Phaeodactylum tricornutum CCAP 1055/1 chromosome 1, 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 CM000605.\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##
cdc45-like protein, essential protein required for initiation of DNA replication. Highly closed to the Thalassiosira protein thaps1 103630.
ATP-dependent phosphorylation of mevalonic acid (MVA pathway)
Fructose-bisphosphate aldolase, cytosolic
Putative subunit of mitochondrial fatty acid synthase. Carrier of the butanoic acid. Requires post-translational modification. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP, enabling acyl-thioester linkages to the sulfhydryl of the prosthetic group. TargetP detects a mitochondrial targeting signal.; ACP), putative mitochondrial precursor
seduheptulose bisphosphatase, probably cytosolic enzyme, does not possess plastid targeting sequence
Inositol phosphatase/fructose-1,6-bisphosphatase, probably plastidic, possesses an N-terminal bipartite plastid targeting sequence
Fructose-1,6-bisphosphatase, chloroplast precursor, possesses N-terminal bipartite targeting sequence
phosphoserine transaminase.Involved in amino acids metabolism
contains a Muts domain 1 found in the Muts family that initiate DNA mismatch repair by recognizing mispaired bases and activating endo and exonucleases to remove the mistmatch. Hihgly closed to the Thalassiosira protein thaps1 150647
2-phosphoglycolate phosphatase catalyzes the cleavage of a phosphate group from phosphoglycolate to generate glycolate. This is the first step in the glycolate (C2) cycle of photorespiration following oxygen fixation.
plastidic ribulose-phosphate 3-epimerase
Ribulose-phosphate 3-epimerase, plastidic enzyme, possesses bipartite N-terminal plastid targeting sequence, involved in Cavin cycle, OPPP, highest similarity to bacterial enzymes
involved in cysteine metabolism; enzyme of cyanobacterial origin, N terminus contains putative mitochondrial transit peptide (TargetP score = 0.900); putatively targeted to mitochondrion; thiol
transporter, major facilitator superfamily and tetracycline resistance protein
The Major Facilitator Superfamily (MFS) transporters are single-polypeptide secondary carriers capable only of transporting small solutes in response to chemiosmotic ion gradients. Also contains sequence similiarities to the transposon Tn10-encoded tetracycline resistance (Tcr) protein. This functions as a metal-tetracycline/H + antiporter
Proteasome (alpha 1 subunit (20S)); 20S; NCBI accession BAA96829
first step in the shikimate pathway; no targeting sequences found
fucoxanhin chlorophyll binding protein related
Fcp related protein, contains bipartite plastid targeting presequence, signal- and transit-peptides at N-terminus with conserved motif at signal peptide cleavage site
expressed protein putatively targeted to plastid, Tryptophan biosynthesis
Promotes transcriptional activity by catalyzing the transfer of acetyl groups from acetyl-CoA to lysine epsilon-amino groups of N-terminal tails of histones
regulatory proteasome non-atpase subunit 8
26S proteasome regulatory non ATPase subunit, homolog to plant RPN8a subunit
putative histone acetyl transferase MYST protein. Highly closed to the protein of Thalassiosira thaps1 118130.
beta-glucan binding protein; homology to endo-1,3-beta-glucanases; located at cell surface
Catalyzes the transfer of an acetyl group from acetyl-CoA to the amine group of an acceptor molecule.
This gene is involved in carbon utilization. Similarity to CAs from other organisms is weak. However, it has a CA domain predicted by Interpro. Signal peptide is encoded at the 5'end that indicates that the gene product is secreted or targeted to the plastid. However, there is almost no evidence for a cTP.
aldehyde dehydrogenase (1.2.1), probable SSDH
beta carbonic anhydrase, GenBank Accession AF414191
replication pre-initiation complex protein
thioredoxin m, contains bipartite plastid targeting presequence, signal- and transit-peptides predicted at N-terminus with phenylalanine at signal peptide cleavage site
precursor of cyclase lycopene beta cyclase
Has EST support. present: 1 || present: 1
cyclization of lycopene to beta-beta carotene
nuclear-encoded-like protein of plastid sec
contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
Early light induced protein-like, contains bipartite plastid targeting presequence, signal- and transit-peptides at N-terminus with conserved motif at signal peptide cleavage site
Unknown permease that contains a xanthine/uracil/vitamin C permease domain. This gene is expressed highly under conditions of nitrogen limitation.
