GREMLIN Database
GYRA - DNA gyrase subunit A
UniProt: P05653 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 821 (738)
Sequences: 5155 (2535)
Seq/√Len: 93.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
75_I86_V5.7191.00
374_E455_K5.5631.00
189_G480_N4.6251.00
200_E469_R4.4501.00
193_D476_K4.2571.00
197_A204_I4.0791.00
665_T691_I3.8991.00
64_Y105_D3.5161.00
197_A212_V3.4271.00
456_D463_K3.3551.00
142_D371_R3.3541.00
456_D460_N3.2211.00
194_G213_I3.1231.00
247_A321_Y3.0501.00
453_E463_K3.0241.00
113_V301_M3.0111.00
392_A413_Q2.9921.00
198_V351_L2.9591.00
618_K648_E2.9351.00
198_V204_I2.9011.00
147_Q158_V2.8641.00
371_R375_A2.8491.00
395_S399_N2.7831.00
453_E456_D2.7611.00
666_K698_V2.6971.00
196_L473_T2.6731.00
60_S133_M2.6621.00
205_T208_E2.6391.00
70_I126_A2.6321.00
207_P235_E2.6111.00
666_K697_D2.6061.00
145_D364_R2.5741.00
385_V416_L2.5651.00
660_Q672_R2.5551.00
189_G482_E2.5531.00
209_L347_L2.5171.00
164_F169_V2.5111.00
69_R77_K2.4901.00
363_R367_A2.4771.00
206_I346_T2.4651.00
644_R686_A2.4401.00
192_I472_L2.4071.00
199_S465_L2.4051.00
694_T736_K2.3971.00
474_E478_R2.3961.00
512_H544_F2.3811.00
422_Q426_D2.3801.00
189_G193_D2.3451.00
375_A419_K2.3111.00
209_L348_K2.2931.00
189_G476_K2.2831.00
134_E479_F2.2801.00
101_Y481_D2.2411.00
257_E313_A2.2351.00
197_A201_N2.2121.00
247_A259_I2.2101.00
248_E262_T2.2081.00
183_I334_L2.2051.00
562_N648_E2.2041.00
689_K692_T2.1941.00
204_I208_E2.1811.00
671_I735_G2.1801.00
455_K459_A2.1781.00
141_K369_E2.1721.00
657_G675_E2.1661.00
246_K486_E2.1621.00
616_T663_I2.1581.00
671_I731_Q2.1551.00
450_L454_L2.1411.00
463_K466_E2.1391.00
681_M685_A2.1251.00
201_N208_E2.1211.00
290_T308_R2.1181.00
261_V305_I2.1111.00
446_S450_L2.1081.00
359_K465_L2.1071.00
105_D127_R2.1041.00
656_D659_K2.0791.00
380_L440_I2.0771.00
616_T702_M2.0701.00
130_K478_R2.0691.00
148_D155_R2.0411.00
372_K375_A2.0341.00
506_I571_G2.0321.00
376_R443_E2.0141.00
618_K647_D2.0091.00
67_S90_M2.0081.00
169_V191_I2.0041.00
338_V345_L1.9931.00
618_K698_V1.9911.00
728_Y740_T1.9841.00
663_I690_G1.9841.00
191_I213_I1.9821.00
207_P231_R1.9811.00
466_E470_E1.9481.00
655_T675_E1.9471.00
247_A317_L1.9461.00
407_R422_Q1.9421.00
442_E446_S1.9351.00
148_D152_G1.9311.00
366_T454_L1.9201.00
362_I468_I1.9191.00
363_R458_L1.9061.00
231_R235_E1.9051.00
408_T412_E1.9041.00
691_I699_V1.9011.00
252_T258_R1.8891.00
551_T555_D1.8881.00
396_L409_G1.8861.00
49_I89_S1.8841.00
359_K461_E1.8711.00
353_H356_D1.8681.00
245_A261_V1.8671.00
503_R552_S1.8461.00
715_T741_A1.8411.00
206_I235_E1.8401.00
563_K595_G1.8381.00
346_T349_Q1.8341.00
438_E442_E1.8311.00
