GREMLIN Database
YTDP - Uncharacterized HTH-type transcriptional regulator YtdP
UniProt: O32071 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 772 (612)
Sequences: 8819 (7987)
Seq/√Len: 322.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
351_P356_E5.2531.00
340_R345_Q3.9121.00
15_K353_N3.7091.00
33_L37_E3.2911.00
346_E370_D3.1941.00
353_N356_E3.0811.00
13_Y325_R2.9461.00
423_Q426_T2.9361.00
338_F365_L2.7371.00
119_T200_A2.6821.00
410_L413_N2.6621.00
218_A293_E2.6481.00
400_E404_R2.6401.00
324_S328_Y2.5141.00
385_Q389_V2.4581.00
444_V448_I2.4251.00
573_K576_A2.4041.00
153_K195_T2.3881.00
11_K14_Y2.3581.00
576_A580_L2.3281.00
441_L444_V2.3011.00
339_A357_L2.2901.00
346_E363_K2.2831.00
439_L443_A2.2561.00
564_L567_A2.2451.00
338_F362_F2.2111.00
477_T480_E2.1941.00
363_K366_K2.1781.00
474_Q549_K2.1771.00
636_K639_E2.1731.00
444_V455_D2.1601.00
404_R407_S2.1591.00
487_E491_M2.1401.00
270_H291_L2.1321.00
505_S526_S2.1291.00
325_R329_K2.1171.00
635_L638_F2.1091.00
303_W307_A2.1061.00
307_A311_I2.0861.00
174_T177_N2.0751.00
106_N110_S2.0731.00
222_F286_F2.0721.00
613_H616_G2.0451.00
575_K578_K2.0381.00
35_S305_T2.0221.00
277_K284_T2.0091.00
613_H617_I1.9961.00
190_L194_N1.9441.00
471_L553_K1.9431.00
341_H365_L1.9381.00
483_A547_D1.9311.00
603_R606_N1.9261.00
596_Q599_I1.9191.00
390_R397_T1.9171.00
334_L338_F1.8991.00
558_K562_H1.8971.00
532_R536_E1.8961.00
505_S523_A1.8941.00
443_A446_S1.8931.00
320_S324_S1.8651.00
618_E625_N1.8491.00
478_K545_D1.8431.00
341_H366_K1.8251.00
390_R394_G1.8181.00
517_K520_T1.7861.00
430_T434_K1.7861.00
478_K549_K1.7611.00
189_P195_T1.7541.00
446_S449_E1.7541.00
566_D569_K1.7461.00
122_S126_K1.7361.00
425_D428_N1.7251.00
250_Q254_A1.7251.00
527_E530_K1.7161.00
626_K630_D1.7131.00
588_F592_T1.7051.00
481_F484_E1.7011.00
376_M380_A1.6951.00
435_K439_L1.6901.00
461_A465_K1.6811.00
611_L625_N1.6661.00
620_F623_E1.6651.00
602_A606_N1.6651.00
403_N407_S1.6641.00
260_G275_Y1.6541.00
335_Y361_S1.6481.00
150_T154_A1.6441.00
625_N629_Y1.6281.00
437_M444_V1.6281.00
63_E67_K1.6251.00
397_T401_V1.6251.00
32_G36_Y1.6221.00
484_E487_E1.6131.00
586_A590_Q1.6051.00
562_H565_F1.5661.00
32_G309_C1.5651.00
390_R395_K1.5641.00
439_L442_F1.5581.00
346_E367_D1.5551.00
625_N638_F1.5411.00
617_I620_F1.5301.00
339_A343_A1.5281.00
490_R536_E1.5211.00
485_L542_F1.5211.00
142_L145_A1.5181.00
426_T429_H1.5161.00
122_S125_K1.5151.00
73_L201_A1.5091.00
623_E627_M1.5071.00
403_N406_E1.5051.00
229_L242_S1.5041.00
392_M396_L1.5031.00
172_E183_N1.5021.00
607_H611_L1.5011.00
335_Y357_L1.4991.00
463_V466_Q1.4891.00
338_F358_I1.4821.00
371_D375_T1.4711.00
436_D439_L1.4691.00
348_Q363_K1.4661.00
560_L564_L1.4651.00
604_F611_L1.4651.00
472_I553_K1.4641.00
540_I544_E1.4601.00
422_L426_T1.4551.00
12_F355_F1.4551.00
