Thalassiosira pseudonana CCMP1335 chromosome 15, 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 CM000650.\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##
Contains wd40 repeats. 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.
TPS_100678 is homologous to EPK2 found in Euglena gracilis Z., which is a PKA homologue in the photosynthetic flagellate. At the timeof annotation (01/03) this was the only occurrence of the PKA catalytic subunit in photosyntheticorganisms.
Putative adenosine deaminase, similar to gi|22831206|dbj|BAC16064.1| (AP004378) adenosine deaminase [Oryza sativa (japonica cultivar-group)] (model%: 99, hit%: 92, score: 448, %id: 33) [Oryza sativa (japonica cultivar-group)]
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
model contains all conserved residues of bacterial response regulator receiver domain including aspartyl residue that is the site of phosphorylation. receiver domain is present DNA binding output domain not found.
Homology to ATP binding domain of cyanobacterial serine/threonine kinas; hypothecial protein
This protein contains InterPro domains IPR004046 and IPR002109. IPR004046 is a glutatione S-transferase, C-terminal domain (GST_C), which, in eukaryotes, participates in the detoxification of reactive electrophilic compounds by catalysing their conjugation to glutathione. IPR002109 is a glutaredoxin domain, which functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides.; NP_488086; putative protein similar to hypothetical protein
probable farnesyl pyrophosphate synthetase
A variety of isoprenoid compounds are synthesized by various organisms. For example in eukaryotes the isoprenoid biosynthetic pathway is responsible for the synthesis of a variety of end products including cholesterol, dolichol, ubiquinone or coenzyme Q. In bacteria this pathway leads to the synthesis of isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids. Among the enzymes that participate in that pathway, are a number of polyprenyl synthetase enzymes which catalyze a 1'4-condensation between 5 carbon isoprene units. It has been shown that all the above enzymes share some regions of sequence similarity. Two of these regions are rich in aspartic-acid residues and could be involved in the catalytic mechanism and/or the binding of the substrates.
Putative protein of unknown function with similarities to NG-dimethylarginine dimethylaminohydrolase 1 (Dimethylargininase 1) (Dimethylarginine dimethylaminohydrolase 1) (DDAHI); similar to gi|6831528|sp|O94760|DDH1_HUMAN NG,NG-dimethylarginine dimethylaminohydrolase 1 (model%: 91, hit%: 93, score: 265, %id: 31) [Homo sapiens]; putative protein of unknown function with similarity to ng-dimethylarginine dimethylaminohydrolase 1 (Dimethylargininase 1) (Dimethylarginine dimethylaminohydrolase 1)
This protein of unknown function contains a 7-Fold repeatfound in clathrin and VPS proteins.Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Also, a homologous protein of unknown function in Mus musculus (Mouse) is inferred tocontain a z inc finger, C3HC4 type (RING finger). This type of RING-finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc,and is probably involved in mediating protein-protein interactions.homologous to Homo Sapien hypotheticalal protein ACCESSION CAD38698; hypothetical protein
similar to SKP1-like protein ASK10 [Arabidopsis thaliana] (model%: 83, hit%: 93, score: 310, %id: 42) [Arabidopsis thaliana]; putative protein similar to SKP1 component of ubiquitin protein degradation pathway
molecular motor involved in microtubule-based transport
nascent-polypeptide-associated complex alpha polypeptide-like protein
no EST data; hypothetical protein with some sequence similarity to a putative oxidoreductase
cystinosin defects in mammals cause lysosomal cystine accumulation secondary to defective lysosomal cystine efflux.; putative protein similar to cystinosin
Contains InterPro domain #IPR002068 for HSP20 proteins. Also contains similarity to Pfam model #00011 for HSP20/alpha crystallin family. This gene has EST support from Phaeodactylum. It is most similar to HSP20 genes from prokaryotes. Possibly mitochondrial?
protein kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases; putative protein kinase
Some similarity to other organisms (54% amino acid identity); Supporting EST data; contains conserved AAA domain (IPR003959), ATPases associated with variuos cellular activities.; nuclear valosin-containing protein
Putative trypsin-like serine protease, similar to At2g47940-68297.m05128 F17A22.33 T9J23.7 DegP2 protease identical to DegP2 protease GI:13172275 from [Arabidopsis thaliana] (model%: 76, hit%: 51, score: 452, %id: 38) [Arabidopsis thaliana]
contains conserved protein phosphatase 2C domain (PP2C); hypothetical protein containing a protein phosphatase 2C domain (PP2C)
Possibly involved in riboflavin metabolism Contains a posphoglycerate mutase domain
Putative protein of unknown function, containing a prolyl aminopeptidase domain, similar to At4g24160-68296.m02554 T19F6.150 putative protein CGI-58 protein - Homo sapiens,PID:g4929585 (model%: 77, hit%: 69, score: 353, %id: 31) [Arabidopsis thaliana]; EST support; putative protein of unknown function, containing a prolyl aminopeptidase domain
sequence similarity to human chromatin assembly factor. presence of multiple WD-40 domains characteristic of this protein. T. pseudonana EST support; CAF-1,retinoblastoma binding protein p48, similar to G1/S transition control protein-binding protein RbAp46
based on presence of urea transporter domain, EST support from T. pseudonana exponentially growing culture, sequence similarity to mamalian sequences and presence of transmembrane domains
Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both side by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).
