GREMLIN Database
TOP1 - DNA topoisomerase 1
UniProt: P06612 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11013
Length: 865 (792)
Sequences: 1704 (875)
Seq/√Len: 31.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
251_K255_Q7.8731.00
74_D77_H5.5841.00
250_N253_Q5.2201.00
662_C665_C4.7121.00
707_P717_E4.3411.00
413_L453_V4.1951.00
277_T407_K4.1671.00
662_C666_G4.0161.00
78_N565_D3.9811.00
815_A818_P3.7001.00
94_S98_Q3.6831.00
716_S732_T3.6341.00
218_E470_F3.6311.00
794_A802_R3.4921.00
553_V563_V3.4341.00
303_K386_D3.4131.00
552_Q557_E3.3601.00
716_S733_N3.2051.00
270_E455_K3.1901.00
664_K668_A3.1671.00
809_E813_Y3.0261.00
105_H135_S3.0171.00
662_C668_A2.9971.00
802_R805_D2.9451.00
34_I126_V2.9201.00
416_G419_D2.9161.00
781_L788_K2.8861.00
791_E794_A2.8621.00
762_P765_K2.8611.00
317_I394_I2.8141.00
665_C668_A2.7731.00
666_G669_M2.7701.00
261_L464_L2.7511.00
426_G451_P2.7361.00
7_I106_I2.6791.00
803_F806_R2.6571.00
664_K667_T2.6481.00
664_K669_M2.6331.00
662_C669_M2.6231.00
683_C689_C2.6171.00
385_A389_K2.5601.00
812_R815_A2.5371.00
665_C669_M2.5231.00
386_D389_K2.4610.99
259_S262_E2.4550.99
663_P667_T2.4460.99
511_R520_E2.4270.99
795_P798_E2.4150.99
222_V257_A2.3960.99
218_E468_Q2.3910.99
5_L100_A2.3870.99
159_I163_N2.3630.99
269_L416_G2.3400.99
219_F469_H2.3310.99
392_Q396_R2.3310.99
762_P767_D2.3200.99
340_S345_K2.3040.99
599_C602_C2.2460.99
710_E717_E2.2330.99
485_E489_R2.2270.99
809_E812_R2.2200.99
78_N561_K2.2170.99
752_K755_P2.2050.99
339_I348_L2.2040.99
693_E696_E2.2020.99
12_A16_T2.1800.99
255_Q258_V2.1450.98
302_K502_S2.1440.98
440_A443_K2.1440.98
651_A655_A2.1440.98
258_V262_E2.1210.98
711_C731_C2.1120.98
804_R808_P2.1100.98
585_G588_R2.1040.98
144_K148_R2.1000.98
814_L817_A2.1000.98
808_P812_R2.0950.98
753_E757_P2.0790.98
662_C667_T2.0590.98
768_A785_T2.0280.98
810_K814_L2.0190.98
83_Y165_Q2.0070.97
377_A380_L1.9980.97
408_Y435_T1.9910.97
559_E562_A1.9880.97
711_C714_C1.9810.97
266_Y417_A1.9720.97
299_F307_M1.9660.97
135_S156_E1.9630.97
811_L814_L1.9600.97
325_T357_S1.9570.97
267_S458_A1.9550.97
100_A106_I1.9460.97
802_R806_R1.9370.97
808_P815_A1.9360.97
666_G671_S1.9220.97
770_F800_L1.9140.97
651_A654_N1.8750.96
773_R782_A1.8750.96
273_D409_D1.8730.96
737_K741_K1.8580.96
108_L120_A1.8570.96
663_P671_S1.8400.96
790_R794_A1.8100.95
279_K405_P1.8090.95
590_N594_L1.8080.95
662_C671_S1.8050.95
746_G749_A1.8040.95
208_E476_R1.7950.95
227_T462_V1.7930.95
663_P668_A1.7840.95
812_R816_D1.7770.95
800_L804_R1.7670.95
502_S506_D1.7670.95
238_V242_N1.7660.95
298_G515_R1.7590.94
411_T428_I1.7470.94
420_F486_L1.7310.94
228_T459_L1.7290.94