242_T327_Q1.8301.00
272_K275_E1.8191.00
457_I467_I1.8161.00
251_Q257_E1.8111.00
84_S88_E1.8081.00
343_K349_Q1.8001.00
731_Q735_G1.7991.00
38_V353_H1.7971.00
264_L303_I1.7931.00
402_T405_I1.7871.00
196_L469_R1.7761.00
377_A444_Y1.7751.00
348_K352_E1.7741.00
198_V352_E1.7691.00
622_S690_G1.7681.00
664_G753_V1.7641.00
85_A89_S1.7591.00
445_Q449_K1.7591.00
460_N463_K1.7381.00
561_S598_I1.7371.00
367_A371_R1.7281.00
204_I212_V1.7241.00
701_G753_V1.7161.00
198_V355_L1.7151.00
464_V467_I1.7071.00
65_K69_R1.7021.00
385_V389_H1.6951.00
206_I348_K1.6921.00
183_I350_C1.6891.00
164_F475_I1.6681.00
195_V355_L1.6641.00
69_R73_E1.6601.00
215_G230_I1.6551.00
614_F661_I1.6321.00
614_F622_S1.6251.00
369_E454_L1.6141.00
441_E445_Q1.6131.00
677_D732_S1.6121.00
145_D158_V1.6091.00
208_E211_E1.6041.00
352_E356_D1.5961.00
404_E408_T1.5791.00
90_M126_A1.5771.00
399_N409_G1.5771.00
403_A430_Q1.5571.00
663_I699_V1.5461.00
38_V350_C1.5451.00
134_E137_R1.5441.00
436_E439_K1.5381.00
393_V410_L1.5261.00
453_E457_I1.5241.00
452_A456_D1.5221.00
621_V689_K1.5201.00
338_V353_H1.5161.00
227_R489_T1.5101.00
339_D356_D1.5031.00
667_N749_Q1.4881.00
450_L453_E1.4661.00
69_R154_E1.4621.00
334_L350_C1.4541.00
242_T329_S1.4531.00
729_R738_L1.4501.00
173_A182_N1.4441.00
52_A73_E1.4431.00
91_V118_A1.4380.99
552_S555_D1.4330.99
660_Q674_P1.4330.99
365_R471_E1.4320.99
513_N540_N1.4140.99
616_T699_V1.4070.99
232_K235_E1.4020.99
201_N204_I1.4000.99
67_S126_A1.3980.99
93_M99_Y1.3840.99
295_E304_V1.3820.99
246_K263_E1.3800.99
384_R444_Y1.3790.99
504_E553_T1.3740.99
612_Y680_E1.3730.99
195_V351_L1.3680.99
69_R76_G1.3680.99
731_Q738_L1.3640.99
277_I292_L1.3640.99
710_H722_R1.3580.99
228_S232_K1.3570.99
136_L160_M1.3530.99
444_Y448_V1.3520.99
481_D484_R1.3490.99
363_R464_V1.3480.99
461_E465_L1.3480.99
512_H546_E1.3460.99
325_A328_T1.3430.99
613_L652_V1.3340.99
562_N597_W1.3240.99
407_R418_E1.3180.99
276_K279_D1.3120.99
723_T728_Y1.3110.99
401_Q405_I1.3100.99
69_R121_M1.3080.99
289_I305_I1.3000.99
274_I303_I1.2950.99
449_K453_E1.2910.99
713_I740_T1.2890.99
52_A75_I1.2880.99
297_D300_G1.2870.99
563_K593_E1.2860.99
182_N331_G1.2840.99
240_S329_S1.2800.99
381_E448_V1.2790.99
411_I421_A1.2730.99
560_F652_V1.2700.99
743_I746_N1.2700.99
456_D459_A1.2660.99
452_A455_K1.2650.99
77_K154_E1.2630.99
396_L413_Q1.2620.99
562_N596_E1.2600.99
256_K290_T1.2590.99
277_I305_I1.2570.99
100_R481_D1.2550.99
234_Y332_I1.2510.99
381_E444_Y1.2510.99
740_T750_L1.2450.99
273_L303_I1.2420.99
73_E77_K1.2420.99
425_L430_Q1.2390.98
234_Y347_L1.2360.98
389_H416_L1.2330.98
359_K464_V1.2320.98
295_E302_R1.2310.98
473_T476_K1.2300.98
