Phaeodactylum tricornutum CCAP 1055/1 chromosome 6, 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 CM000609.\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##
Precise function unknown. A member of a family of related epimerases and dehydratases using bound NAD+ as co-factor.
beta ketoacyl-CoA synthase. Condensing enzyme. Involved in the elongation of acyl-CoAs by 2 carbons. Not predicted to be plastid targeted by TargetP.
Similar to histone acetyltransferases (HATs) which acetylate lysine residues in histone amino-terminal tail regions. HATs are involved in the regulation of both promoter-specific transcription and long-range/chromosome-wide transcription
contains a Muts domain 2. Highly closed to the Thalassiosira protein thaps1 20930.
subunit 1 of the origin recognition complex (ORC) that binds to the ARS consensus sequence of the origins of replication in an ATP-dependent manner. This protein is closed to the Thalassiosira protein thaps1 105635
contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
Hydrolyzes terminal, non-reducing beta-D-glucose residues of beta-glucosides; glycosyl hydrolase family 3
probable 3-hydroxyisobutyrate dehydrogenase. Also close to tartronic semialdehyde reductase glyoxylate metabolism
Gene of unknown function, highly expressed under nitrate starvation and upon exposure to the aldehyde decadienal. Has homology to various transcription factors and does contain a eukaryotic transcription factor binding site.; Pt_50374, Gene of unknownn function
Similar to bacterial and plastidic nucleotide transporters (NTTs), putative bipartite targeting presequence, signal- and transit-peptides predicted at N-terminus.
ribonucleoprotein associated TUDOR protein
putative association with ribonucleoprotein or single-strand DNA-associated complexes; similarity to tudor protein; The tudor domain is found in many proteins that colocalize with ribonucleoprotein or single-strand DNA-associated complexes in the nucleus, in the mitochondrial membrane, or at kinetochores
enzyme close to pyruvate decarboxylase & acetolactate synthase organic acid metabolism
cell wall associated protein, contains a signal peptide
iron-containing alcohol dehydrogenase Close t
Similar to histone H2A core component of nucleosomes, containing two molecules each of H2A, H2B, H3 and H4
Possible oxidoreductase, acting on the aldehyde or oxo of donors with NAD or NADP as the acceptor
Similar to histone H2B core component of nucleosomes, containing two molecules each of H2A, H2B, H3 and H4
1-aminocyclopropane-1-carboxylate synthase
Probable 1- aminocyclopropane-1-carboxylate synthase, a lyase that catalyses an alpha, gama elimination. S-adenosyl-L-methionine =1-aminocyclopropane-1-carboxylate+ methylthioadenosine
Hypothetical protein, no alignments with other genes or protein domains, possible peroxidase-like domain, good EST evidence
contains conserved domain of unknown function, found in Bacteria; located in inner membrane system
enzyme involved in N-Glycan Biosynthesis; transfers GDP-mannose to dolichyl phosphate
In the tricarboxylic acid cycle, catalyzes the reaction: fumarate + H2O = S-malate. The enzyme effects a stereospecific trans hydration and is iron-dependent.
Rab-type small GTPase, ortholog of T. pseudonana TPS_100340, most similar to HsRab18 and AtRabC subtypes among human and plant small GTPases.
fifth step in heme synthesis; extension at the N terminus contains putative ER signal peptide (Signal P score = 0.989); putatively chloroplast targeted
groups with CRTISO in phylogenetic tree containing various PDS ZDS and CRTISO.; phytoene dehydrogenase-related protein
Homologous to the rps19 gene in the chloroplast genome of C. reinhardtii
ATP-dependent helicase. Highly closed to the Thalassiosira protein thaps1 100352.
Medium chain (mu subunit) of AP1 vesicle coat complex, ortholog of T. pseudonana TPS_143660
Arf-subfamily small GTPase, similar to Arf-like proteins (ARL), with no clear ortholog in the T. pseudonana genome.
homology to DnaJ; The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein
Precise function unknown. A member of a family of related epimerases and dehydratases, probably catalyzes the isomerization of nucleotide sugars. Similarity with some bacterial proteins suggests it may be involved in formation of UDP-hexuronic acid derivatives. Uses bound NAD+ as co-factor.
contains a signal peptide, contains a tryptophan rich domain (TRD)
glyceraldehyde-3-phosphate dehydrogenase
putative NADP-dependent Glyceraldehyde-3-phosphate dehydrogenase, bacterial type; Aldehyde dehydrogenases are enzymes which oxidize a wide variety of aliphatic and aromatic aldehydes using NADP as a cofactor
Medium chain (mu subunit) of AP4 complex, ortholog of T. pseudonana TPS_165232
Rab-type small GTPase, ortholog of T. pseudonana TPS_100077
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
Histone linker, necessary for the condensation of nucleosome chains into higher order structures
Similar to histone H3 core component of nucleosomes, containing two molecules each of H2A, H2B, H3 and H4
Similar to histone H4 core component of nucleosomes, containing two molecules each of H2A, H2B, H3 and H4
Probable methylmalonyl-CoA mutase catalyses (R)-methylmalonyl-CoA= succinyl-CoA requires cobamide coenzyme. Involved in valine, leucine and isoleucine degradation and Propanoate metabolism
Probably catalyzes the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate
beta chain succinyl-coa synthetase synthetase
Probable succinate-CoA ligase (GDP forming) catalyses GTP+succinate+CoA =GDP+phosphate+succinyl-CoA. Found in propanoate metabolism and the TCA cycle.
C-type cyclin dependent kinase 2, probably involved in transcriptional control
Has EST support; Alternative splicing variant 2
Has EST support; Alternative splicing variant 1
putative splice variant of Protein ID 26934, Phatr2/chr_6:869375-871526, signal peptide predicted at N-terminus, supported by minority of ESTs; Alternative splicing variant 1
putative splice variant of Protein ID 45333, Phatr2/chr_6:869375-871507, no targeting presequence predicted at N-terminus, supported by majority of ESTs; Alternative splicing variant 2
protein containing a MCM domain and belonging to a family of six proteins. They are required for the initiation of eukariotic DNA replication and interact directly with autonomously replicatig sequences (ARS).Highly closed to the protein of Thalassiosira thaps1 135150.
regulatory proteasome non-atpase subunit 9
26S proteasome regulatory non ATPase subunit, homolog to plant RPN9a subunit