CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources.

Abstract:

BACKGROUND:The functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes) but the experimental determination of the sub-cellular localization of proteomes is laborious and expensive. A fast and low-cost alternative approach is in silico prediction, based on features of the protein primary sequences. However, biologists are confronted with a very large number of computational tools that use different methods that address various localization features with diverse specificities and sensitivities. As a result, exploiting these computer resources to predict protein localization accurately involves querying all tools and comparing every prediction output; this is a painstaking task. Therefore, we developed a comprehensive database, called CoBaltDB, that gathers all prediction outputs concerning complete prokaryotic proteomes. DESCRIPTION:The current version of CoBaltDB integrates the results of 43 localization predictors for 784 complete bacterial and archaeal proteomes (2.548.292 proteins in total). CoBaltDB supplies a simple user-friendly interface for retrieving and exploring relevant information about predicted features (such as signal peptide cleavage sites and transmembrane segments). Data are organized into three work-sets ("specialized tools", "meta-tools" and "additional tools"). The database can be queried using the organism name, a locus tag or a list of locus tags and may be browsed using numerous graphical and text displays. CONCLUSIONS:With its new functionalities, CoBaltDB is a novel powerful platform that provides easy access to the results of multiple localization tools and support for predicting prokaryotic protein localizations with higher confidence than previously possible. CoBaltDB is available at http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten.

journal_name

BMC Microbiol

journal_title

BMC microbiology

authors

Goudenège D,Avner S,Lucchetti-Miganeh C,Barloy-Hubler F

doi

10.1186/1471-2180-10-88

subject

Has Abstract

pub_date

2010-03-23 00:00:00

pages

88

issn

1471-2180

pii

1471-2180-10-88

journal_volume

10

pub_type

杂志文章
  • First isolation and whole-genome sequencing of a Shewanella algae strain from a swine farm in Brazil.

    abstract:BACKGROUND:Infections caused by Shewanella spp. have been increasingly reported worldwide. The advances in genomic sciences have enabled better understanding about the taxonomy and epidemiology of this agent. However, the scarcity of DNA sequencing data is still an obstacle for understanding the genus and its associati...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-020-02040-x

    authors: Alves VBA,Carvalho E,Madureira PA,Marino ED,Vaz ACN,Vidal AMC,Ruiz VLA

    更新日期:2020-11-24 00:00:00

  • Sequence diversity in the A domain of Staphylococcus aureus fibronectin-binding protein A.

    abstract:BACKGROUND:Fibronectin-binding protein A (FnBPA) mediates adhesion of Staphylococcus aureus to fibronectin, fibrinogen and elastin. We previously reported that S. aureus strain P1 encodes an FnBPA protein where the fibrinogen/elastin-binding domain (A domain) is substantially divergent in amino acid sequence from the a...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-8-74

    authors: Loughman A,Sweeney T,Keane FM,Pietrocola G,Speziale P,Foster TJ

    更新日期:2008-05-08 00:00:00

  • Special issue on enhancing vector refractoriness to trypanosome infection-foreword.

    abstract:: ...

    journal_title:BMC microbiology

    pub_type:

    doi:10.1186/s12866-018-1279-4

    authors: Abd-Alla AMM,Tsiamis G,Boucias DG

    更新日期:2018-11-23 00:00:00

  • Biphasic toxicodynamic features of some antimicrobial agents on microbial growth: a dynamic mathematical model and its implications on hormesis.

    abstract:BACKGROUND:In the present work, we describe a group of anomalous dose-response (DR) profiles and develop a dynamic model that is able to explain them. Responses were obtained from conventional assays of three antimicrobial agents (nisin, pediocin and phenol) against two microorganisms (Carnobacterium piscicola and Leuc...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-10-220

    authors: Murado MA,Vázquez JA

    更新日期:2010-08-19 00:00:00

  • Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress.

