Phaeodactylum tricornutum CCAP 1055/1 chromosome 8, 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 CM000611.\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##
cell wall assoiciated protein, contains a signal peptide
phytoene desaturase 1; expressed gene with similarities to higher plant and green algae phytoene desaturases, possibly involved in carotenoid biosynthesis, chloroplast localised
precursor of dehydrogenase pyruvate dehydrogenase E1 component beta subunit
Probably catalyzes the reaction: pyruvate + lipoamide = S-acetyldihydrolipoamide + CO2.
probable D-lactate dehydrogenase (cytochrome) pyruvate metabolism
Catalyzes the liberation of acetyl-CoA from 3-oxoacyl-CoA. Acyl-CoA + CoA = Acetyl-CoA + Acyl-CoA (2 fewer carbons).; 3-oxoacyl-CoA thiolase, putative peroxisomal precursor
Has EST support; Alternative splicing variant 1
Polybiquitin (5 repeats), homolog to mammalian UBC protein; Alternative splicing variant 2
one PAS domain; no evidence to be phototropin
Hypothetical protein. Appears to be a member of the Multi Antimicrobial Extrusion (MATE) family which functions as drug/sodium antiporters. These proteins mediate resistance to a wide range of cationic dyes, fluroquinolones, aminoglycosides and other structurally diverse antibodies and drugs. MATE proteins are found in bacteria, archaea and eukaryotes. These proteins are predicted to have 12 alpha-helical transmembrane regions.; with some similarity to the multi antimicrobial extrusion family
Gene of unknown function. Contain 1 transmembrane domain and a mitochindrial targeting sequence predicted by targetP. There is EST data for this gene under nitrate starvation.; EST support.; Pt_37385, Gene of unknownn function with
regulatory proteasome non-atpase subunit 11
26S proteasome regulatory non ATPase subunit, homolog to animal 14 subunit
Putative formamidase also found in Trytophan and Nitrogen metabolism probably catalzes formamide+H2O =formate+NH3
probable ATP-citrate synthase subunit 1. Involved in TCA cycle
Probably a NAD- or NADP-dependent short-chain dehydrogenase/reductase, possibly a mitochondrial 3-hydroxybutyrate dehydrogenase involved in butanoate metabolism catalyzing the reaction: (R)-3-hydroxybutanoate + NAD+ = acetoacetate + NADH + H+.
Has EST support; Alternative splicing variant 2
intron uncertain, compare to Protein ID 56610; Alternative splicing variant 2
intron uncertain, compare to Protein ID 56611; Alternative splicing variant 1
zeaxanthin epoxidase 1; expressed gene with similarity to zeaxanthin epoxidase, involved in xanthophyll cycling; chloroplast precursor
precursor of protein violaxanthin deepoxidase-like protein
Violaxanthin de-epoxidase-like 2; expressed gene with violaxanthin deepoxidase domain (IPR010788), but low homology with known violaxanthin deepoxidases, possibly involved in xanthophyll cycling
silent information regulator protein Sir2
NAD-dependant histone deacetylase. Yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA
Hydrolyzes terminal, non-reducing beta-D-xylose residues.; glycosyl hydrolase family 3
reduction of ferric iron; contains N-terminal Ferric reductase-like transmembrane component and NADPH oxidase domain; secretory pathway
A-type CDK containing a classical PSTAIRE cyclin-binding motif
Expressed protein with similarity to Xeroderma pigmentosum group A (XPA) protein, probably involved in damage recognition step of Nucleotide Excision Repair (NER) in association with Replication Protein A (RPA)
Deoxyribodipyrimidine photolyase (DNA photolyase) is a DNA repair enzyme. It binds to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), breaks the cyclobutane ring joining the two pyrimidines of the dimer. DNA photolyase is an enzyme that requires two choromophore-cofactors for its activity: a reduced FADH2 and either 5,10-methenyltetrahydrofolate (5,10-MTFH) or an oxidized 8-hydroxy-5- deazaflavin (8-HDF) derivative (F420). The folate or deazaflavin chromophore appears to function as an antenna, while the FADH2 chromophore is thought to be responsible for electron transfer. On the basis of sequence similarities DNA photolyases can be grouped into two classes.
Caspase-like protease. Conserved catalytic Cys-His diad is identified.
In nucleotide-sugar metabolism, catalyzes the reaction: UTP + N-acetyl-alpha-D-glucosamine 1-phosphate = UDP-N-acetyl-D-glucosamine + PPi
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
Oxygen-evolving enhancer protein 3, chloroplast precursor (OEE3,located in the thylakoid lumen, possesses plastid targeting signal
oxygen-evolving enhancer protein 1 precursor
oxygen-evolving enhancer protein 1 precursor (PsbO) gene, GenBank Accession AY191862, contains bipartite plastid targeting presequence, signal- and transit-peptides predicted at N-terminus with conserved motif at signal peptide cleavage site, additional thylakoidal signal peptide present
Glutamate synthase, NADH/NADPH, small subunit
glutathione reductase, N terminus contains putative ER signal peptide (SignalP 0.857); putatively targeted to chloroplast
This gene is involved in malate metabolism. Neuronal networks by SignalP weakly indicate the presence of a signal peptide encoded at the 5'end of the gene. However, there is no clear evidence for a transit peptide because the cleavage site is unusual (SAS-HK) and the putative transit peptide has not enough Serine.
precursor of dehydrogenase pyruvate dehydrogenase E1, alpha and beta subunits
Catalyzes the reaction: pyruvate + lipoamide = S-acetyldihydrolipoamide + CO2
pyruvate kinase, similar to GenBank AY608680 but N-terminus differs, first intron results in frameshift between Phatr2 and AY608680, recent duplication of Protein ID 27502, chr_8:927538-929753
Has EST support. majority of ESTs supports this variant; Alternative splicing variant 1
Has EST support. minority of ESTs supports this variant; Alternative splicing variant 2
pyruvate kinase, similar to GenBank AY608680 but N-terminus differs, first intron results in frameshift between Phatr2 and AY608680, recent duplication of Protein ID 45997, chr_8:912856-914986, Protein ID 46001 might be a splice variant of this gene, but majority of ESTs supports this variant; Alternative splicing variant 1
pyruvate kinase, putative splice variant of Protein ID 27502, identical to GenBank AY608680 but supported by minority of ESTs, recent duplication of Protein ID 45997, chr_8:912856-914986; Alternative splicing variant 2