DOCSLIB.ORG

Bioservices.Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Bioservices.Pdf BioServices Release 1.7.12 Thomas Cokelaer, Lea M. Harder, Jordi Serra-Musach, Dennis Pultz Jul 26, 2021 Contents 1 Installation 5 1.1 User guide................................................5 Python Module Index 195 Index 197 i ii BioServices, Release 1.7.12 Python_version_available BioServices is tested for Python 3.6, 3.7, 3.8 Contributions Please join https://github.com/cokelaer/bioservices and share your notebooks https:// github.com/bioservices/notebooks/ Issues Please use https://github.com/cokelaer/bioservices/issues How to cite Cokelaer et al. BioServices: a common Python package to access biological Web Services programmatically Bioinformatics (2013) 29 (24): 3241-3242 Documentation RTD documentation. Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols). The primary goal of BioServices is to use Python as a glue language to provide a programmatic access to several Bioinformatics Web Services. By doing so, elaboration of new applications that combine several of the wrapped Web Services is fostered. One of the main philosophy of BioServices is to make use of the existing biological databases (not to re-invent new databases) and to alleviates the needs for expertise in Web Services for the developers/users. BioServices provides access to 43 Web Services. For a quick start, look at some notebooks here github coke- laer/bioservices and here github bioservices. Here is a small example using the UniProt Web Service to search for the zap70 specy in human organism: >>> from bioservices import UniProt >>> u= UniProt(verbose= False) >>> data=u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3, ... columns="entry name,length,id, genes") >>> print(data) Entry name Length Entry Gene names ZAP70_HUMAN 619 P43403 ZAP70 SRK B4E0E2_HUMAN 185 B4E0E2 RHOH_HUMAN 191 Q15669 RHOH ARHH TTF More examples and tutorials are available in the On-line documentation Here is the list of services available and their testing status (non exhaustive). Not all services are currently tested (WIP, july 2021) Contents 1 BioServices, Release 1.7.12 Service CI testing arrayexpress bigg biocarta biodbnet biogrid biomart biomodels chebi chembl chemspider clinvitae cog dbfetch ena ensembl eutils eva hgnc intact_complex kegg muscle mygeneinfo ncbiblast omicsdi omnipath panther pathwaycommons pdb pdbe pfam picr pride psicquic pubchem quickgo reactome rhea rnaseq_ebi seqret unichem uniprot wikipathway Note: Contributions to implement new wrappers are more than welcome. See BioServices github page to join the development, and the Developer guide on how to implement new wrappers. Warning: Some of the services may be down. BioServices developers are not responsible for the maintenance or failure of underlying services. Generally speaking (and by experience) the services are up most of the time but 2 Contents BioServices, Release 1.7.12 failure may occur because the site is under maintenance or too many requests have been sent. Another common reason is the fact that the API of the web services has changed: If so, BioServices need to be updated. You may contribute or report such API changes on our Issue page Contents 3 BioServices, Release 1.7.12 4 Contents CHAPTER 1 Installation BioServices is available on PyPi, the Python package repository. The following command should install BioServices and its dependencies automatically provided you have pip on your system: pip install bioservices If not, please see the external pip installation page or pip installation entry. You may also find information in the troubleshootings page section about known issues. Regarding the dependencies, BioServices depends on the following packages: BeautifulSoup4 (for parsing XML), SOAPpy and suds (to access to SOAP/WSDL services; suds is used by ChEBI only for which SOAPpy fails to correctly fetch the service) and easydev. All those packages should be installed automatically when using pip installer. Since version 1.6.0, we also make use of pandas and matplotlib to offer some extra functionalities. 