Thalassiosira pseudonana CCMP1335 chromosome 10, whole genome shotgun sequence.
Eukaryota; Stramenopiles; Bacillariophyta; Coscinodiscophyceae; Thalassiosirophycidae; Thalassiosirales; Thalassiosiraceae; Thalassiosira.
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism
Submitted (15-JUN-2017) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
Submitted (18-SEP-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 CM000646.\nURL -- http://www.jgi.doe.gov/thalassiosira\nJGI Project ID: 2662235\nContacts: E. Virginia Armbrust (armbrust@u.washington.edu)\n Igor Grigoriev (ivgrigoriev@lbl.gov)\nThe clone of P. pseudonana that was sequenced is CCMP1335 and is\navailable from the Center for Culture of Marine Phytoplankton\n(http://ccmp.bigelow.org). This clone was collected in 1958 from\nMoriches Bay (Long Island, New York) and has been maintained\ncontinuously in culture.\nAnnotation was done by the JGI Annotation team and the Diatom\nConsortium.\nChromosomes 7 and 18 are complete and present in GenBank records\nCP001160 and CP001159, 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 January 2009.\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##
HSF12, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF12, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
sir2-type regulatory transcription factor silent information regulator protein
Silent Information Regulator Sir2 protein is one of several factors critical for silencing at least three loci in yeast. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres. Sir2p interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes. Unlike Sir3p and Sir4p, for which no homologues are known, Sir2p is part of a multigene family in yeast (Homologues of Sir Two (HST) 1,2,3,4) that has highly conserved structural homologues in organisms ranging from bacteria to man. Proteins of this family have been proposed to play a role in silencing, chromosome stability and recombination. In addition, an in vitro ADP ribosyltransferase activity has been associated with E. coli and human members of this family. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity
Probable lipase; similar to At1g30370-68300.m03236 T4K22.3 lipase: PF01764: Lipase (model%: 30, hit%: 30, score: 165, %id: 30) [Arabidopsis thaliana]; EST support
Glycoside hydrolase, family 18, putative chitinase, carbohydrate metabolism; hypothetical protein of unknown function, member of glycoside hydrolase, family 18
putative protein with internal repeats that contain integrin-like domains; putative protein containing integrin domains
probably plastid clp protease subunit, most similar to G.theta nucleomorph homologue indicating secodnary gene transfer
Fair to good similarity with known sequences
This protein contains InterPro domain IPR004046. IPR004046 is a glutatione S-transferase, C-terminal domain (GST_C), which, in eukaryotes, participates in the detoxification of reactive electrophilic compounds by catalyzing their conjugation to glutathione.
AP17, clathrin adaptor complex AP2 small chain
This protein has high similarity to other conserved hypothetical proteins. There is EST support for this gene. It contains the domain for DUF160 (InterPro), a family of proteins of unknown function.; conserved hypothetical protein
Probable protein kinase with some similarities to ribosome S6 protein kinase; similar to At3g08720-68298.m00874 F17O14.19 putative ribosomal-protein S6 kinase (ATPK19) identical to putative ribosomal-protein S6 kinase (ATPK19) GB:D42061 [Arabidopsis thaliana] (FEBS Lett. 358 (2), 199-204 (1995)); (model%: 62, hit%: 65, score: 651, %id: 44) [Arabidopsis thaliana]
Putative protein of unknown function containing an esterase/lipase domain; similaritie to At4g24160-68296.m02554 T19F6.150 putative protein CGI-58 protein - Homo sapiens,PID:g4929585 (model%: 99, hit%: 82, score: 208, %id: 24) [Arabidopsis thaliana]; EST support; putative protein of unknown function containing an esterase/lipase domain
based on sequence similarity to hypothetical proteins from bacteria; putative protein of unknown function
This family of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyze the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, E. coli and Bacillus.The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104).; putative protein with oxidoreductase n-terminal domain
Riboflavin kinase, riboflavin metabolism, Vitamin B12 bioynthesis, FAD synthetase domain
putative RNA methyltransferase, supported by phaeodactylum cDNA
Presumably deacetylates chitin or its oligosaccharides (composed of 4-linked N-acetyl-beta-glucosamine residues).; chitin deacetylase
probable dna-directed RNA polymerase II 13.6 kDa polypeptide
This subunit interacts with the RPB36 (36kDa) subunit of RNA polymerase II. Nuclear encoded. Found by blasting with G. theta nucleomorph rpbY.
