GREMLIN Database
PCRA - ATP-dependent DNA helicase PcrA
UniProt: O34580 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 739 (620)
Sequences: 10069 (7276)
Seq/√Len: 292.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
58_N218_Q4.9331.00
565_L608_G4.2051.00
17_Q21_K3.9811.00
204_D234_M3.8231.00
376_L560_I3.7531.00
339_K342_Q3.7281.00
336_V579_M3.7081.00
581_L618_L3.5671.00
574_P614_Q3.4751.00
18_E278_S3.4311.00
339_K577_F3.2851.00
13_N286_Y3.2681.00
12_L20_V3.2651.00
344_H351_L3.1951.00
574_P613_E3.1421.00
575_V615_E3.0981.00
353_D574_P2.9741.00
583_E637_R2.9331.00
352_S558_D2.8881.00
179_D182_K2.7741.00
578_L608_G2.7701.00
198_T201_K2.6621.00
350_K558_D2.6571.00
290_K294_R2.6551.00
341_H374_A2.6231.00
201_K205_R2.6051.00
470_N490_K2.5691.00
233_Y273_D2.5431.00
15_V18_E2.4931.00
22_T27_L2.4421.00
183_K186_K2.4171.00
563_M573_F2.3531.00
359_R601_E2.3481.00
88_W217_F2.3441.00
340_I354_I2.2911.00
55_A58_N2.2881.00
339_K617_Y2.2601.00
351_L377_N2.2561.00
358_Y562_L2.2481.00
407_D410_S2.2201.00
237_K273_D2.2151.00
315_N614_Q2.2131.00
96_C199_T2.2071.00
484_T519_T2.2021.00
577_F617_Y2.1741.00
575_V617_Y2.1321.00
337_A374_A2.1221.00
486_E490_K2.1011.00
342_Q346_T2.0971.00
131_E179_D2.0801.00
47_Y51_E2.0751.00
196_I231_A2.0371.00
43_H79_I2.0251.00
411_F415_V2.0231.00
341_H345_S1.9981.00
338_G374_A1.9671.00
265_T269_S1.9541.00
71_E75_R1.9421.00
183_K187_N1.9351.00
474_M486_E1.9261.00
27_L280_I1.9171.00
207_P210_L1.9161.00
116_L189_S1.9131.00
128_I183_K1.8921.00
39_R43_H1.8801.00
182_K186_K1.8761.00
492_E495_E1.8711.00
391_E511_N1.8601.00
343_L575_V1.8581.00
179_D183_K1.8551.00
103_D212_F1.8521.00
230_R263_D1.8481.00
204_D238_Q1.8481.00
572_E613_E1.8441.00
323_Y620_N1.8431.00
367_I579_M1.8381.00
210_L214_Q1.8341.00
334_Q370_T1.8311.00
343_L354_I1.8311.00
522_F533_A1.8181.00
335_F619_T1.8101.00
90_S95_M1.8071.00
358_Y364_S1.8071.00
190_L198_T1.8041.00
45_I61_A1.7921.00
343_L577_F1.7891.00
344_H354_I1.7641.00
334_Q374_A1.7621.00
149_S193_D1.7551.00
332_E619_T1.7541.00
131_E183_K1.7531.00
203_F210_L1.7311.00
48_L219_Y1.7311.00
400_R539_A1.7291.00
412_T431_A1.7281.00
609_I616_L1.7211.00
326_G335_F1.7201.00
370_T373_K1.6971.00
106_R209_V1.6841.00
446_Q469_E1.6721.00
157_E160_E1.6551.00
29_L247_C1.6481.00
99_I199_T1.6451.00
162_S178_A1.6411.00
495_E498_K1.6391.00
565_L586_F1.6371.00
370_T374_A1.6361.00
493_Y497_L1.6181.00
285_N288_S1.6101.00
93_H195_L1.6091.00
110_N188_Q1.6061.00
350_K353_D1.6001.00
222_V236_V1.5891.00
325_R620_N1.5811.00
344_H350_K1.5711.00
104_I190_L1.5701.00
494_R509_L1.5661.00
253_D306_R1.5651.00
356_I371_L1.5631.00
494_R513_D1.5631.00
234_M237_K1.5611.00