589_T592_T1.4531.00
601_I611_L1.4531.00
450_R453_P1.4521.00
477_T481_F1.4511.00
210_K213_P1.4481.00
606_N609_I1.4481.00
512_F515_L1.4461.00
610_E613_H1.4431.00
620_F624_E1.4401.00
40_Q44_I1.4341.00
385_Q388_M1.4221.00
39_S301_I1.4221.00
446_S450_R1.4191.00
625_N628_L1.4161.00
349_Q363_K1.4011.00
625_N632_I1.3991.00
557_P564_L1.3981.00
478_K481_F1.3931.00
269_I290_S1.3891.00
404_R413_N1.3851.00
573_K580_L1.3821.00
357_L360_Q1.3801.00
179_R206_C1.3791.00
207_S210_K1.3781.00
183_N202_S1.3771.00
585_Q588_F1.3741.00
414_W421_V1.3731.00
358_I362_F1.3721.00
145_A148_A1.3701.00
264_T271_Y1.3701.00
37_E41_K1.3691.00
172_E202_S1.3681.00
616_G620_F1.3631.00
574_E578_K1.3611.00
489_A495_K1.3601.00
225_D229_L1.3591.00
155_S164_N1.3571.00
146_A152_Q1.3531.00
534_K537_N1.3501.00
241_E245_N1.3481.00
467_Q470_I1.3441.00
523_A526_S1.3401.00
606_N610_E1.3371.00
578_K581_H1.3331.00
300_S304_I1.3301.00
299_K302_G1.3271.00
624_E627_M1.3241.00
338_F361_S1.3221.00
384_Q388_M1.3181.00
24_S27_P1.3161.00
291_L295_K1.3131.00
449_E453_P1.3091.00
399_E403_N1.3061.00
565_F569_K1.3001.00
614_V618_E1.2991.00
10_Y14_Y1.2951.00
562_H566_D1.2951.00
375_T378_Q1.2941.00
334_L358_I1.2921.00
567_A570_A1.2891.00
392_M395_K1.2851.00
420_L425_D1.2831.00
34_F38_H1.2811.00
98_Y102_N1.2811.00
595_Y599_I1.2781.00
434_K437_M1.2641.00
150_T153_K1.2641.00
589_T593_N1.2631.00
479_E550_K1.2601.00
220_N234_N1.2591.00
389_V392_M1.2581.00
65_I69_V1.2561.00
601_I605_L1.2561.00
471_L552_F1.2551.00
221_L287_S1.2531.00
608_V618_E1.2521.00
147_S151_K1.2511.00
432_Y436_D1.2481.00
476_G554_T1.2441.00
46_N50_E1.2421.00
39_S43_A1.2361.00
265_V270_H1.2351.00
396_L400_E1.2341.00
362_F366_K1.2331.00
402_D406_E1.2331.00
27_P312_L1.2321.00
334_L359_E1.2291.00
491_M494_E1.2251.00
534_K538_K1.2171.00
306_F310_L1.2161.00
625_N639_E1.2151.00
44_I48_S1.2131.00
51_K55_L1.2091.00
143_H149_Y1.2051.00
488_T535_A1.2041.00
377_K381_T1.2021.00
24_S316_S1.2011.00
437_M441_L1.2011.00
263_E291_L1.2001.00
415_R419_L1.1991.00
582_A585_Q1.1961.00
326_H329_K1.1941.00
210_K214_G1.1921.00
97_I100_Q1.1901.00
31_V35_S1.1901.00
609_I613_H1.1881.00
304_I307_A1.1861.00
339_A361_S1.1851.00
440_L443_A1.1841.00
147_S150_T1.1831.00
444_V452_I1.1761.00
560_L567_A1.1741.00
433_E437_M1.1731.00
489_A493_Q1.1721.00
637_T640_D1.1691.00
145_A153_K1.1671.00
316_S320_S1.1661.00
394_G397_T1.1641.00
120_L188_L1.1641.00
390_R396_L1.1611.00
397_T400_E1.1601.00
271_Y290_S1.1581.00
470_I474_Q1.1571.00
303_W306_F1.1481.00
413_N416_H1.1471.00
438_D442_F1.1461.00
378_Q382_H1.1461.00
115_L201_A1.1451.00
561_Q564_L1.1451.00
366_K370_D1.1411.00
555_H559_Q1.1381.00
448_I451_N1.1371.00
17_I21_C1.1331.00
409_G412_Q1.1331.00
580_L590_Q1.1321.00
376_M379_Q1.1311.00
217_N293_E1.1281.00
13_Y17_I1.1271.00
143_H146_A1.1261.00