469_R473_T1.2250.98
142_D367_A1.2220.98
311_A316_I1.2210.98
223_Q246_K1.2170.98
470_E474_E1.2170.98
249_I259_I1.2140.98
614_F678_V1.2090.98
473_T477_E1.2060.98
349_Q352_E1.2000.98
63_P127_R1.1980.98
293_R306_E1.1970.98
274_I292_L1.1960.98
250_E302_R1.1940.98
384_R441_E1.1940.98
409_G412_E1.1900.98
624_R680_E1.1880.98
568_R633_I1.1870.98
642_S685_A1.1830.98
660_Q730_T1.1820.98
457_I463_K1.1790.98
446_S449_K1.1750.98
206_I210_M1.1740.98
470_E473_T1.1730.98
609_A628_S1.1700.98
405_I409_G1.1690.98
739_K742_K1.1680.98
206_I209_L1.1680.98
258_R306_E1.1620.98
392_A395_S1.1610.98
577_Y581_A1.1570.98
198_V348_K1.1550.98
615_F649_L1.1540.98
192_I476_K1.1520.98
356_D359_K1.1490.98
558_L566_V1.1480.98
223_Q488_V1.1450.97
245_A326_L1.1400.97
379_I423_A1.1380.97
243_I485_T1.1330.97
31_V337_L1.1260.97
354_Y358_Q1.1220.97
230_I241_I1.1200.97
15_S19_R1.1190.97
197_A208_E1.1190.97
335_L344_V1.1190.97
665_T697_D1.1180.97
411_I418_E1.1160.97
22_F32_S1.1140.97
612_Y624_R1.1110.97
378_H417_T1.1100.97
362_I471_E1.1100.97
215_G487_I1.1070.97
13_N16_Q1.0990.97
449_K452_A1.0930.97
75_I150_Y1.0910.97
503_R553_T1.0910.97
667_N697_D1.0900.97
51_Y54_N1.0880.97
56_L73_E1.0870.97
243_I328_T1.0870.97
723_T727_E1.0830.96
20_T24_D1.0800.96
370_L451_I1.0790.96
367_A374_E1.0780.96
383_L440_I1.0760.96
662_I670_L1.0750.96
247_A261_V1.0740.96
578_G581_A1.0700.96
241_I332_I1.0690.96
65_K153_S1.0650.96
621_V686_A1.0610.96
437_R441_E1.0540.96
716_E749_Q1.0540.96
227_R230_I1.0530.96
224_I485_T1.0500.96
362_I464_V1.0490.96
249_I317_L1.0460.96
384_R440_I1.0460.96
222_G245_A1.0420.96
380_L447_L1.0400.96
60_S130_K1.0400.96
307_I311_A1.0390.96
551_T571_G1.0390.96
140_T369_E1.0390.96
336_A350_C1.0390.96
539_T545_V1.0380.95
185_P219_P1.0370.95
614_F655_T1.0350.95
377_A451_I1.0340.95
50_L136_L1.0340.95
653_R702_M1.0330.95
223_Q243_I1.0320.95
662_I711_V1.0290.95
619_H646_D1.0290.95
406_A433_T1.0290.95
692_T736_K1.0270.95
163_R358_Q1.0260.95
233_A332_I1.0260.95
565_K593_E1.0220.95
626_S680_E1.0180.95
193_D196_L1.0180.95
390_L398_R1.0170.95
75_I84_S1.0130.95
46_H98_N1.0090.95
104_V126_A1.0090.95
142_D364_R1.0040.95
221_A246_K1.0030.95
52_A86_V1.0030.95
210_M235_E1.0030.95
193_D473_T0.9950.94
400_S409_G0.9950.94
338_V343_K0.9930.94
59_T62_K0.9920.94
616_T690_G0.9900.94
474_E477_E0.9900.94
462_Y470_E0.9890.94
366_T457_I0.9870.94
135_I162_S0.9870.94
192_I195_V0.9820.94
164_F192_I0.9820.94
74_V86_V0.9780.94
402_T408_T0.9770.94
184_P334_L0.9760.94
376_R380_L0.9750.94
560_F566_V0.9750.94
626_S629_Q0.9750.94
229_G232_K0.9740.94
261_V326_L0.9740.94
445_Q448_V0.9720.94
131_I166_N0.9720.94
250_E260_I0.9720.94