46_A79_I1.5581.00
21_K47_Y1.5521.00
343_L617_Y1.5501.00
479_S482_E1.5461.00
49_M80_L1.5451.00
220_I240_A1.5431.00
322_S615_E1.5141.00
178_A182_K1.5111.00
284_Q312_W1.5091.00
27_L247_C1.5081.00
578_L618_L1.5041.00
184_L194_D1.5041.00
322_S339_K1.4971.00
225_Y233_Y1.4951.00
336_V367_I1.4941.00
211_E214_Q1.4921.00
15_V284_Q1.4921.00
244_Q276_N1.4841.00
211_E215_R1.4771.00
474_M478_L1.4651.00
428_E432_S1.4611.00
60_L220_I1.4551.00
25_G278_S1.4491.00
200_I234_M1.4491.00
269_S273_D1.4461.00
319_I615_E1.4441.00
299_V609_I1.4431.00
401_L414_I1.4431.00
295_A321_I1.4411.00
371_L562_L1.4361.00
74_E78_S1.4351.00
42_T76_V1.4351.00
103_D213_Y1.4331.00
530_T533_A1.4251.00
602_R641_E1.4241.00
45_I76_V1.4141.00
180_Y191_D1.4081.00
270_F277_A1.4051.00
391_E508_R1.4031.00
190_L195_L1.4031.00
581_L605_A1.4001.00
423_G426_S1.3991.00
395_I512_I1.3971.00
336_V577_F1.3971.00
60_L217_F1.3921.00
203_F238_Q1.3891.00
340_I560_I1.3891.00
99_I203_F1.3821.00
443_Q447_Q1.3671.00
284_Q314_E1.3661.00
519_T534_F1.3651.00
124_V183_K1.3651.00
95_M99_I1.3641.00
462_D466_Q1.3621.00
485_E516_L1.3621.00
99_I213_Y1.3611.00
425_T429_K1.3601.00
127_G183_K1.3551.00
271_E279_V1.3531.00
339_K343_L1.3491.00
343_L615_E1.3441.00
363_Q580_G1.3421.00
478_L482_E1.3411.00
302_N641_E1.3331.00
394_D413_R1.3311.00
298_E643_P1.3311.00
454_S457_A1.3271.00
295_A609_I1.3181.00
395_I484_T1.3161.00
181_Q185_L1.3091.00
128_I179_D1.3081.00
207_P211_E1.3081.00
132_R179_D1.3031.00
210_L238_Q1.3021.00
14_P18_E1.3021.00
14_P17_Q1.3021.00
269_S272_K1.3011.00
200_I235_L1.2961.00
355_A573_F1.2941.00
340_I577_F1.2901.00
109_I198_T1.2881.00
104_I107_I1.2871.00
44_R247_C1.2861.00
397_A413_R1.2821.00
206_V209_V1.2751.00
255_S258_R1.2741.00
181_Q184_L1.2721.00
33_A297_N1.2701.00
159_E178_A1.2691.00
15_V283_E1.2671.00
358_Y579_M1.2671.00
172_V175_D1.2671.00
456_K460_A1.2641.00
214_Q242_R1.2621.00
364_S562_L1.2621.00
202_L209_V1.2611.00
494_R498_K1.2601.00
125_I176_V1.2591.00
379_N559_A1.2521.00
481_T523_E1.2391.00
605_A609_I1.2391.00
337_A370_T1.2331.00
25_G245_N1.2301.00
213_Y217_F1.2291.00
635_E639_I1.2281.00
403_S532_V1.2261.00
155_L231_A1.2241.00
107_I202_L1.2201.00
356_I367_I1.2161.00
88_W98_R1.2141.00
48_L54_V1.2111.00
325_R622_K1.2011.00
471_L490_K1.1971.00
642_I646_L1.1931.00
351_L354_I1.1901.00
292_I296_A1.1881.00
200_I238_Q1.1831.00
455_A458_A1.1811.00
96_C235_L1.1791.00
341_H351_L1.1771.00
575_V614_Q1.1721.00
18_E21_K1.1671.00
97_V101_R1.1671.00
340_I351_L1.1551.00
76_V89_I1.1541.00
100_L199_T1.1511.00
106_R206_V1.1511.00
406_D440_S1.1441.00
219_Y245_N1.1421.00
398_Y487_I1.1401.00
230_R234_M1.1391.00
84_A87_I1.1361.00
411_F445_I1.1331.00
