GREMLIN Database
YDJA - Type-2 restriction enzyme BsuMI component YdjA
UniProt: O34303 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 465 (386)
Sequences: 166 (150)
Seq/√Len: 7.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
187_A245_L3.2410.90
351_V354_I3.1610.89
155_P164_Y3.0890.88
297_W392_G2.9370.85
122_D237_R2.6710.78
60_F82_L2.6410.78
267_T392_G2.5770.76
274_W380_P2.5350.75
230_I265_Y2.4920.73
66_C273_V2.4630.72
297_W314_P2.4160.71
122_D184_H2.2880.66
279_K284_H2.2770.66
123_F366_K2.2360.65
128_Y282_F2.2190.64
315_D380_P2.1910.63
331_L378_L2.1300.61
85_I270_F2.0980.59
127_G380_P2.0930.59
146_W149_T2.0370.57
184_H349_P2.0150.56
316_I414_V1.9670.54
131_K229_E1.9570.54
239_V312_L1.9150.52
52_I86_F1.9050.52
334_K360_Y1.8960.51
63_P332_D1.8960.51
332_D360_Y1.8960.51
63_P360_Y1.8960.51
63_P334_K1.8960.51
279_K316_I1.8940.51
127_G274_W1.8610.50
49_V351_V1.8480.49
82_L270_F1.8360.49
355_T359_L1.8270.49
123_F130_Q1.8070.48
127_G146_W1.7960.47
156_V165_F1.7940.47
278_C333_A1.7740.46
128_Y188_L1.7700.46
314_P392_G1.7580.46
331_L376_A1.7540.46
274_W315_D1.7530.46
282_F314_P1.7480.45
312_L355_T1.7170.44
50_G334_K1.6870.43
50_G63_P1.6870.43
50_G360_Y1.6870.43
50_G332_D1.6870.43
46_F278_C1.6770.43
122_D127_G1.6560.42
330_I336_Y1.6380.41
63_P356_K1.6310.41
334_K356_K1.6310.41
332_D356_K1.6310.41
356_K360_Y1.6310.41
188_L366_K1.6210.40
181_V376_A1.6180.40
164_Y238_D1.6180.40
112_D358_L1.6170.40
179_L222_F1.6100.40
234_Y238_D1.6070.40
295_P333_A1.6050.40
123_F223_G1.6010.40
332_D357_Q1.5980.40
357_Q360_Y1.5980.40
63_P357_Q1.5980.40
334_K357_Q1.5980.40
30_L35_I1.5950.39
183_I377_F1.5870.39
266_G377_F1.5830.39
127_G315_D1.5760.39
117_D188_L1.5760.39
164_Y377_F1.5740.39
187_A248_A1.5650.38
404_V422_K1.5520.38
129_Y266_G1.5500.38
121_N125_L1.5450.38
63_P275_E1.5450.38
275_E360_Y1.5450.38
275_E334_K1.5450.38
275_E332_D1.5450.38
146_W334_K1.5440.38
146_W360_Y1.5440.38
63_P146_W1.5440.38
146_W332_D1.5440.38
122_D349_P1.5290.37
379_F408_Y1.5250.37
138_I177_Y1.5230.37
51_V245_L1.5190.37
190_K245_L1.5150.36
97_E294_R1.5070.36
351_V359_L1.5020.36
277_V414_V1.5010.36
267_T297_W1.5010.36
190_K248_A1.5010.36
86_F267_T1.4980.36
57_N416_N1.4950.36
90_S104_E1.4940.36
52_I337_N1.4940.36
409_I414_V1.4850.35
144_I167_T1.4720.35
349_P380_P1.4590.34
128_Y185_K1.4460.34
379_F406_L1.4310.33
199_L216_L1.4200.33
369_R378_L1.4150.33
50_G356_K1.4140.33
241_L244_A1.4130.33
149_T360_Y1.4120.33
149_T334_K1.4120.33
