Dr. J.

Upendar
Assistant Professor
Electrical Engineering Department
University College of Engineering,
Osmania University,Telangana, India
Smt. J. Vijaya Laxmi
M.Sc ( Micro-Biology)
Osmania University
 Protein sequence searches are most impotent
now a days for most biologists.

Most of the researchers in this area design

their own experimental data are they collect
from the reference existing data

The powerful BLAST related search programs

gained an acceptance in this area.

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 2

 In paper [1],a new pLoc-mVirus predictor is developed by the
authors with the help of both optimal GO (Gene Ontology)
information and Chou's general PseAAC.

This pLoc-mVirus predictor is applied to subcellular location

of Virus protein position, when the query virus proteins contains
the multi-label features and occurs at more than two location
sites.

The new pLoc-mVirus predictor method is compared with

iLoc-Virus method .

A BLAST search algorithm is used as important search method to

search the virus proteins in Swiss-Prot database.
The subset of proteins obtained from BLAST search are used

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 3

 Mostly pathogen affected plants and adult higher plants are
concentrated with Chitinases.[2]

Many plant chitinases are small proteins and are glycosyl hydrolases.

The hydrolysis of the N-Acetylglucosamine polymer catalysis enzymes

are called as chitin.

These Chitinases are different sized proteins, having the ability to

degrade chitin.

BLAST search tool is used to detection of homologous sequences and to

analyse the wild type sequence present in the collected database.

The SWISS-MODEL automatic server is used to process the wild type

protein 3D modelling.

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 4

 Intrinsic resistance to most cephalosporins can be
seen in most infections of hospitals, which is because
of Enterococcus faecalis[3].

Sometimes Enterococcus faecalis target the cell-

wall bio-synthesis. transmembrane cognate
phosphatase (IreP) and kinase (IreK) controls the
cephalosporin resistance in Enterococcus Faecalis.

In this BLAST search method is implemented to

extract the features of conserved homolog IreB
action, structure and control of resistance,
antimicrobials in Enterococcus faecalis.

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 5

 The organisms variable genome and core content can be signified by
Pan-genome analysis. Pan genome also aids in organism's lifestyle and
taxonomic classifications.

The authors in paper [4] have studied the pathogenic potential of food
borne pathogen Clostridium botulinum. Clostridium botulinum produces
heat-resistant spores and which is an , spore-forming bacteria and
anaerobic, exist widely in the environment.

Sequential procedure of the paper[4] for synteny analysis contains score

generation, query protein sequence comparison , similarity search
analysis, normalization and maximization of bit score, high scoring
protein analysis and its implementation with the help of BLASTp and
TBLASTN search methods.

Genomic and pan-genomic comparative analysis of multiple Clostridium

botulinum genomes is carried with the help of BLAST method by the
authors of the paper[4].

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 6

 In paper[5], the authors proposed a different type of
search method for low-similarity datasets with the help of
reduced PSSM and position-based secondary structural
features.

In this[5] four different datasets of low-similarity

benchmark are used for the analysis and compared with
the existing methods.

In the earlier developed existing methods some critical

issues are present. In this a PSI-BLAST search method is
applied to selected SWISS-PROT database , to get and align
homogeneous sequences.

This[5] Psi-BLAST method returns a PSSM vector, then this

PSSM vector is scaled down to a range between 0 and 1.

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 7

 In paper[6], the authors have studied the protein
sequences of M. tuberculosis genome strains and human
protein sequences and its increased resistance to the
treatment of tuberculosis.

From the available predicted protein sequences, the

authors have analyzed M. tuberculosis genome strains and
conserved M. tuberculosis proteins absent in human

The authors[6] used PSI_BLAST search algorithm to identify

and separate M. tuberculosis proteins absent in human
against the non-redundant human protein sequences from
their NCBI database.

Finally authors identified conserved proteins, human

protein sequences,

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 8

 In paper[7],the authors said that, Candida
dubliniensis proteomics data analysis showed
some of protein are conserved hypothetical
proteins (HPs).

And the of gene sequence analysis of HP used to

relate the molecular machinery of organisms at
systems level, then assign a precise function to
hypothetical proteins.

The hypothetical proteins used for drug target

for drug design, discovery and screen. BLAST-P,
PSI-BLAST methods are used by the authors

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 9

 Various Protein interactions[8] are important to
understand the mechanisms many biological
functions.

The authors of the paper[8] developed Protein

Association Analyzer (PRASA) for prediction of protein
interactions and the corresponding interaction types.

The PRASA[8] method uses the PSI-BLAST search

method to align the first query protein to all
collected proteins and detects the protein organism
which is having highest bit scores in the analysis.

