.5961.00
197_G237_P1.5911.00
356_G360_K1.5901.00
147_Q153_R1.5851.00
423_L439_V1.5721.00
151_E354_E1.5711.00
379_A382_S1.5641.00
375_V379_A1.5611.00
105_A420_G1.5491.00
200_E221_C1.5381.00
402_R438_S1.5321.00
129_I133_L1.5271.00
342_S345_S1.5201.00
368_L371_K1.5191.00
351_D355_T1.5171.00
317_L349_L1.5021.00
127_K131_K1.4911.00
278_Y306_T1.4821.00
377_L399_I1.4791.00
128_S351_D1.4771.00
285_S394_N1.4751.00
155_M350_A1.4731.00
160_V321_I1.4631.00
376_L399_I1.4611.00
381_R390_I1.4581.00
350_A354_E1.4531.00
239_L274_I1.4481.00
229_P265_W1.4451.00
158_R162_L1.4391.00
230_D261_E1.4371.00
379_A459_K1.4361.00
264_A267_A1.4301.00
168_C321_I1.4251.00
381_R392_G1.4201.00
377_L390_I1.4111.00
409_E427_S1.4071.00
374_A378_E1.4061.00
150_Y170_P1.3931.00
265_W271_S1.3861.00
187_C210_F1.3851.00
195_K236_N1.3841.00
233_Y269_T1.3811.00
266_A271_S1.3791.00
210_F215_M1.3621.00
171_G324_P1.3611.00
197_G220_I1.3561.00
411_E415_A1.3431.00
411_E414_Q1.3411.00
416_A458_L1.3371.00
291_S294_G1.3361.00
382_S459_K1.3161.00
179_T304_L1.3041.00
256_I295_L1.3031.00
448_E452_R1.3021.00
128_S131_K1.2941.00
450_D453_L1.2921.00
456_Q460_T1.2901.00
153_R157_A1.2831.00
368_L372_K1.2781.00
363_N366_R1.2761.00
258_R261_E1.2701.00
163_S359_Q1.2701.00
305_G319_F1.2671.00
265_W269_T1.2651.00
413_I423_L1.2631.00
257_T260_Q1.2631.00
196_I210_F1.2441.00
363_N367_S1.2411.00
334_V338_K1.2401.00
400_L426_V1.2381.00
191_K194_T1.2331.00
410_E427_S1.2201.00
373_H377_L1.2191.00
452_R456_Q1.2131.00
351_D354_E1.2081.00
156_I319_F1.2051.00
186_L274_I1.1971.00
156_I175_I1.1921.00
127_K130_V1.1901.00
267_A300_R1.1881.00
177_A181_V1.1801.00
257_T261_E1.1681.00
195_K237_P1.1661.00
322_V330_I1.1611.00
196_I239_L1.1611.00
240_M271_S1.1601.00
260_Q295_L1.1571.00
328_E332_N1.1441.00
367_S370_R1.1361.00
419_H461_A1.1341.00
373_H443_Y1.1301.00
188_L333_N1.1291.00
402_R437_T1.1291.00
283_R289_I1.1261.00
126_R134_D1.1231.00
169_E324_P1.1231.00
128_S132_S1.1221.00
408_S436_F1.1211.00
172_Q327_M1.1151.00
225_E258_R1.1061.00
152_L175_I1.0961.00
173_I321_I1.0951.00
273_I292_L1.0891.00
169_E172_Q1.0831.00
382_S452_R1.0791.00
207_R211_E1.0721.00
140_F347_L1.0721.00
157_A173_I1.0711.00
99_G103_K1.0691.00
329_P332_N1.0691.00
304_L320_M1.0681.00
378_E452_R1.0671.00
421_V458_L1.0651.00
189_S239_L1.0631.00
227_V240_M1.0631.00
327_M331_Q1.0611.00
174_I327_M1.0571.00
174_I330_I1.0511.00
151_E347_L1.0491.00
375_V378_E1.0461.00
187_C190_L1.0451.00
367_S371_K1.0421.00
302_I322_V1.0411.00
416_A423_L1.0371.00
197_G232_L1.0341.00
