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SENTRA, a database of signal transduction proteins

M. D'Souza
2000 Nucleic Acids Research  
SENTRA, available via URL http://wit.mcs.anl.gov/ WIT2/Sentra/ , is a database of proteins associated with microbial signal transduction.  ...  The database currently includes the classical two-component signal transduction pathway proteins and methylaccepting chemotaxis proteins, but will be expanded to also include other classes of signal transduction  ...  ACKNOWLEDGEMENT This work was supported by the Office of Biological and Environmental Research, US Department of Energy, under Contract W-31-109-Eng-38.  ... 
doi:10.1093/nar/28.1.335 pmid:10592266 pmcid:PMC102390 fatcat:uunfjsxx5fhy5dpy2ckpx3qv6m

Sentra, a database of signal transduction proteins

N. Maltsev
2002 Nucleic Acids Research  
SENTRA, available via URL http://wit.mcs.anl.gov/ WIT2/Sentra/ , is a database of proteins associated with microbial signal transduction.  ...  The database currently includes the classical two-component signal transduction pathway proteins and methylaccepting chemotaxis proteins, but will be expanded to also include other classes of signal transduction  ...  SENTRA, a database of proteins related to signal transduction, was created to address these issues.  ... 
doi:10.1093/nar/30.1.349 pmid:11752334 pmcid:PMC99115 fatcat:n3gwwd4i7bcstizuii5e3dab6y

Sentra: a database of signal transduction proteins for comparative genome analysis

M. D'Souza, E. M. Glass, M. H. Syed, Y. Zhang, A. Rodriguez, N. Maltsev, M. Y. Galperin
2007 Nucleic Acids Research  
Sentra (http://compbio.mcs.anl.gov/sentra), a database of signal transduction proteins encoded in completely sequenced prokaryotic genomes, has been updated to reflect recent advances in understanding  ...  Sentra consists of two principal components, a manually curated list of signal transduction proteins in 202 completely sequenced prokaryotic genomes and an automatically generated listing of predicted  ...  , and perform publicly and display publicly, by or on behalf of the Government.  ... 
doi:10.1093/nar/gkl949 pmid:17135204 pmcid:PMC1751548 fatcat:43t3e72sgjd7bb37u5k4fpled4

STCDB: Signal Transduction Classification Database

M. Chen
2004 Nucleic Acids Research  
The Signal Transduction Classi®cation Database (STCDB) is a database of information relative to the classi®cation of signal transduction.  ...  It is based primarily on a proposed classi®cation of signal transduction and it describes each type of characterized signal transduction for which a unique ST number has been provided.  ...  Fortunately, a number of databases have been constructed to bring signal transduction knowledge into a well-organized format, providing simple and fast access to the signal transduction system.  ... 
doi:10.1093/nar/gkh079 pmid:14681456 pmcid:PMC308813 fatcat:qn4lljv3vffcfhpfyh37xrn5tm

Signal transduction-related bioinformatics services

M. Vihinen
2003 Briefings in Bioinformatics  
Signal transduction pathways are crucial for the regulation of a very wide variety of cellular functions ranging, for example, from translation to intercellular communication, and from metabolism to apoptosis  ...  They also form a substantial part of the genes in genomes and proteins in proteomes in all animals. Signalling can be studied in many different levels and ways.  ...  sites binding to signalling molecules PPDB http://www-lmmb.ncifcrf.gov/phosphoDB/ Phosphoprotein database Sentra http://www-wit.mcs.anl.gov/sentra/ Prokaryotic signal transduction proteins CGRPDB  ... 
doi:10.1093/bib/4.4.325 pmid:14725345 fatcat:4k6qub3tezd33l5gcdp6ka64p4

MiST: a microbial signal transduction database

L. E. Ulrich, I. B. Zhulin
2007 Nucleic Acids Research  
To overcome this problem, we have developed the microbial signal transduction (MiST) database (http://genomics.ornl.gov/mist), a comprehensive library of the signal transduction proteins from completely  ...  Because of their extreme sequence variability and extensive domain shuffling, signal transduction proteins are difficult to identify, and their current annotation in most leading databases is often incomplete  ...  This work was supported in part by a grant GM072285 from the National Institutes of Health to I.B.Z. and funds provided by the UT-ORNL Joint Institute for Computational Sciences.  ... 
doi:10.1093/nar/gkl932 pmid:17135192 pmcid:PMC1747179 fatcat:jhnd255bfjagpafo2irlpzauri

P2CS: a two-component system resource for prokaryotic signal transduction research

Mohamed Barakat, Philippe Ortet, Cécile Jourlin-Castelli, Mireille Ansaldi, Vincent Méjean, David E Whitworth
2009 BMC Genomics  
Description: We present P2CS (Prokaryotic 2-Component Systems), an integrated and comprehensive database of TCS signal transduction proteins, which contains a compilation of the TCS genes within 755 completely  ...  It provides a complete overview of information on TCSs, including predicted candidate proteins and probable proteins, which need further curation/ validation.  ...  Currently, databases describing prokaryotic TCSs contain data from only a subset of available genomes (eg. SENTRA, Genome Atlas) [3, 4] , or analyze TCSs on the basis of predicted proteins (eg.  ... 
doi:10.1186/1471-2164-10-315 pmid:19604365 pmcid:PMC2716373 fatcat:woapzjmclvchxl6xlxihisvq5i