putative protein of unknown function containing a F-box domain; putative protein of unknown function containing a f-box domain
Zinc finger protein similarity, PHD motif, DNA binding, transcription factor; zinc finger protein similarity, PHD motif, DNA binding, transcription factor
P-type (or E1-E2-type) ATPases constitute a superfamily of cation transport enzymes, present both in prokaryota and eukaryota, whose members mediate membrane flux of all common biologically relevant cations
arginine n-methyltransferase-like protein
hypothetical protein, similar to methyltransferase, supported by cDNA; hypothetical protein
based on sequence similarity to cyanobacteria proteins (goxB/thiG) and presence of NAD binding site and FAD dependent oxidoreductase domain appears to be involved in thiamin biosynthesis; Phaeodactylum EST support; putative protein with sequence similarity to thiamin biosynthesis protein
Putative protein of unknown function containing a lipase domain, similar to; gi|22326868|ref|NP_197269.2| (NM_121773) putative protein; protein id: At5g17670.1, gi_17065369 [Arabidopsis thaliana] (model%: 89, hit%: 99, score: 199, %id: 24) [Arabidopsis thaliana]; some EST support; putative protein of unknown function containing a lipase domain
Nuclear encoded hypothetical protein, similar to YCF53 from the plastid genome in red algae and to a hypothetical nuclear encoded protein in Arabidopsis (Acc. No AAL36274). The degree of similarity is highest against Cyanobacteria, followed by Porphyra and Arabidopsis. It is likely that the gene was transferred from the red algal plastid genome to the Diatom nucleus during secondary endosymbiosis (note: there is no ycf53 homologue on the plastid genome in Odontella sinensis, another Diatom).; hypothetical ORF, homologous to plastid ycf53 in porphyra and cyanidium
phenylalanine-trna synthetase-like protein
Strong alignment with other organisms (54% amino acid identity)
1-acyl-sn-glycerol-3-phosphate ACYLTRANSFERASE, lysophosphatidic acid acyltransferase
Similar to Plastidal lysophosphatidic acid acyltransferase[CATALYTIC ACTIVITY] ACYL-COA + 1-ACYL-SN-GLYCEROL 3-PHOSPHATE = COA + 1,2-DIACYL-SN-GLYCEROL 3-PHOSPHATE.[PATHWAY] FIRST STEP IN DE NOVO PHOSPHOLIPID BIOSYNTHESIS.[SIMILARITY] BELONGS TO THE 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE FAMILY
based on sequence similarity to yeast YMC1 and presence of mitochondrial carrier protein domain; with sequence similarity to yeast YMC1 (mitochondrial energy transfer protein)
based on presence of defining chelatase domain, ATPase and vonWillebrand factor domain and sequence similarity and support from Phaeodactylum EST
RT17, ribosomal protein 17 mitochondrial small ribosomal subunit
RT17, ribosomal protein 17, mitochondrial small ribosomal subunit, nuclear encoded, translation, protein biosynthesis
actin-related protein centractin-like protein
No similarity to any known sequences.; hypothetical gene
based on sequence similarity and presence of sodium bile acid symporter domain
Likely amino acid transport. Location unknown.
Shows weak sequence similarity with ATPase alpha subunit 2 in vertebrates.
basic leucine zipper protein smilarity, DNA binding, transcription factor; basic leucine zipper protein similarity, DNA binding, transcription factor
No similarity to any known sequences; hypothetical gene
Partial support by cDNA; unknown protein
Bears sequence similarities to trifunctional enzyme alpha subunit, fatty oxidation complex alpha subunit, 3-hydroxyacyl-CoA dehydrogenase. Very little Phaeodactylum cDNA support.; unknown protein
based on sequence similarity to bacterial proteins and presence of defining domain
The WD40 repeat motif is about 40 residues long, and contains a central Trp-Asp motif. Such a repetitive segment has been shown to exist in a number of proteins, including G-beta-like peptides, yeast STE4, MSI1, CDC4, CDC20, MAK11, PRP4, PWP1 and TUP1, slime-mold AAC3 and coronin, and Drosophila Groucho protein. The number of repeats within these proteins varies between 5 (PRP4, TUP1, and Groucho) and 8 (G-beta, STE4, MSI1, AAC3, CDC4, PWP1, etc.). In G-beta and G-beta like proteins, the repeats span the entire length of the sequence, while in other proteins, they make up the N-terminal, the central or the C-terminal section.
