Phaeodactylum tricornutum CCAP 1055/1 chromosome 4, 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 CM000607.\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##
Participates in the synthesis of GDP-mannose by catalyzing the interconversion of D-fructose 6-phosphate and D-mannose 6-phosphate. Uses zinc as a co-factor.
similarity to 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, that forms part of an alternative nonmevalonate pathway for terpenoid biosynthesis; unknownn protein
probable dihydrolipoamide acetyl transferase Pyruvate metabolism & Glycolysis
Expressed protein similar to histone linker (H1) N-terminal
This family contains the bacterial Ornithine cyclodeaminase enzyme, which catalyses the deamination of ornithine to proline
magnesium-protoporphyrin IX methyltransferase
converts magnesium-protoporphyrin IX to magnesium-protoporphyrin IX metylester
Spc98 are core-protein of the microtubule organizing center (MTOC)
ubiquitin-activating enzyme E1, protein 3
Nedd8 activating enzyme putative, homolog to fungal UbaC
putative Golgi SNARE protein, v-SNARE domain protein with similarity to AtGOS
actin binding protein involved in actin nucleation
Membrane associated nitrate transporter responsible for the active transport of nitrate into the cell. This model has a high level of EST support under conditions of nitrate depletion. The pt genome contains six nitrate transporters. This model is phylogenetically most similar to a nitrtae transporter on scaffold 6 and is also related closely to nitrate transporters from C.fusiformis and Tp model 211471 and 4911.
Aspartate--ammonia ligase (asparagine synthetase) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. This family represents one of two non-homologous forms of aspartate--ammonia ligase found in Escherichia col; Asparagine synthetase A
Gene of unknown function that is upregulated under conditions of nitrate depletion.; Pt_47396, Gene of unknownn function
3-oxoacyl-[acyl-carrier-protein] synthase
Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. May prefer short-chain fatty acid substrates. May use a bipartite plastid targeting signal as predicted by targetP.; Beta-ketoacyl-ACP synthase II; KAS II
Possible oxidoreductase . Acts on the aldehyde or oxo group of donors with NAD or NADP as acceptor.
copper-transporting ATPase, heavy metal transporting ATPase
Kinesin-related motor protein, involved in microtubule-based motility
SET have been shown to contribute to epigenetic mechanisms of gene regulation by methylation of lysine residues in histones and other proteins
enzyme involved in N-glycan biosynthesis; Transfers an alpha-D-mannosyl residue from dolichyl-phosphate D-mannose into membrane lipid-linked oligosaccharide
expressed protein putatively targeted to plastid, biosynthesis of carotenoids
High light induced protein 1b, contains bipartite plastid targeting presequence, signal- and transit-peptides predicted at N-terminus with conserved motif at signal peptide cleavage site
Ca binding and protein chaperoning properties
Gene is involved in carbon utilization. (EST support) There is a signal peptide encoded at the 5'end of the gene. Predicted cleavage site: TTA-QT. However, there are no indications of a cTP. This CA could therefore be secreted.
Involved in carbon utilization. EST support. Signal peptide sequence encoded at 5'end of gene. Predicted cleavage site: ADA-QE. No indications of a cTP (neg. ChloroP prediction, no cTP motif).
C-type cyclin dependent kinase 1, probably involved in transcriptional control
Probable malonyl-CoA decarboxylase catalyses malonyl-CoA = acetyl-CoA + CO2. Involved in beta-Alanine metabolism and Propanoate metabolism
Putative Glycolate- FMN-dependent dehydrogenase. Close to glycolate oxidase & L-lactate dehydrogenase Enzyme involved in glycolate metabolism
putative role in G-protein mediated signal transduction with nucleotidyltransferase activity; contains N-terminal SPX domain assumed to bind G-proteins and C-terminal Cytidylyltransferase domain; unknownn protein
actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments
Ubiquitin-protein ligase, member of cullin family, homolog to mammalian Cul4
epsilon coatomer, subunit of the Coat Protein complex COP I
hydroxymethylbutenyl diphosphate reductase
also called isopentyl-diphosphate:dimethylallyl-diphosphate synthase (IDS) or LytB/IspH: MEP pathway for isoprenoid biosynthesis
Proteasome beta subunit (20s). The proteasome is a 26S (200 kD proteinase complexes; contains a 2OS (673 kD) complex composed of 28 subunits: 14 alpha-subunits and 14-beta-subunits; 20s)(swissprot: locus PSB6_ARATH, accession Q8LD27
homology to RAD21/SCC1/MCD1 family of mitotic cohesin (closer homolog : Double-strand-break repair protein RAD21, by Psi blast iteration 2)
calcium/calmodulin-dependent protein kinase
calcium/calmodulin-dependent protein kinase, with 1 Ser/Thr Kinase domain
protein fucoxanthin chlorophyll a/c protein
adenylosuccinate synthetase Adenylosuccinate synthetase plays an important role in purine biosynthesis, by catalyzing the GTP-dependent conversion of IMP and aspartic acid to AMP. Adenylosuccinate synthetase has been characterized from various sources ranging from Escherichia coli (gene purA) to vertebrate tissues. In vertebrates, two isozymes are present - one involved in purine biosynthesis and the other in the purine nucleotide cycle.
chk2-loki isoform A repair of damaged DNA before its replication in S phase homolog of the yeast Mek1p,Cds1 proteins as well as the human Chk2
sixth step in heme synthesis, putative signal peptide detected by SignalP, putatively chloroplast targeted
unknown function; similarity to protein from Agrobacterium; unknownn protein
[FUNCTION] Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). [CATALYTIC ACTIVITY] Acetyl-CoA + 3-methyl-2-oxobutanoate + H(2)O = (2S)-2-isopropylmalate + CoA. [PATHWAY] Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 1. [SUBUNIT] Homotetramer (By similarity). [SIMILARITY] Belongs to the alpha-IPM synthetase/homocitrate synthase family. LeuA type 1 subfamily.
4-diphosphocytidyl-2c-methyl-d-erythritol kinase
4-diphosphocytidyl-2C-methyl-D-erythritol kinase (also called IspE): MEP pathway for isoprenoid biosynthesis; chloroplast precursor
expressed gene with similarity to violaxanthin deepoxidase, involved in xanthophyll cycling; chloroplast precursor
expressed gene with similarity to zeaxanthin epoxidase, putatively involved in xanthophyll cycling; chloroplast precursor
Has EST support. present: 1 || present: 1
contains bipartite plastid targeting presequence with 'A-W' at signal peptide cleavage site
A flavoprotein (FAD). Acts on primary amines, and usually also on some secondary and tertiary amines.
precursor of desulfurase cysteine desulfurase IscS
involved in FeS clusters assembly; extension at the N terminus contains putative mitochondrial transit peptide (TargetP score= 0.936); putatively targeted to mitochondrion
seventh step in the heme synthesis; enzyme is of cyanobacterial origin, extension at the N terminus (77 aa) contains ER signal peptide (SignalP score = 0.996); putatively chloroplast targeted
Probably an oxidoreductase (acting on CH-OH donors with NAD+ or NADP+ as acceptor); possibly catalyzes stereospecific reduction of 2,5-diketo-D-gluconate (2,5-DKG) to 2-keto-L-gulonate as a precursor to L-ascorbate (vitamin C) synthesis.
Chromokinesin family member are involved in spindle formation and the movements of chromosomes during mitosis. Binds to microtubules and to DNA.; chromokinesin
putative metalloprotease; secretory pathway
phosphoserine phosphatase Enzyme involved in L-serine biosynthesis