310_S358_W1.0301.00
182_L304_L1.0231.00
126_R133_L1.0201.00
188_L330_I1.0101.00
302_I326_L1.0091.00
159_F359_Q1.0081.00
206_S241_Y1.0031.00
150_Y153_R1.0011.00
149_E350_A1.0011.00
182_L320_M0.9911.00
360_K364_R0.9901.00
413_I425_P0.9851.00
200_E432_E0.9851.00
159_F281_E0.9841.00
156_I173_I0.9771.00
388_V401_L0.9751.00
272_F302_I0.9741.00
172_Q298_N0.9721.00
384_L459_K0.9721.00
190_L196_I0.9701.00
148_G153_R0.9651.00
151_E154_H0.9621.00
181_V338_K0.9581.00
158_R161_R0.9531.00
123_N126_R0.9491.00
159_F163_S0.9491.00
410_E414_Q0.9451.00
242_T262_L0.9381.00
263_L301_V0.9331.00
220_I227_V0.9331.00
374_A392_G0.9311.00
110_F451_I0.9301.00
223_D228_L0.9271.00
272_F300_R0.9261.00
208_R211_E0.9261.00
227_V258_R0.9241.00
401_L441_I0.9161.00
166_V293_Q0.9051.00
267_A297_P0.9031.00
186_L330_I0.9021.00
179_T306_T0.8981.00
190_L239_L0.8921.00
293_Q303_Y0.8911.00
290_P295_L0.8901.00
222_S247_Q0.8891.00
184_Q337_M0.8881.00
263_L292_L0.8871.00
361_H364_R0.8821.00
263_L273_I0.8821.00
263_L295_L0.8801.00
417_A422_T0.8791.00
225_E255_T0.8781.00
119_L368_L0.8781.00
155_M353_I0.8771.00
373_H393_K0.8741.00
334_V341_V0.8741.00
416_A461_A0.8721.00
181_V334_V0.8711.00
415_A419_H0.8661.00
285_S373_H0.8651.00
159_F164_R0.8641.00
164_R280_G0.8631.00
285_S370_R0.8591.00
226_G258_R0.8571.00
233_Y265_W0.8551.00
106_P450_D0.8531.00
298_N301_V0.8511.00
163_S281_E0.8501.00
296_D299_G0.8451.00
157_A169_E0.8441.00
160_V303_Y0.8441.00
388_V403_L0.8421.00
230_D234_R0.8391.00
211_E217_V0.8381.00
292_L301_V0.8371.00
210_F217_V0.8351.00
131_K138_G0.8341.00
277_D280_G0.8321.00
347_L350_A0.8311.00
199_E247_Q0.8311.00
364_R367_S0.8281.00
157_A168_C0.8261.00
115_V369_Y0.8231.00
124_A361_H0.8231.00
378_E381_R0.8231.00
299_G323_P0.8221.00
263_L296_D0.8171.00
177_A342_S0.8161.00
412_A461_A0.8151.00
267_A296_D0.8141.00
229_P258_R0.8141.00
384_L387_T0.8091.00
371_K375_V0.8071.00
403_L439_V0.8061.00
364_R368_L0.8021.00
189_S272_F0.8001.00
324_P328_E0.7971.00
127_K134_D0.7961.00
124_A351_D0.7961.00
400_L438_S0.7961.00
153_R170_P0.7951.00
131_K134_D0.7931.00
237_P271_S0.7931.00
373_H392_G0.7901.00
412_A439_V0.7901.00
376_L451_I0.7881.00
106_P420_G0.7881.00
232_L265_W0.7871.00
287_H394_N0.7841.00
154_H354_E0.7831.00
457_K460_T0.7811.00
361_H365_M0.7711.00
132_S348_A0.7711.00
409_E425_P0.7701.00
376_L379_A0.7681.00
124_A127_K0.7671.00
116_D372_K0.7661.00
256_I288_P0.7661.00
359_Q363_N0.7651.00
131_K355_T0.7611.00
421_V457_K0.7601.00
384_L455_I0.7601.00
104_N420_G0.7591.00
254_M259_R0.7591.00
187_C239_L0.7581.00