26S proteasome subunit beta type 1-like protein
Putative proteasome subunit similar to beta type 1 (20S proteasome alpha subunit F) (Proteasome component C5) (TAS-F22/FAFP98) (model%: 100, hit%: 91, score: 307, %id: 37) [Arabidopsis thaliana]
Putative protein of unknown funtion containing a lipase domain, similar to (NC_000917) lysophospholipase [Archaeoglobus fulgidus] (model%: 45, hit%: 86, score: 283, %id: 31) [Archaeoglobus fulgidus]; EST support; putative protein of unknown funtion containing a lipase domain
Topoisomerases catalyse the interconversion of topological isomers of DNA and play a key role in DNA metabolism. Topoisomerase I catalyses an ATP-independent reaction, while topoisomerase II catalyses an ATP-dependent reaction, resulting in the formation of DNA supercoils. Eukaryotic enzymes can form both positive and negative supercoils, while prokaryotic enzymes form only negative supercoils.Eukaryotic topoisomerase II exists as a homodimer; in bacteriophage T4 it consists of three heterologous subunits; in prokaryotes it exists as a tetramer of two subunits (two each of gyrA and gyrB); and in E.coli, a second type II topoisomerase, involved in chromosome segregation (topoisomerase IV), consists of two subunits (parC and parE). GyrB, parE, and the product of bacteriophage T4 gene 39, are all similar to the eukaryotic proteins.Structural studies of E.coli topoisomerase II have shown that the enzyme binds to DNA, forming a complex in which a DNA strand of approximately 120 base pairs is wound around a protein core. At low resolution, this complex resembles a flattened sphere, and may be heart-shaped, with the DNA embedded in the protein. There is evidence for channels or cavities in the complex, which may have a role in the DNA translocation process.The gyrB protein possesses 2 uniquely-folded domains. The N-terminal domain (domain 1) possesses ATP-binding and hydrolysis functions, and forms an 8-stranded anti-parallel beta-sheet with unusual strand connectivities - the structure, which is stabilised by a hydrophobic core, can be subdivided into 6- and 2-stranded anti-parallel sheets, connected by a parallel sheet. The C-terminal domain (domain 2) contains a 4-stranded mixed parallel and anti-parallel beta-sheet. Four helices are also present, 2 of which are rich in arginine residues. The gyrB dimer is punctured by a 20A hole, which may provide a gateway through which DNA is passed during supercoiling. Every arginine of domain 2 protrudes into this hole, possibly creating a DNA-binding surface.From this structural information and results of various biochemical studies, a possible mechanism has been proposed: DNA is first bound by the gyrB dimer, then cleaved by gyrA. A large conformational change allows passage of another DNA strand through the double-stranded break and into the protein complex. This may involve ATP binding, exploiting the energy of association of ATP to the complex to stabilise an unfavourable protein conformation. The DNA break is then repaired by ligation, and the whole DNA molecule released - this possibly involves hydrolysis of ATP to ADP and organic phosphorous, which can dissociate from the protein, allowing the protein complex to return to its favoured conformation, and releasing the DNA.
One region of strong similarity, remainder is very dubious
CATALYZES THE NADP-DEPENDENT REDUCTION OF 2,4-DIENOYL-COA TO YIELD TRANS-2- ENOYL-COA. THE N-TERMINUS MAY CONTAIN THE FAD-BINDING DOMAIN WHEREAS THE NADPH-BINDING DOMAIN MAY BE LOCATED IN THE C-TERMINUS. SIMILAR TO THE OYE FAMILY OF NADH-DEPENDENT FLAVIN OXIDOREDUCTASES.
based on sequence similarity and EST support from Phaeodactylum; putative protein of unknown function with sequence similarity to conserved hypothetical
Good alignment with other organisms. Contains conserved ser/thr kinase domain (IPR002290). Supporting EST data from Phaeodactylum.
Supported by a diatom EST. Hits to peroxisomal proteins from other organisms are weak.; hypothetical protein with similarity to peroxisomal assembly proteins
hypothetical protein; putative RabGAP-contains RabGAP/TBC domain
Supported by sequence simularity only-no EST data
one of 22 hits of a hypothetical helicase from the Gtheta nucleomorph, no EST support; fragment of hypothetical DNA helicase
based on sequence similarity to cobyrinic acid synthase from bacteria and cyanobacteria and presence of defining domains
CONVERSION OF NADPH, GENERATED BY PERIPHERAL CATABOLIC PATHWAYS, TO NADH, WHICH CAN ENTER THE RESPIRATORY CHAIN FOR ENERGY GENERATION. Typically found in prokaryotes and in the eukaryotic mitochondria. In contrast to photosynthetic bacteria, this Nnt appears to be composed of a single polypeptide of the class found in animal mitochondria.; NAD(+) transhydrogenase
contains a Mitochondrial energy transfer protein domain; supported by a cDNA
contains prolyl oligopeptidase domains, partial Phaeodactylum EST support
partial cDNA support; contains Domain in components of the proteasome, COP9-complex and eIF3 (PCI)
protein with peroxisomal targeting peptide
Several matches to peroxisomal targeting peptides, but best hits are only to hypothetical proteins.