1.1 User guide 1.1.1 Quick Start Introduction BioServices provides access to several Web Services. Each service requires some expertise on its own. In this Quick Start section, we will neither cover all the services nor all their functionalities. However, it should give you a good overview of what you can do with BioServices (both from the user and developer point of views). Before starting, let us remind what are Web Services. There provide an access to databases or applications via a web interface based on the SOAP/WSDL or the REST technologies. These technologies allow a programmatic access, which we take advantage in BioServices. The REST technology uses URLs so there is no external dependency. You simply need to build a well-formatted URL and you will retrieve an XML document that you can consume with your preferred technology platform. 5 BioServices, Release 1.7.12 The SOAP/WSDL technology combines SOAP (Simple Object Access Protocol), which is a messaging protocol for transporting information and the WSDL (Web Services Description Language), which is a method for describing Web Services and their capabilities. What methods are available for a given service Usually most of the service functionalities have been wrapped and we try to keep the names as close as possible to the API. On top of the service methods, each class inherits from the BioService class (REST or WSDL). For instance REST service have the useful request method. Another nice function is the onWeb. See also: REST, WSDLService What about the output ? Outputs depend on the service and functionalities of the service. It can be heteregeneous. However, output are mostly XML formatted or in tabulated separated column format (TSV). When XML is returned, it is usually parsed via the BeautilSoup package (for instance you can get all children using getchildren() function). Sometimes, we also convert output into dictionaries. So, it really depends on the service/functionality you are using. Let us look at some of the Web Services wrapped in BioServices. UniProt service Let us start with the UniProt class. With this class, you can access to uniprot services. In particular, you can map an ID from a database to another one. For instance to convert the UniProtKB ID into KEGG ID, use: >>> from bioservices.uniprot import UniProt >>> u= UniProt(verbose= False) >>> u.mapping(fr="ACC+ID", to="KEGG_ID", query='P43403') {'P43403': ['hsa:7535']} Note that the returned response from uniprot web service is converted into a list. The first two elements are the databases used for the mapping. Then, alternance of the queried element and the answer populates the list. You can also search for a specific UniProtKB ID to get exhaustive information: >>> print(u.search("P43403", frmt="txt")) ID ZAP70_HUMAN Reviewed; 619 AA. AC P43403; A6NFP4; Q6PIA4; Q8IXD6; Q9UBS6; DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot. DT 01-NOV-1995, sequence version 1. ... To obtain the FASTA sequence, you can use searchUniProtId(): >>> res=u.searchUniProtId("P09958", frmt="xml") >>> print(u.searchUniProtId("P09958", frmt="fasta")) sp|P09958|FURIN_HUMAN Furin OS=Homo sapiens GN=FURIN PE=1 SV=2 MELRPWLLWVVAATGTLVLLAADAQGQKVFTNTWAVRIPGGPAVANSVARKHGFLNLGQI FGDYYHFWHRGVTKRSLSPHRPRHSRLQREPQVQWLEQQVAKRRTKRDVYQEPTDPKFPQ QWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDP DPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSL (continues on next page) 6 Chapter 1. Installation BioServices, Release 1.7.12 (continued from previous page) GLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREH DSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKC TESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKV SHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNH ITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWD EDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTAPEGLPVPPESSGCKTLTSSQACVVCE EGFSLHQKSCVQHCPPGFAPQVLDTHYSTENDVETIRASVCAPCHASCATCQGPALTDCL SCPSHASLDPVEQTCSRQSQSSRESPPQQQPPRLPPEVEAGQRLRAGLLPSHLPEVVAGL SCAFIVLVFVTVFLVLQLRSGFSFRGVKVYTMDRGLISYKGLPPEAWQEECPSDSEEDEG RGERTAFIKDQSAL See also: Reference guide of bioservices.uniprot.UniProt for more details KEGG service The KEGG interface is similar but contains more methods. The tutorial presents the KEGG itnerface in details, but let us have a quick overview. First, let us start a KEGG instance: from bioservices import KEGG k= KEGG(verbose= False) KEGG contains biological data for many organisms. By default, no organism is set, which can be checked in the following attribute k.organism We can set it to human using KEGG terminology for homo sapiens: k.organis='hsa' You can use the dbinfo() to obtain statistics on the pathway database: >>> print(k.info("pathway")) pathway KEGG Pathway Database path Release 65.0+/01-15, Jan 13 Kanehisa Laboratories 218,277 entries You can see the list of valid databases using the databases attribute. Each of the database entry can also be listed using the list() method. For instance, the organisms can be retrieved with: k.list("organism") However, to extract the Ids extra processing is required. So, we provide aliases to retrieve the organism Ids easily: k.organismIds The human organism is coded as “hsa”. You can also get its T number instead: >>> k.code2Tnumber("hsa") 'T01001' Every elements is referred to with a KEGG ID, which may be difficult to handle at first. There are methods to retrieve the IDs though. For instance, get
