Biological Databases For Microbial Pathways And Enzymes Biology Essay

Microbs are good knows infective entities which are the acute involvement for research worker and scientist for the many infective diseases. The development of the microbs in host -pathogen infection are being analysed by the many microbiological methods and experiments. Insilico attacks and computational methods are besides now added to research these infection and metabolic tracts designations. Enzymes and chemical compounds are the portion of these metabolic tracts, which interconnected to other molecules in formation of assorted proteins, taking to diseases development. The Bioinfor matics has given new manner and attacks to pathologist to observe and ask about the host pathogen interaction by these metabolic tract databases.


Major diseases in Public wellness job are caused due to assorted infective bacteriums globally. These pathogens are being have been reported to dispute the bing intervention by developing drug opposition and in several instances effectual vaccinums are yet to be developed.

Attempts are continuously made by scientist and research workers for the effectual drugs and vaccinums development but the mark accomplishable are non yet successful due to the dynamic adaptability. This consequence due to pathogens is holding frequent stage and antigenic alterations, fluctuations in major virulency factors, and adoptive mutants. The coming of several microbic complete genome sequences along with development of assorted bioinformatics tools, made it faceable for in silico analysis of the genomes and subsequent drug find against deathly human pathogen, NCBI genome database has listed about 1549 to the full sequenced microbic genomes including infective bacteriums till now ( 2011 ) . In add-on, the sum of subsequent informations generated by using genome sequences and related information, including transcriptome, proteome, metabolic, and regulative webs, is besides quickly increasing. assorted combinations of computational methods, mathematics, statistics, and patterning cognition together with traditional and advanced biological methods has become indispensable to obtain biologically meaningful informations from such a inundation of information ( Lee. et al. , 2005 ) .Identification of drug marks in many infective bacteriums done by many Computational attacks based on subtractive genomics have successfully achieved ( Sakharkar et al. , 2004 ; Dutta et al. , 2006 ; Sharma et al. , 2008. ) . The functional and structural word picture of enzymes belonging to microbic metabolic tracts is really of import for structure-based drug design ( Jacobson M. , 2004 ) .There are assorted web resources which can be use to place the pathogen tracts and their manner of actions in different diseases. The chapter is depicting the major microbic tracts and interactions with Bio-molecules.

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1. Useful Internet Resources for Microbial Biotechnology

The list will supply the assorted tools and packages for Microbs. This can be use to place the basic information about microbs. These can be classified in following classs.

Chemical Compounds

Enzymes and their Genes

Metabolic Pathways


Scientific Literature and Related Information

Biodegradation and Biotechnology in General

1a. Chemical Compounds

EPAA PBT Profiler: Persistent, Bioaccumulative, and Toxic Profiles Estimated for Organic Chemicals On-Line

Extension Toxicology NetworkA at Oregon State University

National Pesticide Information Center, Oregon State University

Agricultural Research Service ( ARS ) A Pesticide Properties Database

JINNO Laboratory, Toyohasi University of Technology, Japan

Polycyclic Aromatic Hydrocarbons ( PAHs ) Database

Pesticides Database

Polycyclic Aromatic Hydrocarbon Structure IndexA from the National Institute of Standards and Technology

Search theA EPA Envirofacts Master Chemical IntegratorA ( EMCI )

EPAA Office of Pollution Prevention and Toxics

Pesticide Fact Sheets

IPCSA INCHEM: Chemical Safety Information from Intergovernmental Organizations

National Toxicology Program

SearchA NTP Databases

National Library of Medicine’sA TOXNET: Toxicology Data Network

Agency for Toxic Substances and Disease Registry ( ATSDR ) A ToxFAQs

Environment WriterA Chemical Backgrounders

Hazardous Substances Information SystemA from the Australian Safety and Compensation Council

Environmental Fate DatabaseA from SRC

Scorecard: The Pollution Information Site

Scorecard Chemical Profiles

Collection of Pesticide Common NamesA by Alan Wood

UKA Pesticides Safety Directorate

OSHAA Chemical Sampling Information

Chemical Entities of Biological Interest ( ChEBI ) A at EBI, UK


ChemSpider: Building a Structure Centric Community for Chemists

Molecular ModelsA by Dr. Dave Woodcock

Organic Compounds DatabaseA at Colby College, Maine

IUPAC Goldbook: Collection of Chemical Terminology

ChemFinderA from CambridgeSoft Corporation. Internet Navigator for the Chemical Industry