Highly expressed permease of unknonw function. Contains 9 transmembrane domains and a xanthine/uracil (purine) transporter domain. The gene is highly expressed under condtions of nitrate starvation.
RTX toxins and related Ca2+-binding protein
member of Calcium ATPase family most closely related to ATP2C group (secretory pathway Ca2+ ATPase). Good EST evidence
putative Sec23 homolog, component of the vesicle Coat Protein complex COP II
unknown function; contains tetratricopeptide-like helical domain; secretory pathway; unknownn protein
thioredoxin-o, mitochondrial transit-peptide predicted at N-terminus
Dihydrolipoamide acetyl transferase Pyruvate metabolism & Glycolysis
Phospholipase C, putatively involved in the generation of Ins(1,4,5)P3
DNA mismatch repair belonging to the MUTs family. Highly closed to the Thalassiosira protein thaps1 127172.
DNA replication factor subunit RFC4 closed to the Thalassiosira protein thaps1 111749
udp-n-acetylglucosamine transferase subunit alg13
enzyme involved in N-glycan biosynthesis
Has EST support. unique to Fe-limited library
Zeta-carotene desaturase, expressed gene with high homology to plant and cyanobacterial ZDS, involved in carotenoid biosynthesis, chloroplast localized; chloroplast precursor
phosphoenolpyruvate/phosphate translocator precursor (Tpt1) gene, GenBank Accession AY191864, contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
3-hydroxybutyrate dehydrogenase Amino acid degradation
centrin are components of the MTOC (microtubule organizing center).
Synthesizes and degrades fructose-2,6-bisphosphate, a regulatory molecule for several carbohydrate metabolic pathways. Catalyzes two reactions: (1) ATP + beta-D-fructose 6-phosphate = ADP + beta-D-fructose 2,6-bisphosphate; and (2) beta-D-fructose 2,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate.
close to dihydrolipoamide succinyltransferase : TCA cycle
probable aminotransferase Enzyme involved in amino acids metabolism
unknown function; homology to protein from Cryptosporidium; unknownn protein
Somewhat divergent sequence, doesn't fit into 3 standard categories, but has homologs in Thalassiosira and Cylindrotheca.
F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends
Probably an aldehyde dehydrogenase, catalyzing the reaction: aldehyde + NAD+ + H2O = an acid + NADH
regulatory proteasome non-atpase subunit 3
26S proteasome regulatory non ATPase subunit, homolog to animal subunit
essential conserved nucleolar GTP-binding protein required for synthesis of 40S ribosomal subunits and for processing of the 35S pre-rRNA
Superoxide dismutase [Fe/Mn], likely a mitochondrial precursor; catalyses the conversion of superoxide radicals to molecular oxygen
Arf sybfamily small GTPase, similar to Arf-like (ARL) proteins, ortholog of T. pseudonana TPS_150579
two Phosphoglycerate mutase 1 domains (COG0588, GpmA, residues 176-395 and 572-807) contained in a single ORF, putative bipartite targeting presequence, signal and transit peptide-like domains predicted at N-terminus
protein containing a MCM domain found in DNA-dependent ATPases for the initiation of eukariotic DNA replication. Highly closed to the protein of Thalassiosira thaps1 113896
A short chain acyl-coenzyme A dehydrogenase, catalyzes the first step of beta-oxidation of saturated C-C bonds in acyl compounds using FAD as co-factor.
Hypothetical Cell death related protein, contains Programmed cell death protein 2, C-terminal Pfam domain and expressed exclusively under Ammonia starvation and toxic level of decadienal. Good alignment only in the domain region.
Precise function unknown. Possibly catalyzes the hydrolysis of sulfate ester in N-acetylglucosamine-4-sulfate residues.
putative subunit 2 of the origin recognition complex (ORC) that binds to the ARS consensus sequence of origins of replication.
