GREMLIN Database
DpnII - DpnII restriction endonuclease
PFAM: PF04556 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 278 (276)
Sequences: 1393 (983)
Seq/√Len: 59.2
META: 0.827

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
49_E108_R5.8641.00
47_N50_E4.9971.00
58_K61_E4.0681.00
201_K238_E3.7601.00
55_L62_V3.7151.00
33_K45_K3.5361.00
68_I128_V3.4991.00
45_K51_E3.2401.00
114_D118_N2.9931.00
53_E104_V2.9581.00
41_S45_K2.8841.00
269_N273_N2.8091.00
34_I38_I2.7711.00
38_I59_Y2.7051.00
20_V133_V2.7021.00
204_L237_F2.6881.00
37_N40_N2.5501.00
169_E191_R2.5491.00
33_K41_S2.5041.00
24_K136_D2.4191.00
213_G250_S2.3091.00
5_F9_L2.2541.00
220_T224_Y2.2401.00
146_H169_E2.1801.00
8_T267_N2.1361.00
256_E260_D2.1211.00
153_E168_K2.0631.00
105_E109_K2.0421.00
246_K249_K1.9851.00
229_P261_V1.9641.00
48_I113_F1.9231.00
30_D33_K1.9141.00
41_S51_E1.8801.00
242_I276_L1.8621.00
89_Y105_E1.8361.00
219_E223_S1.8110.99
34_I37_N1.8050.99
49_E104_V1.7820.99
11_E78_K1.7800.99
187_K256_E1.7800.99
53_E101_E1.7310.99
226_T229_P1.7290.99
219_E222_R1.7030.99
153_E157_K1.6980.99
91_F96_Y1.6900.99
148_M268_L1.6710.99
38_I55_L1.5920.99
217_L251_A1.5920.99
29_V125_V1.5840.99
52_F104_V1.5760.99
57_K97_F1.5700.99
107_M113_F1.5650.98
204_L231_L1.5500.98
10_K272_E1.5460.98
271_L276_L1.5440.98
171_Y191_R1.5270.98
39_L62_V1.5220.98
232_K263_D1.5070.98
166_Y169_E1.4790.98
258_T262_I1.4760.98
53_E100_I1.4750.98
165_E178_K1.4470.97
149_E169_E1.4410.97
156_I161_I1.4400.97
20_V25_V1.4120.97
8_T269_N1.4080.97
238_E264_Y1.3930.97
91_F94_K1.3870.97
35_E64_K1.3850.97
173_S189_E1.3770.97
6_L252_K1.3760.97
41_S59_Y1.3740.97
155_Y271_L1.3720.97
79_V83_D1.3640.96
32_I68_I1.3430.96
104_V108_R1.3360.96
162_K277_E1.3330.96
225_K261_V1.3170.96
99_S102_Q1.3050.95
51_E54_E1.3050.95
227_L231_L1.3040.95
190_K222_R1.3010.95
192_F227_L1.2930.95
79_V105_E1.2690.95
57_K100_I1.2680.95
176_K182_D1.2650.94
167_F170_A1.2630.94
26_Y115_L1.2600.94
218_N222_R1.2490.94
218_N223_S1.2450.94
170_A175_I1.2390.94
153_E166_Y1.2270.94
24_K132_E1.2100.93
11_E246_K1.1860.92
79_V84_G1.1790.92
190_K223_S1.1660.92
80_L86_E1.1560.91
14_A22_F1.1510.91
3_E256_E1.1510.91
26_Y120_I1.1330.90
3_E7_S1.1320.90
29_V32_I1.1300.90
196_I205_I1.1280.90
38_I41_S1.1260.90
188_S253_N1.1210.90
54_E58_K1.1170.90
210_Y241_W1.1110.90
27_R30_D1.1060.89
172_A176_K1.0970.89
242_I271_L1.0940.89
35_E38_I1.0940.89
63_L66_I1.0890.89
41_S55_L1.0890.89
176_K189_E1.0830.88
34_I41_S1.0820.88
37_N125_V1.0760.88
36_L125_V1.0760.88
229_P232_K1.0720.88
173_S177_E1.0520.87
66_I223_S1.0510.87
33_K37_N1.0320.86
213_G251_A1.0110.85
89_Y102_Q1.0070.84
146_H191_R1.0060.84
157_K166_Y0.9920.84
253_N256_E0.9870.83
47_N51_E0.9860.83
35_E58_K0.9830.83
190_K218_N0.9810.83
218_N254_N0.9790.83
165_E179_W0.9730.82
63_L103_Y0.9690.82
115_L123_N0.9690.82
154_S158_K0.9630.82
231_L237_F0.9560.81
213_G217_L0.9530.81
26_Y129_F0.9510.81
115_L121_I0.9490.81
30_D45_K0.9440.80