293_A390_L1.7190.94
454_N457_D1.7180.94
689_C692_Y1.7130.94
753_E756_V1.7080.94
224_A415_V1.7050.93
664_K671_S1.7020.93
264_A417_A1.6880.93
668_A671_S1.6830.93
813_Y816_D1.6810.93
145_N149_Q1.6800.93
808_P814_L1.6730.93
204_V510_V1.6650.93
669_M672_Y1.6600.93
652_E655_A1.6550.92
77_H80_E1.6520.92
663_P666_G1.6470.92
760_E771_V1.6450.92
763_C783_A1.6450.92
228_T457_D1.6440.92
408_Y429_L1.6430.92
261_L417_A1.6330.92
599_C619_C1.6150.91
299_F304_T1.6070.91
730_A733_N1.6040.91
803_F808_P1.5930.91
663_P669_M1.5900.91
811_L815_A1.5890.91
809_E817_A1.5880.91
225_S465_T1.5800.91
226_T266_Y1.5690.90
766_S785_T1.5680.90
592_M599_C1.5550.90
226_T422_L1.5530.90
546_M563_V1.5430.89
299_F386_D1.5430.89
664_K670_D1.5410.89
712_E751_P1.5410.89
738_N741_K1.5390.89
662_C670_D1.5380.89
810_K815_A1.5290.89
805_D809_E1.5290.89
414_T423_K1.5120.88
619_C630_C1.5040.88
711_C751_P1.4970.88
688_T691_G1.4920.88
808_P811_L1.4870.88
812_R817_A1.4820.87
776_A792_T1.4820.87
483_V498_A1.4800.87
346_K436_K1.4790.87
806_R810_K1.4750.87
240_H421_R1.4740.87
673_L676_P1.4740.87
741_K749_A1.4680.87
747_E751_P1.4640.87
665_C671_S1.4560.86
226_T415_V1.4550.86
395_W399_V1.4540.86
149_Q153_K1.4520.86
264_A418_G1.4510.86
477_F485_E1.4490.86
668_A672_Y1.4470.86
549_S566_H1.4390.86
265_R458_A1.4370.86
157_L162_V1.4370.86
276_T408_Y1.4350.86
817_A822_P1.4340.86
650_D653_T1.4280.85
414_T421_R1.4270.85
762_P768_A1.4270.85
799_E805_D1.4240.85
804_R816_D1.4230.85
270_E414_T1.4160.85
415_V459_L1.4150.85
782_A787_P1.4070.84
485_E488_K1.4050.84
770_F804_R1.4020.84
801_Y815_A1.4020.84
292_A295_T1.4000.84
799_E803_F1.3970.84
716_S730_A1.3920.84
803_F812_R1.3880.84
216_P470_F1.3880.84
802_R808_P1.3870.84
816_D822_P1.3840.83
593_V600_P1.3820.83
599_C630_C1.3810.83
719_H730_A1.3800.83
759_P772_L1.3700.83
694_I699_F1.3690.83
273_D411_T1.3690.83
409_D430_R1.3680.83
4_A105_H1.3610.82
221_E246_F1.3590.82
667_T671_S1.3580.82
781_L790_R1.3520.82
285_I357_S1.3460.82
799_E806_R1.3420.82
592_M600_P1.3420.82
83_Y166_Q1.3400.81
4_A107_Y1.3390.81
788_K794_A1.3300.81
770_F808_P1.3300.81
223_D235_A1.3290.81
593_V602_C1.3280.81
802_R815_A1.3270.81
38_P199_V1.3250.81
486_L500_I1.3250.81
16_T19_K1.3230.81
721_K728_Y1.3200.80
802_R811_L1.3160.80
378_E381_K1.3130.80
649_E652_E1.3120.80
241_Q420_F1.3090.80
593_V599_C1.3070.80
766_S783_A1.3060.80
299_F303_K1.3030.80
740_R749_A1.3000.79
63_E66_A1.2980.79
68_V71_M1.2880.79
225_S463_E1.2840.79
602_C619_C1.2820.78
293_A304_T1.2790.78
200_A486_L1.2780.78
246_F257_A1.2770.78
124_R134_Y1.2770.78
275_P407_K1.2750.78
808_P813_Y1.2740.78
26_V103_A1.2710.78
62_D69_N1.2710.78
310_R387_A1.2680.78
