Welcome to MAP2.03D Server
Home Submission Instructions References Contact Us

Thank you for using MAP

Input sequence
 Number of nucleotides: 1299
 Number of amino acids: 433
 GC content of the sequence: 53.66
MAP results: Taq (+. G=A. C=T)
(Click on links to get the content and mouseover for description)
a.  Summarized MAP results
Average amino acid substitution per residue: 7.45
Stop codons : 4.69%Gly/Pro residues : 11.60%
Preserved amino acids : 25.47%Codon diversity coefficient : 36.53
Deviation from chemical distribution:   Stop codons: 4.69 % (0.00%);  Charged: 1.39 %  (19.21 %);  Neutral: -4.14 % (35.65 %);  Aromatic: 0.91 % (5.79 %);  Aliphatic: -2.86 % (39.35 %)
b.  Amino acid substitution patternsAmino acid substitutions with secondary structure elements, residue mutability, residue flexibility and solvent accessibility
c.  Amino acid substitutions mappingMapping chemically characterized amino acid substitutions on cartesian coordinates of protein structure
d.  Amino acid substitution patterns with molecular interactionsAmino acid substitutions with molecular interactions like: salt bridges, hydrophobic interactions, aromatic interactions, side chain hydrogen bonds and disulphide bonds
e.  Protein structure indicatorThe structure/function disrupting (stop codons) and likely destabilizing (glycine and proline residues) amino acid substitutions
f.  Amino acid diversity indicatorThe fraction of variants with preserved amino acids and average amino acid substitution per residue after single nucleotide exchange
g.  Chemical diversity indicatorAnalyse the chemical diversity generated by the random mutagenesis method


Amino acid substitution patterns, residue mutability, residue flexibility and solvent accessibility with sequence id, PDB id, aminoacid name and secondary structure elements (H: alpha helix, B: beta bridge and extended strand, T: hydrogen bonded turn and Bend, *: loop or irregular structure)
Amino acid substitutions and mutability
(Horizontal colorbars show substitution probabilities for chemically categorized aminoacid groups)
Residue flexibility
(Normalized b-factor to represent flexible (F) and rigid (R) residues)
Solvent accessibility
(Relative solvent accessibility to differentiate buried (B) and exposed (E) residues)
this is a starthis is a starthis is a star


(The amino acid substitution pattern for mutagenesis methods. The Y-axis shows the original amino acid species and the X-axis shows the substitution pattern.)
this is a star


(Amino acids are divided into six classes for mapping. For each class, amino acid substitution probabilities are shown by color gradient which goes from red (high probability) to blue (low probability) . Please use right mouse click to get access to aditional Jmol functionality Viewing locally the amino acid substitution pattern on structure, download the pdb file by using links (headings) and visualise it with temperature factor option of the visualization tool like VMD, Rasmol).

Stop codon (download)

Gly/Pro (download)

Charged (download)

Neutral (download)

Aromatic (download)

Aliphatic (download)


Amino acid substitution pattern: Salt bridges

(Amino acid substitution pattern with sequence id, PDB id, aminoacid name and chemically categorized amino acid groups)

Saltbridge partner I Saltbridge partner II
this is a star this is a star


(Amino acid substitution pattern with sequence id, PDB id, aminoacid name and chemically categorized aminoacid groups)

Hydrophobic interaction partner I Hydrophobic interaction partner II
this is a star this is a star


(Amino acid substitution pattern with sequence id, PDB id, aminoacid name and chemically categorized aminoacid groups)

Aromatic interaction partner I Aromatic interaction partner II
this is a star this is a star


(Amino acid substitution pattern with sequence id, PDB id, aminoacid name and chemically categorized aminoacid groups)

Side chain hydrogen bond partner I Side chain hydrogen bond partner II
this is a star this is a star


(Amino acid substitution pattern with sequence id, PDB id, aminoacid name and chemically categorized aminoacid groups)