Putative protein similar to DNA-directed DNA polymerase epsilon subunit B; similar to gi|9988418|dbj|BAB12726.1| (AB048257) DNA polymerase epsilon subunit B [Xenopus laevis] (model%: 96, hit%: 96, score: 772, %id: 36) [Xenopus laevis]; putative protein similar to dna-directed DNA polymerase epsilon subunit
methylthioadenosine/S-adenosyl homocysteine nucleosidase
Putative methylthioadenosine/S-adenosyl homocysteine nucleosidase (adenosylhomocysteine nucleosidase) (S-adenosyl-L-homocysteine homocysteinylribohydrolase) very similar to gi|18087497|gb|AAL58883.1|AF458088_1 (AF458088) methylthioadenosine/S-adenosyl homocysteine nucleosidase [Oryza sativa] (model%: 96, hit%: 91, score: 503, %id: 44)
probable function: seems to function as a cochaperonin, along with CPN60, and in certain cases is essential for the discharge of biologically active proteins from CPN60. Belongs to GroES chaperonin family. Putatively targeted to mitochondrion; similar to 10 kDa chaperonin (CPN10) in arabidopsis thaliana, GroES
based on sequence similarity and presence of defining domain for N-terminus of rad21; n-terminus of rad21-like protein
putative protein based on sequence similarity to hypothetical RIKEN cDNA from mouse; putative protein of unknown function
Putative bisphosphate nucleotidase (halotolerance protein); similar to O94505 (O94505) Halotolerance protein (3'(2'),5'-bisphosphate nucleotidase) (model%: 100, hit%: 77, score: 442, %id: 37) [Schizosaccharomyces pombe]
Contains conserved HSP70 domain (IPR001023). Supporting EST data. Weak similarity to other hsp's in database (36% amino acid identity), which is low considering the very high sequence conservation in this family of heat shock proteins among other organisms.
Probable signal peptidase; similar to gi|17230467|ref|NP_487015.1| signal peptidase I [Nostoc sp. PCC 7120] (model%: 99, hit%: 98, score: 223, %id: 31) [Nostoc sp. PCC 7120]
meiotic check point regulator-like protein
based on sequence similarity to FtsH from bacteria and ATPase domain
SUPT6H,-like protein to suppressor of ty 6
SUPT6H, homolog to suppressor of Ty 6 from S. cerevisiae, transcription factor
Glutamine-dependent carbamoyl-phosphate synthase. Catalyzes the first or last step in the synthesis or breakdown of urea.
Part of the valine, leucine, isoleucine biosynthesis pathway. Identified via high similarity to known sequences. Partial Phaeodactylum cDNA support.
Urease transporter inferred from strong homology to other active urase transporters in Oryza, and Arabidopsis. REQUIRED FOR ACTIVE TRANSPORT OF UREA. BELONGS TO THE SODIUM:SOLUTE SYMPORTER FAMILY (SSF).
based on presence of leucine-rich repeats and limited sequence similarity to other proteins containing LRR; putative protein containing leucine-rich repeats including ribonuclease inhibitor family
D-glyceraldehyde 3-phosphate = glycerone phosphate; putative
RS15A, ribosomal protein 15 40S small ribosomal subunit
RS15A, ribosomal protein 15, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
RL35A, ribosomal protein 35A 60S large ribosomal subunit
RL35A, ribosomal protein 35A, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
clathrin is the major protein of the polyhedral coat of coated pits and vesicles trafficking between plasma membrane and trans;golgi network; clathrin has a triskelion structure composed of three heavy chains and three light chains that are the basic subunits of the clathrin coat. The C-terminal domain forms the hub of the triskeleton and contains the trimerization domain and the light chain binding domain involved in the assembly of the clathrin lattice.
based on sequence similarity and presence of defining domains
RS2, ribosomal protein 2, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
probable purine-nucleoside phosphorylase
Probable purine-nucleoside phosphorylase very similar to gi|1311143|pdb|1PBN| Purine Nucleoside Phosphorylase (model%: 100, hit%: 89, score: 564, %id: 45) [Bos taurus]; EST support
Retinal 3',5'-cGMP phosphodiesterase (PDE) is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion.; hypothetical protein with some similarity to cyclic nucleotide phosphodiesterases