169_V188_L0.9690.93
498_E570_K0.9670.93
38_V345_L0.9630.93
213_I347_L0.9610.93
276_K325_A0.9600.93
625_T630_F0.9580.93
307_I316_I0.9550.93
389_H392_A0.9530.93
368_Y372_K0.9510.93
625_T629_Q0.9500.93
619_H647_D0.9480.93
453_E460_N0.9470.93
692_T734_G0.9450.93
196_L476_K0.9410.92
630_F640_A0.9390.92
103_L135_I0.9380.92
101_Y131_I0.9370.92
615_F640_A0.9360.92
621_V644_R0.9360.92
615_F652_V0.9330.92
510_L601_I0.9300.92
741_A746_N0.9300.92
506_I553_T0.9280.92
453_E470_E0.9280.92
58_M70_I0.9240.92
195_V472_L0.9240.92
666_K749_Q0.9230.92
371_R374_E0.9220.92
351_L355_L0.9220.92
223_Q486_E0.9220.92
227_R231_R0.9210.92
201_N205_T0.9200.92
462_Y466_E0.9180.92
642_S684_T0.9150.91
651_G702_M0.9150.91
377_A448_V0.9130.91
418_E422_Q0.9130.91
744_T748_G0.9120.91
553_T571_G0.9100.91
56_L69_R0.9030.91
65_K77_K0.9010.91
268_V273_L0.8990.91
167_L336_A0.8970.91
466_E477_E0.8960.91
385_V415_S0.8950.90
56_L70_I0.8950.90
669_L736_K0.8930.90
61_D133_M0.8920.90
463_K467_I0.8920.90
423_A427_M0.8910.90
224_I243_I0.8900.90
197_A211_E0.8890.90
224_I241_I0.8850.90
369_E450_L0.8840.90
681_M686_A0.8840.90
387_L437_R0.8830.90
453_E467_I0.8780.90
393_V414_F0.8770.90
508_V571_G0.8750.89
396_L421_A0.8750.89
610_E628_S0.8750.89
52_A78_Y0.8740.89
297_D301_M0.8740.89
586_I598_I0.8730.89
665_T699_V0.8680.89
597_W648_E0.8680.89
713_I728_Y0.8670.89
663_I691_I0.8660.89
73_E150_Y0.8630.89
459_A463_K0.8590.89
114_D270_K0.8580.89
204_I355_L0.8580.89
381_E417_T0.8540.88
457_I464_V0.8520.88
617_T641_L0.8510.88
563_K596_E0.8500.88
427_M431_R0.8490.88
559_F601_I0.8480.88
200_E473_T0.8470.88
137_R358_Q0.8450.88
260_I304_V0.8420.88
741_A750_L0.8410.88
128_M132_S0.8380.87
475_I479_F0.8350.87
244_R327_Q0.8310.87
693_L697_D0.8310.87
706_E709_S0.8310.87
17_E21_S0.8310.87
743_I748_G0.8280.87
201_N212_V0.8280.87
199_S469_R0.8260.87
442_E445_Q0.8230.86
396_L414_F0.8230.86
508_V574_I0.8210.86
131_I164_F0.8170.86
614_F690_G0.8160.86
27_M31_V0.8160.86
673_F678_V0.8140.86
247_A313_A0.8140.86
188_L475_I0.8140.86
228_S231_R0.8140.86
142_D375_A0.8110.86
226_G230_I0.8110.86
101_Y480_N0.8100.85
52_A56_L0.8090.85
274_I278_A0.8090.85
103_L166_N0.8090.85
32_S172_A0.8060.85
251_Q254_S0.8060.85
448_V452_A0.8060.85
613_L627_L0.8050.85
555_D605_T0.8050.85
169_V192_I0.8050.85
630_F681_M0.8040.85
189_G477_E0.8040.85
56_L150_Y0.8040.85
732_S735_G0.8030.85
101_Y482_E0.8030.85
393_V416_L0.8000.85
505_N552_S0.7990.85
627_L654_L0.7970.85
259_I317_L0.7970.85
71_V121_M0.7960.84
370_L455_K0.7960.84
226_G229_G0.7960.84
659_K706_E0.7950.84
198_V202_P0.7930.84
196_L200_E0.7930.84
641_L649_L0.7930.84
317_L321_Y0.7910.84