354_I575_V1.1301.00
23_T48_L1.1271.00
399_L484_T1.1241.00
109_I190_L1.1191.00
326_G619_T1.1141.00
439_L444_A1.1141.00
465_R469_E1.1121.00
371_L378_Y1.1121.00
467_M471_L1.1101.00
22_T278_S1.1081.00
98_R102_R1.1071.00
540_L543_D1.1011.00
324_Y335_F1.0991.00
151_A161_F1.0991.00
349_R614_Q1.0981.00
149_S153_N1.0951.00
175_D178_A1.0941.00
22_T25_G1.0841.00
290_K316_D1.0831.00
439_L447_Q1.0831.00
125_I145_L1.0831.00
30_M252_S1.0821.00
433_Y437_N1.0811.00
99_I202_L1.0791.00
398_Y414_I1.0781.00
160_E163_K1.0771.00
327_D622_K1.0741.00
405_P472_T1.0721.00
500_E505_A1.0721.00
577_F619_T1.0711.00
478_L486_E1.0701.00
440_S443_Q1.0691.00
153_N193_D1.0681.00
332_E580_G1.0671.00
341_H344_H1.0631.00
127_G131_E1.0621.00
121_Q180_Y1.0611.00
594_E597_E1.0611.00
199_T235_L1.0591.00
200_I204_D1.0561.00
588_H591_S1.0521.00
90_S94_S1.0481.00
70_R74_E1.0461.00
464_F468_I1.0461.00
349_R575_V1.0461.00
45_I59_I1.0381.00
296_A610_T1.0381.00
335_F339_K1.0301.00
28_L248_V1.0301.00
359_R604_L1.0291.00
102_R216_K1.0281.00
41_L221_H1.0241.00
93_H196_I1.0231.00
400_R410_S1.0211.00
351_L376_L1.0201.00
563_M568_A1.0191.00
128_I176_V1.0141.00
416_N420_R1.0131.00
147_T151_A1.0111.00
379_N561_T1.0051.00
458_A462_D1.0041.00
360_T363_Q1.0021.00
156_T161_F1.0021.00
309_K313_T1.0021.00
28_L279_V0.9971.00
406_D443_Q0.9961.00
395_I515_F0.9961.00
481_T520_K0.9881.00
354_I577_F0.9821.00
463_S466_Q0.9811.00
515_F519_T0.9811.00
469_E472_T0.9791.00
402_V487_I0.9781.00
369_E373_K0.9731.00
365_R369_E0.9711.00
537_D541_I0.9671.00
467_M470_N0.9661.00
534_F538_L0.9651.00
402_V483_L0.9641.00
300_I303_N0.9611.00
401_L411_F0.9601.00
255_S262_A0.9551.00
114_S120_D0.9551.00
128_I132_R0.9541.00
257_Y260_R0.9541.00
44_R245_N0.9531.00
565_L578_L0.9481.00
322_S325_R0.9471.00
334_Q338_G0.9471.00
236_V246_L0.9431.00
185_L198_T0.9411.00
63_T68_A0.9401.00
333_G337_A0.9391.00
150_S153_N0.9381.00
175_D179_D0.9371.00
199_T203_F0.9281.00
446_Q465_R0.9281.00
258_R596_A0.9251.00
485_E489_D0.9251.00
106_R208_E0.9241.00
381_V567_A0.9231.00
328_N331_G0.9201.00
561_T573_F0.9181.00
426_S460_A0.9171.00
103_D106_R0.9151.00
67_K71_E0.9151.00
424_A428_E0.9141.00
430_I441_F0.9121.00
95_M213_Y0.9121.00
19_A29_L0.9121.00
470_N486_E0.9121.00
121_Q145_L0.9111.00
224_E569_K0.9081.00
122_L141_P0.9081.00
146_G150_S0.9071.00
152_K194_D0.9061.00
333_G367_I0.9061.00
554_S557_K0.9041.00
404_N407_D0.9041.00
12_L39_R0.9031.00
289_T614_Q0.9031.00
129_L134_L0.9021.00
161_F165_A0.8981.00
579_M619_T0.8971.00
432_S436_I0.8971.00
228_T266_N0.8961.00
609_I618_L0.8961.00
291_R294_R0.8951.00
196_I235_L0.8941.00
70_R73_K0.8921.00
225_Y228_T0.8921.00
298_E301_K0.8911.00
