GREMLIN Database
XhoI - Restriction endonuclease XhoI
PFAM: PF04555 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 191 (189)
Sequences: 1439 (927)
Seq/√Len: 67.4
META: 0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
128_D133_R5.0421.00
155_A178_T4.4331.00
156_K159_E4.4311.00
29_V77_F4.0801.00
111_A146_F4.0291.00
117_R172_D3.5461.00
126_L155_A2.8961.00
9_D17_T2.7921.00
125_L179_S2.6421.00
131_K134_R2.5601.00
101_T170_L2.4511.00
85_F129_C2.4211.00
93_T161_L2.3991.00
55_F105_T2.3621.00
105_T108_R2.3141.00
148_E164_K2.2921.00
97_I101_T2.2431.00
80_Q158_Y2.1631.00
20_K23_D2.1051.00
180_P183_A2.0711.00
97_I161_L1.9971.00
146_F164_K1.9961.00
108_R168_E1.9541.00
33_L65_V1.9261.00
54_Y164_K1.8311.00
93_T97_I1.8201.00
166_V173_A1.8181.00
18_G21_Q1.8121.00
50_E60_E1.7371.00
7_K10_Q1.7331.00
34_V40_E1.7221.00
13_R17_T1.7131.00
123_L175_C1.7121.00
30_R34_V1.6940.99
83_P129_C1.6510.99
130_P134_R1.6440.99
44_H142_H1.6330.99
12_E15_A1.6250.99
105_T168_E1.5840.99
119_W172_D1.5490.99
103_L120_L1.5460.99
83_P127_E1.5300.99
82_G127_E1.4780.99
39_P42_E1.4500.98
42_E67_H1.4370.98
159_E163_R1.4080.98
85_F127_E1.3610.98
89_F93_T1.3590.98
21_Q119_W1.3430.97
6_G9_D1.3350.97
117_R169_R1.3330.97
183_A186_T1.3330.97
57_P89_F1.3310.97
22_M79_S1.3280.97
140_E150_K1.3200.97
110_G167_R1.2990.97
23_D26_I1.2920.97
80_Q124_M1.2740.96
6_G17_T1.2690.96
147_P150_K1.2640.96
156_K160_L1.2590.96
104_W117_R1.2520.96
47_R60_E1.2370.96
152_A156_K1.2360.96
55_F170_L1.2030.95
89_F158_Y1.2010.95
71_L143_F1.1900.95
104_W169_R1.1840.95
26_I63_L1.1510.94
6_G10_Q1.1400.93
144_P150_K1.1100.92
27_A45_T1.0880.92
58_T163_R1.0860.92
182_S186_T1.0770.91
49_L60_E1.0670.91
55_F101_T1.0530.90
2_Q10_Q1.0430.90
126_L178_T1.0190.89
104_W107_Y1.0080.88
81_V85_F1.0020.88
31_D35_E0.9810.87
133_R178_T0.9740.86
114_P163_R0.9710.86
38_L122_Y0.9570.85
58_T162_C0.9540.85
41_A160_L0.9500.85
22_M125_L0.9470.85
13_R19_G0.9460.85
15_A18_G0.9450.85
163_R167_R0.9350.84
167_R170_L0.9280.84
124_M176_F0.9240.83
138_V145_V0.9230.83
2_Q5_S0.9220.83
3_I27_A0.9150.83
10_Q14_G0.8940.81
124_M163_R0.8930.81
115_S122_Y0.8890.81
100_A104_W0.8880.81
84_S87_N0.8660.79
12_E181_R0.8650.79
21_Q33_L0.8600.79
117_R170_L0.8590.79
101_T161_L0.8520.78
32_L35_E0.8480.78
183_A188_E0.8480.78
178_T190_S0.8410.77
9_D13_R0.8390.77
59_K76_E0.8360.77
80_Q86_G0.8350.77
138_V152_A0.8270.76
180_P188_E0.8270.76
148_E160_L0.8230.76
5_S8_A0.8200.75
156_K163_R0.8190.75
150_K188_E0.8190.75
140_E145_V0.8180.75
185_L188_E0.8140.75
74_A99_S0.8120.75
84_S91_N0.8120.75
54_Y115_S0.8110.74
100_A170_L0.8070.74
185_L189_Y0.7980.73
80_Q122_Y0.7970.73
3_I8_A0.7940.73
15_A21_Q0.7930.73
26_I30_R0.7880.72
54_Y58_T0.7750.71
2_Q8_A0.7740.71
63_L110_G0.7720.71
113_G116_P0.7710.71
43_I63_L0.7670.70
10_Q17_T0.7670.70
58_T140_E0.7650.70
43_I46_K0.7590.69
16_V19_G0.7580.69
6_G14_G0.7570.69
44_H66_V0.7570.69
80_Q83_P0.7550.69
56_R59_K0.7540.69
39_P45_T0.7530.69
122_Y176_F0.7520.69
28_L38_L0.7500.69
170_L175_C0.7490.68
11_G17_T0.7430.68
74_A124_M0.7400.68
184_G189_Y0.7400.68
32_L41_A0.7340.67
31_D34_V0.7340.67
104_W158_Y0.7340.67