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
2-phosphophoglycerate dehydratase. Enzyme involved in glycolysis pathway || contains putative mitochondrial targeting sequence
chloroplast-targeted nuclear-encoded recombinase
RecA/Rad51 proteins are involved in homology searching and strand exchange in homologous recombination. This model was identified by homology with the model in Thalassiosira pseudonana (Thaps2_25358) using tBLASTn and strong support from ESTs in Phaeodactylum. This recA homolog has very high homology to cyanobacterial recA genes and is predicted by the WoLF PSORT subcellular localization program to be in the chloroplast. The sequence contains a signal sequence and transit peptide.
putative synaptobrevin, v-SNARE component, similar to plant vesicle-associated membrane proteins VAMP711, 713, 714
serine hydroxymethyltransferase (aka glycine hydroxymethyltransferase) catalyzes the conversion of glycine to serine. In this model, the presence of a mitochondrial transit peptide suggests this isozyme functions in photorespiration, catalyzing the conversion of two glycine to one serine with the enzyme glycine decarboxylase
plastidic triose-phosphate/phosphate translocator
similar to triose phosphate/phosphate translocator, possesses N-terminal bipartite plastid targeting signal
putative chaperone function, located in cytosol
Spo11/Topoisomerase 6A proteins initiate double strand break formation in meiotic recombination and are related to type II topoisomerase 6 subunit A of archaea. Both the Phaeodactylum tricornutum and Thalassiosira pseudonana genomes contain two spo11 homologs. Phatr2_24838 and Thaps3_269906 are most similar to AtSpo11-3 of Arabidopsis thaliana (green plants) and CMQ111C of Cyanidioschyzon merolae (red algae). Terrestrial plants have three spo11 homologs. AtSpo11-1 is specifically required for meiosis whereas AtSpo11-3 is constitutively expressed and required for general growth and development. AtSpo11-3 interacts with Topoisomerase 6 subunit B, which is also found in diatoms (Phatr_864). Therefore, this spo11 homolog is not expected to be specific to meiosis.; SPO11) homolog 2
precursor of ligase long chain acyl-coa ligase
Catalyzes ester formation of free fatty acids and free CoA. Contains peroxisomal targeting motif, may be involved in beta-oxidation of polyunsaturated fatty acids. When the Thalassiosira pseudonana homolog of this gene was expressed in yeast, it was found to be most specific for DHA, and less specific for EPA and improved accumulation of DHA in triglyceride.; long chain acyl-CoA synthetase
UNC-84 and and Sad1 share a common C-terminal region, that is often termed the SUN (Sad1 and UNC) domain. The C. elegans UNC-84 protein is involved in nuclear anchoring and migration. The S. pombe Sad1 protein localises at the spindle pole body.
regulatory proteasome non-atpase subunit 5
26S proteasome regulatory non ATPase subunit, homolog to animal subunit 12
unknown function; similarity to motif of Tubulin chaperone cofactor A; unknownn protein
ZW10 is a centromere/kinetochore protein involved in mitotic chromosome segregation
protein fucoxanthin chlorophyll a/c protein
Delta subunit of the AP3 complex, ortholog of T. pseudonana TPS_130999
MAP/microtubule affinity-regulating kinase Serine/threonine protein kinase p78 homolog CTAK1 Involved in the specific phosphorylation of microtubule-associated proteins for tau, MAP2 and MAP4. Phosphorylates CDC25C on Ser-216
CRTISO5 carotenoid isomerase 5,phytoene dehydrogenase-related protein
Carotenoid isomerase 5, putative: groups with CRTISO in phylogenetic tree containing various PDS ZDS and CRTISO.
NAPs act as histone chaperones, shuttling both core and linker histones from their site of synthesis in the cytoplasm to the nucleus. The proteins may be involved in regulating gene expression and therefore cellular differentiation
Putative Calcyclin-Binding protein, target of the S100A6 calcium-binding subfamily
ATP-dependent helicase. Highly closed to the Thalassiosira protein thaps1 129208.
