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Does Hypothetical Proteins of Yersinia Pestis CO92 Capable of Coding Enzymes?

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Does Hypothetical Proteins of Yersinia Pestis CO92 Capable of Coding Enzymes? Sunil Pande et al. / Journal of Pharmacy Research 2015,9(4),278-287 Research Article Available online through ISSN: 0974-6943 www.jprsolutions.info Does hypothetical proteins of Yersinia pestis CO92 Capable of Coding Enzymes? Sunil Pande1 and Dilip Gore2* 1Rajiv Gandhi Biotechnology Centre, Rashtrasant Tukdoji Maharaj Nagpur University, L.I.T. Premises, Nagpur, Maharashtra, India. 440 033 2Sai Bioinfosys Institute of Bioinformatics Research, Plot No. 271 Raghuji Nagar, Nagpur (Maharashtra), India.440009 Received on:25-03-2015; Revised on:16-04-2015 ; Accepted on: 12-05-2015 ABSTRACT Background: Yersinia pestis are known for the plague outbreak and when it has been sequenced for the genome; more than 900 hypothetical proteins have been marked but still the exact functions about those are obscure. Methods: The evidences brought up by the combined results of CDD BLAST, INTERPRSCAN, PFAM and CATH domain search programs enabled to search enzyme functions based on conserved domains available in hypothetical proteins. Results and Discussion: Y. pestis is showcasing 210 hypothetical proteins with enzyme coding ability evident from conserved domains. Conclusion: These Y. pestis hypothetical proteins possesing conserved domains of enzymes may be functioning in cellular metabolism to bring about the virulence. KEYWORDS: Bioinformatics, Enzyme conserved domain, Hypothetical proteins. INTRODUCTION The deadly plague brought about by the bacterium, Yersinia pestis MATERIALS AND METHODS as previously diverged from Yersinia pseudotuberculosis (YPT) some 5000–15,000 years ago.1 Y. pestis reported to transmits in human by Data Collection: the bite of infected rodents. Once inside the human, the transmission The total 998 hypothetical protein sequences marked for Y. pestis of bacteria occurred through skin and progress towards lymph nodes, CO92 strain (biovar Orientalis) and those were retrieved in FASTA establishing bubonic type plague, ultimately lead to septicemia and format available at the website: www.genome.jp/kegg/. death within seven days if not medicated properly. Human to human transmission is another deadly mode recorded which causes rapid Search for Conserved Sequences spread among highly crowded community as in Madagascar and in The Y. pestis genome encoding 998 hypothetical proteins were the Democratic Republic of Congo.2, 3 screened for the presence of enzyme domains in the query sequences when input given to the four conserved domain searching programs. The early genome sequenced for Y. pestis CO92 offered first-time These programs remain linked with the conserved domain databases opportunities for understanding the virulence traits of the deadly and reported particular protein family showing best scored homology pathogen.4 Additionally, two other Y. pestis strain whole genomes, for the given query sequence. KIM and 91001, were sequenced.5-8 These findings provided an in- The programs used as:- creasing opportunity to uncover virulence-associated genes linked A) CDD-BLAST (http://www.ncbi.nlm.nih.gov/BLAST/) 10 11 12 for the pathogenicity associated with humans. 9 In the present study, B) INTERPROSCAN (http://www.abi.ac.uk/interpro) 13 genomic information has been used for the functional annotation of C) PFAM (http://www.pfam.sanger.ac.uk/) 14 the hypothetical proteins of Y. pestis have been investigated by con- D) CATH (http://www.cathdb.info/) 15 served domain analysis using four bioprograms. Functional Categorization *Corresponding author. The hypothetical proteins possess enzyme domains as reported by Dilip Gore four programs were categorized in percent confidence levels using Sai Bioinfosys Institute of Bioinformatics Research, following parameters:- Plot No. 271 Raghuji Nagar, 1. Four tools indicate the same enzyme functions then confidence Nagpur (Maharashtra), India.440009 level set as 100 percent. Journal of Pharmacy Research Vol.9 Issue 4.April 2015 278-287 Table 1 : Enzyme function prediction in the hypothetical proteins of Y. pestis KEGG NO CDD BLAST INTERPROSCAN PFAM CATH % YPO0032 N-Acyltransferase superfamily Thioesterase Putative thioesterase (yiiD_Cterm) NO 50 YPO0042 UPF0126 domain UPF0126 Isoprenylcysteine carboxyl methyltransfe NO 25 YPO0063 Peptidase family M23 Duplicated hybrid motif Peptidase family M23 Lipoprotein -like domain 50 YPO0065 Rhodanese Homology Domain (RHOD) Rhodanese Rhodanese-like domain tRNA sulfurtransferase -like domain 75 YPO0076 YhgA-like Transposase_31 Putative transposase, YhgA-like NO 75 YPO0082 hypothetical protein RraA-like Demethylmenaquinone methyltransferase 4-hydroxy-4-methyl-2-oxoglutarate 25 Sunil Pande aldolase -like domain YPO0083 Uncharacterized proteins, LmbE