417_L421_V1.1251.00
359_E363_K1.1251.00
374_E377_K1.1241.00
349_Q359_E1.1241.00
416_H419_L1.1171.00
560_L563_E1.1171.00
358_I365_L1.1171.00
632_I639_E1.1161.00
475_S553_K1.1151.00
102_N106_N1.1141.00
462_V466_Q1.1121.00
271_Y288_L1.1121.00
339_A364_Q1.1111.00
442_F446_S1.1111.00
149_Y153_K1.1081.00
578_K582_A1.1031.00
531_Y534_K1.1001.00
608_V611_L1.1001.00
444_V451_N1.0981.00
299_K303_W1.0961.00
29_I33_L1.0931.00
248_F252_V1.0891.00
59_Q63_E1.0871.00
453_P456_K1.0861.00
567_A571_G1.0861.00
437_M447_L1.0851.00
636_K640_D1.0841.00
561_Q565_F1.0841.00
607_H625_N1.0801.00
55_L59_Q1.0791.00
530_K534_K1.0771.00
317_L321_W1.0771.00
412_Q416_H1.0761.00
526_S530_K1.0731.00
431_P438_D1.0721.00
373_E376_M1.0721.00
70_D74_T1.0711.00
250_Q253_L1.0681.00
145_A149_Y1.0671.00
627_M630_D1.0641.00
220_N288_L1.0611.00
338_F341_H1.0611.00
475_S546_L1.0591.00
99_N103_Q1.0581.00
179_R204_P1.0571.00
220_N233_H1.0541.00
20_F320_S1.0531.00
185_I198_L1.0491.00
346_E366_K1.0471.00
585_Q589_T1.0421.00
318_L322_L1.0411.00
206_C210_K1.0401.00
474_Q477_T1.0371.00
37_E40_Q1.0361.00
434_K438_D1.0361.00
146_A149_Y1.0351.00
523_A527_E1.0331.00
435_K438_D1.0331.00
490_R540_I1.0331.00
440_L444_V1.0301.00
336_E339_A1.0281.00
437_M440_L1.0261.00
473_N477_T1.0261.00
590_Q593_N1.0261.00
563_E567_A1.0261.00
445_N449_E1.0251.00
472_I554_T1.0251.00
559_Q562_H1.0241.00
146_A150_T1.0201.00
390_R393_L1.0191.00
608_V625_N1.0141.00
251_K257_A1.0141.00
145_A150_T1.0131.00
365_L369_N1.0131.00
67_K70_D1.0111.00
627_M631_Q1.0091.00
59_Q278_S1.0091.00
463_V467_Q1.0061.00
587_I590_Q1.0031.00
592_T596_Q1.0031.00
471_L556_F1.0021.00
55_L287_S1.0011.00
127_W130_N0.9981.00
28_V31_V0.9971.00
451_N454_T0.9921.00
324_S327_F0.9921.00
335_Y339_A0.9911.00
370_D374_E0.9911.00
553_K557_P0.9901.00
614_V625_N0.9891.00
393_L397_T0.9871.00
417_L424_I0.9861.00
613_H620_F0.9851.00
226_E282_A0.9831.00
73_L186_K0.9821.00
430_T433_E0.9821.00
352_Q356_E0.9801.00
416_H425_D0.9781.00
544_E548_Q0.9771.00
605_L609_I0.9771.00
44_I295_K0.9761.00
10_Y18_T0.9721.00
356_E359_E0.9671.00
273_V286_F0.9671.00
416_H420_L0.9661.00
332_R335_Y0.9641.00
190_L196_K0.9641.00
333_V336_E0.9621.00
397_T402_D0.9611.00
367_D371_D0.9601.00
164_N189_P0.9601.00
512_F521_A0.9591.00
438_D447_L0.9571.00
397_T404_R0.9571.00
314_T318_L0.9561.00
148_A153_K0.9551.00
337_S362_F0.9541.00
537_N541_I0.9531.00
401_V405_F0.9531.00
419_L423_Q0.9531.00
390_R401_V0.9531.00
119_T202_S0.9511.00
103_Q106_N0.9501.00
580_L583_I0.9491.00
249_V252_V0.9481.00
349_Q353_N0.9421.00
399_E402_D0.9391.00
170_T227_K0.9391.00
171_K225_D0.9381.00
377_K380_A0.9351.00
36_Y302_G0.9341.00
462_V465_K0.9341.00
423_Q427_L0.9331.00
15_K326_H0.9321.00
396_L399_E0.9301.00
541_I545_D0.9281.00
381_T384_Q0.9261.00
144_E148_A0.9261.00