ChemSpyA Environment News

Zinc: a free database of commercially-available compounds, from UCSF

Online Chemical Database

NIST Chemical WebBookA from the National Institute of Standards and Technology

Chemical Information PageA at the National Library of Medicine

1b. Enzymes and their Genes

IntEnz: Integrated Enzyme Database at EBI

Ligand Chemical DatabaseA at Kyoto University

ExPASy ENZYME DatabaseA at the University of Geneva

BRENDA: The Comprehensive Enzyme Information System

The Enzyme Database, Trinity College, Dublin

Enzyme NomenclatureA from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology.

E-zyme: for anticipation of enzymatic reactions, at Kyoto University

Thermodynamicss of Enzyme-Catalyzed ReactionsA from the National Institute of Standards and Technology

Sequence Retrieval SystemA at the European Bioinformatics Institute

a/b hydrolase fold households databaseA at the University of Stuttgart

Catalytic Site AtlasA at EMBL-EBI

EzCatDB: Enzyme Catalytic Mechanism Database from AIST, Japan

BiocatCollection: International Collection of Biocatalysts

GenBankA at the National Center for Biotechnology Information

Microbial Genomics GatewayA by the US Department of Engergy

MBGD: Microbial Genome DatabaseA for Comparative Analysis at the University of Tokyo

The Enhanced Microbial Genomes LibraryA at Pole Bio-Informatique Lyonnais, France

PGD: The Plasmid Genome Database from the Centre of Ecology and Hydrology-Oxford, UK

GenProtEC: A E. coliA cistrons and proteins at the Woods Hole Marine Biological Laboratory

1c. Metabolic Pathways

KEGG: A Kyoto Encyclopedia of Genes and Genomes

PathPred: Biodegradation/biosynthesis tract anticipation

Boehringer Mannheim Biochemical PathwaysA on the ExPASy waiter, Geneva, Switzerland

IUBMB-Nicholson Metabolic Maps, Minimaps and Animaps

International Society for the Study of Xenobiotics

Biopathways Consortium

BioCyc: A Knowledge Library of Pathway/Genome Databases

MetaCycA Biodegradation Pathways

Yeast Genome PathwaysA at MIPS, Germany

GREP: Generator of Reaction Equations and Pathways at Trinity College Dublin, Ireland

1d. Microorganisms

Biodegradative Strain DatabaseA at Michigan State University

American Type Culture Collection

DSMZ: German Collection of Microorganisms and Cell Cultures

SearchA Bacterial Nomenclature Up-To-Date

List of bacterial names with standing in terminology

Centraalbureau voor Schimmelcultures ( CBS ) A SearchA the NCCB Bacteria/Plasmids Database

WFCC-MIRCENA World Data Centre for Microorganisms The Microbiology Information Portal

Microbes Online

MicrobeWikiA at Kenyon College

Taxonomy BrowserA at the National Center for Biotechnology Information

Toxic Waste SiteA in theA Microbe ZooA at Michigan State University

Microbial WorldA at University of Edinburgh

Environmental Procedures

Wood Biodegradation

American Society for Microbiology

Society for Industrial Microbiology

1e. Scientific Literature and Related Information

Entrez PubMedA at the National Center for Biotechnology Information

Entrez cross-database hunt page

Journal of Biological Chemistry Online

Journal of Biochemistry Online

Nucleic Acids Research Online

Bioinformatics Online

BMC Bioinformatics

Journal of Chemical Information and Modeling

American Society for Microbiology Diaries

Genamics JournalSeek: Molecular Biology, Biochemistry and Science Journals

National Academy Press

SearchA text of NAP books for “ biodegradation ”

Natural Attenuation for Groundwater Remediation ( 2000 )

In Situ Bioremediation: When Does It Work? ( 1993 )

U.S. EPAA A Citizen ‘s Guide to BioremediationA PDF File

U.S. EPAA Hazardous Waste Clean-Up Information ( CLU-IN )