63_P149_T1.4120.33
149_T332_D1.4120.33
371_K383_N1.4110.33
351_V355_T1.4100.33
358_L404_V1.4030.32
63_P335_Y1.3940.32
332_D335_Y1.3940.32
335_Y360_Y1.3940.32
273_V370_G1.3860.32
184_H295_P1.3850.32
50_G357_Q1.3790.32
265_Y273_V1.3690.31
306_N409_I1.3580.31
48_Y266_G1.3570.31
229_E284_H1.3540.31
275_E336_Y1.3470.30
136_Y145_D1.3460.30
297_W317_I1.3380.30
223_G293_S1.3370.30
330_I418_Y1.3250.30
152_E415_Y1.3220.30
166_S169_N1.3210.30
50_G275_E1.3090.29
270_F333_A1.3030.29
118_Y122_D1.3030.29
312_L351_V1.3020.29
50_G146_W1.3020.29
315_D356_K1.2880.29
47_N420_E1.2870.28
274_W333_A1.2790.28
165_F294_R1.2700.28
245_L409_I1.2640.28
288_Y318_K1.2600.28
163_Y407_V1.2590.28
113_F187_A1.2580.28
202_T223_G1.2540.27
275_E356_K1.2490.27
333_A349_P1.2370.27
250_D326_E1.2370.27
196_G293_S1.2330.27
146_W356_K1.2190.26
275_E357_Q1.2090.26
266_G349_P1.2080.26
354_I394_V1.2060.26
133_F282_F1.2050.26
115_I358_L1.1930.26
50_G149_T1.1880.25
229_E333_A1.1880.25
184_H377_F1.1860.25
373_K413_Q1.1850.25
155_P377_F1.1790.25
64_K234_Y1.1770.25
146_W357_Q1.1740.25
315_D332_D1.1640.25
315_D360_Y1.1640.25
63_P315_D1.1640.25
315_D334_K1.1640.25
67_N84_K1.1590.24
62_L292_I1.1570.24
119_L246_K1.1560.24
50_G335_Y1.1520.24
58_V77_T1.1500.24
142_G380_P1.1490.24
90_S159_K1.1440.24
123_F380_P1.1440.24
64_K164_Y1.1430.24
266_G363_A1.1370.24
144_I234_Y1.1300.24
316_I401_I1.1270.24
243_K421_N1.1260.24
359_L363_A1.1260.24
149_T315_D1.1250.24
127_G149_T1.1240.23
314_P380_P1.1070.23
149_T356_K1.1070.23
149_T164_Y1.1070.23
266_G317_I1.0990.23
122_D126_N1.0980.23
62_L364_L1.0960.23
187_A414_V1.0950.23
187_A338_I1.0950.23
121_N168_Y1.0900.23
145_D337_N1.0890.22
146_W275_E1.0850.22
61_I278_C1.0830.22
149_T357_Q1.0780.22
335_Y356_K1.0710.22
279_K401_I1.0690.22
269_Y330_I1.0610.22
163_Y385_T1.0590.22
73_H280_T1.0520.21
315_D349_P1.0510.21
223_G259_R1.0470.21
304_E308_E1.0450.21
277_V311_T1.0430.21
86_F144_I1.0360.21
335_Y357_Q1.0300.21
147_S167_T1.0300.21
30_L354_I1.0300.21
278_C363_A1.0280.21
184_H229_E1.0270.21
125_L410_S1.0250.21
81_K415_Y1.0240.21
83_L265_Y1.0180.21
149_T275_E1.0020.20
151_N228_K0.9980.20
41_S105_L0.9980.20
65_Y351_V0.9960.20
150_V171_V0.9940.20
64_K330_I0.9940.20
88_K421_N0.9930.20
36_L187_A0.9850.20
164_Y182_K0.9770.20
86_F191_Y0.9750.19
164_Y184_H0.9740.19
376_A407_V0.9690.19
336_Y377_F0.9660.19
65_Y401_I0.9600.19
250_D273_V0.9590.19
219_A223_G0.9580.19
356_K380_P0.9550.19
316_I333_A0.9530.19
281_V414_V0.9520.19
338_I345_L0.9470.19
