Abstract：
:As the protein databases continue to expand at an exponential rate, fed by daily uploads from multiple large scale genomic and metagenomic projects, the problem of assigning a function to each new protein has become the focus of significant research interest in recent times. Herein, we review the most recent advances in the field of automated function prediction (AFP). We begin by defining what is meant by biological "function" and the means of describing such functions using standardised machine readable ontologies. We then focus on the various function-prediction programs available, both sequence and structure based, and outline their associated strengths and weaknesses. Finally, we conclude with a brief overview of the future challenges and outstanding questions in the field, which still remain unanswered.
journal_name
Arch Microbioljournal_title
Archives of microbiologyauthors
Sleator RD,Walsh Pdoi
10.1007/s00203-010-0549-9subject
Has Abstractpub_date
2010-03-01 00:00:00pages
151-5issue
3eissn
0302-8933issn
1432-072Xjournal_volume
192pub_type
杂志文章,评审abstract：:In this study, on evaluating the physiological function and mechanism of putrescine, we found that putrescine supplementation (1 mM) increases transcription of the putrescine aminotransferase gene, ygjG. Putrescine-dependent expression was confirmed by measuring β-galactosidase activity and with reverse transcription-...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-014-0991-1
更新日期：2014-09-01 00:00:00
abstract：:Studies are presented of the biliproteins of Anabaena sp. This filamentous cyanobacterium contains three major biliproteins. Whereas two of these, C-phycocyanin and allophycocyanin, are common to all cyanobacteria, the third, phycoerythrocyanin (gammamax approximately 568 nm) has hitherto not been described and its di...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/BF00416970
更新日期：1976-10-11 00:00:00
abstract：:The ability of soil microorganisms to solubilize phosphate is an important trait of plant growth-promoting bacteria leading to increased yields and smaller use of fertilizers. This study presents the isolation and characterization of phosphobacteria from Puna, northwestern Argentina and the ability to produce phosphat...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-011-0692-y
更新日期：2011-07-01 00:00:00
abstract：:Acinetobacter calcoaceticus LMD 79.41 produced significant amounts of pyrrolo-quinoline quinone (PQQ) in its culture medium when grown on quinic acid or shikimic acid. Studies with LMD 79.41 and PQQ- -mutants of this strain demonstrated that this organism contains an NAD(P)-independent quinate dehydrogenase (QDH) (EC ...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/BF00409714
更新日期：1988-05-01 00:00:00
abstract：:The role of the genomic bipyrimidine nucleotide frequency in pyrimidine dimer formation caused by germicidal UV radiation was studied in three microbial reference organisms (Escherichia coli K12, Deinococcus radiodurans R1, spores and cells of Bacillus subtilis 168). The sensitive HPLC tandem mass spectrometry assay w...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-010-0579-3
更新日期：2010-07-01 00:00:00
abstract：:The site of integration of phage M mu d (Ap lac) in mutant M9s which leads to deficiency of formic dehydrogenase (benzylviologen-linked) activity was determined. It was shown that the phage had inserted into the gene for the seleno-polypeptide of the enzyme (80 kd) leading to the formation of a truncated peptide (60 k...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/BF00428850
更新日期：1985-05-01 00:00:00
abstract：:The ontogeny of the myxomycete Physarum globuliferum was observed on corn meal agar and hanging drop cultures without adding sterile oat flakes, bacteria or other microorganisms. Its complete life cycle including spore germination, myxamoebae, swarm cells, plasmodial development, and maturity of fructifications was de...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-009-0533-4
更新日期：2010-02-01 00:00:00
abstract：:Synthetic biology, the design and synthesis of synthetic biological systems from DNA to whole cells, has provided us with the ultimate tools for space exploration and colonisation. Herein, we explore some of the most significant advances and future prospects in the field of synthetic biology, in the context of astrobi...
journal_title：Archives of microbiology
pub_type： 信件
doi：10.1007/s00203-019-01651-x
更新日期：2019-08-01 00:00:00
abstract：:We report on the genome-wide response, based on DNA microarrays, of the cyanobacterium Synechocystis sp. PCC 6803 wild type and DeltasigB to a 15 min heat shock. Approximately 9% of the genes in wild type and DeltasigB were significantly regulated (P < 0.001) following this treatment, with chaperones induced the most....