161_I165_E0.9430.80
50_E54_E0.9380.80
231_L262_I0.9380.80
190_K219_E0.9370.80
15_T147_L0.9340.80
170_A195_V0.9340.80
52_F56_L0.9320.80
186_G190_K0.9310.79
73_R132_E0.9270.79
228_A232_K0.9250.79
259_F265_I0.9200.79
15_T150_N0.9160.78
166_Y170_A0.9120.78
184_S192_F0.9110.78
195_V204_L0.9100.78
146_H168_K0.9100.78
27_R31_K0.9030.77
36_L128_V0.8950.77
17_D23_E0.8930.77
226_T230_E0.8910.76
52_F103_Y0.8840.76
171_Y174_E0.8830.76
161_I167_F0.8810.76
163_K167_F0.8770.75
146_H150_N0.8750.75
56_L62_V0.8710.75
113_F117_Q0.8710.75
104_V113_F0.8710.75
212_G250_S0.8700.75
240_V276_L0.8650.74
225_K258_T0.8630.74
97_F100_I0.8620.74
81_D84_G0.8570.74
270_M273_N0.8460.73
39_L55_L0.8380.72
218_N251_A0.8310.71
14_A147_L0.8290.71
100_I104_V0.8270.71
221_A241_W0.8270.71
220_T225_K0.8250.71
186_G230_E0.8250.71
56_L100_I0.8220.70
243_T248_W0.8200.70
181_I237_F0.8160.70
80_L105_E0.8160.70
249_K252_K0.8140.70
156_I196_I0.8120.69
6_L9_L0.8100.69
205_I242_I0.8030.69
4_E7_S0.8030.69
192_F204_L0.8000.68
150_N168_K0.8000.68
66_I100_I0.7990.68
29_V133_V0.7980.68
167_F172_A0.7970.68
217_L221_A0.7960.68
93_K96_Y0.7940.68
35_E61_E0.7910.67
258_T265_I0.7900.67
154_S157_K0.7870.67
21_D139_G0.7870.67
7_S27_R0.7860.67
37_N41_S0.7830.67
14_A18_Y0.7820.67
32_I55_L0.7760.66
181_I202_I0.7730.66
189_E253_N0.7730.66
34_I58_K0.7720.66
17_D154_S0.7710.65
218_N221_A0.7680.65
107_M112_L0.7680.65
102_Q105_E0.7670.65
49_E53_E0.7670.65
56_L89_Y0.7570.64
90_N95_N0.7560.64
192_F231_L0.7550.64
172_A188_S0.7540.64
222_R257_E0.7520.63
189_E226_T0.7500.63
210_Y221_A0.7500.63
71_A133_V0.7490.63
9_L252_K0.7490.63
40_N123_N0.7480.63
49_E113_F0.7470.63
48_I71_A0.7460.63
269_N272_E0.7450.63
210_Y224_Y0.7400.62
137_S172_A0.7400.62
217_L220_T0.7380.62
5_F13_I0.7370.62
185_V233_S0.7370.62
233_S238_E0.7340.62
146_H149_E0.7340.62
36_L69_L0.7340.62
25_V133_V0.7290.61
249_K253_N0.7260.61
32_I125_V0.7250.61
130_G141_K0.7240.61
23_E27_R0.7210.60
70_L110_T0.7200.60
238_E263_D0.7200.60
14_A19_F0.7190.60
98_E102_Q0.7180.60
95_N98_E0.7180.60
30_D51_E0.7170.60
130_G145_G0.7110.59
167_F171_Y0.7050.58
227_L238_E0.7040.58
225_K229_P0.7000.58
101_E104_V0.6970.58
143_R248_W0.6970.58
39_L65_V0.6960.58
267_N276_L0.6940.57
130_G206_E0.6920.57
73_R133_V0.6910.57
29_V38_I0.6910.57
108_R117_Q0.6890.57
31_K129_F0.6880.57
68_I72_V0.6880.57
40_N125_V0.6850.56
67_P106_F0.6830.56
43_I259_F0.6810.56
196_I274_G0.6800.56
166_Y172_A0.6770.55
172_A189_E0.6740.55
70_L157_K0.6720.55
33_K122_K0.6700.55
46_K118_N0.6700.55
137_S146_H0.6670.54
155_Y158_K0.6660.54
133_V136_D0.6660.54
52_F113_F0.6650.54
12_S18_Y0.6640.54
19_F151_L0.6640.54
153_E156_I0.6640.54
108_R113_F0.6630.54
220_T223_S0.6620.54
188_S220_T0.6600.54
4_E8_T0.6590.53
90_N94_K0.6580.53
7_S11_E0.6550.53
208_N243_T0.6540.53
229_P240_V0.6520.53
135_L144_G0.6420.52
33_K125_V0.6420.52
66_I103_Y0.6390.51
140_R143_R0.6370.51
25_V139_G0.6340.51
141_K216_K0.6330.51
223_S254_N0.6280.50
66_I107_M0.6270.50
