Phaeodactylum tricornutum CCAP 1055/1 chromosome 7, 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 CM000610.\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##
contains a signal peptide, FAS1 domain represents an ancient cell adhesion domain common to plants and animals
Precise function unknown. A member of a family of related epimerases and dehydratases, probably catalyzes either of two reactions: (1) the interconversion of UDP-D-glucose and UDP-D-galactose; or (2) the dehydration of dTDP-glucose in pathways leading to synthesis of nucleotide-6-deoxysugars by the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-D-glucose + H2O. Uses bound NAD+ as co-factor.
Gene is involved in carbon utilization. EST support. Signal peptide is encoded at the 5'end of this gene. Predicted cleavage site: VDA-QE. No signs of a cTP (neg. ChoroP prediction, no cTP motif). Has high similarity to NCBI Acc. No. BAD6744.1 (New Phaeo CA). Possibly beta CA.
Catalyzes the two-electron reduction of biliverdin IX-alpha to the tetrapyrrole chromophore phytochromobilin (PPhiB). Signal peptide and transit peptide is predicted (SignalP, ChloroP). Protein is therefore probably targeted to the plastid
This protein belongs to a family that contains nitrilases that break carbon-nitrogen bonds and appear to be involved in the reduction of organic nitrogen compounds and ammonia production. They all have distinct substrate specificity and include cyanide hydratases, aliphatic amidases, beta-alanine synthase, and a few other proteins with unknown molecular function; Formamide amidohydrolase
contains conserved ferric reductase domain. Also similar to respiratory burst oxidase
cell wall assoiciated protein, contains a signal peptide
eighth step in heme synthesis; contains ER signal peptide at extended N terminus (2 versions possible, extension of 99 aa / SignalP score = 0.953; extension of 109 aa / SignalP score = 0.912); putatively chloroplast targeted
groups with CRTISO in phylogenetic tree containing various PDS ZDS and CRTISO.; phytoene dehydrogenase-related protein
Probably catalyzing the reaction myoinositol+NAD=2,4,6/3, 5-pentahydroxycyclohexanone+NADH+H
Has EST support; Alternative splicing variant 2
Phatr_46077 has weak homology to proteins involved in sister chromatid cohesion and was found using tblastn with the mammalian protein Stag3; Alternative splicing variant 1
Phatr_ 35208 has weak homology to proteins involved in sister chromatid cohesion. Closest to Thaps3_24333, but proteins are quite divergent.; Alternative splicing variant 2
enzyme involved in N-glycan biosynthesis; 1,2
Sar1-like small GTPase, ortholog of T. pseudonana TPS_8056
Catalyzes the formation of acyl-CoA from free fatty acid and CoA. Similar to metazoan long-chain acyl-CoA ligases. Lacks transmembrane domains by computer-prediction.; long chain acyl-CoA ligase
Rad50 is involved in recombination, recombinational repair, and/or non-homologous end joining. It is a component of an exonuclease complex with MRE11 homologs. The Saccharomyces cerevisiae Rad50/MRE11 complex possesses single-stranded endonuclease activity and ATP-dependent double-strand-specific exonuclease activity. Rad50 provides an ATP-dependent control of MRE11 by unwinding and repositioning DNA ends into the MRE11 active site. This family is distantly related to the SbcC family of bacterial proteins.; Alternative splicing variant 1
Rad50 pairs with Mre11 to repair double strand breaks. This complex functions in DNA repair, telomere maintenance, and meiotic recombination. The Rad50 signature motif is very highly conserved in this model. The Q loop, CxxC motif, Walker B motif, and H-loop are well conserved in this model with Rad50 sequences from other organisms but the conserved Walker A motif is missing from the model. The closest homolog in version 3 of the Thalassiosira pseudonana genome is Thaps3_9195; Alternative splicing variant 2
Catalyzes the desaturation of very long chain acyl-CoA to 2-trans-enoyl-CoA. Acyl-CoA + O(2) = trans-2,3-dehydroacyl-CoA + H(2)O(2). Uses FAD cofactor. First step of peroxisomal fatty acid beta-oxidation.
F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments thereby blocking the exchange of subunits at these ends
fusion protein that is cleaved to yield Ubiquitin and a ribosomal protein of the small (40S) subunit, homolog to mammalian Ub-CEP80 protein
chitinase glycoside hydrolase family 18, ribosome-binding factor
Putative chitinase with glycosode hydrolase and ribosomal binding factor A domains. Chitinase active site detected in amino acid translation. 5' end has signal peptide. Similarity to T. pseudonana gene.
CDH1 co-activator of the anaphase-promoting complex (APC).
Catalyzes the interconversion of D-ribulose 5-phosphate and D-xylulose 5-phosphate in the pentose phosphate pathway.
DNA replication factor C subunit RFC5, highly closed to the Thalassiosira protein thaps1 131057.
2-hydroxyacid-dehydrogenase. oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor. close to 3-phosphoglycerate dehydrogenase; 2-hydroxyacid dehydrogenase
alpha-adaptin subunit of the AP1 vesicle coat complex; ortholog of T. pseudonana TPS_142116
putative synaptobrevin, v-SNARE component, similar to animal SYBL1 and plant VAMP722
Most similar to flavohemoproteins from bacteria and fungi and consist of two distinct domains, an N-terminal globin domain and a C-terminal FAD-containing reductase domain. flavohaemoglobins are involved in responding to nitric oxide (NO) and nitrosative stresses catalyzing the production of nitrate from NO and O2. EST support in the Fe-limit which is also known to be regulated by nitrosative stress.
Gene is involved in carbon utilization but has no EST support. There is a signal peptide encoded at the 5'end of this gene. Predicted cleavage site is VRC-RS.
Contains a reliabel signal peptide and severn transmembrane domains. The model contains a glutamate-like receptor that is in the GPCR family. There is also a GABA receptor domain. The gene is upregulated under conditions of nitrate depletion.
poorly characterized function; C3HC4-type RING finger
reductase of ferredoxin thioredoxin reductase
Has EST support. present: 1 || present: 1
Ferredoxin-thioredoxin reductase subunit B, plastidic enzyme
Adenylate kinase, plastidic enzyme, possesses N-terminal bipartite plastid targeting sequence
putative Uncoordinated protein Unc18 homolog, Sec1 domain-containing protein, syntaxin-binding protein
Plastidial HCO3-transporter, eukaryote. Protein has a signal peptide with the cleavage site: SAA-FA. N-terminal protein part is ChloroP positive and the putative transit peptide is similar to T.p. transit peptides.
Gene of unknown function contains domain for pathogenesis-related genes transcriptional activator and ethylene-responsive factors.
The MutS homolog 4 (MSH4) interacts with MSH5 to promote cross-over formation during meiotic recombination. Phatr3_45661 appears to be an MSH4 and is closest to Thaps3_ 261368.; MSH4) DNA recombination protein
ubiquitin-activating enzyme E1, protein 1
Ubiquitin activating enzyme E1, homolog to animal UBA
Kinesin-related motor protein, involved in microtubule-based motility
Possibly hydrolyzes terminal, non-reducing beta-D-galactose residues of galactosides; glycoside hydrolase family 35
Catalyzes the formation of acyl-CoA from free fatty acid and CoA. Similar to metazoan long-chain acyl-CoA ligases. Has 1 computer-predicted transmembrane domain.; long chain acyl-CoA ligase
ATP-dependent helicase. Highly closed to the Thalassiosira protein thaps1 101888.
protein fucoxanthin chlorophyll a/c protein
unknown protein; highly expressed under iron starvation; secretory pathway