183_I222_F0.9450.19
219_A249_I0.9440.19
171_V234_Y0.9440.19
162_P418_Y0.9420.19
275_E335_Y0.9420.19
156_V160_G0.9410.19
64_K140_G0.9380.19
278_C359_L0.9350.18
116_A191_Y0.9340.18
46_F314_P0.9330.18
55_G94_K0.9220.18
297_W349_P0.9220.18
82_L194_D0.9130.18
126_N377_F0.9130.18
65_Y363_A0.9110.18
236_D239_V0.9050.18
50_G315_D0.9030.18
229_E233_T0.9010.18
353_D359_L0.8990.18
273_V392_G0.8980.18
145_D250_D0.8980.18
179_L191_Y0.8950.18
226_I341_D0.8940.18
143_I319_A0.8920.17
58_V68_R0.8920.17
246_K250_D0.8900.17
274_W349_P0.8890.17
327_Y407_V0.8880.17
188_L317_I0.8850.17
56_R130_Q0.8820.17
123_F176_E0.8810.17
122_D138_I0.8750.17
105_L294_R0.8740.17
359_L364_L0.8730.17
297_W377_F0.8700.17
404_V421_N0.8690.17
228_K328_F0.8680.17
241_L282_F0.8680.17
104_E194_D0.8620.17
226_I334_K0.8610.17
226_I332_D0.8610.17
63_P226_I0.8610.17
226_I360_Y0.8610.17
92_L148_K0.8610.17
184_H266_G0.8600.17
88_K105_L0.8590.17
169_N288_Y0.8580.17
65_Y233_T0.8570.17
351_V396_F0.8560.17
181_V274_W0.8540.17
354_I377_F0.8510.17
86_F325_K0.8490.17
229_E278_C0.8440.16
267_T314_P0.8440.16
278_C297_W0.8420.16
241_L405_T0.8400.16
287_E290_K0.8360.16
64_K216_L0.8360.16
52_I315_D0.8330.16
225_V247_T0.8320.16
166_S377_F0.8290.16
139_D333_A0.8260.16
149_T380_P0.8250.16
85_I267_T0.8240.16
55_G209_S0.8220.16
239_V295_P0.8190.16
242_L295_P0.8190.16
59_I64_K0.8180.16
131_K238_D0.8150.16
30_L157_F0.8080.16
242_L265_Y0.8060.16
155_P239_V0.8060.16
49_V82_L0.8050.16
49_V278_C0.8040.16
62_L297_W0.8030.16
44_L239_V0.8010.15
410_S414_V0.8010.15
284_H295_P0.7990.15
63_P380_P0.7980.15
360_Y380_P0.7980.15
332_D380_P0.7980.15
334_K380_P0.7980.15
233_T331_L0.7960.15
63_P336_Y0.7960.15
336_Y360_Y0.7960.15
332_D336_Y0.7960.15
123_F274_W0.7960.15
249_I320_F0.7960.15
120_L293_S0.7930.15
49_V381_S0.7920.15
316_I410_S0.7890.15
218_Y367_L0.7850.15
144_I164_Y0.7840.15
315_D357_Q0.7810.15
121_N228_K0.7810.15
44_L144_I0.7800.15
126_N238_D0.7780.15
64_K248_A0.7770.15
111_S363_A0.7760.15
292_I406_L0.7750.15
152_E159_K0.7750.15
297_W386_N0.7730.15
282_F297_W0.7690.15
393_S405_T0.7680.15
164_Y336_Y0.7670.15
157_F328_F0.7660.15
42_G414_V0.7630.15
198_I354_I0.7600.15
161_V182_K0.7560.15
113_F116_A0.7550.15
168_Y330_I0.7540.15
312_L363_A0.7500.14
290_K303_I0.7490.14
327_Y374_H0.7470.14
316_I358_L0.7460.14
178_H328_F0.7440.14
53_S232_N0.7390.14
229_E363_A0.7390.14
148_K166_S0.7390.14
31_K77_T0.7390.14
282_F409_I0.7380.14
65_Y297_W0.7370.14
84_K201_F0.7350.14