649_L652_V0.7900.84
366_T467_I0.7890.84
214_P227_R0.7880.84
206_I212_V0.7870.84
195_V354_Y0.7860.84
138_D141_K0.7860.84
292_L305_I0.7860.84
366_T458_L0.7850.84
345_L353_H0.7840.84
59_T133_M0.7840.84
39_R159_V0.7840.84
664_G740_T0.7830.84
213_I346_T0.7810.83
240_S331_G0.7800.83
387_L440_I0.7800.83
397_I429_L0.7780.83
551_T603_P0.7770.83
163_R474_E0.7760.83
403_A422_Q0.7760.83
137_R163_R0.7750.83
388_D437_R0.7740.83
616_T622_S0.7730.83
56_L77_K0.7730.83
150_Y153_S0.7700.82
163_R475_I0.7690.82
401_Q434_G0.7680.82
64_Y107_H0.7680.82
70_I75_I0.7670.82
333_N344_V0.7670.82
279_D283_D0.7650.82
235_E348_K0.7650.82
428_R431_R0.7640.82
275_E279_D0.7630.82
192_I475_I0.7610.82
377_A381_E0.7610.82
193_D480_N0.7600.82
439_K442_E0.7590.82
611_L654_L0.7580.81
191_I194_G0.7570.81
561_S567_Y0.7570.81
456_D461_E0.7570.81
395_S398_R0.7550.81
370_L374_E0.7550.81
193_D214_P0.7550.81
510_L549_I0.7550.81
63_P153_S0.7550.81
614_F702_M0.7540.81
115_G269_N0.7520.81
212_V348_K0.7510.81
386_A390_L0.7510.81
364_R367_A0.7510.81
519_L523_T0.7500.81
65_K154_E0.7480.81
75_I89_S0.7480.81
606_E609_A0.7480.81
230_I233_A0.7470.81
389_H396_L0.7460.80
35_L336_A0.7460.80
270_K294_D0.7450.80
102_M129_S0.7430.80
460_N466_E0.7420.80
149_N153_S0.7420.80
653_R704_I0.7410.80
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540_N582_K0.6600.72
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65_K121_M0.5540.58
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194_G197_A0.5530.58
750_L753_V0.5530.58
667_N694_T0.5520.58
490_S493_E0.5520.58
397_I433_T0.5520.58
319_N323_Q0.5510.58
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402_T430_Q0.5470.57
653_R703_E0.5470.57
56_L75_I0.5470.57
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244_R321_Y0.5450.57
38_V336_A0.5450.57
260_I303_I0.5440.57
656_D675_E0.5440.57
456_D462_Y0.5440.57
445_Q452_A0.5440.57
77_K153_S0.5430.57
136_L139_I0.5430.57
665_T693_L0.5420.57
524_Y550_S0.5420.57
173_A267_Q0.5410.57
433_T438_E0.5410.57
402_T406_A0.5410.57
84_S118_A0.5410.57
390_L447_L0.5400.56
401_Q433_T0.5390.56
659_K704_I0.5380.56
410_L415_S0.5380.56
224_I332_I0.5380.56
329_S332_I0.5380.56
661_I675_E0.5370.56
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134_E475_I0.5370.56
607_F611_L0.5360.56
299_T302_R0.5360.56
462_Y465_L0.5360.56
513_N542_D0.5360.56
430_Q433_T0.5350.56
251_Q255_G0.5350.56
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336_A345_L0.5350.56
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284_K287_E0.5330.56
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714_V720_G0.5280.55