    abstract:BACKGROUND:Lactic acid bacteria (LAB) has been considered a beneficial bacterial group, found as part of the microbiota of diverse hosts, including humans and various animals. However, the mechanisms of how hosts and LAB interact are still poorly understood. Previous work demonstrates that 13 species of Lactobacillus a...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-13-235

    authors: Butler È,Alsterfjord M,Olofsson TC,Karlsson C,Malmström J,Vásquez A

    更新日期:2013-10-22 00:00:00

  • Bacterial diversity analysis of larvae and adult midgut microflora using culture-dependent and culture-independent methods in lab-reared and field-collected Anopheles stephensi-an Asian malarial vector.

    abstract:BACKGROUND:Mosquitoes are intermediate hosts for numerous disease causing organisms. Vector control is one of the most investigated strategy for the suppression of mosquito-borne diseases. Anopheles stephensi is one of the vectors of malaria parasite Plasmodium vivax. The parasite undergoes major developmental and matu...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-9-96

    authors: Rani A,Sharma A,Rajagopal R,Adak T,Bhatnagar RK

    更新日期:2009-05-19 00:00:00

  • Chemical modulators of the innate immune response alter gypsy moth larval susceptibility to Bacillus thuringiensis.

    abstract:BACKGROUND:The gut comprises an essential barrier that protects both invertebrate and vertebrate animals from invasion by microorganisms. Disruption of the balanced relationship between indigenous gut microbiota and their host can result in gut bacteria eliciting host responses similar to those caused by invasive patho...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-10-129

    authors: Broderick NA,Raffa KF,Handelsman J

    更新日期:2010-04-27 00:00:00

  • Study on the community structure and function of symbiotic bacteria from different growth and developmental stages of Hypsizygus marmoreus.

    abstract:BACKGROUND:The symbiotic bacteria associated with edible fungi are valuable microbial resources worthy of in-depth exploration. It is important to analyze the community structure and succession of symbiotic bacteria in mushrooms. This can assist in the isolation of growth-promoting strains that have an essential relati...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-020-01998-y

    authors: Sun S,Li F,Xu X,Liu Y,Kong X,Chen J,Liu T,Chen L

    更新日期:2020-10-14 00:00:00

  • Low phosphatase activity of LiaS and strong LiaR-DNA affinity explain the unusual LiaS to LiaR in vivo stoichiometry.

    abstract:BACKGROUND:LiaRS mediates Bacillus subtilis response to cell envelope perturbations. A third protein, LiaF, has an inhibitory role over LiaRS in the absence of stimulus. Together, LiaF and LiaRS form a three-component system characterized by an unusual stoichiometry, a 4:1 ratio between LiaS and LiaR, the significance ...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-020-01796-6

    authors: Jani S,Sterzenbach K,Adatrao V,Tajbakhsh G,Mascher T,Golemi-Kotra D

    更新日期:2020-04-29 00:00:00

  • Annexin A2 (ANXA2) interacts with nonstructural protein 1 and promotes the replication of highly pathogenic H5N1 avian influenza virus.

    abstract:BACKGROUND:Non-structural protein 1 (NS1) is a multifunctional protein and a crucial regulatory factor in the replication and pathogenesis of avian influenza virus (AIV). Studies have shown that NS1 can interact with a variety of host proteins to modulate the viral life cycle. We previously generated a monoclonal antib...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-017-1097-0

    authors: Ma Y,Sun J,Gu L,Bao H,Zhao Y,Shi L,Yao W,Tian G,Wang X,Chen H

    更新日期:2017-09-11 00:00:00

  • Comparison between Gram stain and culture for the characterization of vaginal microflora: definition of a distinct grade that resembles grade I microflora and revised categorization of grade I microflora.