271_E307_K0.8901.00
125_I129_L0.8861.00
54_V58_N0.8851.00
253_D300_I0.8831.00
495_E499_A0.8831.00
57_W86_D0.8781.00
225_Y248_V0.8781.00
463_S467_M0.8751.00
337_A371_L0.8741.00
348_K575_V0.8731.00
457_A460_A0.8721.00
514_E517_S0.8721.00
293_L311_L0.8711.00
299_V605_A0.8701.00
483_L487_I0.8701.00
368_E372_L0.8691.00
293_L296_A0.8651.00
270_F274_Y0.8641.00
456_K459_N0.8641.00
159_E163_K0.8631.00
125_I148_I0.8621.00
49_M87_I0.8621.00
352_S559_A0.8621.00
361_N364_S0.8611.00
538_L541_I0.8611.00
150_S154_E0.8601.00
215_R242_R0.8591.00
471_L487_I0.8591.00
368_E378_Y0.8571.00
396_L538_L0.8541.00
385_K388_D0.8531.00
498_K509_L0.8531.00
509_L513_D0.8491.00
400_R407_D0.8491.00
26_P244_Q0.8491.00
162_S174_S0.8481.00
442_F446_Q0.8481.00
169_Y173_V0.8471.00
367_I562_L0.8441.00
422_V426_S0.8441.00
151_A173_V0.8441.00
197_M231_A0.8411.00
392_I515_F0.8391.00
97_V195_L0.8381.00
237_K274_Y0.8371.00
93_H193_D0.8361.00
339_K615_E0.8361.00
459_N463_S0.8341.00
252_S309_K0.8331.00
83_G86_D0.8311.00
148_I152_K0.8311.00
587_P601_E0.8301.00
105_D111_R0.8291.00
433_Y447_Q0.8291.00
529_K533_A0.8281.00
272_K306_R0.8261.00
441_F444_A0.8241.00
125_I141_P0.8231.00
582_E621_A0.8221.00
333_G366_V0.8211.00
23_T219_Y0.8201.00
337_A341_H0.8201.00
291_R646_L0.8181.00
255_S259_W0.8161.00
437_N447_Q0.8151.00
21_K51_E0.8131.00
338_G342_Q0.8121.00
518_V534_F0.8121.00
402_V471_L0.8111.00
393_K397_A0.8091.00
395_I488_L0.8081.00
290_K313_T0.8051.00
23_T47_Y0.8051.00
327_D331_G0.8051.00
144_I173_V0.8051.00
470_N474_M0.8020.99
171_Q175_D0.8010.99
26_P245_N0.7980.99
296_A609_I0.7970.99
72_M75_R0.7940.99
471_L483_L0.7940.99
532_V536_T0.7930.99
165_A174_S0.7920.99
93_H100_L0.7920.99
221_H247_C0.7900.99
593_M597_E0.7890.99
294_R317_E0.7880.99
24_D219_Y0.7860.99
155_L197_M0.7850.99
294_R298_E0.7840.99
107_I206_V0.7840.99
322_S617_Y0.7830.99
116_L184_L0.7810.99
301_K308_P0.7780.99
433_Y444_A0.7780.99
15_V312_W0.7780.99
156_T160_E0.7780.99
141_P145_L0.7770.99
33_A606_Y0.7770.99
336_V619_T0.7760.99
122_L142_R0.7760.99
174_S178_A0.7760.99
264_I267_I0.7750.99
426_S429_K0.7740.99
291_R321_I0.7740.99
291_R317_E0.7730.99
586_F589_S0.7720.99
62_I95_M0.7720.99
578_L605_A0.7710.99
62_I236_V0.7700.99
390_K417_V0.7700.99
267_I270_F0.7690.99
294_R646_L0.7690.99
118_T122_L0.7680.99
426_S461_L0.7680.99
368_E562_L0.7680.99
177_Y181_Q0.7660.99
118_T121_Q0.7650.99
44_R219_Y0.7650.99
598_M637_R0.7630.99
459_N462_D0.7620.99
196_I200_I0.7620.99
218_Q243_F0.7610.99
182_K185_L0.7600.99
351_L558_D0.7600.99
181_Q198_T0.7580.99
180_Y184_L0.7580.99
481_T516_L0.7570.99
29_L280_I0.7560.99
43_H47_Y0.7540.99
466_Q470_N0.7540.99
240_A246_L0.7540.99