PublicationsA from the Canadian Network of Toxicology Centers

1f. Biodegradation and Biotechnology in General

U.S. Geological SurveyA BioremediationA andA Toxic Substances Hydrology Program

Biodegradation, from Environmental Inquiry, Cornell University

U.S. Department of Energy, A Office of Biology and Environmental ResearchA Program

Google Directory of Biotechnology

The microbs tracts, enzymes and marks can be besides search by these web resources the inside informations of web resources have been provided to research the related information.



a searchable database of metabolic tracts, enzymes, substrates and merchandises. Has links toA ENZYMEA ( see below ) . Constructed in concurrence withA Boehringer Mannheim Corp.Produces a in writing representation of the metabolic tracts ensuing from the hunt within the context of an tremendous metabolic map – neighbouring metabolic reactions can be viewed.




The information base is implemented in a relational information base and covers some 40 informations Fieldss with information about terminology, reaction and specificity, enzyme construction, isolation/preparation, stableness, literature mentions and cross mentions to sequence and 3D-structure informations Bankss. The information base is made available via the Internet through cooperation with the European Bioinformatics Institute. The enzyme information contained in this database is comprehensive and utile covering many facets including substrates, inhibitors, optimum conditions for activity, locations and beginnings. Searching the database requires the EC figure for the mark enzyme – seeA EC Enzyme orA ENZYMEA in this database. Linkss are provided to several other enzyme and metabolic tracts databases. Brenda is one of several databases nested within the metabolic tract database set of theA SRS5A sequence retrieval system at EBI. To happen the database follow these links fromA SRS entryway page -A START, expand theA Metabolic PathwaysA bill of fare ( snap on ) , click onA BRENDA. nexus to travel to theA BRENDAA front page and the concluding nexus to the hunt page.



ECEnzymeA -A

Enzyme committee database: this Web version of EC Enzyme has hot links among its ain entries and to the undermentioned Databases.A

OMIMA -OnlineMendelianInheritanceinManA

SWISSPROTA – The Swiss Protein Database EC Enzyme comes with a users manual that gives an extended description of the database.



EcoCycA –

A Encyclopedia ofA E.coliA Genes and Metabolism – needs a watchword but free enrollment for non-profit administrations.




Enzyme terminology database – a depository of information relation to the terminology of enzymes. It is chiefly based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology ( IUBMB ) and it describes each type of characterized enzyme for which an EC ( Enzyme Commission ) figure has been provided.




Ligand Chemical Database for Enzyme Reactions at Kyoto, Japan. TheA ENZYMEA subdivision is a aggregation of all known enzymatic reactions classified harmonizing to the terminology of the International Union of Biochemistry and Molecular Biology ( IUBMB ) . TheA COMPOUNDA subdivision is a aggregation of metabolic compounds including substrates, merchandises, and inhibitors.



Metabolic DatabaseA -A

The metabolic constituent ofA SoyBase, a soybean familial database, contains reaction and pathway descriptions and diagrams for a figure of basic metabolicpathways.A SoybaseA is anA ACEDBA database ; the metabolic information has been made available on the Web via a interlingual rendition plan that is still under development, and has some bugs. AGISA = Agricultural Genome Information Service, an incorporate system for agricultural genome analysis. ( See entry inA Plant CornerA andA AGIS genome siteA ) .



a peptidase and peptidase inhibitor Web waiter at the University of Tours, France. PROLYSISA is intended as a Web resource for those interested in peptidases and their natural or man-made inhibitors. This page contains informations of general involvement every bit good as utile links to other Internet resources.



All enzymes are given an Enzyme Commission ( E.C. ) figure leting it to be unambiguously identified.

All E.C. Numberss have four Fieldss separated by periods: e.g. “ ” .

The left-hand-most field represents the most wide categorization for the enzyme. The following field represents a finer division of that wide class. The 3rd field is adds more elaborate information and the 4th field defines the specific enzyme. The E.C. Classification Page has three columns stand foring the first three Fieldss of the E.C. figure of an enzyme. Snaping on an point in the 1st column alters the 2nd column to demo the subclassifications for that major header. Snaping on an point in the 2nd column alters the 3rd column to demo the appropriate subclassifications. Snaping on the 3rd column opens another window that will incorporate all possible full E.C. Numberss that conform to your first three picks. Snaping on a specific figure will take you to the E.C. database entry for that enzyme, in that window.




an Integration of Biological Data to Support the Interpretation of Genomes. PUMA is a web-based system that offers incorporate entree to biological informations. It is intended as an environment to back up the reading and presentation of genomes.A PUMAA is a system that attempts to incorporate entree to the emerging organic structure of biological sequence informations from within a functional context ; it is an integrating based on a functional overview of an being and offers entree through structured presentations of the informations — most notably, metabolic tracts, alliances, and phyletic trees. ( See besides new site onreconstructed metamorphosis ) .