P2CS: a database of prokaryotic two-component systems

Mohamed Barakat, Philippe Ortet, David E. Whitworth
2010 Nucleic Acids Research  
P2CS (http://www.p2cs.org) is a specialized database for prokaryotic two-component systems (TCSs), virtually ubiquitous signalling proteins which regulate a wide range of physiological processes.  ...  Alternatively a variety of database-wide or taxon-specific searches are supported.  ...  Compared to more generalized databases of signal-transduction proteins such as MiST, Genome Atlas and SENTRA (6, 7, 8) , P2CS provides a relative diversity of information for each protein entry and a  ... 
doi:10.1093/nar/gkq1023 pmid:21051349 pmcid:PMC3013651 fatcat:bncswe3gqjevhf2m4bjos5h6mu

A Framework for Classification of Prokaryotic Protein Kinases

Nidhi Tyagi, Krishanpal Anamika, Narayanaswamy Srinivasan, Alan Ruttenberg
2010 PLoS ONE  
Many prokaryotic Ser/Thr kinases exhibit a wide variety of modular organization which indicates a degree of complexity and protein-protein interactions in the signaling pathways in these microbes.  ...  After series of searches in a comprehensive sequence database we recognized that 38 subfamilies of prokaryotic protein kinases are associated to a specific taxonomic level.  ...  Apart from KinG, SENTRA [45, 46, 47] which is a manually curated database provides information on signal transduction proteins.  ... 
doi:10.1371/journal.pone.0010608 pmid:20520783 pmcid:PMC2877116 fatcat:6l56cxcomnho5btgqv5bx3h25y

A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts

Michael Y Galperin
2005 BMC Microbiology  
The total number of signal transduction proteins grows approximately as a square of genome size.  ...  This paper presents results of a comprehensive census of signal transduction proteins--histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases  ...  The SENTRA [44, 45] ), SMART [11, 12] and COG [46, 47] databases have a good coverage of the first sequenced genomes but have not been updated in a while, whereas data in other databases, such as  ... 
doi:10.1186/1471-2180-5-35 pmid:15955239 pmcid:PMC1183210 fatcat:dhuv25pc5fcntehgqf4n5yfrnm

Structural Classification of Bacterial Response Regulators: Diversity of Output Domains and Domain Combinations

M. Y. Galperin
2006 Journal of Bacteriology  
CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems.  ...  ), protein-or ligand-binding (PAS, GAF, TPR, CAP_ED, and HPt) domains, or newly described domains of unknown function.  ...  databases, such as KEGG, SENTRA, and COG (60, 84, 134) .  ... 
doi:10.1128/jb.01887-05 pmid:16740923 pmcid:PMC1482966 fatcat:knxbfoo5anhafc6na3gqhtufvq

Survey of the number of two-component response regulator genes in the complete and annotated genome sequences of prokaryotes

Mark K. Ashby
2004 FEMS Microbiology Letters  
The survey shows that for Bacteria there is a link between the total number of potential response regulator genes and both the genome complexity (number of potential protein-coding genes) and the organism's  ...  requires a higher level of control of gene expression and cellular activity.  ...  A survey of the number of response regulators for 34 organisms can be found in the Sentra database (http://www-wit.mcs. anl.gov/sentra/).  ... 
doi:10.1016/s0378-1097(04)00004-7 pmid:14987775 fatcat:gs5m2tb4rbd25ngsyzgpnk76bq

Evolution and applications of plant pathway resources and databases

Y. Sucaet, T. Deva
2011 Briefings in Bioinformatics  
We propose Good Database Practice as a possible model for collaboration and to ease future integration efforts.  ...  We lay out trends and challenges in the ongoing efforts to integrate plant pathway databases and the applications of database integration.  ...  Eve Syrkin Wurtele and Dr Julie Dickerson at Iowa State University, who supported us in a number of ways with encouragement, sound advice, guidance and lots of good ideas.  ... 
doi:10.1093/bib/bbq083 pmid:21949268 fatcat:v4w7i5b47zhj7idwb7k5wrpdgi

Environmental conditions and transcriptional regulation inEscherichia coli: a physiological integrative approach

Agustino Martínez-Antonio, Heladia Salgado, Socorro Gama-Castro, Rosa María Gutiérrez-Ríos, Verónica Jiménez-Jacinto, Julio Collado-Vides
2003 Biotechnology and Bioengineering  
The link between growth conditions, signal transduction, and transcriptional regulation is modeled in the database in a simple format that highlights biological relevant information.  ...  literature and incorporated into Regulon-DB, a database on transcriptional regulation and operon organization in E. coli.  ...  The Sentra database contains a classification of signaltransduction proteins for over 43 prokaryote genomes (Maltsev et al., 2002) .  ... 
doi:10.1002/bit.10846 pmid:14708114 fatcat:rrjrm7evo5g2tmxkai6lurdsau

Different Evolutionary Modifications as a Guide to Rewire Two-Component Systems

Beate Krueger, Torben Friedrich, Frank Förster, Jörg Bernhardt, Roy Gross, Thomas Dandekar
2012 Bioinformatics and Biology Insights  
As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here.  ...  Designed connector proteins may also be useful to modify TCS in selected cases.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank Dr. Ulrike Rapp-Galmiche for stylistic and language corrections.  ... 
doi:10.4137/bbi.s9356 pmid:22586357 pmcid:PMC3348925 fatcat:golacxy7n5gh3eh7hlugebr22i
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