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 10

 The authors of the paper[9] mentioned that Type six
secretion systems (T6SSs) will present in most of the
Gram-negative bacteria and are important

These are responsible for the translocation of effector

molecules into target eukaryotic. The Francisella
novicida ia impoetent for intramacrophage growth.

The authors presented the X-ray crystal structure of

the conserved type six secretion component from F.
Novicida in paper[9].

To find the conserved residues in the TssL group,

PSI-BLAST search method

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 11

 In signaling, metabolism, immune responses
and gene expression like biological
processes, Proteinprotein interactions are
crucial things and its crowded cellular
environments.

PSI-Blast sequence profile is used as one of

the approach in paper[10] for statistical
quality of interface residue detection, and the
average fraction of its.

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 12

 Salivary, sweat, and lacrimal glands[11] like exocrine
organs can be expressed by hormonally responsive
prolactin-induced protein.

In paper[11], authors did sequencing of the PIP

coding, phylogenetic relationship and analysis of this
gene. DNA sequencing of primate PIP genes[11] .

PSI-BLASTsearch method is used to PIP and related

gene with the help of NCBI non-redundant protein
database to analyse homologous sequences, amino
acid sequences and amino acid Residues

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 13

1) Xiang Cheng, Xuan Xiao, Kuo-Chen Chou, pLoc-mVirus: Predict
subcellular localization of multi-location virus proteins via
incorporating the optimal GO information into general PseAAC Gene
journal (Elsevier) , 628 (2017) page 315321
2) Bipasha Bhattacharjee , Neeta Pathaw, Nikhil K. Chrungoo, Atanu
Bhattacharjee, Molecular modelling, dynamics simulation and
characterization of antifungal chitinase from Sechium edule Gene
journal, 606 (2017) page 3946.
3) Cherisse L. Hall, Betsy L. Lytle , Davin Jensen, Jessica S. Hoff , Francis
C. Peterson, Brian F. Volkman and Christopher J. Kristich Structure
and Dimerization of IreB, a Negative Regulator of Cephalosporin
Resistance in Enterococcus faecalis Journal of Micro Biology(Elsevier)
(2017) 429, page 23242336.
4) Tulika Bhardwaj, Pallavi Somvanshi, Pan-genome analysis of
Clostridium botulinum reveals unique targets for drug development,
Gene journal, 623 (2017) page 4862
5) Junru Wang , Cong Wang , Jiajia Cao , Xiaoqing Liu , Yuhua Yao , Qi
Dai, Prediction of protein structural classes for low-similarity
sequences using reduced PSSM and position-based secondary
structural features Gene journal (elsevier)554 (2015) page 241248

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 14

6) Settu Sridhar, Pallabini Dash, Kunchur Guruprasad, Comparative analyses of
the proteins from Mycobacterium tuberculosis and human genomes:
Identification of potential tuberculosis drug targets, Gene journal (Elsevier) ,
579 (2016) page 6974
7) Kundan Kumar, Amresh Prakash, Munazzah Tasleem, Asimul Islam, Faizan
Ahmad, Md. Imtaiyaz Hassan, Functional annotation of putative hypothetical
proteins from Candida dubliniensis, Gene journal (Elsevier) 543 (2014)page
93100.
8) Chen-Yu Fan, Yi-Han Bai, Cheng-Yi Huang, Tsung-Ju Yao, Wen-Hao Chiang,
Darby Tien-Hao Chang;, PRASA: An integrated web server that analyzes protein
interaction types, Gene journal, (elsevier) 518 (2013) page 7883
9) Craig S. Robb, Francis E. Nano and Alisdair B. Boraston, The Structure of the
Conserved Type Six Secretion Protein TssL (DotU) from Francisella novicida,
Journal of Molecular Biology, (Elsevier), (2012) 419, page 277283.
10) Sophie Sacquin-Mora, Alessandra Carbone, and Richard Lavery, Identification
of Protein Interaction Partners and ProteinProtein Interaction Sites, Journal of
Molecular Biology, (Elsevier). (2008) 382, page 12761289.
11) Takashi Kitano , Wei Tian , Kazuo Umetsu , Isao Yuasa ,Kentaro Yamazaki ,
Naruya Saitou , Motoki Osawa, Origin and evolution of gene for prolactin-
induced protein, Gene journal (Elsevier) 383 (2006), page 6470.

Dr. J.Upendar Asst. Prof. EED,UCE, OU, Hyderabad 15

Thank You

Dr. J.Upendar Asst. Prof.

EED,UCE, OU, Hyderabad 16