187_C241_Y0.7581.00
409_E437_T0.7571.00
246_H395_S0.7541.00
317_L341_V0.7531.00
426_V438_S0.7501.00
446_L450_D0.7381.00
174_I331_Q0.7381.00
185_N330_I0.7371.00
174_I322_V0.7371.00
302_I320_M0.7371.00
227_V232_L0.7331.00
407_A411_E0.7321.00
232_L240_M0.7321.00
409_E413_I0.7251.00
449_E452_R0.7221.00
376_L441_I0.7221.00
181_V185_N0.7191.00
290_P294_G0.7191.00
206_S210_F0.7171.00
200_E430_Y0.7161.00
160_V319_F0.7151.00
360_K363_N0.7151.00
187_C213_N0.7141.00
228_L258_R0.7131.00
180_T205_R0.7131.00
421_V454_G0.7121.00
175_I317_L0.7121.00
195_K235_Q0.7081.00
372_K448_E0.7081.00
224_A391_L0.7071.00
293_Q296_D0.7071.00
119_L125_W0.7051.00
384_L388_V0.7041.00
149_E343_A0.7031.00
380_I455_I0.7031.00
380_I390_I0.7021.00
124_A355_T0.7011.00
108_I457_K0.7011.00
230_D233_Y0.7011.00
296_D300_R0.6991.00
144_G343_A0.6991.00
371_K374_A0.6941.00
307_F319_F0.6941.00
365_M369_Y0.6901.00
144_G149_E0.6891.00
247_Q250_I0.6881.00
240_M265_W0.6841.00
328_E331_Q0.6831.00
357_E360_K0.6831.00
460_T463_A0.6831.00
204_H428_P0.6801.00
179_T278_Y0.6781.00
414_Q418_D0.6771.00
456_Q459_K0.6721.00
219_P431_I0.6711.00
374_A377_L0.6701.00
380_I401_L0.6701.00
175_I341_V0.6691.00
132_S351_D0.6691.00
198_F217_V0.6661.00
376_L443_Y0.6651.00
272_F326_L0.6651.00
256_I294_G0.6621.00
123_N134_D0.6621.00
457_K461_A0.6621.00
223_D231_E0.6611.00
224_A389_E0.6611.00
221_C228_L0.6601.00
126_R129_I0.6581.00
362_I366_R0.6581.00
430_Y435_P0.6561.00
407_A415_A0.6561.00
283_R286_G0.6521.00
317_L345_S0.6521.00
197_G240_M0.6501.00
113_G398_H0.6491.00
240_M266_A0.6481.00
107_A420_G0.6481.00
242_T254_M0.6481.00
293_Q301_V0.6481.00
355_T359_Q0.6461.00
109_D422_T0.6461.00
198_F210_F0.6441.00
159_F280_G0.6431.00
347_L351_D0.6421.00
427_S436_F0.6421.00
124_A357_E0.6401.00
245_S277_D0.6401.00
100_L105_A0.6401.00
199_E220_I0.6391.00
177_A341_V0.6371.00
311_L349_L0.6351.00
281_E310_S0.6341.00
196_I215_M0.6341.00
199_E227_V0.6331.00
389_E404_L0.6321.00
144_G340_T0.6311.00
296_D301_V0.6301.00
229_P233_Y0.6281.00
283_R288_P0.6271.00
263_L267_A0.6271.00
187_C215_M0.6241.00
96_V99_G0.6231.00
128_S348_A0.6231.00
129_I344_H0.6181.00
445_G450_D0.6171.00
423_L441_I0.6171.00
222_S252_T0.6161.00
185_N333_N0.6151.00
254_M258_R0.6141.00
379_A451_I0.6141.00
410_E425_P0.6121.00
366_R370_R0.6121.00
404_L437_T0.6111.00
254_M262_L0.6101.00
176_G320_M0.6091.00
391_L402_R0.6091.00
183_L274_I0.6091.00
186_L304_L0.6061.00
195_K238_Y0.6041.00
182_L318_S0.6031.00
407_A412_A0.6021.00
266_A270_N0.6021.00
229_P262_L0.6011.00
