Phaeodactylum tricornutum CCAP 1055/1 chromosome 21, whole genome shotgun sequence.
Eukaryota; Stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Naviculales; Phaeodactylaceae; Phaeodactylum.
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
Submitted (15-JUN-2017) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
Submitted (12-AUG-2008) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
PROVISIONAL REFSEQ: This record has not yet been subject to final\nNCBI review. The reference sequence is identical to CM000623.\nURL -- http://www.jgi.doe.gov/phaeodactylum\nJGI Project ID: 3634397\nContacts: Chris Bowler (cbowler@biologie.ens.fr)\n Igor Grigoriev (ivgrigoriev@lbl.gov)\nThe clone of P. tricornutum that was sequenced is CCAP1055/1 and is\navailable from the Culture collection of Algae and Protozoa\n(http://www.ccap.ac.uk). This clone represents a monoclonal culture\nderived from a fusiform cell in May 2003 from strain CCCP632, which\nwas originally isolated in 1956 off Blackpool (U.K.). It has been\nmaintained in culture continuously in F/2 medium.\nAnnotation was done by the JGI Annotation team and the Diatom\nConsortium.\nChromosomes 3 and 11 are complete and present in GenBank records\nCP001142 and CP001141, respectively.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376)\nAnnotated scaffolds were added in December 2008.\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: INSDC submitter\nAnnotation Status :: Full annotation\nAnnotation Pipeline :: Eukaryotic Annotation Propagation Pipeline\n##Genome-Annotation-Data-END##
Possible glucoamylase precursor. Glucoamylase breaks 1,4-glycosidic bonds. No interpro domains detected.
Rab-type small GTPase, ortholog of T. pseudonana TPS_98341
Citrate synthase, Citrate + CoA = acetyl-CoA + H(2)O + oxaloacetate. The gene model contains a mitochondrial trageting sequence predicted by signalP. Appears to be upregulation under N limitation with NH4 as the sole N source.
Protein involved in determining life span
involved in aminoacid metabolism, no targeting sequences found, enzyme is probably cytosolic
Highly expressed gene of unknown function. Contains a pyridoxal-dependent decarboxylase interpro domain. Many ESTs under nitrate deplete conditions.; Pt_50312 Highly expressed gene of unknownn function
putative N methyl transferase; N terminus contains putative ER signal peptide (SignalP prediction score = 0.990), putatively chloroplast targeted
formate-tertahydrofolate ligase Enzyme involved in folic acid biosynthesis
Aspartate amino transferase Catalyzes reversible reaction glutamate+oxaloacetate-aspartate+2oxoglutatrate. Enzyme involved in amino acids metabolism
Kinesin-related motor protein, involved in microtubule-based motility
Catalyzes the reaction: oxaloacetate + ATP = phosphoenolpyruvate + ADP + CO2. Requires divalent cations. Has a potential role in C4 photosynthetic metabolism.; ATP), mitochondrial precursor
Homologous to tufA in the chloroplast genome of C. reinhardtii
SOD's are catalyzing the dismutation of superoxide into molecular oxygen and hydrogen peroxide using Cu/Zn as a metal cofactor. Partial EST support only from low dose of decadienal library.
translation start unclear, compare to Protein ID 56587
contains conserved domain UPF0047; unknownn protein
pds-like3, phytoene desaturase-like protein
Phytoene desaturase-like3, expressed gene with similarities to cyanobacterial phytoene desaturases/dehydrogenases, possibly involved in carotenoid biosynthesis
2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor
succinate dehydrogenase iron sulfur protein
A component of a mitochondrial enzyme complex that interconverts succinate and fumarate in the citric acid cycle. Reaction catalyzed: succinate + ubiquinone = fumarate + ubiquinol. This subunit uses an iron-sulfur cluster as co-factor.
Mer3 is a DNA helicase involved in class I (interference-sensitive) cross-overs. In Arabidopsis it is expressed specifically in buds. Curiously, there is EST support for this gene under several conditions, but the ESTs are directed in the opposite direction to the predicted gene. Closest to Thaps3_ 11979.
This gene is involved in carbon utilization. Signal peptide is encoded at the 5'end of this gene. No evidence for cTP (no ChloroP prediction, no cTP motif). Protein is possibly secreted.
putative role in formation of polyphenolic compounds; Tyrosinase is a copper monooxygenases that catalyzes the hydroxylation of monophenols and the oxidation of o-diphenols to o-quinols; similarity to Elicitin-like protein from Phytophthora
unknown protein with similarity to iron regulated protein from Dunaliella salina; similarity to Quinonprotein alcohol dehydrogenase-like protein with 8-bladed beta-propeller motif; highly expressed under iron starvation; secretory pathway
precursor of carboxylase pyruvate carboxylase
Replenishes the supply of oxaloacetate for the tricarboxylic acid cycle by catalyzing the reaction: pyruvate + ATP + HCO3- = oxaloacetate + ADP + Pi.
Rab-type small GTPase, ortholog of T. pseudonana TPS_110754
precursor of dehydrogenase pyruvate dehydrogenase E1 component alpha subunit
Probably catalyzes the reaction: pyruvate + lipoamide = S-acetyldihydrolipoamide + CO2.