Load more

Recommended publications
  • Lineage-Specific Evolution of the Vertebrate Otopetrin Gene Family Revealed by Comparative Genomic Analyses
    Hurle et al. BMC Evolutionary Biology 2011, 11:23 http://www.biomedcentral.com/1471-2148/11/23 RESEARCHARTICLE Open Access Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses Belen Hurle1, Tomas Marques-Bonet2,3, Francesca Antonacci3, Inna Hughes4, Joseph F Ryan1, NISC Comparative Sequencing Program1,5, Evan E Eichler3, David M Ornitz6, Eric D Green1,5* Abstract Background: Mutations in the Otopetrin 1 gene (Otop1) in mice and fish produce an unusual bilateral vestibular pathology that involves the absence of otoconia without hearing impairment. The encoded protein, Otop1, is the only functionally characterized member of the Otopetrin Domain Protein (ODP) family; the extended sequence and structural preservation of ODP proteins in metazoans suggest a conserved functional role. Here, we use the tools of sequence- and cytogenetic-based comparative genomics to study the Otop1 and the Otop2-Otop3 genes and to establish their genomic context in 25 vertebrates. We extend our evolutionary study to include the gene mutated in Usher syndrome (USH) subtype 1G (Ush1g), both because of the head-to-tail clustering of Ush1g with Otop2 and because Otop1 and Ush1g mutations result in inner ear phenotypes. Results: We established that OTOP1 is the boundary gene of an inversion polymorphism on human chromosome 4p16 that originated in the common human-chimpanzee lineage more than 6 million years ago. Other lineage- specific evolutionary events included a three-fold expansion of the Otop genes in Xenopus tropicalis and of Ush1g in teleostei fish. The tight physical linkage between Otop2 and Ush1g is conserved in all vertebrates.
    [Show full text]
  • Geomicrobiological Processes in Extreme Environments: a Review
    202 Articles by Hailiang Dong1, 2 and Bingsong Yu1,3 Geomicrobiological processes in extreme environments: A review 1 Geomicrobiology Laboratory, China University of Geosciences, Beijing, 100083, China. 2 Department of Geology, Miami University, Oxford, OH, 45056, USA. Email: [email protected] 3 School of Earth Sciences, China University of Geosciences, Beijing, 100083, China. The last decade has seen an extraordinary growth of and Mancinelli, 2001). These unique conditions have selected Geomicrobiology. Microorganisms have been studied in unique microorganisms and novel metabolic functions. Readers are directed to recent review papers (Kieft and Phelps, 1997; Pedersen, numerous extreme environments on Earth, ranging from 1997; Krumholz, 2000; Pedersen, 2000; Rothschild and crystalline rocks from the deep subsurface, ancient Mancinelli, 2001; Amend and Teske, 2005; Fredrickson and Balk- sedimentary rocks and hypersaline lakes, to dry deserts will, 2006). A recent study suggests the importance of pressure in the origination of life and biomolecules (Sharma et al., 2002). In and deep-ocean hydrothermal vent systems. In light of this short review and in light of some most recent developments, this recent progress, we review several currently active we focus on two specific aspects: novel metabolic functions and research frontiers: deep continental subsurface micro- energy sources. biology, microbial ecology in saline lakes, microbial Some metabolic functions of continental subsurface formation of dolomite, geomicrobiology in dry deserts, microorganisms fossil DNA and its use in recovery of paleoenviron- Because of the unique geochemical, hydrological, and geological mental conditions, and geomicrobiology of oceans. conditions of the deep subsurface, microorganisms from these envi- Throughout this article we emphasize geomicrobiological ronments are different from surface organisms in their metabolic processes in these extreme environments.
    [Show full text]
  • Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.
