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Computational Molecular Biology 2014, Vol. 4, No. 14, 1-9
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Sequence alignment
The cytokinin dehydrogenase enzymes of all the
plants were subjected for multiple sequence
alignment using ClustalW2 (http://www.ebi.ac.uk/
Tools/msa/clustalw2/) analysis (Thompson et al.,
1994). The alignment file was saved in clustal
format and conserved residues were identified
successfully. A phylogenetic tree was generated.
The conserved residues of all the enzymes are
shown in Figure 1.
Figure 1 the multiple sequence alignment result of all the enzyme
Physico-Chemical Characterization of all the
enzymes
The amino acid sequences of all the enzymes were
subjected to ProtParamtool (http://web.expasy.org/
protparam/) for further analysis, from where we got
the physical and chemical properties of all the
enzymes including molecular weight, theoretical PI,
extinction coefficients, instability index, aliphatic
index, grand average of hydrophobicity, total
number of positively and negatively charged
residues [9]. Detail information is shown in Table 2,
Table 3, Table 4.
Secondary structure prediction of enzymes
The CFFSP server (http://www.biogem.org/tool/
chou-fasman/) was used for secondary structure
analysis where we submitted the amino acid
sequences as an input and the result showed the details
about helices, sheets and turns respectively (David et
al., 1999). The detail information is shown in Table 5
and Figure 2-Figure 11.