Kinesin-related motor protein required for mitotic spindle assembly and chromosome segregation; related to DSK1 of the diatom Cylindrotheca fusiformis
1-acyl-sn-glycerol-3-phosphate acyltransferase
Catalyzes the conversion of Acyl-CoA and 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid) to CoA and 1,2-diacyl-sn-glycerol 3-phosphate (phosphatidic acid). Membrane bound.; Lysophosphatidic acid acyltransferase
Possibly creates an amide linkage that joins the free carboxyl group of a fatty acid to the epsilon-amino group of a specific lysine residue in lipoate-dependent enzymes
Has EST support; Alternative splicing variant 2
Has EST support; Alternative splicing variant 1
Synthesizes 1,3-beta-D-glucan. Reaction catalyzed: UDP-glucose + [(1,3)-beta-D-glucosyl]n = UDP + [(1,3)-beta-D-glucosyl]n+1.; Alternative splicing variant 1
catalyzes the dephosphorylation of 2-phosphoglycolate. Is involved in the dissimilation of the intracellular 2-phosphoglycolate formed during the DNA repair of 3'-phosphoglycolate ends, a major class of DNA lesions induced by oxidative stress
Putative microtubule associated protein / MAP65_ASE1 family (essential for anaphase spindle elongation)
ADA2 ortholog with ZZ finger. motif found in a number of eukaryotic transcriptional regulatory proteins. SANT domain is essential for the in vivo functions of yeast Swi3p, Ada2p, and Rsc8p, subunits of three distinct chromatin remodeling complexes
probable Sec13 protein, component of the Coat Protein complex COP II
putative transcription factor; contains DNA-binding part of Transcriptional factor tubby; N-terminal part shows weak similarity to F-box domain, that serves as a link between a target protein and a ubiquitin-conjugating enzyme
A hydrophobic, multiple transmembrane protein, possibly located in the ER-Golgi network and involved in the O-acetylation of carbohydrates of glycosphingolipids.
precursor of protein zeaxanthin epoxidase-like protein
expressed gene with similarity to zeaxanthin epoxidase, putatively involved in xanthophyll cycling
pds-like2, phytoene desaturase-like protein
Phytoene desaturase-like2, expressed gene with similarities to cyanobacterial phytoene desaturases/dehydrogenases, possibly involved in carotenoid biosynthesis
Plastidial HCO3-transporter, eukaryote. Protein has a signal peptide with the cleavage site: GSA-FT. N-terminal protein part is ChloroP positive and the putative transit peptide is similar to T.p. transit peptides.
Has EST support. unique to Fe-limitation
putative Sly1p, syntaxin-binding protein, Sec1 domain-containing protein
1-deoxy-d-xylulose-5-phosphate reductoisomerase
second step in MEP pathway, first intermediate unique for isoprenoid biosynthesis; chloroplast precursor
violaxanthin deepoxidase-related, chloroplast precursor
Similar to histone H3 core component of nucleosomes, containing two molecules each of H2A, H2B, H3 and H4
putative vesicle transport involved protein, distantly similar to plant VTI12
Similar to the subunit C of the chromatin assembly factor 1 (CAF1) bringing newly synthesized histones H3 and H4 tetramer to replicating DNA. This subunit (p55 in fruit fly) associates with acetyltransferases and deacetylases in cell extracts and is also a component of the nucleosome remodeling factor complex (NURF); Other definition: nucleosome remodeling factor 55kDa subunit
Arf-type small GTPase, probable Arf1, ortholog of T. pseudonana TPS_121381
unknown function; weak similarity to mitochondrial Rf1 protein (restorer for CMS) and pentatricopeptide (PPR) repeat-containing protein; unknownn protein
Putative synaptobrevin, v-SNARE component, similar to plant, animal, and yeast SEC22
Putative transcription factor CBF/NF-Y/archaeal histone binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin
n-acetylglucosaminyl-phosphatidylinositol biosynthetic protein
Involved in the first step of glycosylphosphatidylinositol (GPI) Catalyses UDP-N-acetyl-D-glucosamine + 1-phosphatidyl-1D-myo-inositol = UDP + 6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo- inositol
homolog to fungal NDK, mitochondrial signal peptide
[CATALYTIC ACTIVITY] Chorismate = prephenate. [ENZYME REGULATION] Allosterically regulated. [PATHWAY] Branch point of the biosynthetic pathway leading to the three aromatic amino acids, phenylalanine, tyrosine and tryptophan (the shikimate pathway); CM