274_W335_Y0.7340.14
77_T133_F0.7320.14
44_L312_L0.7310.14
126_N164_Y0.7310.14
281_V377_F0.7290.14
205_E287_E0.7280.14
127_G349_P0.7270.14
39_D223_G0.7270.14
140_G169_N0.7260.14
132_K308_E0.7250.14
123_F146_W0.7220.14
101_F250_D0.7220.14
216_L330_I0.7210.14
295_P359_L0.7200.14
270_F420_E0.7170.14
249_I379_F0.7160.14
274_W334_K0.7150.14
274_W360_Y0.7150.14
274_W332_D0.7150.14
63_P274_W0.7150.14
148_K228_K0.7110.14
326_E404_V0.7100.14
270_F332_D0.7100.14
270_F334_K0.7100.14
63_P270_F0.7100.14
270_F360_Y0.7100.14
303_I307_K0.7100.14
149_T335_Y0.7090.14
92_L208_K0.7090.14
195_F281_V0.7070.14
117_D226_I0.7050.14
49_V355_T0.7040.14
362_K401_I0.7040.14
229_E349_P0.7020.14
188_L245_L0.7010.13
51_V391_F0.7010.13
292_I313_E0.7000.13
282_F377_F0.6990.13
190_K290_K0.6990.13
234_Y345_L0.6980.13
123_F127_G0.6980.13
160_G243_K0.6980.13
278_C378_L0.6970.13
249_I349_P0.6970.13
394_V408_Y0.6940.13
171_V293_S0.6940.13
206_F241_L0.6920.13
297_W331_L0.6900.13
305_V353_D0.6890.13
42_G114_M0.6840.13
320_F326_E0.6810.13
58_V87_K0.6810.13
169_N355_T0.6810.13
142_G349_P0.6770.13
274_W356_K0.6760.13
66_C314_P0.6740.13
278_C295_P0.6740.13
401_I414_V0.6730.13
275_E315_D0.6730.13
191_Y282_F0.6710.13
179_L183_I0.6700.13
124_S180_I0.6690.13
49_V129_Y0.6660.13
238_D271_H0.6640.13
263_S399_L0.6550.13
150_V335_Y0.6550.13
115_I348_N0.6530.13
332_D377_F0.6500.13
334_K377_F0.6500.13
360_Y377_F0.6500.13
63_P377_F0.6500.13
265_Y407_V0.6460.12
409_I413_Q0.6430.12
37_Y158_S0.6430.12
265_Y396_F0.6420.12
179_L378_L0.6400.12
111_S183_I0.6400.12
30_L33_K0.6390.12
255_Q373_K0.6380.12
228_K409_I0.6380.12
355_T396_F0.6360.12
241_L331_L0.6350.12
278_C353_D0.6340.12
89_Y220_D0.6320.12
266_G333_A0.6310.12
65_Y355_T0.6300.12
297_W406_L0.6300.12
421_N425_S0.6300.12
249_I398_F0.6290.12
120_L148_K0.6270.12
133_F174_K0.6240.12
129_Y312_L0.6220.12
160_G404_V0.6210.12
294_R404_V0.6200.12
217_D415_Y0.6190.12
86_F120_L0.6190.12
69_H145_D0.6170.12
111_S328_F0.6140.12
108_D294_R0.6140.12
86_F285_V0.6140.12
275_E330_I0.6130.12
278_C355_T0.6120.12
171_V420_E0.6120.12
119_L199_L0.6090.12
262_L393_S0.6070.12
182_K211_D0.6070.12
221_F311_T0.6060.12
349_P392_G0.6050.12
65_Y229_E0.6040.12
120_L225_V0.6040.12
241_L287_E0.6040.12
333_A380_P0.6040.12
92_L276_E0.6030.12
281_V339_N0.6030.12
126_N341_D0.6000.12
172_V177_Y0.6000.12
270_F284_H0.5990.12
56_R141_E0.5970.12
184_H363_A0.5970.12
340_F410_S0.5950.12
273_V336_Y0.5950.12
119_L251_R0.5940.12
35_I379_F0.5940.12
79_F378_L0.5930.12