127_E181_R0.7330.67
72_V165_L0.7300.66
14_G17_T0.7260.66
76_E92_R0.7260.66
140_E144_P0.7240.66
30_R40_E0.7230.66
87_N94_E0.7210.66
60_E99_S0.7210.66
91_N95_E0.7090.64
110_G174_A0.6990.63
57_P161_L0.6990.63
2_Q6_G0.6970.63
38_L65_V0.6960.63
75_I155_A0.6910.62
27_A31_D0.6900.62
155_A159_E0.6890.62
131_K185_L0.6890.62
133_R190_S0.6880.62
39_P46_K0.6870.62
104_W120_L0.6870.62
128_D190_S0.6860.62
54_Y105_T0.6840.61
26_I77_F0.6810.61
36_A124_M0.6760.61
77_F125_L0.6760.61
130_P133_R0.6740.60
85_F132_S0.6710.60
56_R98_G0.6700.60
33_L175_C0.6700.60
55_F74_A0.6670.60
99_S171_Y0.6660.59
110_G135_P0.6640.59
28_L177_L0.6630.59
54_Y124_M0.6630.59
88_N92_R0.6600.59
38_L72_V0.6560.58
126_L176_F0.6550.58
60_E103_L0.6530.58
90_N98_G0.6510.58
138_V151_G0.6460.57
105_T114_P0.6420.57
45_T63_L0.6420.57
103_L112_F0.6390.56
86_G91_N0.6380.56
116_P119_W0.6370.56
39_P67_H0.6350.56
7_K39_P0.6340.56
176_F180_P0.6340.56
126_L158_Y0.6330.56
80_Q176_F0.6330.56
105_T109_E0.6310.55
75_I147_P0.6310.55
41_A67_H0.6310.55
77_F124_M0.6300.55
159_E176_F0.6300.55
63_L164_K0.6290.55
55_F137_R0.6260.55
177_L180_P0.6250.55
182_S190_S0.6250.55
78_K91_N0.6240.55
75_I115_S0.6190.54
72_V116_P0.6160.54
29_V75_I0.6120.53
29_V170_L0.6110.53
53_G161_L0.6080.53
132_S153_S0.6080.53
22_M123_L0.6070.52
180_P190_S0.6070.52
50_E139_R0.6070.52
127_E158_Y0.6040.52
39_P114_P0.6030.52
59_K78_K0.6010.52
56_R76_E0.5990.52
29_V79_S0.5980.51
44_H64_L0.5930.51
161_L165_L0.5930.51
80_Q89_F0.5890.50
84_S94_E0.5860.50
77_F103_L0.5860.50
166_V174_A0.5850.50
80_Q87_N0.5840.50
16_V81_V0.5840.50
34_V41_A0.5830.50
93_T136_V0.5820.50
111_A122_Y0.5810.49
65_V74_A0.5800.49
42_E68_D0.5780.49
101_T105_T0.5780.49
64_L103_L0.5770.49
30_R107_Y0.5760.49
9_D12_E0.5750.49
33_L73_A0.5740.49
80_Q93_T0.5730.48
136_V152_A0.5730.48
96_A99_S0.5720.48
114_P167_R0.5610.47
92_R95_E0.5600.47
114_P150_K0.5590.47
175_C190_S0.5590.47
30_R45_T0.5580.47
179_S184_G0.5550.46
57_P85_F0.5540.46
23_D27_A0.5530.46
80_Q104_W0.5510.46
68_D185_L0.5490.46
76_E94_E0.5470.45
78_K86_G0.5440.45
136_V177_L0.5430.45
136_V140_E0.5390.44
180_P184_G0.5330.44
31_D63_L0.5320.44
48_A166_V0.5300.43
149_F160_L0.5290.43
15_A20_K0.5270.43
38_L119_W0.5270.43
105_T162_C0.5260.43
56_R94_E0.5250.43
116_P151_G0.5240.43
31_D46_K0.5240.43
93_T156_K0.5230.43
125_L150_K0.5210.42
66_V143_F0.5190.42
57_P138_V0.5160.42
123_L177_L0.5130.41
186_T190_S0.5130.41
28_L35_E0.5060.41
101_T154_Y0.5060.41
60_E74_A0.5060.41
41_A144_P0.5050.40
75_I159_E0.5050.40
113_G167_R0.5030.40
29_V63_L0.5010.40
57_P162_C0.5000.40
55_F168_E0.5000.40
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  
2wcwA 2 0.6492 14.2 0.966 Contact Map
1j3gA 1 0.3822 8.6 0.969 Contact Map
3mtxA 1 0.4136 7.3 0.97 Contact Map
1t8hA 1 0.3822 5.8 0.972 Contact Map
4b94A 1 0.3613 5.1 0.972 Contact Map
4qbnA 2 0.4607 4.9 0.973 Contact Map
3h1tA 1 0.7801 4.7 0.973 Contact Map
4bzjA 2 0.7277 4.7 0.973 Contact Map
4knkA 1 0.4084 4.5 0.973 Contact Map
3ld2A 1 0.6649 4.5 0.973 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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