Thalassiosira pseudonana CCMP1335 chromosome 22, 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 CM000653.\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##
No reasonable similarity to any known sequences.; hypothetical gene
similar to TIM23, translocase of inner mitochondrial membrane
Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Ascorbate peroxidase is the main enzyme responsible for hydrogen peroxide removal in chloroplasts and cytosol of higher plants. Although this gene lacks the domain for 'plant ascorbate peroxidase', the fact that it is currently trucated must be taken into consideration. This gene has EST support from Phaeodactylum, but not T. pseudonana. It contains InterPro domain #IPR002016 for haem peroxidases and strong similarity to Pfam model #PF00141 for peroxidases. The best hit to this protein (score of 643) was to ascorbate peroxidase from Euglena gracilis.
hypothetical protein with homology to formins
member of the clp superfamily, regulatory beta subunit
Clp proteins are involved in protein degradation, chaperone function and heat shock response. The given gene by similarity seems to be involved in protein degradation. It is ost similar to cyanobacterial beta subunits. At least 6 more regulative subunits are in the T. pseudonana genome.
sequence similarity to other proteins of unknown function from cyanobacteria; putatative protein with transmembrane domain of unknown function
It is part of the hererodimer that is required for meiotic recombination; homologous to MutL (
contains a conserved phosphatidylinositol-4-phosphate 5-kinase domain; PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate a precursor in the phosphinositide signaling pathway; hypothetical protein containing a phosphatidylinositol-4-phosphate 5-kinase domain
RPC6, dna-directed RNA polymerases III 39 kDa polypeptide
Contains an iron-sulfur cluster binding domain, a CO dehydrogenase flavoprotein C-terminal domain, and aldehyde oxidase/xanthine dehydrogenase a/b hammerhead and molybdopterin binding domains. Partial support by Phaeodactylum cDNA.; hypothetical gene
Fucoxanthin chlorophyll a/c protein, member of LHC superfamily. No introns; FCP4
No reasonable similarity to known sequences.; hypothetical gene
An enzyme involved in glycolysis. Reaction catalyzed: fructose 1,6-bisphosphate = dihydroxyacetone phosphate + glyceraldehyde 3-phosphate.; putative
[FUNCTION] PROBABLY PLAYS A ROLE IN FACILITATING THE ASSEMBLY OF MULTIMERIC PROTEIN COMPLEXES INSIDE THE ER. [SUBCELLULAR LOCATION] ENDOPLASMIC RETICULUM LUMEN. [SIMILARITY] BELONGS TO THE HEAT SHOCK PROTEIN 70 FAMILY.
High homology to hypothetical proteins from a variety of organisms. May contain a beta lactamase motif
intraflagellar transport protein, bld1, osm-6
IFT proteins are part of a large complex that are transported along ciliary microtubules and are required for assembly of cilia.
Unknown function; putative protein of unknown function, supported by EST data
Unknown protein.; putative protein, supported by EST data
Possible V-ATPase proteolipid subunit. Less significant hit than other gene model however. EST support.
This model contains the motif for the prolyl 4-hydroxylase alpha subunit C-terminus. It is most similar to unknown proteins in Arabidopsis thaliana. There is partial EST support for this model; hypothetical protein similar to prolyl 4-hydroxylase alpha subunit C-terminus
histone deacetylase HDAC silent information regulator protein 2 Sir2 sirtuin
Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are all members of this ancient protein superfamily. One family of histone deacetylases is known as the Sir2 family.
based on sequence similarity to metazoan proteins, presence of domain found in other hypothetical proteins and predicted transmembrane domains; hypothetical protein with transmembrane domains
MYB DNA binding protein/ transcription factor-like protein
Member of MYB DNA binding protein/ transcription factor family.
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.
