GREMLIN Database
YCXD - Uncharacterized HTH-type transcriptional regulator YcxD
UniProt: Q08792 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 444 (350)
Sequences: 33314 (22972)
Seq/√Len: 1227.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
103_N107_D3.5811.00
348_E430_T3.2371.00
347_K351_L2.9991.00
169_K190_P2.9071.00
134_A139_F2.8731.00
352_R434_E2.7661.00
207_E246_A2.6771.00
234_E238_Q2.6221.00
163_F189_I2.6051.00
148_T154_A2.4691.00
369_T383_V2.4531.00
435_R439_L2.3781.00
128_V331_K2.3361.00
124_S327_E2.3161.00
168_E216_K2.2901.00
396_R399_K2.2581.00
96_L100_H2.2281.00
356_A437_V2.0591.00
299_L304_T1.9921.00
130_R142_E1.9891.00
354_H372_S1.9541.00
356_A438_K1.9391.00
352_R430_T1.9351.00
354_H358_R1.9301.00
156_S160_A1.9191.00
123_P127_R1.8981.00
233_S236_D1.8931.00
205_K209_L1.8801.00
104_K328_I1.8661.00
244_A251_L1.8541.00
203_I239_E1.8461.00
131_K331_K1.8211.00
83_F436_G1.8181.00
122_L324_A1.8141.00
174_Q193_G1.8141.00
169_K192_I1.8091.00
248_D277_H1.8071.00
197_T236_D1.8071.00
429_K432_D1.7931.00
389_P392_R1.7541.00
127_R142_E1.7341.00
158_L279_I1.7311.00
128_V131_K1.7211.00
252_V281_L1.7181.00
238_Q242_R1.7091.00
355_Q359_T1.7041.00
435_R438_K1.6821.00
356_A359_T1.6821.00
345_S430_T1.6541.00
100_H104_K1.6521.00
127_R131_K1.6481.00
99_Q103_N1.6441.00
234_E267_D1.6371.00
356_A441_M1.6281.00
352_R356_A1.6191.00
239_E242_R1.6141.00
144_H301_E1.6131.00
358_R370_F1.6071.00
202_D205_K1.6021.00
205_K208_R1.6011.00
390_A408_D1.5991.00
207_E239_E1.5901.00
120_K308_Y1.5701.00
356_A360_H1.5571.00
404_L421_L1.5351.00
256_Y283_S1.5341.00
356_A434_E1.5291.00
284_F326_L1.5261.00
333_G337_R1.5201.00
353_L380_T1.5181.00
217_F252_V1.5181.00
184_L189_I1.5151.00
242_R246_A1.5101.00
353_L437_V1.5091.00
392_R396_R1.5061.00
165_N188_G1.4991.00
133_L298_V1.4991.00
174_Q195_K1.4971.00
195_K205_K1.4951.00
204_A239_E1.4881.00
169_K214_S1.4801.00
297_A307_F1.4771.00
319_S322_S1.4711.00
140_A298_V1.4511.00
100_H103_N1.4501.00
104_K108_T1.4491.00
354_H370_F1.4461.00
294_V326_L1.4451.00
124_S331_K1.4281.00
430_T434_E1.4261.00
101_C328_I1.4251.00
345_S348_E1.4251.00
210_F243_L1.4241.00
78_P401_G1.4181.00
395_H398_E1.4121.00
360_H441_M1.4101.00
203_I243_L1.4051.00
351_L355_Q1.4021.00
171_A215_I1.3991.00
354_H380_T1.3991.00
327_E331_K1.3901.00
400_Q439_L1.3871.00
207_E211_Q1.3861.00
207_E247_Y1.3821.00
102_I325_A1.3821.00
128_V327_E1.3811.00
120_K126_I1.3781.00
102_I106_I1.3691.00
197_T200_G1.3621.00
159_C184_L1.3581.00
123_P142_E1.3531.00
244_A249_V1.3401.00
392_R395_H1.3391.00
359_T441_M1.3391.00
181_V185_E1.3391.00
328_I332_S1.3341.00
151_V281_L1.3291.00
243_L249_V1.3251.00
235_R238_Q1.3251.00
242_R245_E1.3191.00
171_A194_V1.3191.00
101_C104_K1.3191.00
129_L296_A1.3181.00
243_L247_Y1.3111.00
383_V420_L1.3101.00
170_I184_L1.3081.00
360_H438_K1.2971.00
234_E272_Y1.2871.00