Probable betaine aldehyde dehydrogenase; similar to gi|23501441|ref|NP_697568.1| (NC_004310) betaine aldehyde dehydrogenase [Brucella suis 1330] (model%: 88, hit%: 90, score: 1181, %id: 51) [Brucella suis 1330]
Looks like targeted to mitochondrion; UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase
Putative protein, similar to dihydroorate oxidase (DHOdehase) (dihydroorotate dehydrogenase) (dihydoorotic acid dehydrogenase) (DHO dehydrogenase) (4,5-L-dihydroorotate:oxygen oxidoreductase) (S-dihydroorotate:oxygen oxidoreductase); seeAt5g23300-68299.m02351 MKD15.16 dihydroorotate dehydrogenase precursor (dihydroorotate oxidase) (sp|P32746); supported by cDNA: gi_16448_emb_X62909.1_ATPYRD (model%: 81, hit%: 79, score: 764, %id: 47) [Arabidopsis thaliana]; weak EST support; putative protein
No reasonable similarity to any known sequences. Partial cDNA support.; hypothetical gene
Ribosomal protein (nuclear-encoded), part of 60S subunit of cytoplasmic ribosome.
Weak similarity to other organisms, but strong supporting EST data suggest this is a real gene; contains conserved putative tRNA binding domain (IPR002547)
Protein phosphatase 2C (PP2C) is one of the four major classes of mammalian serine/threonine specific protein phosphatases; shows broad substrate specificity and is dependent on divalent cations; contains conserved PP2C domain; putative protein phosphatase
eukaryotic translation initiation factor
Synonym(s): Suvar3-9,Enhancer-of-zeste,Trithorax Several proteins that contribute to epigenetic mechanisms of gene regulation contain a characteristic 130 amino acid motif of unknown function called the SET domain. The SET domain genes are widely represented in the eukaryotic genomes,and proteins were initially distributed into four families,SU(VAR)3-9,E(Z),ASH1 and TRITHORAX based on the homology of their SET domains. Addtional proteins have now been identified which do not fit into this classification [PMID: 12039029]. The SET domain is mainly found in proteins with multi-cellular functions,although some exceptions to this are found in yeasts. It appears to be a protein-protein interaction domain,however histone-specific methylase activity has been associated with the SET-domain of SU(VAR)3-9 family members. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control. The SET domain containing Drosophila protein,enhancer of zeste,has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure.
Zinc finger protein similarity, PHD motif, DNA binding, transcription factor; zinc finger protein similarity, PHD motif, DNA binding, transcription factor
No EST evidence, but several alignments with cytochrome P450s from Arabidopsis. Also good hits to Pfam and InterPro P450 domains.; hypothetical protein similar to cytochrome P450, possibly vitamin D(3) 24-hydroxylase
Function unkown.; hypothetical protein with weak similarity to putative UDP-glucose:sterol glucosyltransferase
Phytoene dehydrogenase (phytoene desaturase) is an enzyme of carotenoid biosynthesis that converts phytoene into zeta-carotene via the symmetrical introduction of two double bonds at the C-11 and C-11' positions of phytoene. The sequence of phytoene dehydrogenase from bacteria (gene crtI or carC) and fungi (gene AL-1) are not related to that from cyanobacteria and plants but is evolutionary related to that of another enzyme of carotenoid biosynthesis, methoxyneurosporene dehydrogenase (gene crtD). There are two glycine-rich conserved regions, both of which probably play a role in the binding of either FAD or NAD. The first conserved region is in the N-terminal section while the second one is in the C-terminal section.; putative protein with some similarity to phytoene dehydrogenase
function: reduction of geranylgeranyl pyrophosphate and geranylgeranyl chlorophyll; similar to similar to geranylgeranyl hydrogenase in nostoc sp
Contains RCC1 repeats. RCC1 (regulator of chromosome condensation 1) binds chromatin and serves as GEF for Ran-type small GTPases; however, RCC1 repeats are found in other GEFS as well (not a Ran-specific feature)
phosphatidylinositol-4-phosphate 5-kinase (PIP5K)-like protein
PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate a precursor in the phosphinositide signaling pathway; contains conserved PIP5K domains.
Putative protein of unknown function, similar to gi|23100447|ref|NP_693914.1| (NC_004193) hypothetical conserved protein [Oceanobacillus iheyensis] (model%: 65, hit%: 58, score: 154, %id: 24) [Oceanobacillus iheyensis]; EST support; putative protein of unknown function containing a trypsin-like serine protease domain
sequence similarity and Phaeodactylum EST support
hypothetical protein with similarity to atp-dependent RNA helicases
putative GTP pyrophosphokinase based on sequence similarity and defining domains
3',5'-cyclic nucleotide phosphodiesterase
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.
The SpoU_methylase protein of Saccharomyces cerevisiae hasn been shown to be required for ribose methylation at a universally conserved nucleotide in the peptidyl transferase center of the mitohondrial large ribosomal RNA (21S rRNA).
HSF45, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF45, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
similar to mitochondrial precursor, 39 kDA subunit found in human and cow.
putative protein, zinc finger motif, supported by EST data, Cx2Cx11Hx4H; putative protein, zinc finger motif
succinate/fumarate mitochondrial transporter
based on sequence similarity and mitochondrial substrate carrier domain