    [Show full text]
  • Brian W. Waters
    INVESTIGATION OF 2-OXOACID OXIDOREDUCTASES IN METHANOCOCCUS MARIPALUDIS AND LARGE-SCALE GROWTH OF M. MARIPALUDIS by BRIAN W. WATERS (Under the direction of Dr. William B. Whitman) ABSTRACT With the emergence of Methanococcus maripaludis as a genetic model for methanogens, it becomes imperative to devise inexpensive yet effective ways to grow large numbers of cells for protein studies. Chapter 2 details methods that were used to cut costs of growing M. maripaludis in large scale. Also, large scale growth under different conditions was explored in order to find the conditions that yield the most cells. Chapter 3 details the phylogenetic analysis of 2-oxoacid oxidoreductase (OR) homologs from M. maripaludis. ORs are enzymes that catalyze the oxidative decarboxylation of 2-oxoacids to their acyl-CoA derivatives in many prokaryotes. Also in chapter 3, a specific OR homolog in M. maripaludis, an indolepyruvate oxidoreductase (IOR), was mutagenized, and the mutant was characterized. PCR and Southern hybridization analysis showed gene replacement. A no-growth phenotype on media containing aromatic amino acid derivatives was found. INDEX WORDS: Methanococcus maripaludis, fermentor, 2-oxoacid oxidoreductase, indolepyruvate oxidoreductase INVESTIGATION OF 2-OXOACID OXIDOREDUCTASES IN METHANOCOCCUS MARIPALUDIS AND LARGE-SCALE GROWTH OF M. MARIPALUDIS by BRIAN W. WATERS B.S., The University of Georgia,1999 A Thesis Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE ATHENS, GEORGIA 2002 © 2002 Brian W. Waters All Rights Reserved INVESTIGATION OF 2-OXOACID OXIDOREDUCTASES IN METHANOCOCCUS MARIPALUDIS AND LARGE-SCALE GROWTH OF M. MARIPALUDIS by BRIAN W.
    [Show full text]
  • MUTED Antibody - C-Terminal Region (ARP63301 P050) Data Sheet
    MUTED antibody - C-terminal region (ARP63301_P050) Data Sheet Product Number ARP63301_P050 Product Name MUTED antibody - C-terminal region (ARP63301_P050) Size 50ug Gene Symbol BLOC1S5 Alias Symbols DKFZp686E2287; MU; MUTED Nucleotide Accession# NM_201280 Protein Size (# AA) 187 amino acids Molecular Weight 21kDa Product Format Lyophilized powder NCBI Gene Id 63915 Host Rabbit Clonality Polyclonal Official Gene Full Name Muted homolog (mouse) Gene Family BLOC1S This is a rabbit polyclonal antibody against MUTED. It was validated on Western Blot by Aviva Systems Biology. At Aviva Systems Biology we manufacture rabbit polyclonal antibodies on a large scale (200-1000 Description products/month) of high throughput manner. Our antibodies are peptide based and protein family oriented. We usually provide antibodies covering each member of a whole protein family of your interest. We also use our best efforts to provide you antibodies recognize various epitopes of a target protein. For availability of antibody needed for your experiment, please inquire (). Partner Proteins BLOC1S2,DTNBP1,BLOC1S1,BLOC1S2,CNO,DTNBP1,SNAPIN,BLOC1S2,BLOC1S3,DTNBP1,PLDN,SQS TM1,YOD1 This gene encodes a component of BLOC-1 (biogenesis of lysosome-related organelles complex 1). Components of this complex are involved in the biogenesis of organelles such as melanosomes and platelet- Description of Target dense granules. A mouse model for Hermansky-Pudlak Syndrome is mutated in the murine version of this gene. Alternative splicing results in multiple transcript variants. Read-through transcription exists between this gene and the upstream EEF1E1 (eukaryotic translation elongation factor 1 epsilon 1) gene, as well as with the downstream TXNDC5 (thioredoxin domain containing 5) gene.