499_E506_I0.9241.00
107_Y110_S0.9221.00
614_V617_I0.9221.00
464_D467_Q0.9211.00
167_L185_I0.9211.00
557_P560_L0.9191.00
311_I315_L0.9191.00
63_E280_Y0.9181.00
611_L618_E0.9181.00
472_I557_P0.9181.00
248_F253_L0.9171.00
189_P193_T0.9171.00
257_A260_G0.9161.00
372_L376_M0.9131.00
447_L450_R0.9131.00
420_L427_L0.9121.00
401_V407_S0.9101.00
101_V105_L0.9071.00
48_S52_F0.9071.00
151_K155_S0.9051.00
434_K441_L0.9051.00
486_N490_R0.9021.00
32_G305_T0.9021.00
630_D634_E0.9011.00
387_F390_R0.9011.00
501_Q526_S0.9001.00
557_P567_A0.9001.00
481_F538_K0.8991.00
363_K367_D0.8971.00
388_M392_M0.8951.00
514_V525_G0.8951.00
630_D633_F0.8911.00
457_H460_P0.8901.00
235_N238_D0.8901.00
341_H369_N0.8881.00
149_Y198_L0.8881.00
340_R365_L0.8881.00
443_A447_L0.8861.00
612_M619_L0.8821.00
16_L20_F0.8821.00
151_K154_A0.8801.00
71_H74_T0.8801.00
21_C317_L0.8781.00
604_F608_V0.8781.00
144_E149_Y0.8771.00
485_L536_E0.8751.00
433_E436_D0.8751.00
431_P434_K0.8751.00
548_Q551_T0.8751.00
233_H238_D0.8751.00
584_L590_Q0.8721.00
461_A464_D0.8711.00
66_L69_V0.8711.00
556_F564_L0.8711.00
461_A567_A0.8691.00
252_V286_F0.8671.00
222_F233_H0.8641.00
615_L619_L0.8631.00
173_G178_C0.8631.00
487_E490_R0.8601.00
330_P351_P0.8591.00
251_K254_A0.8561.00
532_R542_F0.8561.00
432_Y435_K0.8541.00
146_A153_K0.8531.00
473_N476_G0.8521.00
470_I473_N0.8511.00
538_K541_I0.8501.00
125_K144_E0.8501.00
537_N540_I0.8491.00
100_Q103_Q0.8481.00
298_A302_G0.8481.00
409_G413_N0.8481.00
144_E147_S0.8461.00
374_E378_Q0.8461.00
610_E614_V0.8451.00
411_K414_W0.8451.00
447_L451_N0.8431.00
187_Q195_T0.8431.00
395_K399_E0.8401.00
476_G480_E0.8391.00
406_E409_G0.8391.00
72_S75_H0.8391.00
331_I358_I0.8351.00
451_N455_D0.8341.00
64_H67_K0.8331.00
333_V337_S0.8331.00
372_L380_A0.8331.00
171_K180_Y0.8331.00
604_F607_H0.8321.00
330_P334_L0.8311.00
580_L594_P0.8301.00
272_K291_L0.8291.00
12_F327_F0.8281.00
25_T313_L0.8281.00
302_G306_F0.8271.00
58_T61_S0.8241.00
168_I184_L0.8241.00
557_P561_Q0.8221.00
10_Y15_K0.8201.00
169_S183_N0.8191.00
579_C590_Q0.8191.00
169_S172_E0.8181.00
347_K363_K0.8171.00
448_I452_I0.8171.00
573_K590_Q0.8171.00
593_N600_A0.8161.00
224_I286_F0.8151.00
494_E506_I0.8141.00
421_V428_N0.8141.00
617_I621_E0.8121.00
563_E566_D0.8101.00
599_I603_R0.8101.00
344_I365_L0.8101.00
441_L455_D0.8051.00
420_L423_Q0.8021.00
19_F323_G0.8021.00
50_E53_D0.8001.00
52_F56_Q0.7991.00
181_N202_S0.7981.00
321_W325_R0.7941.00
405_F408_L0.7931.00
35_S39_S0.7931.00
453_P457_H0.7921.00
42_T46_N0.7921.00
69_V72_S0.7921.00
300_S303_W0.7911.00
625_N636_K0.7901.00
77_V186_K0.7881.00
155_S165_N0.7881.00
297_E300_S0.7851.00
631_Q635_L0.7851.00
469_T561_Q0.7841.00
394_G400_E0.7831.00
404_R410_L0.7831.00
555_H558_K0.7821.00
626_K629_Y0.7821.00
480_E551_T0.7811.00
502_L510_Q0.7781.00
