GREMLIN Database
RE_LlaJI - LlaJI restriction endonuclease
PFAM: PF09563 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 374 (345)
Sequences: 578 (495)
Seq/√Len: 26.7
META: 0.735

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
142_C200_L4.7821.00
33_L37_L4.0541.00
233_D268_T3.8571.00
178_I201_I3.8401.00
300_N304_T3.7331.00
279_L327_A3.5231.00
182_N201_I3.3761.00
299_I328_F3.3451.00
181_L197_L3.2871.00
181_L201_I3.2711.00
99_I122_F3.0031.00
77_D192_R2.9841.00
29_D33_L2.8411.00
174_K204_L2.6960.99
86_E184_E2.5970.99
296_S300_N2.5560.99
185_L194_K2.3840.99
77_D139_H2.3750.99
264_L300_N2.3320.98
142_C203_Y2.3290.98
111_I120_L2.3030.98
296_S304_T2.3010.98
185_L198_K2.2950.98
83_L140_K2.2840.98
145_E203_Y2.2200.98
66_F69_A2.2000.98
232_I268_T2.1960.98
296_S299_I2.1940.98
184_E197_L2.1890.98
251_W279_L2.1850.98
178_I205_E2.1490.97
344_N348_E2.0950.97
110_P119_Y2.0890.97
289_T292_N2.0620.96
73_E195_R2.0580.96
279_L329_I2.0420.96
232_I281_A2.0290.96
15_F19_Y2.0170.96
191_D194_K2.0140.96
221_T251_W2.0100.96
33_L36_L1.9740.95
112_I117_P1.9370.95
34_I37_L1.9210.95
277_Y327_A1.8840.94
120_L196_L1.8750.94
146_S203_Y1.8740.94
343_G348_E1.8370.93
201_I205_E1.8330.93
196_L228_W1.8020.93
27_R30_I1.7640.92
1_F14_Y1.7620.92
27_R33_L1.7620.92
302_Q305_Y1.7520.92
89_K125_R1.7410.91
241_D244_K1.7330.91
100_N125_R1.7010.90
143_V163_L1.7000.90
223_S226_Y1.6880.90
340_K345_V1.6820.90
91_Y123_V1.6690.89
343_G349_N1.6610.89
192_R196_L1.6340.88
86_E193_K1.6240.88
249_P261_K1.6170.88
309_L312_F1.5930.87
345_V350_I1.5910.87
139_H228_W1.5900.87
83_L196_L1.5740.86
102_K106_K1.5660.86
264_L308_A1.5650.86
294_P328_F1.5540.86
30_I33_L1.5420.85
295_G298_D1.5350.85
301_K305_Y1.5290.85
103_K107_K1.5190.84
267_D281_A1.5060.84
56_F59_E1.4980.83
343_G350_I1.4840.83
345_V348_E1.4800.83
37_L224_F1.4750.82
285_K292_N1.4600.82
190_N193_K1.4550.82
224_F228_W1.4430.81
282_K302_Q1.4250.80
139_H197_L1.4230.80
264_L304_T1.4180.80
3_G16_P1.4120.80
104_T229_E1.4080.79
326_N331_P1.3970.79
182_N205_E1.3940.79
147_F159_P1.3930.79
41_L96_S1.3920.79
343_G346_N1.3910.79
163_L273_N1.3780.78
239_I242_K1.3750.78
232_I329_I1.3680.77
251_W266_P1.3680.77
108_S123_V1.3640.77
138_I152_W1.3450.76
249_P283_Y1.3450.76
40_V44_Y1.3380.76
12_L17_K1.3250.75
264_L299_I1.3190.75
270_M277_Y1.2980.73
246_F265_R1.2980.73
73_E77_D1.2810.72
284_Y302_Q1.2720.72
134_L180_I1.2570.71
233_D237_N1.2520.71
282_K301_K1.2510.71
266_P281_A1.2420.70
123_V181_L1.2420.70
107_K123_V1.2390.70
278_I299_I1.2380.70
93_T123_V1.2360.70
267_D294_P1.2320.69
280_D302_Q1.2080.68
82_G189_F1.2020.67
343_G347_F1.2020.67
29_D32_K1.1980.67
219_F269_I1.1980.67
134_L177_I1.1960.67
328_F331_P1.1930.67
71_Y146_S1.1890.67
220_G294_P1.1800.66
65_D78_Y1.1720.65