TheA RestrictionA Enzyme DatabaseA – a aggregation of information about limitation enzymes, methylases, and the micro-organism from which they have been isolated – isoschizomers, acknowledgment sequences, cleavage sites, methylation specificity, commercial handiness, and mentions – both published and unpublished. Maintained by Dr Richard J. Roberts and Dana Macelis.


Metabolic pathwaysA -A

Metabolic tracts of the morbid murphy and disease resistance-related proteins in murphy at Scots Crop Reseach Institute ( SCRI ) . Poster-sized representation of the extended metabolic events taking topographic point in the murphy challenged by pathogens or injuring. Proteins included in the Metabolic tracts of the morbid murphy are listedA here. Many of these proteins have enzyme activity, exist as multiple isozymes, and may be involved in the biogenesis of either signalling molecules or antimicrobic compounds. Enzyme activity, subcellular localisation and map can be controlled by post-translational alteration affecting add-on of phosphates, methyl groups, saccharides or lipoids to the proteins. Isozymes can be differentially regulated with some up-regulated by injuring whilst others are up-regulated by pathogens. Many enzymes are able to move on a figure of substrates and ‘enzyme reactions’listed below are lone illustrations instead than being an thorough listing. Many more proteins are associated with opposition of murphy to bacterial and fungous diseases but have non been included in the tabular array because they have either non been good characterised or are non yet included in the metabolic tracts chart.

Cell signalling tracts




( What Is There ) A The WIT system helps users create metabolic Reconstructions, which is made possible by the recent copiousness of complete bacterial genomic sequences. Such Reconstructions will for the first clip set the phase for meaningful simulations of the basic behavior of bugs, and may therefore significantly beforehand microbic biological science.

2. Online Web Portals for Pathogenic

Nerve pathwaies Analysis

This is good known that pathogen doing terrible disease epidemics and lower economic outputs. In human wellness, there is turning concern over fungous infections in immunocompromised patients. Over the last 15 old ages, the figure of cistrons coni¬?rmed by cistron and/or transcript break experiments to be required for the disease doing ability of a bug has bit by bit increased. These cistrons are termed pathogenicity cistrons if the consequence on the phenotype is qualitative, or virulence/aggressiveness cistrons if the consequence is quantitative ( Shaner et al.,1992 ) .the undermentioned resources are besides helpfull to follow the infective cistrons function and their maps.

2a. BRITE- Biomolecular Relations in Information Transmission and Expression

hypertext transfer protocol: //


Molecular interactions and tracts database, portion of the KEGG system

2b. MiST – Microbial Signal Transduction database

hypertext transfer protocol: //


Signal transduction systems link environmental stimulations with adaptative cellular responses and enable an being to last and accommodate to altering conditions. This communicating web of signaling tracts regulates critical cellular activities in all beings from bacteriums to worlds. The MiST ( Microbial Signal Transduction ) database is a comprehensive catalog of the signal transduction proteins ( two- and one-component systems ) within wholly sequenced bacterial and archaeal genomes. These are identified with assorted sphere profiles that straight or indirectly implicate a peculiar protein as take parting in signal transduction. MiST presently contains information on the signal transduction proteins within more than 365 genomes and freshly, available genomes are added on a monthly footing. We have designed a user-friendly interface to ease the comparing and analysis of bacterial signal transduction repertories.

2c. VirHostNet

hypertext transfer protocol: //


A knowledgebase of virus-host molecular interaction webs

2d.CPA – Comparative Pathway Analyzer

hypertext transfer protocol: //


The Comparative Pathway Analyzer ( CPA ) is a web tool for comparative metabolic web analysis. The differences in metabolic reaction content between two sets of beings are computed and displayed on KEGG tract maps.

