Phaeodactylum tricornutum CCAP 1055/1 chromosome 9, 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 CM000612.\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##
Similar to histone H2A core component of nucleosomes, containing two molecules each of H2A, H2B, H3 and H4
beta prime (beta', beta2) coatomer, subunit of the Coat Protein complex COP I
involved in actin nucleation, contains a Formin homology 2 domain
beta coatomer, subunit of the Coat Protein complex COP I
Membrane targted urea transporter. Phylogenetically, this is a plant-like urea transporter. This urea transporter is the second most highly expressed gene in the nitrate starved EST library.; DUR3
chitin binding gene with signal peptide, two chitin binding domains, and a plant lectin/antimicrobial domain
regulatory proteasome non-atpase subunit 12
26S proteasome regulatory non ATPase subunit, homolog to plant RPN12a subunit
CDC20 co-activator of the anaphase-promoting complex (APC).
tocopherol O-methyltransferase, converts gamma-tocopherol to alpha-tocopherol; tocopherol is used to scanvenge reactive oxygen species
Calcium dependent protein kinase of the CaMK subfamily, containing a Ser/Thr Protein Kinase domain and 2 EF Hand Domains
actin binding protein involved in actin nucleation
enzyme involved in N-glycan biosynthesis; 1,3
hypothetical protein similar to gi|35213617 glr3047 [Gloeobacter violaceus PCC 7421
bifunctional trehalose-6-phosphate synthase
Dual function enzyme which catalyzes the synthesis of trehalose. The two reactions catalyzed: (1) UDP-glucose + D-glucose 6-phosphate = UDP + trehalose 6-phosphate; and (2) trehalose 6-phosphate + H2O = trehalose + phosphate.; glycosyl transferase family 20
unknown function; weak similarity to fission yeast PWWP domain protein, but without PWWP motif; unknownn protein
enzyme invovled in N-glycan biosynthesis
delta 6 elongase, microsomal precursor. Involved in the biosynthesis of polyunsaturated fatty acids. 7 predicted transmembrane domains. Catalyzes conversion of acyl -CoAs such as alpha-linoleoyl-CoA or stearidonyl-CoA to eicosatrienoyl-CoA or eicosatetraenoyl-CoA via the addition of two carbons from malonyl CoA.
Probable enoyl-CoA hydratase catalyses (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H2O Also found in fatty acid elongation in mitochondria, fatty acid metabolism Valine, leucine and isoleucine degradation, Lysine degradation, Tryptophan metabolism, beta-Alanine metabolism, Benzoate degradation via CoA ligation, Propanoate metabolism, Butanoate metabolism, Limonene and pinene degradation, Caprolactam degradation
precursor of protein violaxanthin deepoxidase-like protein
Violaxanthin de-epoxidase-like 1; expressed gene with violaxanthin deepoxidase domain (IPR010788), but low homology with known violaxanthin deepoxidases, possibly involved in xanthophyll cycling
rab-type small GTPase, ortholog of T. pseudonana TPS_105101
Similar to homeobox containing transcription factors
Rad51 is the eukaryotic homolog of RecA and is involved in homology searching and strand exchange in homologous recombination during DNA repair and meiosis. Phatr2_54533 is closest to the Thalassiosira pseudonana protein Thaps3_ 255596 and both have very high homology to Rad51 and DMC1 (meiotic-specific Rad51 homologs) in animals, plants, and yeasts. This gene is expected to be expressed constitutively (and there is some EST support under standard, 'silica minus' and 'Fe minus' conditions) but it might be expected to be up-regulated during meiosis.
Alpha tubulin is a major constituent of microtubules. This particular alpha tubulin gene is highly expressed; particularly under conditions of nitrate depletion.
thioredoxin h, probably cytosolic, 5 bp micro-exon 'G-TGT-G' encodes first cysteine of 'WCGPC' thioredoxin motif
methylmalonate semialdhyde dehydrogenase
aldehyde dehydrogenase probable MMSDH : inositol & propanoate metabolism, amino acids degradation.
unknown function; weak similarity to yeast peptidyl-prolyl cis-trans isomerase; secretory pathway; unknownn protein
Chromokinesin family member are involved in spindle formation and the movements of chromosomes during mitosis. Binds to microtubules and to DNA.; chromokinesin
TCA cycle & reductive carboxylate cycle. catalyze reaction between malate & fumarate
small (sigma) subunit of the AP1 vesicle coat complex, ortholog of T. pseudonana TPS_104515
GrpE protein, HSP90 cofactor, chloroplast targeted
GrpE protein, N terminus contains putative ER signal peptide; putatively chloroplast targeted
Prohibitin-like Protein, used in cell defense
Rb-related protein. Involved in control of G1-S transition during the cell cycle
EC 6.2.1.4: Succinyl CoA ligase alpha chain
precursor of mutase superoxide dismutase [Fe/Mn]
Superoxide dismutase [Fe/Mn], likely a mitochondrial precursor; catalyses the conversion of superoxide radicals to molecular oxygen
precursor of ATPase ATPase gamma subunit
Has EST support. present: 1 || present: 1
ATPase gamma subunit, GenBank Accession AAA73506, contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
probable zinc containing alcohol dehydrogenase : aldehyde & ketone synthesis
putative ATPase activity; contains tetratricopeptide repeat (TPR) domain
thioredoxin f, contains bipartite plastid targeting presequence, signal- and transit-peptides predicted at N-terminus with phenylalanine at signal peptide cleavage site
Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins, homolog to fungal Smt3p
CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism].
Probable aldehyde lyase catalyses D-Ribulose 5-phosphate+Formaldehyde <=> D-arabino-6-Hexulose 3-phosphate