319_I324_Y0.7540.99
394_D493_Y0.7510.99
486_E489_D0.7490.99
635_E640_A0.7490.99
386_F392_I0.7460.99
88_W216_K0.7440.99
329_E366_V0.7440.99
158_P177_Y0.7430.99
469_E473_N0.7430.99
115_I195_L0.7420.99
266_N270_F0.7420.99
340_I371_L0.7400.99
47_Y50_A0.7390.99
234_M238_Q0.7380.99
366_V370_T0.7370.99
93_H190_L0.7370.99
396_L400_R0.7360.99
267_I271_E0.7350.99
337_A376_L0.7350.99
289_T292_I0.7330.99
151_A156_T0.7330.99
455_A459_N0.7320.99
319_I322_S0.7300.99
414_I464_F0.7260.99
581_L586_F0.7260.99
32_G35_S0.7250.99
222_V248_V0.7240.99
303_N602_R0.7240.99
335_F617_Y0.7240.99
250_G254_Q0.7240.99
417_V496_M0.7230.99
283_E312_W0.7220.99
147_T150_S0.7220.99
319_I325_R0.7200.99
481_T485_E0.7190.99
46_A50_A0.7180.99
607_V611_R0.7180.99
47_Y52_K0.7180.99
288_S292_I0.7150.99
324_Y617_Y0.7120.99
200_I231_A0.7120.99
533_A537_D0.7110.99
156_T164_V0.7100.99
484_T516_L0.7090.99
73_K77_E0.7090.99
389_R392_I0.7090.99
453_V457_A0.7090.99
489_D494_R0.7070.99
19_A247_C0.7050.99
264_I268_L0.7050.99
212_F216_K0.7030.99
93_H229_N0.7030.99
97_V115_I0.7030.99
23_T52_K0.6990.99
296_A299_V0.6990.99
386_F511_N0.6980.99
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501_K505_A0.5210.92
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135_D139_F0.5130.92
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124_V129_L0.5130.92
72_M89_I0.5130.92
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415_V445_I0.5120.92
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63_T71_E0.5110.92
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60_L88_W0.5110.92
289_T318_G0.5110.92
381_V559_A0.5110.92
535_L539_A0.5100.92
121_Q191_D0.5090.91
534_F537_D0.5090.91
335_F338_G0.5080.91
45_I49_M0.5080.91
505_A509_L0.5070.91
364_S368_E0.5070.91
295_A642_I0.5060.91
59_I219_Y0.5060.91
48_L53_H0.5060.91
224_E570_G0.5040.91
448_V451_I0.5040.91
213_Y216_K0.5040.91
82_P86_D0.5040.91
321_I325_R0.5030.91
122_L145_L0.5030.91
451_I454_S0.5030.91
454_S460_A0.5020.91
23_T245_N0.5020.91
252_S268_L0.5020.91
64_F232_Q0.5010.91
333_G336_V0.5010.91
515_F518_V0.5010.91
543_D546_Q0.5010.91
120_D123_S0.5010.91
493_Y496_M0.5000.91
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  
1pjrA 1 0.843 100 0.103 Contact Map
4c2tA 1 0.8769 100 0.113 Contact Map
1uaaA 2 0.8539 100 0.242 Contact Map
4c2uA 1 0.8796 100 0.252 Contact Map
3u4qA 1 0.9337 100 0.252 Contact Map
3lfuA 1 0.8512 100 0.255 Contact Map
1w36B 1 0.9378 100 0.312 Contact Map
3u4qB 1 0.9188 100 0.4 Contact Map
4pj3A 1 0.6631 100 0.595 Contact Map
2xzlA 1 0.5575 100 0.664 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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