GREMLIN Database
DP2S - DNA polymerase II small subunit
UniProt: Q9HMR7 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 508 (390)
Sequences: 392 (284)
Seq/√Len: 14.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
448_V495_L8.9581.00
252_S496_D6.4811.00
386_L450_H6.4521.00
255_A384_V5.1101.00
257_L292_L3.9731.00
384_V448_V3.7921.00
416_L449_F3.7050.99
464_N476_Q3.4520.99
172_V217_I3.2480.99
243_T447_D3.2250.98
293_I327_L3.1250.98
414_E460_G3.1160.98
258_I291_L3.0680.98
144_Q420_R2.9770.97
459_V479_F2.9400.97
291_L334_M2.8460.97
196_V232_A2.6170.94
252_S498_D2.5130.93
280_L291_L2.4480.92
387_Y391_S2.4400.92
190_T490_A2.4020.91
293_I338_M2.3960.91
106_A111_V2.3650.91
117_M372_S2.3580.91
409_P455_H2.2750.89
254_Q496_D2.1670.86
323_F327_L2.1500.86
408_D411_N2.1480.86
171_M216_V2.0720.84
262_H487_P2.0530.83
392_L416_L2.0450.83
217_I284_A2.0280.82
256_A492_A1.9360.79
235_I238_P1.9320.79
154_T157_L1.9270.79
262_H343_H1.9100.78
364_R392_L1.9040.78
241_P445_V1.8390.75
352_Q373_N1.8350.75
337_V375_S1.8220.75
491_T504_V1.8200.75
339_I450_H1.8030.74
371_T375_S1.7370.71
308_D311_L1.7350.71
140_R437_E1.7110.70
420_R464_N1.6950.69
334_M365_A1.6920.69
395_V416_L1.6890.69
256_A280_L1.6680.68
218_A450_H1.6670.68
417_L421_H1.6590.67
172_V287_S1.6550.67
157_L227_G1.6420.67
304_Y307_Q1.6100.65
255_A497_L1.6040.65
294_A450_H1.6000.65
237_F483_V1.5970.64
256_A291_L1.5960.64
307_Q311_L1.5900.64
417_L507_F1.5760.63
108_A111_V1.5490.62
223_L398_E1.5480.62
176_R180_S1.5460.62
319_Q420_R1.5310.61
196_V425_P1.5280.61
393_D458_G1.5240.61
322_T325_E1.5170.60
492_A507_F1.5090.60
445_V464_N1.4980.59
170_G221_G1.4870.59
262_H298_V1.4610.57
130_F391_S1.4460.56
113_I120_A1.4450.56
227_G394_E1.4430.56
339_I385_L1.4420.56
106_A109_R1.4230.55
252_S287_S1.4210.55
391_S433_A1.4210.55
307_Q310_E1.4200.55
328_K362_I1.4040.54
277_A329_D1.4040.54
324_A386_L1.3880.53
259_S452_G1.3870.53
238_P350_E1.3720.52
135_R319_Q1.3710.52
378_T383_S1.3590.52
280_L431_R1.3580.52
236_Y395_V1.3250.50
117_M120_A1.3200.50
255_A383_S1.3110.49
175_I178_T1.3100.49
251_R384_V1.3100.49
297_M323_F1.3090.49
302_G343_H1.3050.49
280_L492_A1.3030.49
329_D332_G1.2980.48
326_H439_H1.2960.48
216_V395_V1.2870.48
193_V232_A1.2850.48
347_R480_Q1.2790.47
492_A505_H1.2770.47
339_I388_H1.2730.47
169_V310_E1.2730.47
239_E418_K1.2700.47
279_W417_L1.2690.47
396_I409_P1.2650.47
158_A192_G1.2570.46
264_G421_H1.2560.46
413_M480_Q1.2560.46
339_I386_L1.2480.46
149_V218_A1.2460.45
165_D233_D1.2420.45
291_L336_I1.2380.45