453_L460_T0.6011.00
190_L194_T0.6011.00
412_A416_A0.5991.00
111_H422_T0.5971.00
168_C172_Q0.5951.00
246_H283_R0.5941.00
369_Y444_G0.5941.00
390_I399_I0.5931.00
121_P124_A0.5931.00
185_N334_V0.5921.00
106_P453_L0.5891.00
104_N107_A0.5891.00
345_S348_A0.5881.00
156_I305_G0.5851.00
284_Y370_R0.5841.00
175_I346_Q0.5801.00
220_I231_E0.5801.00
414_Q417_A0.5801.00
267_A299_G0.5801.00
259_R295_L0.5771.00
232_L262_L0.5761.00
149_E346_Q0.5761.00
198_F207_R0.5751.00
375_V451_I0.5751.00
124_A128_S0.5731.00
402_R436_F0.5721.00
178_G316_R0.5701.00
202_G207_R0.5701.00
406_P437_T0.5701.00
380_I384_L0.5701.00
259_R292_L0.5681.00
194_T236_N0.5671.00
245_S259_R0.5651.00
426_V430_Y0.5641.00
323_P326_L0.5641.00
161_R165_G0.5641.00
356_G359_Q0.5631.00
412_A462_W0.5611.00
430_Y438_S0.5611.00
379_A384_L0.5601.00
98_P102_Q0.5581.00
253_I283_R0.5581.00
275_E292_L0.5581.00
127_K355_T0.5581.00
291_S303_Y0.5561.00
322_V326_L0.5561.00
176_G318_S0.5531.00
344_H348_A0.5521.00
110_F441_I0.5511.00
130_V133_L0.5501.00
283_R366_R0.5481.00
184_Q213_N0.5481.00
154_H157_A0.5461.00
184_Q209_M0.5451.00
132_S347_L0.5441.00
261_E265_W0.5431.00
124_A360_K0.5431.00
100_L103_K0.5431.00
227_V262_L0.5411.00
225_E257_T0.5411.00
292_L295_L0.5411.00
284_Y443_Y0.5401.00
207_R219_P0.5401.00
218_T237_P0.5401.00
370_R373_H0.5401.00
98_P101_H0.5391.00
186_L239_L0.5381.00
263_L266_A0.5351.00
240_M273_I0.5331.00
413_I417_A0.5281.00
284_Y373_H0.5271.00
157_A161_R0.5271.00
387_T390_I0.5241.00
147_Q174_I0.5241.00
183_L209_M0.5231.00
118_T447_S0.5221.00
228_L233_Y0.5211.00
153_R173_I0.5211.00
277_D291_S0.5201.00
280_G305_G0.5191.00
413_I439_V0.5161.00
106_P457_K0.5151.00
109_D112_Q0.5141.00
378_E392_G0.5141.00
245_S253_I0.5141.00
108_I454_G0.5131.00
107_A422_T0.5121.00
307_F353_I0.5101.00
186_L189_S0.5101.00
193_G216_D0.5101.00
325_E329_P0.5091.00
181_V184_Q0.5091.00
189_S302_I0.5051.00
156_I307_F0.5041.00
282_F366_R0.5031.00
343_A347_L0.5031.00
125_W352_F0.5021.00
227_V230_D0.5011.00
259_R275_E0.5001.00
108_I453_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 0.968 100 0.272 Contact Map
3pplA 2 0.8252 100 0.379 Contact Map
3qguA 2 0.8252 100 0.402 Contact Map
3f6tA 2 0.8763 100 0.407 Contact Map
3ez1A 2 0.8038 100 0.417 Contact Map
1vp4A 2 0.8571 100 0.436 Contact Map
2r2nA 2 0.8337 100 0.44 Contact Map
3d6kA 2 0.8102 100 0.441 Contact Map
2x5fA 2 0.8401 100 0.444 Contact Map
3aowA 2 0.823 100 0.445 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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