    [Show full text]
  • University of California, San Diego
    UC San Diego UC San Diego Electronic Theses and Dissertations Title The post-terminal differentiation fate of RNAs revealed by next-generation sequencing Permalink https://escholarship.org/uc/item/7324r1rj Author Lefkowitz, Gloria Kuo Publication Date 2012 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO The post-terminal differentiation fate of RNAs revealed by next-generation sequencing A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Gloria Kuo Lefkowitz Committee in Charge: Professor Benjamin D. Yu, Chair Professor Richard Gallo Professor Bruce A. Hamilton Professor Miles F. Wilkinson Professor Eugene Yeo 2012 Copyright Gloria Kuo Lefkowitz, 2012 All rights reserved. The Dissertation of Gloria Kuo Lefkowitz is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2012 iii DEDICATION Ma and Ba, for your early indulgence and support. Matt and James, for choosing more practical callings. Roy, my love, for patiently sharing the ups and downs
    [Show full text]
  • Fmicb-08-02642
    Edinburgh Research Explorer Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using DiverseBreeds and Basal Diets Citation for published version: Auffret, MD, Stewart, R, Dewhurst, R, Duthie, C-A, Rooke, JA, Wallace, R, Freeman, T, Snelling, TJ, Watson, M & Roehe, R 2018, 'Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using DiverseBreeds and Basal Diets', Frontiers in Microbiology, vol. 8, 2642. https://doi.org/10.3389/fmicb.2017.02642, https://doi.org/10.3389/fmicb.2017.02642 Digital Object Identifier (DOI): 10.3389/fmicb.2017.02642 10.3389/fmicb.2017.02642 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Frontiers in Microbiology Publisher Rights Statement: This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation.
    [Show full text]
  • The NIH Catalyst from the Deputy Director for Intramural Research
    — Fostering Communication and Collaboration The nihCatalyst A Publication for NIH Intramural Scientists National Institutes of Health Office of the Director Volume 15 Issue 6 November-Dece.mber i , 2007 Research Festival Research Festival of Age: Getting to the Bottom Coming Tissue Engineering and Regenerative Medicine Of the Beta Cell by Fran Pollner by Julie Wallace or some, the quest is to increase the progenitor pool of pancre- anel chair Rocky F atic beta cells, to derive stem Tuan noted that cells that can be controlled in cul- P this was the NIH ture and serve as replacements for Research Festival’s damaged or lost beta cells; for oth- first dedicated sympo- ers, the quest is for new treatments. sium on tissue engi- neering and regenera- Stem Cell Studies tive medicine, a re- Typically, cul- flection that the field tured human beta is steadily approach- cells do not prolif- ing the threshold of erate well or retain clinical application. the mature pheno- Indeed, applying type, noted Marvin biological and engi- neering principles to Gershengorn, chief Fran Pollner The Re-Generation: (left to right): Pamela Robey, N1DCR; of the Clinical En- Marvin repairing and replac- Cynthia Dunbar, NHLB1; Catherine Kuo, NIAMS; and panel docrinology Branch Gershengorn ing damaged and de- chair Rocky Tuan, NIAMS and scientific director, NIDDK, who stroyed tissues has at- has been exploring the optimization tracted researchers across NIH; scientists adipocytes, and chondrocytes derived of hIPCs (human islet cell-derived from three institutes described their on- from MSCs could indeed be made to precursor cells) for about five years.
    [Show full text]
  • Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
    GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs.
    [Show full text]
  • Human BLOC1S2 / BLOS2 Protein (GST Tag)
    Human BLOC1S2 / BLOS2 Protein (GST Tag) Catalog Number: 13916-H09E General Information SDS-PAGE: Gene Name Synonym: BLOS2; CEAP; CEAP11 Protein Construction: A DNA sequence encoding the human BLOC1S2 (Q6QNY1-2) (Met1- Arg99) was fused with the GST tag at the N-terminus. Source: Human Expression Host: E. coli QC Testing Purity: > 74 % as determined by SDS-PAGE Endotoxin: Protein Description Please contact us for more information. BLOC1S2, also known as BLOS2, belongs to the BLOC1S2 family. It is a Stability: component of BLOC-1 complex. The BLOC-1 complex is composed of BLOC1S1, BLOC1S2, BLOC1S3, DTNBP1, MUTED, PLDN, Samples are stable for up to twelve months from date of receipt at -70 ℃ CNO/cappuccino and SNAPIN. The BLOC-1 complex is required for normal biogenesis of lysosome-related organelles, such as platelet dense Predicted N terminal: Met granules and melanosomes. BLOC1S2 interacts directly with BLOC1S1, Molecular Mass: BLOC1S3, MUTED, CNO/cappuccino and SNAPIN. It may play a role in cell proliferation. It also plays a role in intracellular vesicle trafficking. The recombinant human BLOC1S2 /GST chimera consists of 333 amino Functionally, BLOC1S2 gene has been proposed to participate in acids and has a predicted molecular mass of 38.7 kDa. It migrates as an processes (melanosome organization, microtubule nucleation, platelet approximately 39 KDa band in SDS-PAGE under reducing conditions. dense granule organization, positive regulation of cell proliferation, positive regulation of transcription, regulation of apoptosis, positive regulation of Formulation: transcription from RNA polymerase II promoter). Lyophilized from sterile PBS, pH 7.4 References Normally 5 % - 8 % trehalose, mannitol and 0.01% Tween80 are added as 1.Sowa ME, et al.