339_I371_T1.2350.45
173_N193_V1.2280.44
292_L386_L1.2220.44
485_I488_D1.2200.44
334_M392_L1.2180.44
172_V491_T1.2130.44
440_L444_T1.2130.44
381_G475_H1.2130.44
397_A451_T1.2100.44
223_L230_L1.2070.43
112_E219_V1.2040.43
393_D409_P1.1980.43
194_F197_L1.1940.43
390_V429_R1.1900.42
474_Q477_T1.1900.42
300_G343_H1.1890.42
180_S491_T1.1790.42
343_H388_H1.1770.42
217_I235_I1.1730.42
108_A120_A1.1710.41
298_V481_E1.1650.41
334_M507_F1.1630.41
385_L483_V1.1630.41
292_L379_I1.1550.41
298_V305_P1.1470.40
223_L234_D1.1460.40
142_A194_F1.1430.40
220_S234_D1.1420.40
285_A444_T1.1410.40
185_V327_L1.1300.39
166_A230_L1.1290.39
425_P430_T1.1280.39
241_P420_R1.1260.39
230_L350_E1.1170.39
196_V486_S1.1100.38
169_V448_V1.1080.38
330_V443_D1.1030.38
276_F297_M1.1020.38
462_H480_Q1.1010.38
258_I279_W1.0960.37
216_V227_G1.0910.37
393_D479_F1.0850.37
215_E387_Y1.0780.37
237_F338_M1.0740.36
219_V444_T1.0650.36
302_G305_P1.0650.36
192_G490_A1.0640.36
354_A430_T1.0640.36
353_P433_A1.0630.36
208_V330_V1.0630.36
141_L504_V1.0630.36
125_G298_V1.0600.36
347_R445_V1.0570.35
279_W285_A1.0550.35
227_G433_A1.0530.35
306_G310_E1.0530.35
288_V338_M1.0530.35
278_D321_E1.0490.35
140_R441_A1.0440.35
253_V380_D1.0410.35
133_V432_L1.0390.35
211_L238_P1.0370.34
194_F449_F1.0320.34
146_R169_V1.0280.34
241_P392_L1.0280.34
173_N429_R1.0240.34
187_L499_T1.0230.34
454_V484_N1.0210.34
127_Y359_L1.0200.34
218_A355_F1.0180.34
272_A490_A1.0160.33
439_H486_S1.0160.33
457_L502_I1.0150.33
111_V114_D1.0150.33
130_F436_A1.0130.33
263_V272_A1.0120.33
382_V447_D1.0100.33
264_G417_L1.0060.33
441_A492_A1.0030.33
320_Y357_E1.0030.33
241_P423_A1.0020.33
249_A255_A1.0000.33
116_D338_M0.9980.33
263_V488_D0.9940.32
272_A417_L0.9930.32
157_L192_G0.9870.32
392_L438_D0.9870.32
149_V294_A0.9860.32
248_T336_I0.9850.32
213_L428_G0.9800.32
253_V274_R0.9700.31
186_E192_G0.9660.31
410_Q486_S0.9610.31
163_G360_R0.9540.30
394_E498_D0.9510.30
185_V336_I0.9450.30
387_Y480_Q0.9430.30
263_V270_A0.9380.30
112_E378_T0.9380.30
496_D506_K0.9360.30
122_T435_E0.9350.30
153_P276_F0.9350.30
168_I408_D0.9330.30
385_L422_V0.9300.29
271_D276_F0.9260.29
254_Q331_P0.9260.29
172_V185_V0.9250.29
167_A234_D0.9220.29
211_L499_T0.9180.29
185_V490_A0.9160.29
357_E418_K0.9160.29
375_S400_P0.9140.29
290_Y337_V0.9120.29
182_H217_I0.9110.29
257_L483_V0.9100.28
280_L330_V0.9070.28
191_N454_V0.9030.28
264_G442_I0.8990.28
481_E495_L0.8990.28
268_F343_H0.8970.28
347_R421_H0.8960.28
157_L194_F0.8880.28
216_V256_A0.8870.27
388_H465_V0.8820.27
237_F263_V0.8810.27
