Title

Substitutional Analysis of Orthologous Protein Families Using BLOCKS

Authors

Parth Sarthi Sen Gupta¹, Shyamashree Banerjee¹, Rifat Nawaz Ul Islam¹, Vishma Pratap Sur² and Amal K. Bandyopadhyay¹٭

Affiliation

¹Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India;

²Indian Institute of Chemical Biology, Animal House (IICB), Kolkata, West Bengal, India

Email

akbanerjee@biotech.buruniv.ac.in; Phone - +91-342-2657231(O), 9474723882(M), Fax - +91-3422657231;

Article Type

Hypothesis

Date

Received December 14, 2016; Revised December 26, 2016; Accepted December 27, 2016; Published January 19, 2017

Orthologous proteins, form due to divergence of parental sequence, perform similar function under different environmental and biological conditions. Amino acid changes at locus specific positions form hetero-pairs whose role in BLOCK evolution is yet to be understood. We involve eight protein BLOCKs of known divergence rate to gain insight into the role of hetero-pairs in evolution. Our procedure APBEST uses BLOCK-FASTA file to extract BLOCK specific evolutionary parameters such as dominantly used hetero-pair (D), usage of hetero-pairs (E), non-conservative to conservative substitution ratio (R), maximally-diverse residue (MDR), residue (RD) and class (CD) specific diversity. All these parameters show BLOCK specific variation. Conservative nature of D points towards restoration of function of BLOCK. While E sets the upper-limit of usage of hereto-pairs, strong correlation of R with divergence-rate indicates that the later is directly dependent on non-conservative substitutions. The observation that MDR, measure of positional diversity, occupy very limited positions in BLOCK indicates accommodation of diversity is positionally restricted. Overall, the study extract observed hetero-pair related quantitative and multi-parametric details of BLOCK, which finds application in evolutionary biology.

Keywords:

evolution, substitution, non-conservative, conservative, hetero-pairs, divergence rate.

Citation

Sen Gupta, Bioinformation 13(1): 1-7 (2017)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.