Disulphide bond partner I Disulphide bond partner II
this is a star this is a star


(The structure/function disrupting (stop codons) and likely destabilizing (glycine and proline residues) amino acid substitutions. Bar colors show the mutagenesis method employed for nucleotide substitution: enzyme based methods in red, whole cell methods in green, synthetic chemistry based methods in blue and theoretical nonbiased method in black colour.)
Fraction of variants with stop codons Fraction of variants with Gly or Pro
this is a star this is a star


(The fraction of variants with preserved amino acids and average amino acid substitution per residue after single nucleotide exchange. Bar colors show the mutagenesis method employed for nucleotide substitution: enzyme based methods in red, whole cell methods in green, synthetic chemistry based methods in blue and theoretical nonbiased method in black color.)
Fraction of variants with preserved amino acids Average amino acid substitution per residue
this is a star this is a star


(Codon diversity coefficient shows the distribution of random mutations among codons of a gene for mutagenesis methods (enzyme based methods in red, whole cell methods in green, synthetic chemistry based methods in blue and theoretical nonbiased method in black color). Chemical diversity indicator shows the percentages of stop codon (red), charged (pink), neutral (yellow), aromatic (cyan) and aliphatic (blue) amino acid substitutions generated by random mutagenesis methods.)
Codon diversity coefficient Amino acid substitutions
this is a star this is a star


(The values represent the deviation from the chemical distribution of the sequence for random mutagenesis methods)
Methods/Amino Acid Classes Stop Charge Neutral Aromatic Aliphatic
Chemical distribution 0.00 % 19.21 % 35.65 % 5.79 % 39.35 %
Non-biased 4.11 % 3.14 % -3.16 % -0.30 % -3.79 %
Taq (-. G>A=C=T) 3.08 % 2.85 % -3.33 % -0.85 % -1.75 %
Taq (+. G=A=C=T) 2.58 % 3.69 % -3.75 % -1.69 % -0.84 %
Taq (+. G>A=C=T) 3.67 % 2.36 % -3.50 % -0.29 % -2.23 %
Taq (+. G>>A=C=T) 1.80 % 3.96 % -3.47 % -2.12 % -0.16 %
Taq (+. G=A. C=T) 4.69 % 1.39 % -4.14 % 0.91 % -2.86 %
Taq (+. G=T. A=C) 2.61 % 3.12 % -2.90 % -1.82 % -1.00 %
Taq (I614K) 3.91 % 1.86 % -3.17 % -0.51 % -2.10 %
Mutazyme I 5.41 % 1.07 % -1.65 % 0.05 % -4.88 %
Mutazyme II 5.23 % 1.18 % -2.98 % 0.74 % -4.17 %
Pfu (exo-. D473G) 4.81 % 1.65 % -3.29 % 0.44 % -3.61 %
Transcriptase 3.48 % 1.12 % -1.05 % -0.14 % -3.42 %
Taq (dPTP/8-oxodGTP) 1.49 % 3.99 % -2.55 % -2.92 % -0.03 %
epRCA 5.88 % -0.32 % -0.88 % -0.15 % -4.54 %
Pol I 4.64 % 0.64 % -1.80 % -0.62 % -2.85 %
E. coli (mutA) 5.48 % 1.44 % -2.59 % 0.91 % -5.24 %
Nitrous acid 5.84 % -3.33 % -7.83 % -0.21 % 5.52 %
Formic acid 3.91 % -2.63 % 1.37 % 2.38 % -5.04 %
Hydrazine 3.27 % -0.46 % -2.76 % -1.09 % 1.04 %
EMS 3.37 % 2.76 % -2.25 % -2.10 % -1.77 %
 
Reference: Verma R, Schwaneberg U, Roccatano D 2012. MAP2.03D: A sequence/structure based server for protein engineering  
Website copyright 2005 Mutagenesis Assistant Program. All rights reserved