Phaeodactylum tricornutum CCAP 1055/1 chromosome 2, 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 CM000606.\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##
xeroderma pigmentosum group D complementing protein
Probable 5'-3' ATP-dependent DNA helicase as a subunit of the basal transcription factor TFIIH, involved in DNA Nucleotide Excision Repair (NER) and RNA transcription
expressed protein probably contains signal ER presequence and it seems to be targeted to plastid
nuclear-encoded-like protein of chloroplast gro
47% identity with plastid groEL suggests a copy recently transferred to nucleus.
protein fucoxanthin chlorophyll a/c protein
protein fucoxanthin chlorophyl a/c protein
3rd of four closely-related genes in tandem
2nd of 4 closely-related genes in tandem
First of 4 very closely-related genes in tandem
mitochondrial transit peptide predicted at N-terminus
expressed protein putatively targeted to plastid, carotenoid cleavage enzyme; CCD1
adenylosuccinate lyase A number of enzymes, belonging to the lyase class, for which fumarate is a substrate have been shown to share a short conserved sequence around a methionine which is probably involved in the catalytic activity of this type of enzymes.; Adenylosuccinase; ASL; ASASE
Homologous to the atpB gene in the chloroplast genome of C. reinhardtii
Putative isochorismatase involve in siderophore biosynthesis in bacteria. Higher number of ESTs found in low decadienal library. Predicted to have 4 transmembrane domains.
unknown function; weak similarity to vWA-like and TPR-like domains and to proteins involved in signal transduction; unknownn protein
enoyl-ACP reductase. Reduces the 2-trans enoyl-ACP of a growing fatty acyl-ACP. Part of the type II fatty acid synthase of the plastid. Probably contains a typical bipartite plastid targeting signal. Predicted to have both ER and plastid targeting signals by targetP.
seventh step in the shikimate pathway; contains putative ER signal peptide at the N terminus (SignalP score = 0.999); putatively chloroplast targeted
splicing coactivator subunit-like protein
Rab-family small GTPase, ortholog of T. pseudonana TPS_7642
medium subunit of AP2 complex (putative clathrin vesicle coat component); ortholog of T. pseudonana TPS_102502
gamma-interferon-inducible lysosomal thiol reductase
This gene has good EST support and is most similar to the gamma-interferon-inducible lysosomal thiol reductase (GILT) family. These sequences are associated with disulphide bond reduction and antigen processing in mammals.; GILT) protein-family homolog
Phosphoglucomutase, plastidic enzyme, possesses N-terminal bipartite plastid targeting signal
Putative Glutaredoxin, involved in redox reactions, contains a presequence for either ER or plastids; probably glutaredoxin
Homologous to Rh1 from Chlamydomonas, putative CO2 channel, Homologous to ammonium transporters
Membrane associated nitrate transporter responsible for actively transporting nitrate ions into the cell. The Pt genome contains 6 nitrate transporters. Phylogenetically, this model is closely related to the nitrate transporter on scaffold 6, which has a very high level of EST support under nitrate depletion. There is only very limited EST support for this nitrate transporter.
triosephosphate isomerase/glyceraldehyde-3-phosphate dehydrogenase precursor
mitochondrial triosephosphate isomerase/glyceraldehyde-3-phosphate dehydrogenase fusion protein, GenBank Accession AF063804
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
D-type CDK. Interacts with H-type cyclin and forms a CDK activating kinase (CAK)
ATP-dependent helicase highly closed to the Thalassiosira protein thaps1 97518
Probably involved in damage recognation initiation step of DNA Nucleotide Excision Repair (NER), in association with a RAD4 (alias Xeroderma pigmentosum group C, XPC) protein homolog
Similar to bacterial and plastidic nucleotide transporters (NTTs)
Probably triosephosphate isomerase Catalyzies D-glyceraldhyde 3-phosphate to glycerone phosphate
homology to DnaJ; The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein
short-chain dehydrogenase/reductase acting with NAD or NADP as acceptor
Probably a short-chain dehydrogenase/reductase, possibly acting on ketone groups with NAD+ or NAD+ as acceptor
Medium chain (small subunit) of AP3 complex, ortholog of T. pseudonana TPS_115537
3-phosphoshikimate 1-carboxyvinyltransferase
sixth step in the shikimate pathway; extensions at the N terminus contains putative ER signal peptides; putatively chloroplast targeted
Glycine decarboxylase H-protein (also known as glycine cleavage system H-protein, GCSH, GCVH). Catalyzes the formation of serine from two glycine with consequent production of CO2 and NH3. Part of the glycolate cycle (C2 cycle) in photorespiration.