262_I265_I0.6250.50
228_A262_I0.6250.50
155_Y159_A0.6240.50
115_L120_I0.6230.49
83_D105_E0.6230.49
81_D85_N0.6200.49
48_I104_V0.6190.49
134_G141_K0.6190.49
191_R220_T0.6180.49
13_I147_L0.6160.49
221_A224_Y0.6140.48
266_Y270_M0.6140.48
203_Y240_V0.6130.48
56_L224_Y0.6100.48
116_F124_L0.6090.48
156_I160_G0.6080.48
174_E178_K0.6050.47
141_K206_E0.6050.47
202_I237_F0.6050.47
115_L147_L0.6040.47
23_E53_E0.6030.47
87_F102_Q0.6030.47
42_L51_E0.6020.47
254_N270_M0.6000.47
98_E168_K0.6000.47
206_E216_K0.5970.47
50_E57_K0.5890.46
31_K64_K0.5880.46
219_E224_Y0.5860.45
160_G190_K0.5850.45
112_L116_F0.5840.45
18_Y144_G0.5820.45
231_L234_I0.5810.45
115_L129_F0.5780.44
17_D150_N0.5780.44
186_G261_V0.5770.44
170_A179_W0.5770.44
222_R227_L0.5730.44
61_E64_K0.5710.44
156_I166_Y0.5710.44
20_V122_K0.5700.44
34_I62_V0.5680.43
144_G147_L0.5670.43
157_K165_E0.5670.43
10_K13_I0.5660.43
201_K264_Y0.5650.43
88_L96_Y0.5650.43
40_N43_I0.5600.42
174_E177_E0.5600.42
12_S39_L0.5590.42
174_E181_I0.5570.42
136_D139_G0.5560.42
14_A211_S0.5560.42
175_I179_W0.5560.42
91_F95_N0.5540.42
160_G270_M0.5510.41
61_E93_K0.5500.41
40_N124_L0.5500.41
127_Y133_V0.5500.41
46_K50_E0.5500.41
225_K230_E0.5490.41
33_K51_E0.5490.41
160_G218_N0.5480.41
43_I116_F0.5480.41
18_Y139_G0.5450.41
251_A254_N0.5450.41
148_M203_Y0.5430.41
35_E59_Y0.5420.41
21_D108_R0.5410.40
37_N44_G0.5410.40
72_V77_I0.5410.40
177_E246_K0.5340.40
93_K273_N0.5340.40
169_E172_A0.5340.40
50_E53_E0.5310.39
67_P115_L0.5300.39
161_I198_T0.5290.39
136_D143_R0.5280.39
75_K93_K0.5280.39
77_I81_D0.5270.39
14_A144_G0.5260.39
179_W197_K0.5260.39
21_D137_S0.5260.39
20_V124_L0.5240.39
141_K208_N0.5240.39
45_K55_L0.5230.38
19_F224_Y0.5220.38
127_Y132_E0.5210.38
222_R254_N0.5190.38
89_Y135_L0.5190.38
211_S247_G0.5190.38
130_G216_K0.5190.38
220_T258_T0.5180.38
85_N98_E0.5160.38
14_A20_V0.5160.38
48_I117_Q0.5150.38
16_Y81_D0.5150.38
71_A74_E0.5140.38
128_V258_T0.5140.38
82_D88_L0.5140.38
17_D233_S0.5130.37
170_A178_K0.5120.37
167_F178_K0.5120.37
144_G217_L0.5120.37
238_E265_I0.5110.37
2_F259_F0.5100.37
226_T238_E0.5100.37
79_V89_Y0.5100.37
83_D88_L0.5070.37
31_K158_K0.5070.37
201_K227_L0.5060.37
8_T11_E0.5060.37
130_G134_G0.5050.37
165_E197_K0.5050.37
173_S253_N0.5040.37
43_I48_I0.5030.36
114_D232_K0.5030.36
219_E254_N0.5020.36
22_F160_G0.5020.36
95_N100_I0.5020.36
103_Y113_F0.5020.36
36_L65_V0.5010.36
89_Y96_Y0.5010.36
91_F103_Y0.5000.36
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  
2gb7A 2 0.8058 81.5 0.95 Contact Map
3bm3A 2 0.7302 64.7 0.956 Contact Map
1na6A 2 0.7878 34.5 0.964 Contact Map
1y88A 5 0.4209 30.5 0.965 Contact Map
4qs4A 3 0.5827 12.1 0.971 Contact Map
3oyyA 1 0.3309 9.9 0.972 Contact Map
1gefA 2 0.3849 9.5 0.972 Contact Map
3h1tA 1 0.4496 9.3 0.972 Contact Map
3hrlA 1 0.3273 9.1 0.972 Contact Map
1uebA 1 0.3237 8.8 0.972 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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