2e. PID ( Pathway interaction database )

hypertext transfer protocol: //


NCI-Nature Pathway Interaction Database

2f. Pathway Resource List

hypertext transfer protocol: //


The Pathway Resource List ( PRL ) is a database of 150+ links to resources for protein-protein interactions, metabolic and signalling tracts, written text factor and familial interaction webs, tract diagrams, protein sequences, and protein-compound interactions.

2g. ProdoNet

hypertext transfer protocol: //


A web-based application for the function of procaryotic cistrons and the corresponding proteins to common cistron regulative and metabolic webs. Users input a list of cistrons from which shared operons, co-expressed cistrons and shared regulators are detected. Common metabolic tracts are so viewed on KEGG maps.

2h. Pal

hypertext transfer protocol: //


Pathway and Literature Strainer ( PaLS ) high spots those members on a user inputted list that portion forms from PubMed, GO, KEGG and Reactome.

2i.CPA -Comparative Pathway Analyzer

hypertext transfer protocol: //


The Comparative Pathway Analyzer ( CPA ) is a web tool for comparative metabolic web analysis. The differences in metabolic reaction content between two sets of beings are computed and displayed on KEGG tract maps.

3. Israel Science and Technology Homepage

The Israelian authorities besides supplying the assorted resources for the pathogenic and non infective microbs tracts and their mark sensing by on-line resources. The undermentioned mentioned web resources besides helpful to research the information of micorbs.


BioCarta Charts – Dynamic graphical theoretical accounts of biological tracts

Biocatalysis/Biodegradation Database – Microbial biocatalytic reactions and biodegradation tracts chiefly for xenobiotic, chemical compounds


CellML Model Repository


Comprehensive Systems-Biology Database of transcriptional co-responses


E-Cell Project to pattern and retrace biological phenomena in silico


Golm Metabolome Database


Human Metabolome Database

IUBMB-Nicholson Metabolic Maps

JWS Online Cellular Systems Modelling

Metabolic Pathways

Metabolic Pathways of Biochemistry


MetaCyc database of metabolic tracts

Microbial biocatalytic reactions and biodegradation tracts

Molecule Pages: A comprehensive signaling database

NuGO – Nutritional Metabolomics Database


Pathcase Metabolic Pathway Database System


Reactome – a curated knowledgebase of biological tracts


Signing and metabolic human biological tract maps

UniPathway, metabolic tracts for the UniProtKB/Swiss-Prot

Despite rapid progresss on certain facets of works infective bacteriums, many economically of import pathosystems are mostly undiscovered and biologically relevant life phases of even familiar systems remain ill understood. We know unusually small about end-stage disease, latent infections, survival off from the host, interactions among multiple bugs in a works, and the effects of quantitative virulency factors.

Biochemical reactions in a cell can be diagrammatically represented as metabolic tract mapsin the signifier of webs of interrelated molecules, picturing the relationships between enzymes and the chemical compounds they transform. The major challenge is that the metabolic web of even a simple bacteria is so complex that it is really hard for a individual scientist to hold on all the inside informations ( Karp. , 2001 ) . Computer databases for metabolic tracts and informations on the participant enzymes and metabolites are hence an indispensable tool for the analysis of biochemical webs of whole beings. Metabolic tracts can be used to look into the cogency of the functional assignments by analyzing whether any given tract is complete. If an enzyme is apparently absent from an otherwise complete tract, it may bespeak that the cistron coding for this enzyme was wrongly classified.Alternatively, if the cistron for this enzyme is genuinely absent from the genome, the tract may either hold a different design or may non be operative in that peculiar species [ Ogata et al,1996 ) .

Metabolic tracts have attracted much involvement, as they enable analysis of the functional capacities of beings based on their genome sequences. Comparisons of metabolic tracts from different species facilitate word picture of their evolutionary relationships and designation of suited marks for development of fresh anti-microbial drugs. Integration of look informations for cistrons encoding metabolic enzymes with metabolic tract maps enables understanding of how the metabolic procedures of the being are affected by different growing conditions and facilitates the finding of cistron map. This cognition is utile for the scientific discipline of metabolic technology, which aims at modifying the metabolic tracts of bacteriums or workss in order to increase the production of certain compounds, or the debasement of toxic compounds ( Sanford et al. , 2002, Stephanopoulos, 2001 ) .


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