358_R372_S1.2741.00
170_I217_F1.2591.00
238_Q272_Y1.2551.00
236_D239_E1.2471.00
99_Q107_D1.2461.00
282_K296_A1.2451.00
135_T336_G1.2451.00
210_F249_V1.2411.00
263_N375_A1.2381.00
235_R239_E1.2361.00
432_D435_R1.2321.00
381_H407_I1.2191.00
245_E275_S1.2171.00
344_D347_K1.2101.00
169_K215_I1.2001.00
391_S408_D1.1981.00
340_E344_D1.1951.00
218_F249_V1.1851.00
164_P168_E1.1841.00
124_S324_A1.1811.00
143_R301_E1.1801.00
276_S300_P1.1751.00
211_Q247_Y1.1681.00
126_I130_R1.1641.00
350_S425_I1.1581.00
340_E343_R1.1541.00
144_H275_S1.1511.00
306_T309_A1.1451.00
159_C163_F1.1451.00
160_A187_L1.1411.00
345_S349_R1.1401.00
158_L252_V1.1331.00
394_I404_L1.1311.00
385_P419_N1.1291.00
251_L269_L1.1231.00
434_E438_K1.1181.00
311_K315_D1.0891.00
352_R355_Q1.0871.00
169_K211_Q1.0851.00
269_L278_V1.0731.00
268_P271_A1.0711.00
162_P217_F1.0681.00
350_S354_H1.0641.00
146_F304_T1.0611.00
328_I331_K1.0611.00
125_L147_I1.0581.00
113_L324_A1.0481.00
149_S153_Q1.0481.00
132_L135_T1.0471.00
305_D309_A1.0451.00
141_D144_H1.0371.00
163_F170_I1.0341.00
299_L307_F1.0341.00
261_E266_A1.0331.00
144_H304_T1.0271.00
130_R145_I1.0241.00
104_K107_D1.0201.00
245_E277_H1.0151.00
337_R341_K1.0041.00
159_C219_Y1.0031.00
351_L372_S0.9981.00
129_L147_I0.9981.00
153_Q311_K0.9971.00
402_V440_L0.9961.00
391_S395_H0.9901.00
245_E276_S0.9891.00
355_Q434_E0.9821.00
207_E243_L0.9801.00
161_M310_Y0.9771.00
383_V419_N0.9761.00
389_P418_E0.9761.00
141_D301_E0.9731.00
122_L327_E0.9711.00
96_L99_Q0.9691.00
234_E271_A0.9691.00
172_I191_A0.9671.00
382_L423_I0.9661.00
279_I299_L0.9641.00
204_A208_R0.9641.00
360_H437_V0.9601.00
200_G236_D0.9571.00
281_L297_A0.9561.00
181_V193_G0.9541.00
99_Q106_I0.9531.00
145_I298_V0.9531.00
100_H107_D0.9521.00
171_A209_L0.9511.00
132_L259_D0.9511.00
123_P126_I0.9481.00
184_L191_A0.9471.00
101_C105_A0.9451.00
163_F217_F0.9441.00
336_G340_E0.9351.00
135_T259_D0.9331.00
124_S127_R0.9291.00
324_A327_E0.9291.00
241_V278_V0.9291.00
79_G401_G0.9271.00
304_T308_Y0.9241.00
97_D328_I0.9211.00
151_V283_S0.9201.00
199_E236_D0.9181.00
131_K134_A0.9171.00
341_K344_D0.9151.00
211_Q215_I0.9141.00
185_E191_A0.9141.00
279_I303_L0.9111.00
220_T240_L0.9101.00
250_Y277_H0.8991.00
180_M219_Y0.8991.00
97_D332_S0.8991.00
261_E264_K0.8951.00
171_A206_V0.8931.00
129_L145_I0.8921.00
344_D348_E0.8911.00
154_A281_L0.8891.00
396_R400_Q0.8881.00
154_A297_A0.8851.00
196_R225_H0.8851.00
355_Q358_R0.8821.00
138_V270_Y0.8801.00
270_Y280_Y0.8791.00
162_P250_Y0.8781.00
153_Q315_D0.8761.00
338_H341_K0.8761.00
194_V209_L0.8751.00
182_E185_E0.8751.00
384_L421_L0.8641.00
250_Y279_I0.8631.00
263_N347_K0.8631.00
350_S373_G0.8621.00
173_E194_V0.8601.00
368_F384_L0.8601.00
161_M307_F0.8591.00
390_A419_N0.8591.00
349_R430_T0.8581.00
132_L336_G0.8561.00
394_I406_A0.8541.00
130_R141_D0.8541.00
201_L236_D0.8481.00