    [Show full text]
  • A BLOC-1 Mutation Screen Reveals That PLDN Is Mutated in Hermansky-Pudlak Syndrome Type 9
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector ARTICLE A BLOC-1 Mutation Screen Reveals that PLDN Is Mutated in Hermansky-Pudlak Syndrome Type 9 Andrew R. Cullinane,1,* James A. Curry,1 Carmelo Carmona-Rivera,1 C. Gail Summers,2 Carla Ciccone,1 Nicholas D. Cardillo,1 Heidi Dorward,1 Richard A. Hess,1 James G. White,3 David Adams,1,4 Marjan Huizing,1 and William A. Gahl1,4 Hermansky-Pudlak Syndrome (HPS) is an autosomal-recessive condition characterized by oculocutaneous albinism and a bleeding diath- esis due to absent platelet delta granules. HPS is a genetically heterogeneous disorder of intracellular vesicle biogenesis. We first screened all our patients with HPS-like symptoms for mutations in the genes responsible for HPS-1 through HPS-6 and found no functional muta- tions in 38 individuals. We then examined all eight genes encoding the biogenesis of lysosome-related organelles complex-1, or BLOC-1, proteins in these individuals. This identified a homozygous nonsense mutation in PLDN in a boy with characteristic features of HPS. PLDN is mutated in the HPS mouse model pallid and encodes the protein pallidin, which interacts with the early endosomal t-SNARE syntaxin-13. We could not detect any full-length pallidin in our patient’s cells despite normal mRNA expression of the mutant transcript. We could detect an alternative transcript that would skip the exon that harbored the mutation, but we demonstrate that if this transcript is translated into protein, although it correctly localizes to early endosomes, it does not interact with syntaxin-13.
    [Show full text]
  • Adaptations of Methanococcus Maripaludis to Its Unique Lifestyle
    ADAPTATIONS OF METHANOCOCCUS MARIPALUDIS TO ITS UNIQUE LIFESTYLE by YUCHEN LIU (Under the Direction of William B. Whitman) ABSTRACT Methanococcus maripaludis is an obligate anaerobic, methane-producing archaeon. In addition to the unique methanogenesis pathway, unconventional biochemistry is present in this organism in adaptation to its unique lifestyle. The Sac10b homolog in M. maripaludis, Mma10b, is not abundant and constitutes only ~ 0.01% of the total cellular protein. It binds to DNA with sequence-specificity. Disruption of mma10b resulted in poor growth of the mutant in minimal medium. These results suggested that the physiological role of Mma10b in the mesophilic methanococci is greatly diverged from the homologs in thermophiles, which are highly abundant and associate with DNA without sequence-specificity. M. maripaludis synthesizes lysine through the DapL pathway, which uses diaminopimelate aminotransferase (DapL) to catalyze the direct transfer of an amino group from L-glutamate to L-tetrahydrodipicolinate (THDPA), forming LL-diaminopimelate (LL-DAP). This is different from the conventional acylation pathway in many bacteria that convert THDPA to LL-DAP in three steps: succinylation or acetylation, transamination, and desuccinylation or deacetylation. The DapL pathway eliminates the expense of using succinyl-CoA or acetyl-CoA and may represent a thriftier mode for lysine biosynthesis. Methanogens synthesize cysteine primarily on tRNACys via the two-step SepRS/SepCysS pathway. In the first step, tRNACys is aminoacylated with O-phosphoserine (Sep) by O- phosphoseryl-tRNA synthetase (SepRS). In the second step, the Sep moiety on Sep-tRNACys is converted to cysteine with a sulfur source to form Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS).
    [Show full text]