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-006-0138-0
更新日期：2006-10-01 00:00:00
abstract：:Maize is highly responsive to the application of nitrogen to achieve high productivity. Inoculation with diazotrophic bacteria can improve plant growth with low N fertilization. The objective was to evaluate the inoculation of two species of diazotrophs on N metabolism in maize plants, in the presence of two concentra...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-018-1594-z
更新日期：2019-05-01 00:00:00
abstract：:The mechanism of the massive extracellular production of citric and isocitric acids by Saccharomycopsis lipolytica grown on n-paraffins has been studied. When growth stops, because of nitrogen limitation, the intracellular concentration of ATP sharply rises whereas that of AMP and ADP decreases to a low level. At the ...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/BF00428588
更新日期：1977-05-13 00:00:00
abstract：:The hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough consists of six genes (hmcA to hmcF) that encode structural components of the high-molecular-mass cytochrome redox protein complex (the Hmc complex). Two genes (rrf1 and rrf2) encoding regulatory proteins are present downstream of hmcF. Expression ...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s002030050458
更新日期：1997-06-01 00:00:00
abstract：:Edwardsiella tarda (E. tarda) is distributed widely in a variety of hosts including humans, other mammals and fish, and it is worthwhile to notice that E. tarda -caused fish infections lead to the most important bacterial disease in fish. Considering Eha acting as a transcriptional regulator in E. tarda strain ET13 ha...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-019-01794-x
更新日期：2020-05-01 00:00:00
abstract：:Polyaromatic hydrocarbons (PAHs) are considered as hazardous organic priority pollutants. PAHs have immense public concern and critical environmental challenge around the globe due to their toxic, carcinogenic, and mutagenic properties, and their ubiquitous distribution, recalcitrance as well as persistence in environ...
journal_title：Archives of microbiology
pub_type： 杂志文章,评审
doi：10.1007/s00203-020-01929-5
更新日期：2020-10-01 00:00:00
abstract：:Beta-Lactamase (penicillinase) activity was found in a number of strains of blue-green algea. In some cases, this enzyme permitted algae to overcome the inhibitory effects of penicillin. Production and localization of beta-lactamase were studied in a unicellular species, Coccochloris elabens (strain 7003), and in a fi...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/BF00429338
更新日期：1977-03-01 00:00:00
abstract：:BvgAS is a two-component system of Bordetella pertussis involved in the reciprocal regulation of the virulence genes and the flagellar biosynthesis. In this study, we found that expression of bvgAS in Escherichia coli also results in reduced motility. The repression was relieved by the addition of known chemical modul...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s002030050688
更新日期：1999-01-01 00:00:00
abstract：:Peptidoglycan of Corynebacterium species Co 112 (DSM 20606) exhibits an unknown amino acid. The amino acid was isolated from cell wall hydrolysates and identified as threo-beta-hydroxyornithine. This amino acid is found in the interpeptide bridge of the peptidoglycan of Corynebacterium sp. Co 112. The primary structur...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/BF00407766
更新日期：1983-06-01 00:00:00
abstract：:Serine (Ser)/threonine (Thr) or tyrosine (Tyr) protein kinases in eukaryotes contain RDxKxxN or RDx(A/R)A(A/R)N sequences, respectively, in the catalytic loop. Myxococcus xanthus DspB is a dual-specificity kinase that contains an atypical sequence, RDVAQKN, in the catalytic loop. The DspB mutant (A165K), which contain...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-015-1181-5
更新日期：2016-04-01 00:00:00
abstract：:Mycothiol (MSH) plays important roles in maintaining cytosolic redox homeostasis and in adapting to reactive oxygen species in the high-(G + C)-content Gram-positive Actinobacteria. However, its physiological roles are ill defined compared to glutathione, the functional analog of MSH in Gram-negative bacteria and most...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-013-0889-3
更新日期：2013-06-01 00:00:00