228_T232_E1.2660.78
308_A317_I1.2650.77
226_T236_L1.2640.77
669_M673_L1.2600.77
799_E813_Y1.2590.77
800_L810_K1.2500.77
348_L429_L1.2440.76
347_Y431_F1.2430.76
305_M317_I1.2310.76
754_D757_P1.2270.75
757_P771_V1.2270.75
805_D812_R1.2250.75
549_S558_A1.2240.75
805_D811_L1.2230.75
255_Q259_S1.2220.75
652_E657_R1.2180.75
92_V95_E1.2130.74
234_L453_V1.2120.74
589_P594_L1.2110.74
720_L745_N1.2080.74
179_V537_L1.2070.74
225_S235_A1.2030.74
592_M602_C1.1990.74
803_F811_L1.1950.73
756_V807_L1.1950.73
512_V515_R1.1920.73
765_K768_A1.1920.73
706_G720_L1.1830.73
805_D816_D1.1830.73
739_T743_L1.1810.72
296_R440_A1.1790.72
788_K791_E1.1730.72
660_R663_P1.1680.72
707_P719_H1.1670.71
657_R660_R1.1650.71
758_L806_R1.1650.71
416_G421_R1.1640.71
504_I508_G1.1620.71
806_R811_L1.1620.71
803_F810_K1.1600.71
801_Y804_R1.1570.71
224_A464_L1.1560.71
202_R531_E1.1500.70
785_T802_R1.1500.70
404_T407_K1.1460.70
779_V796_L1.1450.70
597_I602_C1.1430.70
178_M575_L1.1430.70
777_A780_F1.1420.70
300_G453_V1.1400.70
598_D603_G1.1400.70
772_L781_L1.1380.70
805_D808_P1.1370.69
815_A822_P1.1290.69
384_E387_A1.1270.69
665_C672_Y1.1250.69
332_V354_Q1.1220.68
148_R152_N1.1200.68
721_K730_A1.1200.68
575_L579_E1.1180.68
779_V789_S1.1160.68
276_T410_S1.1160.68
343_F399_V1.1140.68
720_L736_C1.1110.68
818_P822_P1.1100.68
426_G450_L1.1060.67
597_I600_P1.1020.67
74_D80_E1.1010.67
141_E146_A1.1000.67
805_D822_P1.0990.67
335_V399_V1.0990.67
665_C670_D1.0950.66
810_K816_D1.0940.66
249_V253_Q1.0930.66
226_T453_V1.0900.66
306_M310_R1.0900.66
655_A659_K1.0890.66
729_M742_I1.0860.66
651_A657_R1.0850.66
662_C672_Y1.0840.66
25_Y107_Y1.0810.65
606_M632_T1.0760.65
164_A291_Q1.0750.65
138_V147_I1.0730.65
260_L420_F1.0720.65
337_G341_D1.0700.65
760_E769_Y1.0680.65
201_V504_I1.0670.64
234_L459_L1.0670.64
593_V597_I1.0670.64
275_P411_T1.0660.64
664_K672_Y1.0620.64
584_E587_M1.0620.64
736_C745_N1.0620.64
372_D375_V1.0590.64
718_M729_M1.0570.64
812_R818_P1.0560.64
256_A260_L1.0530.63
756_V760_E1.0510.63
303_K306_M1.0490.63
799_E810_K1.0480.63
762_P769_Y1.0460.63
790_R793_R1.0460.63
447_D685_N1.0460.63
655_A658_A1.0450.63
644_N650_D1.0400.62
658_A661_R1.0360.62
592_M604_R1.0350.62
592_M595_T1.0340.62
663_P670_D1.0330.62
766_S770_F1.0330.62
761_L800_L1.0300.62
803_F813_Y1.0300.62
763_C804_R1.0260.61
598_D604_R1.0260.61
28_K96_L1.0230.61
589_P600_P1.0230.61
289_L304_T1.0210.61
254_T464_L1.0190.61
36_D169_R1.0140.60
809_E815_A1.0120.60
665_C673_L1.0100.60
805_D813_Y1.0090.60
301_V498_A1.0090.60
758_L774_D1.0080.60
766_S804_R1.0080.60
764_E783_A1.0070.60
591_Q600_P1.0070.60
40_S43_A1.0050.60
623_A630_C1.0030.60