157_L490_A0.8790.27
257_L450_H0.8770.27
123_G444_T0.8730.27
240_V445_V0.8730.27
414_E496_D0.8700.27
299_E302_G0.8680.27
350_E387_Y0.8670.27
293_I395_V0.8660.27
187_L414_E0.8660.27
115_G355_F0.8590.26
392_L412_A0.8570.26
408_D476_Q0.8570.26
158_A454_V0.8560.26
432_L448_V0.8560.26
265_S315_D0.8520.26
227_G496_D0.8520.26
434_P483_V0.8510.26
137_R424_P0.8490.26
161_P222_T0.8440.26
279_W334_M0.8440.26
129_D193_V0.8430.26
178_T182_H0.8420.26
185_V211_L0.8380.25
317_Y397_A0.8370.25
273_W346_V0.8340.25
158_A191_N0.8330.25
140_R298_V0.8310.25
217_I253_V0.8310.25
138_Y190_T0.8300.25
141_L263_V0.8280.25
296_D413_M0.8280.25
186_E336_I0.8280.25
283_P399_H0.8260.25
123_G153_P0.8250.25
321_E381_G0.8250.25
337_V432_L0.8250.25
236_Y414_E0.8220.25
208_V257_L0.8200.25
130_F175_I0.8200.25
130_F395_V0.8180.25
143_A495_L0.8170.25
148_R497_L0.8170.25
351_P374_P0.8160.24
351_P389_G0.8160.24
374_P389_G0.8160.24
295_G351_P0.8160.24
295_G374_P0.8160.24
295_G389_G0.8160.24
256_A494_I0.8120.24
157_L198_V0.8120.24
157_L191_N0.8120.24
337_V377_V0.8090.24
155_S496_D0.8060.24
242_R336_I0.8060.24
383_S444_T0.7980.24
193_V327_L0.7970.24
423_A500_L0.7950.24
491_T506_K0.7950.24
355_F449_F0.7940.24
104_A108_A0.7940.24
283_P330_V0.7910.23
334_M370_I0.7890.23
291_L330_V0.7880.23
324_A450_H0.7880.23
193_V486_S0.7870.23
128_Q152_R0.7850.23
307_Q455_H0.7830.23
440_L459_V0.7820.23
141_L144_Q0.7810.23
304_Y477_T0.7790.23
142_A168_I0.7780.23
348_L375_S0.7760.23
242_R425_P0.7750.23
249_A257_L0.7750.23
399_H412_A0.7750.23
298_V350_E0.7740.23
186_E276_F0.7710.23
397_A410_Q0.7700.23
187_L261_V0.7690.23
143_A364_R0.7670.23
421_H507_F0.7660.22
263_V326_H0.7640.22
165_D420_R0.7640.22
132_S416_L0.7630.22
173_N229_I0.7620.22
391_S439_H0.7600.22
108_A274_R0.7590.22
177_S408_D0.7590.22
339_I358_E0.7570.22
172_V502_I0.7540.22
119_G288_V0.7520.22
239_E421_H0.7490.22
405_T408_D0.7440.22
132_S256_A0.7420.22
456_K485_I0.7400.22
417_L506_K0.7390.21
341_G351_P0.7380.21
295_G341_G0.7380.21
341_G389_G0.7380.21
341_G374_P0.7380.21
424_P434_P0.7350.21
409_P412_A0.7340.21
213_L486_S0.7320.21
189_D373_N0.7310.21
131_V432_L0.7300.21
259_S423_A0.7290.21
158_A173_N0.7270.21
388_H453_H0.7260.21
271_D465_V0.7260.21
262_H485_I0.7230.21
243_T338_M0.7190.21
296_D455_H0.7180.21
165_D280_L0.7180.21
316_I322_T0.7180.21
285_A298_V0.7170.21
131_V238_P0.7170.21
166_A390_V0.7170.21
409_P454_V0.7170.21
137_R446_P0.7160.21
144_Q464_N0.7150.21
298_V349_A0.7140.21
214_D484_N0.7130.21
429_R435_E0.7100.20
369_R448_V0.7090.20