295_G304_T1.1710.65
95_G124_T1.1700.65
299_I303_I1.1570.64
84_Y184_E1.1430.63
226_Y298_D1.1390.63
27_R181_L1.1350.63
253_L259_K1.1240.62
33_L38_L1.1130.61
41_L221_T1.1120.61
11_I78_Y1.1100.61
341_I344_N1.1070.61
10_N13_V1.1030.61
105_I120_L1.0980.60
273_N290_P1.0980.60
251_W286_Y1.0940.60
184_E188_T1.0880.60
130_N221_T1.0790.59
134_L138_I1.0740.59
190_N279_L1.0700.58
41_L115_G1.0660.58
173_D176_Y1.0660.58
22_P143_V1.0640.58
40_V224_F1.0570.57
86_E196_L1.0520.57
71_Y203_Y1.0490.57
264_L296_S1.0450.56
73_E199_S1.0400.56
41_L227_V1.0330.56
341_I348_E1.0300.55
198_K271_I1.0300.55
139_H235_V1.0220.55
2_V299_I1.0180.54
139_H294_P1.0170.54
76_N96_S1.0140.54
251_W294_P1.0090.54
249_P308_A1.0080.54
59_E208_D1.0060.54
274_D322_K1.0050.54
307_E330_M1.0040.53
118_I178_I1.0010.53
15_F196_L1.0000.53
65_D127_K0.9990.53
138_I181_L0.9980.53
181_L196_L0.9970.53
138_I328_F0.9930.53
77_D81_N0.9910.52
49_D52_E0.9830.52
340_K344_N0.9800.52
92_K95_G0.9750.51
300_N307_E0.9730.51
77_D205_E0.9710.51
143_V227_V0.9700.51
225_E296_S0.9700.51
346_N349_N0.9680.51
15_F236_F0.9660.51
196_L224_F0.9650.51
106_K132_D0.9640.50
106_K120_L0.9570.50
280_D301_K0.9520.50
224_F281_A0.9470.49
74_L187_N0.9470.49
101_W104_T0.9460.49
337_N340_K0.9450.49
119_Y189_F0.9440.49
25_D214_N0.9430.49
188_T197_L0.9410.49
114_N181_L0.9400.49
114_N134_L0.9330.48
37_L40_V0.9270.48
335_K340_K0.9190.47
160_E257_K0.9150.47
49_D78_Y0.9130.47
72_L194_K0.9050.46
103_K183_K0.9050.46
339_F344_N0.9030.46
57_L65_D0.9000.46
280_D284_Y0.8940.45
139_H146_S0.8930.45
195_R198_K0.8900.45
83_L136_T0.8870.45
344_N347_F0.8850.45
264_L327_A0.8770.44
227_V233_D0.8730.44
190_N204_L0.8720.44
300_N303_I0.8720.44
284_Y301_K0.8670.43
89_K201_I0.8670.43
41_L44_Y0.8590.43
249_P295_G0.8580.43
74_L79_L0.8580.43
196_L283_Y0.8570.42
104_T305_Y0.8570.42
4_I102_K0.8540.42
17_K285_K0.8540.42
113_S116_S0.8520.42
15_F18_G0.8500.42
340_K343_G0.8480.42
232_I264_L0.8450.42
327_A332_Y0.8450.42
265_R300_N0.8440.42
40_V43_K0.8430.41
249_P296_S0.8430.41
242_K264_L0.8400.41
278_I309_L0.8400.41
177_I204_L0.8340.41
218_Y238_G0.8330.41
101_W305_Y0.8270.40
77_D294_P0.8270.40
1_F146_S0.8260.40
264_L328_F0.8250.40
249_P300_N0.8250.40
17_K189_F0.8250.40
340_K348_E0.8240.40
30_I35_K0.8230.40
72_L76_N0.8200.40
29_D37_L0.8190.40
268_T298_D0.8180.40
138_I251_W0.8170.40
31_R37_L0.8170.40
31_R35_K0.8160.40
62_S209_E0.8150.39
232_I333_N0.8130.39
281_A306_G0.8100.39
293_L303_I0.8100.39
345_V349_N0.8100.39
220_G328_F0.8040.39
70_A300_N0.8030.39
26_L160_E0.8020.39
82_G331_P0.8000.38
281_A294_P0.8000.38
124_T225_E0.7990.38
176_Y180_I0.7990.38
18_G139_H0.7910.38
67_P70_A0.7890.38
109_T118_I0.7860.37
93_T281_A0.7850.37
341_I345_V0.7850.37
186_N213_D0.7810.37
341_I346_N0.7770.37
231_M286_Y0.7730.36