720_L742_I1.0030.60
254_T466_P1.0020.60
505_Q512_V0.9980.59
602_C606_M0.9960.59
753_E768_A0.9950.59
806_R812_R0.9910.59
15_K282_A0.9900.59
670_D676_P0.9840.58
640_N643_L0.9810.58
295_T440_A0.9810.58
666_G670_D0.9800.58
654_N657_R0.9790.58
655_A661_R0.9780.58
4_A24_D0.9770.58
670_D674_I0.9770.58
432_D436_K0.9770.58
669_M677_K0.9740.57
672_Y675_D0.9710.57
738_N743_L0.9710.57
649_E656_L0.9700.57
809_E814_L0.9700.57
677_K692_Y0.9680.57
766_S811_L0.9670.57
799_E808_P0.9660.57
708_I729_M0.9660.57
604_R621_G0.9650.57
205_V519_A0.9620.56
667_T674_I0.9610.56
243_D268_V0.9600.56
294_S480_A0.9590.56
766_S789_S0.9590.56
267_S416_G0.9580.56
590_N596_S0.9580.56
269_L421_R0.9580.56
810_K813_Y0.9560.56
251_K455_K0.9540.56
796_L802_R0.9540.56
285_I325_T0.9530.56
217_E249_V0.9520.56
741_K745_N0.9510.55
67_L71_M0.9500.55
40_S44_A0.9490.55
708_I720_L0.9490.55
589_P592_M0.9480.55
287_S490_G0.9480.55
592_M597_I0.9470.55
266_Y461_L0.9460.55
762_P804_R0.9420.55
178_M408_Y0.9400.55
238_V241_Q0.9370.54
590_N593_V0.9340.54
422_L464_L0.9330.54
412_T425_R0.9330.54
327_L398_F0.9300.54
791_E802_R0.9280.54
756_V771_V0.9270.54
653_T657_R0.9270.54
806_R815_A0.9260.53
622_Y630_C0.9250.53
290_Q498_A0.9250.53
346_K389_K0.9230.53
343_F506_D0.9220.53
27_V32_G0.9210.53
792_T795_P0.9210.53
44_A62_D0.9190.53
665_C675_D0.9180.53
799_E804_R0.9170.53
743_L759_P0.9150.53
671_S675_D0.9140.53
648_G651_A0.9120.52
337_G340_S0.9120.52
574_Q578_A0.9110.52
593_V596_S0.9090.52
814_L818_P0.9090.52
725_F739_T0.9080.52
764_E804_R0.9060.52
141_E329_Q0.9050.52
802_R813_Y0.9050.52
764_E768_A0.9040.52
806_R809_E0.9040.52
417_A422_L0.8990.51
667_T672_Y0.8990.51
766_S769_Y0.8980.51
671_S674_I0.8970.51
346_K407_K0.8940.51
376_M379_S0.8940.51
707_P710_E0.8910.51
666_G672_Y0.8890.50
667_T670_D0.8890.50
782_A785_T0.8880.50
271_R413_L0.8880.50
755_P760_E0.8880.50
544_A609_R0.8860.50
770_F803_F0.8840.50
655_A660_R0.8840.50
799_E802_R0.8820.50
160_D163_N0.8790.50
261_L466_P0.8780.50
790_R797_V0.8770.50
268_V413_L0.8760.49
179_V325_T0.8750.49
595_T598_D0.8750.49
813_Y817_A0.8730.49
772_L788_K0.8720.49
137_V151_F0.8690.49
791_E798_E0.8690.49
777_A787_P0.8680.49
757_P773_R0.8670.49
85_V88_G0.8660.49
791_E804_R0.8660.49
241_Q257_A0.8640.48
783_A786_F0.8640.48
804_R817_A0.8630.48
222_V466_P0.8630.48
602_C630_C0.8610.48
794_A805_D0.8580.48
90_E94_S0.8570.48
793_R796_L0.8570.48
722_M728_Y0.8570.48
63_E68_V0.8560.48
62_D66_A0.8560.48
78_N102_K0.8560.48
669_M675_D0.8550.48
594_L602_C0.8550.48
700_R743_L0.8550.48
813_Y818_P0.8520.47
781_L806_R0.8520.47
768_A811_L0.8520.47
12_A140_N0.8510.47
310_R314_A0.8510.47
334_M372_D0.8510.47