Putative metalloprotease (metallopeptidase); similar to gi|417743|sp|Q02038|NEUL_PIG Neurolysin, mitochondrial precursor (Neurotensin endopeptidase) (Mitochondrial oligopeptidase M) (Microsomal endopeptidase) (MEP) (Soluble angiotensin-binding protein) (SABP) (Endopeptidase 24.16) (model%: 100, hit%: 91, score: 798, %id: 32) [Sus scrofa]
Thioredoxin, two peculiar one base misfits between EST data and genomic sequence
20S proteasome alpha subunit B) (20S proteasome subunit alpha-2
contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
translation initiation factor eif-2b alpha subunit
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
Contains homology to cytochrome C/heme binding site
heme regulated eukaryotic translation initiation factor-like protein
TPS_108356 is similar to many alpha kinase eukaryotic translation inititation factor proteins.Also, TPS_108356 is significantly homologous to the known heme-regulated eIF-2 alpha kinasegenes in vertebrates. At present, there are two distinct mammalian eIF-2alpha kinases that have been cloned, the double-stranded-RNA-dependent eIF-2 alpha kinase(PKR) and the heme-regulated eIF-2 alpha kinase (HRI). HRI is activated under conditions ofheme deficiency in immature erythroid cells, and its activity is inhibited by heme.
catalyzes the formation of spermidine (from putrescine) or spermine (spermidine) EST support
one of 22 hits of a hypothetical DNA helicase forn the Gtheta nucleomorph, EST support; fragment of putative DNA helicase
Function unknown.; hypothetical protein with weak similarity to phosphoglucomutase
based on sequence similarity to sur1 protein from yeast
HSF31, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF31, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
N-acetylglutamate synthase. Amino Acid Metabolism; Urea cycle and metabolism of amino groups. Converts glutamate to N-Acetylglutamate for Aginine synthesis.
Putative papain cysteine protease, similar to At3g45310-68298.m04185 F18N11.70 cysteine proteinase AALP, putative similar to AALP protein GI:7230640 from [Arabidopsis thaliana] and barley aleurain (model%: 90, hit%: 60, score: 343, %id: 35) [Arabidopsis thaliana]
histone deacetylase Rpd3 HDA2 HDA1 HDAC HD2
Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are all members of this ancient protein superfamily
Presumably effects the conversion of GDP-4-keto-6-deoxy-D-mannose to GDP-L-fucose via a GDP-4-dehydro-L-fucose intermediate.; putative; gdp-4-keto-6-deoxy-d-mannose epimerase-reductase
homology to putative serine/threonine kinases of cyanobacteria and ATP binding domain; hypothetical protein
most similar to animal homologues, much less similar to G. theta, i.e. the ancestral red algal gene was lost
dual-specificity tyrosine-phosphorylation regulated kinase 1a-like protein
Contains conserved ser/thr protein kinase domains (IPR002290) and tyr kinase domain (IPR001245). Aligns with dual specificity kinase in humans with 52% identity on the amino acid level.
Serine/threonine (S/T) phosphatases catalyse the dephosphorylation of phosphoserine and phosphothreonine residues; contains conserved serine/threonine protein phosphatase.
Putative protein belongs to a family of flavoprotein monooxygenase proteins.; similar to polyketide hydroxylase; hypothetical protein
One of main fucoxanthin chlorophyll a/c proteins; member of LHC superfamily.; FCP1
Supported by EST data; conserved hypothetical protein
similar to acyl-CoA binding protein; hypothetical protein
Contains homology to hypothetical proteins from a variety of organisms
cold-shock DNA-binding domain-containing protein
Contains InterPro domain #IPR002059 which is a cold-shock DNA-binding domain. Contains some similarity to Pfam model #PF00313 for cold-shock DNA-binding domain (CSD). This protein has EST support. The best hit was to a cold shock protein from Triticum aestivum (E=3e-25).
Eukaryotic 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. There are a number of conserved regions in the catalytic domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a glycine-rich stretch of residues in the vicinity of a lysine residue, which has been shown to be involved in ATP binding. In the central part of the catalytic domain there is a conserved aspartic acid residue which is important for the catalytic activity of the enzyme.
Similar to ATP-dependent RNA-helicase of yeast
typical eukaryotic GS isoform (GSII), ammonium assimilation; GLNA