Phaeodactylum tricornutum CCAP 1055/1 chromosome 10, 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 CM000613.\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##
One of six nitrate transporters in the Pt genome. The expression level for this transporter is quite low according to the EST data. Phylogenetically, this transporter is in a Pheaodactylum specific clade that also includes the nitrate transporter on scaffold 22.
Putative glutathione peroxidase; involved in response to oxidative stress; catalyses the reduction of hydroxyperoxides using glutathione: 2 Glutathione + H 2 O(2) = oxidised Glutathione + 2H 2 O
Membrane targeted protein that facilitates the active transport of ammonium into the cell. Highly expressed across many EST libraries and second most highly expressed gene in N limited EST library. One of 8 ammonium transporters in Pt and is most similar to Phatr1/scaffold_4:716626-718010
sevenths step in the heme synthesis; enzyme is of cyanobacterial origin, extension at the N terminus (27 aa) contains ER signal peptide (SignalP score = 0.998); putatively chloroplast targeted
Similar to drosophila ash2 protein involved in transcriptional activation maintenance in association with the H3K4 histone-methyltransferase trithorax protein
One of four component proteins of the enzyme glycine decarboxylase. Together with serine hydroxymethyltransferase this complex catalyzes the formation of one serine from two glycine. This reaction is part of the photorespiratory pathway (glycolate metabolism).; glycine cleavage system T-protein, glycine dehydrogenase T-protein, GCST, GCVT
This family of sequences is a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine sulfhydrylase (OAH, ) and O-acetylserine sulfhydrylase (OAS, ). An alternate name for OAH sulfhydrylase is homocysteine synth; Thiol)-lyase (O-acetylhomoserine sulfhydrylase)(OAH sulfhydrylase; Homocysteine synthase
Has EST support. present: 1 || present: 1
Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea, which are member of the MipB/TalC subfamily of class I aldolases, plastidic
60 kDa plastid protein, involved in protein translocation, possesses plastid targeting sequence
unknown function; contains tetratricopeptide-like helical domain; weak similarity to bacterial putative phosphatase; unknownn protein
ATP-dependent helicase. Highly closed to the Thalassiosira protein thaps1 162922.
second step in the shikimate pathway; contains ER signal peptide at the N terminus (SignalP score = 0.995); putatively chloroplast targeted
unknown function; partial similarity to Ferredoxin
This dehydrogenase is close to D-lactate dehydrogenase || Most probably a 2-hydroxyacid dehyrdogenase, similar to D-lactate dehydrogenase, with NAD+ or NADP+ as acceptor. The model encodes for an N-terminal transcription factor domain of the CAP family, presumably activated by binding of an effector molecule.; 2-hydroxyacid dehydrogenase
Possibly contains domains similar to disease resistance proteins and apoptpsis/cell death proteins - but this model needs some serious work. Probably more than one gene product represented by this model. Seems to have arginine and serine rich domains but this might be non-coding. All the ests are closer to the 3' end.
translation initiation factor eif-2bgamma
Potentially a component of translation initiation factor eIF-2B, a complex of five subunits that promotes the exchange of eIF2-bound GDP for GTP.
putative glycosylphosphatidylinostol (GPI)- anchored protein transfer 1 ortholog
putative Tic22 protein; N terminus contains putative ER signal peptide (SignalP predisction score = 0.999); putatively chloroplast targeted; involved in transport of nuclear encoded proteins into the primary chloroplast
Sec7 domain-containing expressed protein of unknown function, distantly similar to plant and animal GDP/GTP exchange factors
phosphoenolpyruvate carboxylase with a mitochondrial precursor sequence.
Kinesin-related motor protein, involved in microtubule-based motility
Possibly an L-ascorbate peroxidase, catalyzing the reaction ascorbate + H2O2 -> dehydroascorbate + 2H2O, using heme as co-factor
phenylalanyl-trna synthetase class IIc family protein
catalizes the coupling of phenylalanine to phenylalanyl-tRNA, contains a Ferredoxin-fold anticodon binding domain
EDS5 has an essential function in the SA-dependent pathway of plant defense against pathogens response and induced by UV-C. It is homologous with members of the MATE (multidrug and toxin extrusion) transporter family. As in plants, the protein is predicated to have 9 transmembrane domains with additional signal peptide (0.96). Good EST coverage.
Spo11/Topoisomerase VIA proteins initiate double strand break formation in meiotic recombination and are related to type II topoisomerase VI subunit A of archaea. Both the Phaeodactylum tricornutum and Thalassiosira pseudonana genomes contain two spo11 homologs. This homolog is most similar to Tps_101261 and may represent the meiotically regulated spo11 homolog.; SPO11) homolog 1
contains Tetratricopeptide TPR_1; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; unknownn protein
contains Tetratricopeptide repeat domain involved in protein-protein interaction
Involved in iron transport. Contains transmembrane domains.
Component of fatty acid synthase. Reduces 3-ketoacyl-[acyl carrier protein] intermediates to 3R-hydroxyacyl-[acyl carrier protein] during saturated fatty acid biosynthesis. Probably plastid targeted, but targetP only detects secretory half of putative bipartite signal.
Putative clathrin light chain, clathrin vesicle coat component
Has EST support. 5'-end and intron only, EST incomplete at 3'-end
unknown function; similarity to Galactose-3-O-sulfotransferase; secretory pathway; unknownn protein
Expressed protein containing ERCC4 domain and with similarity to the XPF/MUS81 nuclease family
3-isopropylmalate dehydrogenase Amino acids metabolism