Copine, calcium-dependent membrane-binding protein with two C2 Calcium Binding Domain
Expressed protein with similarity to Rad7 protein, probable subunit of Nucleotide Excision Factor 4 (NEF4) involved in DNA-damaged Global Genome Repair (GGR) Nucleotide Excision repair (NER) by generating superhelicity in DNA through the catalytic activity of the Rad16-like subunit of NEF4 complex
Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes.
Similar to dRING motif-containing drosophila Sce polycomb protein involved in transcriptional repression maintenance
In nucleotide sugar metabolism, generates an intermediate in the formation of GDP-fucose. Catalyzes the reaction: GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H2O.
DNA replication factor C subunit RFC3. Hightly closed to the Thalassiosira protein thaps1 132932.
enzyme involved in N-Glycan Biosynthesis
similar to coumaryl-CoA ligase; coumaryl-CoA synthetase
S-adenosyl-L-homocysteine hydrolase is responsible for the reversible hydration of S-adenosyl-L-homocysteine into adenosine and homocysteine. This gene appears to be highly expressed in response to nitrogen limitation.
replication protein A is athree-subunit protein that plays a central role in eukaryotic DNA replication, homologous recombination, and excision repair
WD40 mitotic checkpoint-like protein similar to spleen mitotic checkpoint BUB3
BUB3 is a mitotic checkpoint protein involved in sensing of unattached chromosomes. deletion abolishes mitotic checkpoint function in Saccharomyces cerevisiae.
possible a ferric reductase similar to Dcytb involved in iron uptake in the duodenal mucosa
second step in heme biosynthesis, contains ER signal peptide (SignalP score 0.994), putatively chloroplast targeted
Probably Triosephosphate isomerase catalyzes D-glyceraldhyde 3-phosphate to glycerone phosphate
Caspase-like protease. Conserved catalytic Cys-His diad is identified.
regulatory proteasome non-atpase subunit 7
26S proteasome regulatory non-ATPase subunit, homolog to plant RPN7 subunit
Rad51 is the eukaryotic homolog of RecA and is involved in homology searching and strand exchange in homologous recombination during DNA repair and meiosis. Phatr2_54137 is closest to the Thalassiosira pseudonana protein Thaps3_257784 and both have homology to Rad51 homologs in plants and animals. No automatic model was present for Phatr1 assembly and this predicted gene was identified by homology to Thaps1_113675 (by tblastn). The amino acid sequence of the open reading frame has high homology to the Rad51C sequence of Chlamydomonas (2e-48) and human (2e-46) and is predicted by Interpro scan to be a member of the RecA/Rad51 family and part of the P-loop containing ATPase superfamily. There is EST support under 'ammonium low' and 'silicon plus' conditions. As a Rad51 homolog, it is expected to be constitutively expressed at a low level but likely upregulated during meiosis.
Probably a short-chain dehydrogenase/reductase with NAD+ or NAD+ as acceptor
DNA polymerase epsilon, subunit D, catalytic subunit participating with PCNA in DNA replication late in S phase
RB and hbrm cooperate to repress the activation functions of E2F1 RB requires the presence of the hbrm/BRG-1 proteins, which are components of the coactivator SWI/SNF complex.
peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation; secretory pathway
unknown function; similarity to Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor; unknownn protein
SMC proteins family (6) form heterodimers and act as a essential regulator of chromosome condensation. Hihly closed to the Thalassiosira protein 188447.
Putative plastidic triose phosphate/phosphate translocator, homologous to TPT1 (duplication?), but without plastid targeting signal, possibly located in CER membrane
Some sequence similarity to tetracycline resistance (Tcr) protein which functions as a metal-tetracycline/H+ antiporter. Most EST support on 5' end, 7 predicted transmembrane domains.
This ion channel sequence clusters in bacterial (ERiC etc) group of chloride channels. Ortholog in T.pseudonana (Tp_96497 and Tp_4666). Predicted 10 TM domains. HP plot suggests possible '5 extension required, this is supported by EST.