homologs N-ACETYLGLUCOSAMINYL- GlcNAc-PI de-N-acetylase 1D-myo-inositol -like domain 50 PHOSPHATIDYLINOSITOL DE-N-ACETYLASE-RELATED YPO0141 HAD_like HADHALOGNASE Haloacid dehalogenase-like hydrolase Putative hydrolase -like domain 100 et al./JournalofPharmacyResearch2015,9(4),278-287 YPO0275 SirA, YedF, and YeeD SirA-like Sulfurtransferase TusA Sulfurtransferase TusA -like domain 50 Journal ofPharmacy Research YPO0284 nucleoside-diphosphate-sugar epimerases NO NADH(P)-binding UPF0659 protein YMR090W -like domain 50 YPO0290 PELOTA RNA binding domain PRTase_1 Phosphoribosyl transferase NO 75 YPO0291 NO HAD-like Sucrose-6F-phosphate phosphohydrolase Glycerol-3-phosphate acyltransferase 6 - 50 like domain YPO0292 TRSP domain C terminus to PRTase_2 Uncharacterised conserved protein, TRSP domain C terminus to PRTase_2 Phosphoribosyltransferase -like domain 75 UCP020967 type YPO0293 ATP-grasp domain Uncharacterised conserved protein, ATP-grasp in the biosynthetic pathway with Succinyl-CoA ligase [ADP-forming] subunit 50 UCP029120 type Ter operon beta -like domain YPO0368 Uncharacterized conserved protein yjeF_cterm: YjeF family C-terminal YjeF-related protein N-terminus Hydroxyethylthiazole kinase -like domain 50 domain YPO0392a HTH_Tnp_1 HTH_Tnp_1 Transposase NO 75 YPO0392 Histidine kinase-like ATPases ATPase domain of HSP90 Histidine kinase-, DNA gyrase B-, and HSP90 Sensor protein -like domain 75 V ol.9 Issue4.April 2015 chaperone/DNA topoisomerase -like ATPase II/histidine kinase YPO0396 SbcCD_C SbcCD_C Putative exonuclease SbcCD, C subunit HTH-type transcriptional regulator malT - 75 like domain YPO0433 Pat_hypo_Ecoli_yjju_like Patatin Patatin-like phospholipase Lysophospholipase -like domain 100 YPO0466 Acetyltransferase (GNAT) family GNAT Acetyltransferase (GNAT) family Mycothiol acetyltransferase -like domain 1/2/3 100 YPO0489a NO NO Cdc14 phosphatase binding protein N-terminus NO 25 YPO0593 Protein phosphatase 2C PP2C-like Protein phosphatase 2C Ca(2+)/calmodulin-dependent protein kinase - 75 like domain YPO0601 V-type ATP synthase subunit E NO Pre-toxin domain with VENN motif NO 25 YPO0608 Glycoamylase super family Glycoamylase Putative glucoamylase NO 75 YPO0610 Cellobiose phosphorylase Six-hairpin glycosidases NO NO 25 YPO0624 ArsB_NhaD_permease super family Na_H_antiporter Na+/H+ antiporter family NO 50 YPO0625 PYR_PYL_RCAR_like Polyketide_cyc2 Polyketide cyclase / dehydrase and lipid transport S-norcoclaurine synthase -like domain 75 YPO0629 putative monooxygenase Dimeric alpha+beta barrel Putative mono-oxygenase ydhR NO 50 YPO0636 NO NO Protein-kinase domain of FAM69 NO 25 YPO0652 CYTH-like_Pase_CHAD CYTH-like phosphatases CYTH domain Adenylate cyclase -like domain 75 YPO0655 putative transporter AA_permease_2 Amino acid permease NO 50 YPO0659 45_DOPA_Dioxygenase LigB Catalytic LigB subunit of aromatic ring-opening 4,5-DOPA dioxygenase extradiol -like domain 100 dioxygenase 278-287 YPO0660 Glutathionylspermidine synthase GSP_synth Glutathionylspermidine synthase preATP-grasp NO 75 YPO0695 Flp pilus assembly protein Peptidase_A24 Type IV leader peptidase family NO 50 KEGG NO CDD BLAST INTERPROSCAN PFAM CATH % YPO0757 Cellulase-like super family no description Sugar-binding cellulase-like ABeta-agarase -like domain 50 YPO0763 Soluble NSF attachment protein, SNAP TPR_1 Tetratricopeptide repeat -Receptor-associated protein of the synapse 50 like domain 1/2 YPO0769 NO NO Spi protease inhibitor NO 25 YPO0774 Oxidoreductase family GFO_IDH_MocA ,yOxidoreductase NAD-binding famil Inositol 2-dehydrogenase -like domain 50 Rossmann fold YPO0775 NADB_Rossmann super family Saccharop_dh Saccharopine dehydrogenase Saccharopine dehydrogenase -like domain 75 YPO0790a DUF2058 super family NO Glutathione S-transferase, C-terminal domain NO 25 YPO0800 Zn-dependent hydrolases, including Metallo-beta-lactamase superfamily Metallo-beta-lactamase superfamily NO 50 glyoxylases YPO0840 LanC_like superfamily Six-hairpin glycosidases Glycosyl Hydrolase Family 88 Unsaturated rhamnogalacturonyl hydrolase 50 yesR -like domain Sunil Pande YPO0897 hypothetical protein Journal ofPharmacy Research Sdh5 Flavinator of succinate dehydrogenase -Succinate dehydrogenase assembly factor 2, 75 like domain YPO0908 Ubiquinone biosynthesis hydroxylase FAD_binding_3 FAD binding domain NO 50 YPO0936 Tfp pilus assembly protein, pilus retraction T2SP_E Uncharacterized ACR, COG1678 UPF0301 protein MCA2336 2 -like domain 50 TPaseA PilT et al./JournalofPharmacyResearch2015,9(4),278-287 YPO0940 Tfp pilus assembly protein, pilus retraction T2SP_E Type II/IV secretion system protein General secretion pathway protein E -like 50 TPaseA PilT domain YPO0941 PLPDE_III_Yggs_like Ala_racemase_N Alanine racemase, N-terminal domain Alanine racemase -like domain 75 YPO0955 Periplasmic binding protein TroA_f Peripla_BP_2 Periplasmic binding protein Light-independent
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