82_G228_W0.7670.36
15_F21_L0.7660.36
107_K111_I0.7650.36
99_I105_I0.7610.36
98_K102_K0.7580.35
55_L61_E0.7580.35
13_V118_I0.7560.35
339_F343_G0.7560.35
286_Y293_L0.7470.35
32_K189_F0.7470.35
140_K143_V0.7460.35
81_N121_D0.7460.35
339_F345_V0.7450.35
209_E322_K0.7430.34
5_K14_Y0.7430.34
53_E58_N0.7390.34
86_E133_N0.7390.34
27_R31_R0.7370.34
70_A145_E0.7360.34
108_S197_L0.7340.34
78_Y109_T0.7330.34
141_Y146_S0.7330.34
236_F279_L0.7320.34
148_K161_K0.7320.34
138_I217_F0.7270.33
193_K264_L0.7210.33
18_G138_I0.7190.33
80_E259_K0.7180.33
148_K241_D0.7140.32
201_I204_L0.7100.32
117_P178_I0.7060.32
184_E196_L0.7050.32
173_D177_I0.7040.32
135_I184_E0.7030.32
76_N179_S0.6990.32
90_I269_I0.6990.32
82_G101_W0.6990.32
137_R172_G0.6970.31
47_K110_P0.6960.31
246_F249_P0.6930.31
227_V306_G0.6930.31
94_N215_Q0.6890.31
196_L199_S0.6860.31
111_I240_E0.6850.31
188_T266_P0.6850.31
42_A75_I0.6840.31
81_N200_L0.6840.31
220_G267_D0.6830.30
205_E210_K0.6820.30
220_G326_N0.6790.30
267_D328_F0.6770.30
221_T264_L0.6760.30
34_I143_V0.6750.30
75_I79_L0.6740.30
100_N273_N0.6720.30
143_V147_F0.6710.30
336_D340_K0.6710.30
251_W281_A0.6700.30
139_H184_E0.6690.30
128_T174_K0.6670.29
194_K199_S0.6660.29
26_L29_D0.6660.29
124_T145_E0.6650.29
294_P298_D0.6650.29
212_S291_K0.6640.29
115_G158_M0.6630.29
149_K281_A0.6610.29
139_H192_R0.6600.29
68_L335_K0.6600.29
136_T228_W0.6600.29
175_E187_N0.6590.29
119_Y137_R0.6580.29
221_T283_Y0.6570.29
122_F202_A0.6540.29
15_F270_M0.6530.29
88_E143_V0.6530.29
282_K294_P0.6520.29
111_I175_E0.6520.29
41_L179_S0.6510.28
219_F266_P0.6480.28
280_D305_Y0.6470.28
186_N248_K0.6460.28
2_V221_T0.6460.28
142_C146_S0.6460.28
13_V69_A0.6450.28
142_C154_F0.6440.28
233_D281_A0.6440.28
346_N350_I0.6430.28
122_F231_M0.6410.28
41_L132_D0.6400.28
341_I347_F0.6400.28
267_D282_K0.6390.28
246_F330_M0.6390.28
34_I210_K0.6370.28
103_K123_V0.6360.28
269_I276_F0.6330.27
84_Y296_S0.6320.27
294_P299_I0.6310.27
103_K114_N0.6300.27
221_T232_I0.6280.27
24_D35_K0.6280.27
123_V143_V0.6280.27
76_N337_N0.6270.27
68_L209_E0.6270.27
143_V170_D0.6270.27
79_L191_D0.6260.27
9_D323_K0.6260.27
337_N348_E0.6250.27
173_D273_N0.6240.27
128_T212_S0.6230.27
249_P303_I0.6210.27
5_K41_L0.6190.27
76_N125_R0.6170.26
100_N185_L0.6140.26
277_Y325_Y0.6130.26
117_P192_R0.6120.26
197_L201_I0.6110.26
78_Y122_F0.6100.26
70_A142_C0.6100.26
237_N309_L0.6090.26
43_K161_K0.6080.26
66_F142_C0.6060.26
154_F293_L0.6060.26
4_I126_K0.6050.26
98_K138_I0.6050.26
336_D345_V0.6040.26
94_N175_E0.6040.26
142_C293_L0.6040.26
294_P302_Q0.6030.26
150_L153_L0.6010.26
221_T227_V0.6000.25
116_S148_K0.5990.25
232_I239_I0.5990.25
228_W298_D0.5980.25
233_D245_Y0.5980.25
294_P301_K0.5960.25
46_K112_I0.5950.25
99_I189_F0.5940.25
189_F193_K0.5930.25