301_V503_T0.7070.20
380_D436_A0.7060.20
270_A379_I0.7030.20
256_A290_Y0.7030.20
256_A379_I0.7020.20
372_S429_R0.7000.20
192_G310_E0.7000.20
238_P441_A0.6990.20
130_F262_H0.6990.20
390_V426_F0.6980.20
419_K486_S0.6980.20
244_Y502_I0.6960.20
294_A359_L0.6960.20
460_G501_D0.6950.20
347_R377_V0.6920.20
265_S476_Q0.6910.20
108_A211_L0.6910.20
342_N388_H0.6900.20
178_T359_L0.6870.20
194_F286_E0.6860.20
215_E419_K0.6860.20
367_D438_D0.6840.19
212_L259_S0.6830.19
182_H443_D0.6830.19
294_A386_L0.6770.19
164_S310_E0.6760.19
185_V309_E0.6760.19
296_D361_S0.6750.19
262_H463_H0.6750.19
311_L319_Q0.6740.19
422_V442_I0.6720.19
303_V392_L0.6690.19
350_E390_V0.6680.19
322_T460_G0.6660.19
130_F321_E0.6640.19
422_V496_D0.6630.19
220_S223_L0.6630.19
300_G462_H0.6620.19
234_D293_I0.6620.19
426_F432_L0.6610.19
445_V476_Q0.6600.19
108_A496_D0.6600.19
109_R336_I0.6590.19
397_A429_R0.6590.19
288_V490_A0.6590.19
110_S327_L0.6590.19
415_L419_K0.6570.19
136_D140_R0.6520.18
218_A483_V0.6520.18
397_A423_A0.6510.18
262_H268_F0.6510.18
337_V447_D0.6490.18
217_I459_V0.6470.18
169_V305_P0.6460.18
193_V275_S0.6460.18
141_L441_A0.6450.18
268_F300_G0.6440.18
285_A507_F0.6420.18
109_R359_L0.6420.18
350_E438_D0.6410.18
275_S428_G0.6400.18
421_H446_P0.6390.18
442_I501_D0.6370.18
257_L453_H0.6360.18
148_R409_P0.6350.18
497_L500_L0.6350.18
212_L253_V0.6350.18
272_A318_D0.6340.18
321_E330_V0.6330.18
240_V288_V0.6330.18
359_L411_N0.6310.18
280_L334_M0.6300.18
310_E319_Q0.6290.18
312_D334_M0.6280.18
237_F384_V0.6280.18
124_T168_I0.6280.18
347_R375_S0.6270.18
266_Q380_D0.6260.18
361_S505_H0.6230.17
220_S230_L0.6230.17
160_M337_V0.6220.17
320_Y490_A0.6210.17
185_V399_H0.6200.17
184_R455_H0.6190.17
361_S487_P0.6180.17
325_E448_V0.6150.17
191_N457_L0.6140.17
461_I489_V0.6130.17
156_A159_S0.6130.17
489_V500_L0.6110.17
163_G335_E0.6110.17
166_A171_M0.6100.17
392_L449_F0.6060.17
122_T411_N0.6030.17
143_A381_G0.6020.17
427_G484_N0.6020.17
109_R114_D0.6020.17
218_A237_F0.6010.17
241_P258_I0.6000.17
172_V492_A0.5990.17
346_V353_P0.5980.17
163_G359_L0.5970.17
269_A436_A0.5970.17
304_Y379_I0.5950.17
189_D352_Q0.5950.17
286_E444_T0.5950.17
177_S180_S0.5940.17
192_G243_T0.5930.17
283_P444_T0.5930.17
302_G477_T0.5860.16
134_F426_F0.5840.16
453_H485_I0.5830.16
417_L446_P0.5830.16
240_V420_R0.5830.16
361_S458_G0.5820.16
374_P438_D0.5810.16
351_P438_D0.5810.16
389_G438_D0.5810.16
295_G438_D0.5810.16
254_Q332_G0.5800.16
320_Y350_E0.5800.16
314_V333_D0.5790.16
255_A292_L0.5790.16
265_S268_F0.5780.16
277_A326_H0.5780.16