    abstract:BACKGROUND:The microbiological diagnosis of bacterial vaginosis is usually made using Nugent's criteria, a useful but rather laborious scoring system based on counting bacterial cell types on Gram stained slides of vaginal smears. Ison and Hay have simplified the score system to three categories and added a fourth cate...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-5-61

    authors: Verhelst R,Verstraelen H,Claeys G,Verschraegen G,Van Simaey L,De Ganck C,De Backer E,Temmerman M,Vaneechoutte M

    更新日期:2005-10-14 00:00:00

  • The role of interactions between bacterial chaperone, aspartate aminotransferase, and viral protein during virus infection in high temperature environment: the interactions between bacterium and virus proteins.

    abstract:BACKGROUND:The life cycle of a bacteriophage has tightly programmed steps to help virus infect its host through the interactions between the bacteriophage and its host proteins. However, bacteriophage-host protein interactions in high temperature environment remain poorly understood. To address this issue, the protein ...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-13-48

    authors: Chen Y,Wei D,Wang Y,Zhang X

    更新日期:2013-02-26 00:00:00

  • Influence of internalin A murinisation on host resistance to orally acquired listeriosis in mice.

    abstract:BACKGROUND:The bacterial surface protein internalin (InlA) is a major virulence factor of the food-born pathogen Listeria monocytogenes. It plays a critical role in the bacteria crossing the host intestinal barrier by a species-specific interaction with the cell adhesion molecule E-cadherin. In mice, the interaction of...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-13-90

    authors: Bergmann S,Beard PM,Pasche B,Lienenklaus S,Weiss S,Gahan CG,Schughart K,Lengeling A

    更新日期:2013-04-23 00:00:00

  • Identification and characterization of intervening sequences within 23S rRNA genes from more than 200 Campylobacter isolates from seven species including atypical campylobacters.

    abstract:BACKGROUND:Identification and characterization of intervening sequences (IVSs) within 23S rRNA genes from Campylobacter organisms including atypical campylobacters were carried out using two PCR primer pairs, designed to generate helix 25 and 45 regions. RESULTS:Only C. sputorum biovar sputorum LMG7975 and fecalis LMG...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-9-256

    authors: Tazumi A,Kakinuma Y,Misawa N,Moore JE,Millar BC,Matsuda M

    更新日期:2009-12-11 00:00:00

  • Proteome profiling of Pseudomonas aeruginosa PAO1 identifies novel responders to copper stress.

    abstract:BACKGROUND:The opportunistic pathogen, Pseudomonas aeruginosa is well known for its environmental and metabolic versatility, yet many of the functions of its gene-products remain to be fully elucidated. This study's objective was to illuminate the potential functions of under-described gene-products during the medicall...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-019-1441-7

    authors: Wright BW,Kamath KS,Krisp C,Molloy MP

    更新日期:2019-04-01 00:00:00

  • Characterization of Mycobacterium tuberculosis Beijing isolates from the Mediterranean area.

    abstract:BACKGROUND:The Beijing lineage of Mycobacterium tuberculosis is causing concern due to its global distribution and its involvement in severe outbreaks. Studies focused on this lineage are mainly restricted to geographical settings where its prevalence is high, whereas those in other areas are scarce. In this study, we ...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-10-151

    authors: Alonso M,Alonso Rodriguez N,Garzelli C,Martínez Lirola M,Herranz M,Samper S,Ruiz Serrano MJ,Bouza E,García de Viedma D

    更新日期:2010-05-25 00:00:00

  • Bactericidal activity of M protein conserved region antibodies against group A streptococcal isolates from the Northern Thai population.

    abstract:BACKGROUND:Most group A streptococcal (GAS) vaccine strategies have focused on the surface M protein, a major virulence factor of GAS. The amino-terminus of the M protein elicits antibodies, that are both opsonic and protective, but which are type specific. J14, a chimeric peptide that contains 14 amino acids from the ...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-6-71

    authors: Yoonim N,Olive C,Pruksachatkunakorn C,Pruksakorn S

    更新日期:2006-08-09 00:00:00

  • Global regulation of gene expression in response to cysteine availability in Clostridium perfringens.