353_L356_A0.8441.00
395_H399_K0.8431.00
368_F382_L0.8411.00
369_T385_P0.8361.00
132_L136_Q0.8311.00
393_V421_L0.8301.00
279_I297_A0.8281.00
146_F307_F0.8271.00
133_L296_A0.8271.00
121_G126_I0.8231.00
294_V318_C0.8231.00
206_V218_F0.8221.00
301_E305_D0.8201.00
83_F433_I0.8141.00
215_I249_V0.8101.00
72_K76_G0.8041.00
173_E201_L0.8031.00
157_L307_F0.8001.00
128_V330_L0.7961.00
404_L423_I0.7941.00
337_R340_E0.7921.00
206_V243_L0.7921.00
427_N432_D0.7911.00
88_P346_Y0.7911.00
149_S319_S0.7901.00
97_D338_H0.7841.00
203_I236_D0.7841.00
250_Y303_L0.7831.00
108_T328_I0.7821.00
241_V272_Y0.7801.00
97_D100_H0.7801.00
341_K345_S0.7801.00
353_L425_I0.7791.00
350_S372_S0.7771.00
197_T202_D0.7691.00
77_Q401_G0.7691.00
263_N350_S0.7661.00
342_I346_Y0.7611.00
245_E274_L0.7551.00
348_E352_R0.7551.00
159_C217_F0.7531.00
156_S314_N0.7531.00
79_G432_D0.7511.00
158_L307_F0.7501.00
130_R140_A0.7491.00
390_A418_E0.7451.00
225_H228_L0.7451.00
267_D271_A0.7431.00
136_Q258_G0.7421.00
194_V205_K0.7381.00
431_E434_E0.7381.00
201_L218_F0.7371.00
359_T434_E0.7361.00
171_A218_F0.7341.00
203_I207_E0.7341.00
126_I142_E0.7341.00
79_G435_R0.7311.00
348_E351_L0.7281.00
173_E225_H0.7261.00
408_D418_E0.7241.00
311_K318_C0.7241.00
241_V251_L0.7231.00
360_H364_G0.7231.00
390_A394_I0.7211.00
397_L440_L0.7181.00
210_F247_Y0.7161.00
353_L433_I0.7151.00
152_Q179_L0.7141.00
89_D349_R0.7111.00
390_A406_A0.7111.00
105_A325_A0.7091.00
151_V256_Y0.7071.00
339_K343_R0.7061.00
351_L354_H0.7011.00
402_V439_L0.7011.00
381_H420_L0.6991.00
391_S406_A0.6981.00
172_I184_L0.6961.00
133_L280_Y0.6951.00
170_I189_I0.6931.00
353_L423_I0.6891.00
320_M324_A0.6841.00
388_L396_R0.6841.00
393_V396_R0.6831.00
294_V322_S0.6821.00
96_L107_D0.6801.00
127_R130_R0.6791.00
108_T113_L0.6781.00
163_F168_E0.6761.00
338_H342_I0.6731.00
160_A310_Y0.6721.00
192_I209_L0.6721.00
194_V201_L0.6711.00
262_E347_K0.6711.00
174_Q411_Y0.6701.00
199_E233_S0.6691.00
305_D308_Y0.6661.00
267_D272_Y0.6651.00
169_K213_E0.6621.00
324_A328_I0.6611.00
146_F308_Y0.6591.00
273_D276_S0.6551.00
352_R437_V0.6531.00
372_S375_A0.6531.00
204_A207_E0.6471.00
269_L272_Y0.6441.00
259_D287_M0.6421.00
347_K350_S0.6391.00
241_V245_E0.6391.00
232_L237_K0.6381.00
332_S336_G0.6381.00
407_I420_L0.6381.00
265_K375_A0.6381.00
438_K441_M0.6371.00
302_A305_D0.6341.00
388_L392_R0.6331.00
122_L320_M0.6321.00
92_V98_F0.6311.00
237_K272_Y0.6301.00
201_L206_V0.6301.00
230_C375_A0.6301.00
127_R331_K0.6281.00
154_A295_G0.6271.00
180_M184_L0.6221.00
258_G282_K0.6221.00
244_A248_D0.6221.00
370_F380_T0.6201.00
255_D258_G0.6201.00
245_E273_D0.6191.00
91_D99_Q0.6191.00
105_A328_I0.6181.00
147_I294_V0.6181.00
169_K216_K0.6171.00
153_Q157_L0.6171.00
73_S78_P0.6161.00
284_F296_A0.6161.00
224_F376_P0.6161.00
149_S318_C0.6161.00
352_R433_I0.6151.00
105_A108_T0.6151.00
206_V240_L0.6141.00