129_D419_K0.5770.16
185_V401_S0.5760.16
250_D298_V0.5750.16
247_S255_A0.5750.16
355_F502_I0.5740.16
157_L229_I0.5730.16
158_A398_E0.5730.16
155_S240_V0.5720.16
285_A417_L0.5710.16
129_D171_M0.5700.16
413_M451_T0.5700.16
299_E343_H0.5700.16
383_S441_A0.5690.16
423_A451_T0.5680.16
293_I417_L0.5670.16
330_V477_T0.5660.16
314_V323_F0.5650.16
134_F427_G0.5640.16
130_F379_I0.5630.16
431_R492_A0.5630.16
178_T296_D0.5630.16
342_N367_D0.5620.16
221_G355_F0.5610.16
390_V394_E0.5590.16
360_R386_L0.5590.16
239_E420_R0.5590.16
365_A383_S0.5580.16
343_H488_D0.5570.15
415_L418_K0.5560.15
246_P497_L0.5550.15
297_M505_H0.5540.15
108_A232_A0.5530.15
178_T331_P0.5520.15
291_L492_A0.5510.15
164_S336_I0.5500.15
421_H497_L0.5500.15
279_W288_V0.5500.15
324_A360_R0.5490.15
212_L428_G0.5490.15
187_L233_D0.5480.15
254_Q494_I0.5470.15
195_P384_V0.5470.15
306_G311_L0.5460.15
350_E448_V0.5460.15
256_A276_F0.5450.15
298_V479_F0.5450.15
141_L350_E0.5430.15
180_S392_L0.5430.15
157_L358_E0.5430.15
238_P262_H0.5430.15
238_P303_V0.5420.15
257_L475_H0.5420.15
218_A445_V0.5420.15
160_M233_D0.5410.15
257_L337_V0.5400.15
112_E293_I0.5380.15
426_F484_N0.5340.15
214_D427_G0.5310.15
133_V496_D0.5300.15
156_A505_H0.5290.15
146_R379_I0.5280.15
356_D450_H0.5270.15
430_T449_F0.5250.15
372_S409_P0.5240.15
293_I336_I0.5240.15
247_S283_P0.5240.15
331_P421_H0.5230.15
190_T355_F0.5230.15
123_G250_D0.5230.15
257_L499_T0.5220.14
425_P486_S0.5220.14
217_I376_T0.5220.14
365_A483_V0.5200.14
241_P379_I0.5190.14
337_V358_E0.5190.14
301_V304_Y0.5180.14
208_V491_T0.5160.14
320_Y391_S0.5160.14
301_V444_T0.5160.14
193_V213_L0.5160.14
140_R216_V0.5150.14
385_L458_G0.5140.14
284_A321_E0.5140.14
237_F284_A0.5110.14
123_G435_E0.5090.14
212_L314_V0.5090.14
304_Y343_H0.5070.14
331_P487_P0.5070.14
257_L448_V0.5070.14
342_N453_H0.5060.14
279_W421_H0.5050.14
325_E338_M0.5040.14
377_V393_D0.5040.14
141_L192_G0.5040.14
264_G388_H0.5030.14
459_V502_I0.5020.14
288_V392_L0.5020.14
285_A288_V0.5000.14
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  
3e0jA 1 0.7579 100 0.467 Contact Map
3floA 3 0.7421 100 0.594 Contact Map
4y97A 1 0.7854 100 0.618 Contact Map
2yvtA 1 0.4488 99.6 0.897 Contact Map
3ib7A 2 0.4626 99.5 0.905 Contact Map
3av0A 1 0.4429 99.5 0.907 Contact Map
3d03A 5 0.4429 99.5 0.907 Contact Map
1su1A 3 0.3346 99.4 0.909 Contact Map
2kknA 1 0.3031 99.4 0.909 Contact Map
1s3lA 1 0.3248 99.4 0.909 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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