    abstract:BACKGROUND:Cysteine has a crucial role in cellular physiology and its synthesis is tightly controlled due to its reactivity. However, little is known about the sulfur metabolism and its regulation in clostridia compared with other firmicutes. In Clostridium perfringens, the two-component system, VirR/VirS, controls the...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-10-234

    authors: André G,Haudecoeur E,Monot M,Ohtani K,Shimizu T,Dupuy B,Martin-Verstraete I

    更新日期:2010-09-07 00:00:00

  • The canine oral microbiome: variation in bacterial populations across different niches.

    abstract:BACKGROUND:Microbiota from different niches within the canine oral cavity were profiled and compared. Supragingival plaque and stimulated saliva, were collected alongside samples from the buccal and tongue dorsum mucosa, from 14 Labrador retrievers at three timepoints within a 1 month timeframe. The V3-V4 region of the...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-020-1704-3

    authors: Ruparell A,Inui T,Staunton R,Wallis C,Deusch O,Holcombe LJ

    更新日期:2020-02-28 00:00:00

  • Synergism and the mechanism of action of the combination of α-mangostin isolated from Garcinia mangostana L. and oxacillin against an oxacillin-resistant Staphylococcus saprophyticus.

    abstract:BACKGROUND:Globally, staphylococci have developed resistance to many antibiotics. New approaches to chemotherapy are needed and one such approach could be to use plant derived actives with conventional antibiotics in a synergestic way. The purpose of this study was to isolate α-mangostin from the mangosteen (Garcinia m...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-016-0814-4

    authors: Phitaktim S,Chomnawang M,Sirichaiwetchakoon K,Dunkhunthod B,Hobbs G,Eumkeb G

    更新日期:2016-08-26 00:00:00

  • Whole genome analysis of hypervirulent Klebsiella pneumoniae isolates from community and hospital acquired bloodstream infection.

    abstract:BACKGROUND:Hypervirulent K. pneumoniae (hvKp) causes severe community acquired infections, predominantly in Asia. Though initially isolated from liver abscesses, they are now prevalent among invasive infections such as bacteraemia. There have been no studies reported till date on the prevalence and characterisation of ...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-017-1148-6

    authors: Shankar C,Veeraraghavan B,Nabarro LEB,Ravi R,Ragupathi NKD,Rupali P

    更新日期:2018-01-08 00:00:00

  • Analysis of stress- and host cell-induced expression of the Mycobacterium tuberculosis inorganic pyrophosphatase.

    abstract:BACKGROUND:The gene encoding the inorganic pyrophosphatase (PPase) of the intracellular pathogen Legionella pneumophila is induced during intracellular infection, but is constitutively expressed in Escherichia coli. The causative agent of tuberculosis, Mycobacterium tuberculosis, contains a well conserved copy of PPase...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-1-3

    authors: Triccas JA,Gicquel B

    更新日期:2001-01-01 00:00:00

  • Roles of iron acquisition systems in virulence of extraintestinal pathogenic Escherichia coli: salmochelin and aerobactin contribute more to virulence than heme in a chicken infection model.

    abstract:BACKGROUND:Avian pathogenic Escherichia coli (APEC) and uropathogenic E. coli (UPEC) are the two main subsets of extraintestinal pathogenic E. coli (ExPEC). Both types have multiple iron acquisition systems, including heme and siderophores. Although iron transport systems involved in the pathogenesis of APEC or UPEC ha...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-12-143

    authors: Gao Q,Wang X,Xu H,Xu Y,Ling J,Zhang D,Gao S,Liu X

    更新日期:2012-07-20 00:00:00

  • Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing.