379_Q382_H0.7771.00
364_Q368_R0.7771.00
242_S245_N0.7751.00
105_L109_Q0.7751.00
343_A364_Q0.7731.00
413_N417_L0.7721.00
546_L550_K0.7721.00
596_Q600_A0.7711.00
593_N596_Q0.7711.00
149_Y152_Q0.7701.00
141_T146_A0.7701.00
541_I544_E0.7681.00
21_C27_P0.7681.00
497_E526_S0.7630.99
296_K300_S0.7630.99
601_I604_F0.7630.99
67_K71_H0.7630.99
337_S347_K0.7620.99
474_Q552_F0.7610.99
166_H186_K0.7610.99
222_F288_L0.7600.99
543_Y547_D0.7580.99
325_R332_R0.7560.99
117_N202_S0.7550.99
290_S293_E0.7550.99
195_T198_L0.7540.99
68_T71_H0.7520.99
548_Q552_F0.7480.99
472_I475_S0.7460.99
328_Y332_R0.7430.99
557_P563_E0.7420.99
174_T178_C0.7410.99
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586_A593_N0.5410.95
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335_Y355_F0.5400.95
27_P316_S0.5400.95
339_A342_G0.5400.95
547_D554_T0.5390.95
13_Y328_Y0.5390.95
277_K282_A0.5380.95
588_F593_N0.5380.95
54_T58_T0.5370.95
58_T221_L0.5370.95
515_L520_T0.5350.95
590_Q594_P0.5350.95
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597_F607_H0.5330.95
592_T595_Y0.5320.95
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488_T529_L0.5320.95
142_L150_T0.5310.95
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183_N200_A0.5300.95
465_K560_L0.5300.95
149_Y155_S0.5290.95
345_Q365_L0.5290.95
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312_L316_S0.5280.94
615_L622_L0.5280.94
414_W420_L0.5260.94
489_A496_A0.5260.94
442_F445_N0.5260.94
481_F542_F0.5240.94
586_A589_T0.5240.94
619_L625_N0.5240.94
468_A556_F0.5240.94
229_L232_L0.5230.94
577_D581_H0.5230.94
503_S507_G0.5230.94
36_Y40_Q0.5220.94
330_P358_I0.5220.94
173_G180_Y0.5210.94
505_S530_K0.5200.94
525_G531_Y0.5200.94
20_F23_L0.5200.94
322_L326_H0.5180.94
337_S340_R0.5180.94
17_I22_L0.5180.94
507_G510_Q0.5160.94
338_F369_N0.5140.94
543_Y546_L0.5140.94
580_L593_N0.5140.94
417_L428_N0.5130.94
404_R408_L0.5130.94
605_L618_E0.5120.94
349_Q356_E0.5110.93
582_A586_A0.5100.93
479_E483_A0.5070.93
418_A421_V0.5070.93
467_Q559_Q0.5070.93
70_D280_Y0.5060.93
384_Q390_R0.5050.93
104_E107_Y0.5030.93
25_T29_I0.5030.93
512_F517_K0.5030.93
486_N539_S0.5020.93
35_S316_S0.5020.93
292_P295_K0.5020.93
507_G525_G0.5010.93
60_Q63_E0.5010.93
622_L628_L0.5010.93
415_R418_A0.5000.93
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  
4rnhA 2 0.3873 100 0.763 Contact Map
3pjxA 1 0.3886 100 0.769 Contact Map
4j40A 2 0.1775 100 0.77 Contact Map
3gbgA 1 0.3251 100 0.803 Contact Map
1bl0A 1 0.1399 100 0.803 Contact Map
3oioA 1 0.1438 100 0.803 Contact Map
3oouA 1 0.136 100 0.804 Contact Map
3mn2A 1 0.1373 100 0.806 Contact Map
3mklA 1 0.1438 100 0.808 Contact Map
2k9sA 1 0.1373 100 0.809 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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