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142_D155_R0.5270.55
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616_T650_M0.5260.55
622_S663_I0.5260.55
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248_E661_I0.5260.55
162_S358_Q0.5260.55
509_T524_Y0.5260.55
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58_M90_M0.5260.55
207_P211_E0.5250.54
292_L303_I0.5250.54
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437_R440_I0.5250.54
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264_L271_A0.5240.54
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226_G233_A0.5230.54
412_E415_S0.5230.54
273_L277_I0.5230.54
517_K583_G0.5230.54
345_L350_C0.5220.54
443_E446_S0.5220.54
194_G351_L0.5220.54
22_F333_N0.5210.54
497_D573_E0.5210.54
389_H414_F0.5210.54
543_D583_G0.5200.54
135_I160_M0.5190.54
126_A129_S0.5190.54
733_R736_K0.5190.54
715_T743_I0.5180.53
134_E140_T0.5180.53
651_G663_I0.5180.53
235_E346_T0.5160.53
616_T661_I0.5160.53
599_N643_L0.5150.53
295_E306_E0.5150.53
131_I479_F0.5140.53
164_F358_Q0.5140.53
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395_S419_K0.5140.53
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298_R301_M0.5130.53
664_G741_A0.5130.53
666_K696_D0.5130.53
518_R553_T0.5120.53
58_M126_A0.5120.53
56_L59_T0.5110.52
629_Q680_E0.5110.52
179_M335_L0.5100.52
391_D397_I0.5100.52
400_S406_A0.5100.52
628_S631_A0.5090.52
56_L126_A0.5090.52
51_Y139_I0.5090.52
717_K748_G0.5080.52
46_H97_F0.5080.52
85_A97_F0.5080.52
434_G438_E0.5080.52
374_E377_A0.5080.52
238_R331_G0.5080.52
274_I297_D0.5080.52
368_Y371_R0.5070.52
318_N499_D0.5070.52
640_A683_R0.5060.52
78_Y139_I0.5060.52
379_I427_M0.5060.52
114_D296_S0.5050.52
585_P741_A0.5050.52
162_S167_L0.5050.52
423_A434_G0.5050.52
359_K468_I0.5050.52
384_R447_L0.5050.52
183_I327_Q0.5040.51
384_R445_Q0.5040.51
371_R419_K0.5030.51
137_R474_E0.5030.51
307_I313_A0.5030.51
744_T749_Q0.5030.51
609_A631_A0.5030.51
717_K746_N0.5020.51
728_Y731_Q0.5020.51
362_I465_L0.5020.51
18_M336_A0.5020.51
403_A431_R0.5010.51
385_V441_E0.5010.51
619_H696_D0.5000.51
98_N267_Q0.5000.51
409_G413_Q0.5000.51
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  
1zvuA 2 0.8136 100 0.204 Contact Map
2inrA 2 0.5384 100 0.332 Contact Map
4i3hA 2 0.5883 100 0.336 Contact Map
2novA 2 0.5518 100 0.336 Contact Map
2xcsB 2 0.5859 100 0.338 Contact Map
2xkjE 2 0.5822 100 0.346 Contact Map
3ilwA 2 0.5591 100 0.351 Contact Map
4ckkA 2 0.5505 100 0.362 Contact Map
4gfhA 2 0.5493 100 0.468 Contact Map
3l4jA 1 0.553 100 0.483 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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