178_H409_R0.6131.00
382_L420_L0.6131.00
159_C187_L0.6121.00
92_V345_S0.6111.00
218_F244_A0.6111.00
157_L311_K0.6071.00
160_A314_N0.6051.00
173_E218_F0.6051.00
333_G336_G0.6041.00
270_Y273_D0.6041.00
218_F243_L0.6021.00
195_K202_D0.6011.00
132_L258_G0.6011.00
202_D236_D0.6001.00
103_N106_I0.5981.00
172_I193_G0.5981.00
117_G122_L0.5981.00
156_S187_L0.5971.00
146_F299_L0.5971.00
203_I240_L0.5961.00
117_G317_D0.5961.00
210_F215_I0.5951.00
394_I421_L0.5951.00
81_I439_L0.5941.00
174_Q416_P0.5941.00
97_D101_C0.5921.00
117_G320_M0.5911.00
262_E425_I0.5911.00
148_T297_A0.5901.00
105_A324_A0.5891.00
402_V436_G0.5881.00
84_A403_L0.5871.00
241_V269_L0.5851.00
164_P216_K0.5851.00
147_I318_C0.5841.00
102_I321_I0.5831.00
166_G190_P0.5831.00
237_K269_L0.5811.00
97_D333_G0.5811.00
208_R211_Q0.5811.00
241_V273_D0.5801.00
81_I435_R0.5781.00
176_G221_M0.5771.00
86_S379_H0.5741.00
98_F329_Y0.5731.00
273_D278_V0.5731.00
255_D268_P0.5701.00
80_P403_L0.5701.00
237_K253_E0.5681.00
357_I437_V0.5681.00
260_L343_R0.5681.00
357_I382_L0.5671.00
273_D277_H0.5671.00
150_G293_R0.5661.00
241_V274_L0.5661.00
223_R231_S0.5651.00
241_V244_A0.5631.00
95_Y99_Q0.5631.00
159_C189_I0.5621.00
101_C325_A0.5611.00
262_E350_S0.5601.00
98_F289_F0.5591.00
157_L310_Y0.5591.00
343_R347_K0.5581.00
140_A144_H0.5581.00
244_A247_Y0.5581.00
284_F330_L0.5581.00
211_Q246_A0.5571.00
155_L183_Q0.5571.00
163_F216_K0.5551.00
232_L236_D0.5551.00
261_E265_K0.5531.00
244_A277_H0.5501.00
108_T112_D0.5501.00
158_L281_L0.5481.00
172_I181_V0.5471.00
299_L303_L0.5471.00
104_K332_S0.5421.00
397_L404_L0.5421.00
276_S302_A0.5411.00
97_D337_R0.5411.00
80_P401_G0.5411.00
158_L162_P0.5371.00
300_P303_L0.5311.00
325_A328_I0.5301.00
140_A270_Y0.5301.00
223_R255_D0.5281.00
156_S183_Q0.5281.00
193_G412_L0.5271.00
134_A137_Q0.5261.00
371_S383_V0.5241.00
356_A433_I0.5221.00
253_E269_L0.5211.00
336_G339_K0.5211.00
287_M339_K0.5191.00
82_D403_L0.5171.00
232_L240_L0.5171.00
255_D280_Y0.5161.00
257_L379_H0.5151.00
192_I215_I0.5151.00
87_A115_I0.5141.00
388_L393_V0.5111.00
108_T324_A0.5111.00
268_P280_Y0.5111.00
168_E214_S0.5101.00
160_A186_T0.5101.00
147_I323_Q0.5101.00
125_L327_E0.5091.00
285_S293_R0.5081.00
253_E280_Y0.5071.00
137_Q271_A0.5041.00
152_Q177_Y0.5041.00
398_E403_L0.5041.00
134_A138_V0.5031.00
262_E346_Y0.5011.00
230_C236_D0.5001.00
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 0.9617 100 0.255 Contact Map
3pplA 2 0.8671 100 0.327 Contact Map
3f6tA 2 0.8851 100 0.363 Contact Map
3qguA 2 0.8671 100 0.369 Contact Map
3ez1A 2 0.8514 100 0.371 Contact Map
3d6kA 2 0.8559 100 0.392 Contact Map
2x5fA 2 0.8874 100 0.396 Contact Map
2r2nA 2 0.8829 100 0.399 Contact Map
1vp4A 2 0.8896 100 0.405 Contact Map
4je5A 2 0.8941 100 0.416 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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