238_V243_D0.8500.47
708_I718_M0.8480.47
23_S101_E0.8480.47
278_S434_W0.8470.47
149_Q152_N0.8460.47
759_P813_Y0.8450.47
779_V795_P0.8440.47
222_V254_T0.8440.47
124_R128_G0.8440.47
66_A71_M0.8430.47
137_V154_P0.8420.47
801_Y812_R0.8410.47
476_R509_Y0.8400.47
762_P812_R0.8390.46
376_M380_L0.8380.46
802_R810_K0.8380.46
268_V455_K0.8370.46
593_V598_D0.8370.46
273_D455_K0.8360.46
251_K258_V0.8350.46
335_V807_L0.8350.46
407_K431_F0.8340.46
143_T550_L0.8320.46
263_K389_K0.8300.46
292_A296_R0.8300.46
221_E467_A0.8290.46
10_S13_K0.8280.46
171_M550_L0.8280.46
123_L126_V0.8260.45
783_A807_L0.8260.45
183_L193_A0.8250.45
298_G389_K0.8250.45
738_N753_E0.8230.45
204_V281_G0.8200.45
804_R809_E0.8190.45
785_T811_L0.8190.45
635_N638_P0.8180.45
801_Y808_P0.8170.45
143_T146_A0.8160.45
228_T460_T0.8150.45
270_E569_S0.8130.44
677_K680_L0.8110.44
801_Y805_D0.8090.44
562_A565_D0.8080.44
788_K810_K0.8080.44
605_K609_R0.8060.44
651_A658_A0.8050.44
138_V155_G0.8050.44
654_N658_A0.8040.44
775_G778_G0.8030.44
340_S348_L0.8020.43
141_E328_S0.8000.43
246_F249_V0.8000.43
594_L597_I0.7980.43
767_D796_L0.7970.43
112_L140_N0.7950.43
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178_M578_A0.5120.23
25_Y147_I0.5120.23
230_S270_E0.5120.23
439_P442_R0.5120.23
141_E550_L0.5120.23
233_A329_Q0.5110.23
363_E369_R0.5110.23
595_T600_P0.5110.23
14_A140_N0.5110.23
222_V263_K0.5110.23
379_S382_D0.5110.23
3_K26_V0.5100.23
766_S782_A0.5100.23
719_H740_R0.5100.23
804_R815_A0.5090.23
140_N499_S0.5090.23
689_C693_E0.5090.23
761_L769_Y0.5090.23
592_M596_S0.5090.23
785_T813_Y0.5080.23
290_Q496_T0.5070.23
296_R441_L0.5070.23
155_G174_V0.5070.23
755_P795_P0.5070.23
265_R345_K0.5060.23
242_N337_G0.5060.23
269_L418_G0.5050.23
125_E407_K0.5050.23
781_L786_F0.5040.23
13_K37_L0.5040.23
412_T532_E0.5040.23
418_G453_V0.5040.23
18_N26_V0.5040.23
284_F437_V0.5030.23
766_S806_R0.5030.23
790_R798_E0.5020.23
805_D814_L0.5020.23
436_K490_G0.5020.23
17_I21_L0.5020.23
781_L805_D0.5020.23
725_F729_M0.5020.23
378_E385_A0.5020.23
14_A474_P0.5020.23
619_C622_Y0.5010.23
650_D656_L0.5010.23
32_G309_Q0.5000.22
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  
2gaiA 1 0.6578 100 0.337 Contact Map
1mw9X 1 0.6428 100 0.354 Contact Map
4cgyA 1 0.6624 100 0.354 Contact Map
1i7dA 1 0.6497 100 0.384 Contact Map
4dduA 1 0.6035 100 0.436 Contact Map
1gkuB 1 0.5746 100 0.44 Contact Map
1vddA 7 0.1283 99.9 0.917 Contact Map
3vdpA 2 0.1249 99 0.956 Contact Map
2fcjA 2 0.1318 98.8 0.96 Contact Map
1yuaA 1 0.141 98.8 0.96 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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