    abstract:BACKGROUND:Several plant-pathogenic bacteria are transmitted by insect vector species that often also act as hosts. In this interface, these bacteria encounter plant endophytic, insect endosymbiotic and other microbes. Here, we used high throughput sequencing to examine the bacterial communities of five different psyll...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-020-01895-4

    authors: Morrow JL,Om N,Beattie GAC,Chambers GA,Donovan NJ,Liefting LW,Riegler M,Holford P

    更新日期:2020-07-20 00:00:00

  • Brucella melitensis VjbR and C12-HSL regulons: contributions of the N-dodecanoyl homoserine lactone signaling molecule and LuxR homologue VjbR to gene expression.

    abstract:BACKGROUND:Quorum sensing is a communication system that regulates gene expression in response to population density and often regulates virulence determinants. Deletion of the luxR homologue vjbR highly attenuates intracellular survival of Brucella melitensis and has been interpreted to be an indication of a role for ...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-10-167

    authors: Weeks JN,Galindo CL,Drake KL,Adams GL,Garner HR,Ficht TA

    更新日期:2010-06-08 00:00:00

  • Statistical characterization of the GxxxG glycine repeats in the flagellar biosynthesis protein FliH and its Type III secretion homologue YscL.

    abstract:BACKGROUND:FliH is a protein involved in the export of components of the bacterial flagellum and we herein describe the presence of glycine-rich repeats in FliH of the form AxxxG(xxxG)mxxxA, where the value of m varies considerably in FliH proteins from different bacteria. While GxxxG and AxxxA patterns have previously...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-9-72

    authors: Trost B,Moore SA

    更新日期:2009-04-16 00:00:00

  • Nuclear and Wolbachia-based multimarker approach for the rapid and accurate identification of tsetse species.

    abstract:BACKGROUND:Tsetse flies (Diptera: Glossinidae) are solely responsible for the transmission of African trypanosomes, causative agents of sleeping sickness in humans and nagana in livestock. Due to the lack of efficient vaccines and the emergence of drug resistance, vector control approaches such as the sterile insect te...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/s12866-018-1295-4

    authors: Augustinos AA,Meki IK,Demirbas-Uzel G,Ouédraogo GMS,Saridaki A,Tsiamis G,Parker AG,Abd-Alla AMM,Bourtzis K

    更新日期:2018-11-23 00:00:00

  • Persistent, triple-virus co-infections in mosquito cells.

    abstract:BACKGROUND:It is known that insects and crustaceans can carry simultaneous, active infections of two or more viruses without showing signs of disease, but it was not clear whether co-infecting viruses occupied the same cells or different cells in common target tissues. Our previous work showed that successive challenge...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-10-14

    authors: Kanthong N,Khemnu N,Pattanakitsakul SN,Malasit P,Flegel TW

    更新日期:2010-01-20 00:00:00

  • Characterization of the Bat proteins in the oxidative stress response of Leptospira biflexa.

    abstract:BACKGROUND:Leptospires lack many of the homologs for oxidative defense present in other bacteria, but do encode homologs of the Bacteriodes aerotolerance (Bat) proteins, which have been proposed to fulfill this function. Bat homologs have been identified in all families of the phylum Spirochaetes, yet a specific functi...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-12-290

    authors: Stewart PE,Carroll JA,Dorward DW,Stone HH,Sarkar A,Picardeau M,Rosa PA

    更新日期:2012-12-13 00:00:00

  • Doxycycline-regulated gene expression in the opportunistic fungal pathogen Aspergillus fumigatus.

    abstract:BACKGROUND:Although Aspergillus fumigatus is an important human fungal pathogen there are few expression systems available to study the contribution of specific genes to the growth and virulence of this opportunistic mould. Regulatable promoter systems based upon prokaryotic regulatory elements in the E. coli tetracycl...

    journal_title:BMC microbiology

    pub_type: 杂志文章

    doi:10.1186/1471-2180-5-1

    authors: Vogt K,Bhabhra R,Rhodes JC,Askew DS

    更新日期:2005-01-13 00:00:00