229_E242_L0.5910.12
267_T358_L0.5900.12
152_E378_L0.5890.12
185_K411_A0.5870.12
354_I358_L0.5870.12
159_K187_A0.5860.11
140_G362_K0.5850.11
186_W363_A0.5830.11
248_A317_I0.5820.11
277_V358_L0.5790.11
239_V350_G0.5750.11
265_Y281_V0.5740.11
30_L34_G0.5720.11
146_W335_Y0.5700.11
139_D380_P0.5700.11
278_C318_K0.5620.11
31_K341_D0.5620.11
282_F338_I0.5590.11
29_L32_S0.5590.11
172_V259_R0.5580.11
120_L211_D0.5580.11
170_E277_V0.5580.11
131_K312_L0.5580.11
123_F315_D0.5570.11
329_L376_A0.5560.11
64_K222_F0.5560.11
47_N294_R0.5550.11
181_V407_V0.5520.11
195_F233_T0.5520.11
249_I274_W0.5490.11
48_Y169_N0.5480.11
48_Y140_G0.5430.11
49_V267_T0.5430.11
123_F246_K0.5430.11
198_I243_K0.5430.11
50_G336_Y0.5420.11
373_K420_E0.5410.11
311_T351_V0.5400.11
345_L348_N0.5390.11
188_L412_E0.5390.11
162_P167_T0.5390.11
103_S160_G0.5380.11
362_K379_F0.5370.11
197_V230_I0.5360.11
286_N414_V0.5360.11
77_T250_D0.5350.11
47_N145_D0.5330.11
302_D307_K0.5330.11
54_N236_D0.5320.11
146_W315_D0.5320.11
192_F195_F0.5310.11
261_T331_L0.5290.11
122_D229_E0.5280.11
314_P333_A0.5280.11
46_F297_W0.5270.11
83_L249_I0.5240.11
41_S126_N0.5230.10
164_Y284_H0.5220.10
50_G380_P0.5220.10
189_S200_G0.5220.10
86_F388_F0.5220.10
149_T274_W0.5210.10
249_I307_K0.5190.10
115_I155_P0.5190.10
113_F327_Y0.5180.10
330_I334_K0.5180.10
63_P330_I0.5180.10
330_I360_Y0.5180.10
65_Y406_L0.5180.10
267_T288_Y0.5180.10
274_W314_P0.5170.10
270_F381_S0.5160.10
129_Y267_T0.5150.10
247_T421_N0.5150.10
80_N414_V0.5120.10
223_G280_T0.5110.10
184_H354_I0.5110.10
359_L381_S0.5110.10
157_F423_T0.5100.10
65_Y331_L0.5100.10
33_K86_F0.5100.10
155_P331_L0.5090.10
59_I107_S0.5070.10
65_Y183_I0.5070.10
52_I231_V0.5070.10
266_G274_W0.5070.10
373_K404_V0.5040.10
134_T170_E0.5040.10
229_E249_I0.5030.10
48_Y274_W0.5020.10
188_L282_F0.5020.10
65_Y242_L0.5010.10
65_Y184_H0.5010.10
197_V348_N0.5010.10
160_G206_F0.5010.10
49_V189_S0.5000.10
41_S383_N0.5000.10
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  
4qlbG 1 0.0688 4.9 0.981 Contact Map
4b0aA 1 0.1978 3.1 0.983 Contact Map
2lc5A 1 0.1828 2.8 0.983 Contact Map
5bt3A 1 0.2258 2.7 0.983 Contact Map
3o6qB 1 0.0774 2.5 0.984 Contact Map
3mb4A 1 0.2344 2.4 0.984 Contact Map
1e0nA 1 0.0581 2.3 0.984 Contact Map
1rm1A 1 0.1978 2.3 0.984 Contact Map
2q6qA 2 0.1183 2.2 0.984 Contact Map
1avsA 1 0.1763 2.2 0.984 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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