abstract：:The isolated cell wall of Streptomyces griseus 52-1 strain labelled with fluorescein isothiocyanate (FITC) and containing wall-bound autolytic enzyme was lysed as a function of different cations. The autolysis was accelerated by aminoglycoside antibiotics (streptomycin and the structurally closely related neomycin) wh...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/BF00291282
更新日期：1990-01-01 00:00:00
abstract：:Grasses of the Urochloa genus have been widely used in crop-livestock integration systems or as cover crops in no-till systems such as in rotation with maize. Some species of Urochloa have mechanisms to reduce nitrification. However, the responses of microbial functions in crop-rotation systems with grasses and its co...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-020-01910-2
更新日期：2020-09-01 00:00:00
abstract：:An isoeugenol-degrading enzyme was purified to homogeneity from Pseudomonas putida IE27, an isoeugenol-assimilating bacterium. The purified enzyme was a 55 kDa monomer and catalyzed the initial step of isoeugenol degradation, the oxidative cleavage of the side chain double-bond of isoeugenol, to form vanillin. Another...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-007-0218-9
更新日期：2007-06-01 00:00:00
abstract：:The mechanism of lysis of Eubacterium alactolyticum cell walls by Streptomyces albus G enzyme was studied. The analysis of the peptide terminal groups and peptide subunits isolated from the cell wall digest, released during solubilization of the cell walls, revealed that lytic action of S. albus G enzyme was mainly du...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/BF00406563
更新日期：1989-01-01 00:00:00
abstract：:The histidine protein kinase SppK is a peptide pheromone-activated kinase that regulates the production of the bacteriocin sakacin P in Lactobacillus sakei. SppK belongs to subfamily 10 of histidine protein kinases (HPKs), which regulate important processes in Gram-positive bacteria, including virulence, competence an...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-005-0049-5
更新日期：2006-01-01 00:00:00
abstract：:Lipase is an important commercial enzyme with unique and versatile biotechnological applications. This study was conducted to biosynthesize and characterizes alkaliphilic lipase by Exiguobacterium sp. strain AMBL-20T isolated from the glacial water samples of the northeastern (Gilgit-Baltistan) region of Pakistan. The...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-020-02133-1
更新日期：2020-12-15 00:00:00
abstract：:The methanotrophic bacterium Methylomicrobium album BG8 uses methane as a sole source of carbon and energy. This bacterium forms an extensive intracytoplasmic membrane. The first enzymes of the methane oxidation pathway are the membrane-bound particulate methane monooxygenase and the periplasmic methanol dehydrogenase...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-002-0426-2
更新日期：2002-07-01 00:00:00
abstract：:The L-alanine mediated germination of food isolated Bacillus cereus DSA 1 spores, which lacked an intact exosporium, increased in the presence of D-cycloserine (DCS), which is an alanine racemase (Alr) inhibitor, reflecting the activity of the Alr enzyme, capable of converting L-alanine to the germination inhibitor D-...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-013-0946-y
更新日期：2014-02-01 00:00:00
abstract：:Pseudomonas putida CSV86 utilizes benzyl alcohol via catechol and methylnaphthalenes through detoxification pathway via hydroxymethylnaphthalenes and naphthaldehydes. Based on metabolic studies, benzyl alcohol dehydrogenase (BADH) and benzaldehyde dehydrogenase (BZDH) were hypothesized to be involved in the detoxifica...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-011-0697-6
更新日期：2011-08-01 00:00:00
abstract：:The study was conducted to evaluate the microbiological and chemical profiles of elephant grass inoculated with and without different wild strains of lactic acid bacteria. Silage was prepared of four treatments and one control with three replicates as control (EKC, adding 2 ml/kg sterilizing water), Lactobacillus plan...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/s00203-017-1447-1
更新日期：2018-03-01 00:00:00
abstract：:Photosynthesis was measured by the 14C method on natural as well as low light adapted populations of Chloroflexus (a photosynthetic bacterium) and Synechococcus (a blue-green alga) from hot springs in Yellowstone National Park (Wyoming U.S.A.), to test the ability of these phototrophs to photosynthesize at a variety o...
journal_title：Archives of microbiology
pub_type： 杂志文章
doi：10.1007/BF00428590
更新日期：1977-05-13 00:00:00