232_I246_F0.5920.25
247_P264_L0.5900.25
249_P330_M0.5900.25
1_F220_G0.5900.25
151_G281_A0.5890.25
41_L207_L0.5870.25
238_G270_M0.5870.25
264_L294_P0.5860.25
296_S303_I0.5850.25
5_K303_I0.5850.25
136_T197_L0.5850.25
135_I188_T0.5850.25
305_Y331_P0.5850.25
80_E133_N0.5840.25
157_F161_K0.5820.24
75_I160_E0.5810.24
337_N343_G0.5810.24
61_E65_D0.5810.24
199_S268_T0.5790.24
179_S193_K0.5780.24
27_R35_K0.5770.24
340_K346_N0.5760.24
70_A199_S0.5750.24
176_Y254_D0.5740.24
84_Y220_G0.5740.24
13_V349_N0.5740.24
338_K348_E0.5720.24
83_L236_F0.5710.24
43_K68_L0.5710.24
110_P179_S0.5710.24
67_P330_M0.5690.24
5_K285_K0.5690.24
26_L212_S0.5670.24
301_K331_P0.5670.24
127_K143_V0.5660.24
263_T308_A0.5660.24
61_E64_V0.5650.24
191_D306_G0.5590.23
93_T114_N0.5590.23
26_L33_L0.5590.23
84_Y188_T0.5580.23
284_Y294_P0.5580.23
151_G155_G0.5580.23
58_N63_S0.5560.23
174_K212_S0.5550.23
194_K300_N0.5540.23
41_L248_K0.5540.23
255_G290_P0.5530.23
9_D116_S0.5510.23
6_I213_D0.5500.23
297_S300_N0.5500.23
200_L232_I0.5490.23
4_I40_V0.5490.23
249_P304_T0.5490.23
2_V232_I0.5480.23
36_L78_Y0.5470.23
267_D299_I0.5460.23
110_P149_K0.5400.22
80_E202_A0.5400.22
120_L211_D0.5390.22
139_H204_L0.5380.22
162_P189_F0.5370.22
121_D164_I0.5360.22
40_V271_I0.5360.22
173_D204_L0.5350.22
15_F144_Y0.5350.22
261_K276_F0.5350.22
152_W293_L0.5330.22
75_I147_F0.5320.22
204_L281_A0.5320.22
98_K231_M0.5300.22
115_G154_F0.5300.22
17_K232_I0.5300.22
83_L139_H0.5290.22
103_K202_A0.5260.22
253_L256_G0.5260.22
231_M270_M0.5250.21
189_F269_I0.5250.21
236_F266_P0.5240.21
240_E252_K0.5240.21
168_L171_L0.5230.21
62_S65_D0.5230.21
300_N328_F0.5220.21
261_K320_K0.5220.21
151_G154_F0.5220.21
126_K348_E0.5220.21
304_T307_E0.5220.21
81_N192_R0.5210.21
24_D212_S0.5210.21
282_K305_Y0.5210.21
77_D267_D0.5200.21
286_Y290_P0.5190.21
269_I294_P0.5190.21
81_N196_L0.5190.21
181_L185_L0.5180.21
74_L133_N0.5180.21
181_L252_K0.5180.21
278_I282_K0.5160.21
107_K119_Y0.5160.21
47_K219_F0.5160.21
104_T280_D0.5130.21
138_I294_P0.5110.21
84_Y197_L0.5100.21
184_E303_I0.5100.21
36_L40_V0.5090.21
189_F295_G0.5070.21
155_G164_I0.5060.21
111_I121_D0.5060.21
121_D295_G0.5060.21
302_Q331_P0.5060.21
2_V37_L0.5050.20
45_S174_K0.5040.20
81_N112_I0.5000.20
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  
4z9nA 2 0.2861 3.5 0.977 Contact Map
3n4sA 2 0.115 2.9 0.978 Contact Map
4qlbG 1 0.0909 2.9 0.978 Contact Map
2j5lA 1 0 2.8 0.978 Contact Map
4obiA 1 0.0722 2.4 0.979 Contact Map
1y88A 5 0.3422 1.6 0.98 Contact Map
2g7hA 1 0.1497 1.5 0.981 Contact Map
4hs4A 6 0.131 1.5 0.981 Contact Map
2pi2E 1 0.139 1.2 0.982 Contact Map
4khaA 1 0.1711 1.2 0.982 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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