Thalassiosira pseudonana CCMP1335 chromosome 13, 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 CM000648.\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##
Guanylate cyclases catalyze the formation of cyclic GMP(cGMP) from GTP. cGMP acts as an intracellular messenger, activating cGMP-dependent kinases and regulating CGMP-sensitive ion channels. The role of cGMP as a second messenger in vascular smooth muscle relaxation and retinal photo-transduction is well established. Guanylate cyclase is found both in the soluble and particular fraction of eukaryotic cells. The soluble and plasma membrane-bound forms differ in structure, regulation and other properties. Most currently known plasma membrane-bound forms are receptors for small polypeptides. The soluble forms of guanylate cyclase are cytoplasmic heterodimers having alpha and beta subunits.
rna-binding protein of the pumilio family
presence of pumilio domains and sequence similiarity suggest may be RNA binding protein involved in tranlational repression
Poor alignment with other organisms, but very strong EST data suggests this is a gene. Contains guanylate cylase domains (IPR001054).
MYB DNA binding protein/ transcription factor-like protein
Member of MYB DNA binding protein/ transcription factor family.
RanGAP, ran-binding protein 1-like protein
C-terminal half is lacking, putative pseudogene; delta subunit of clathrin adaptor protein complex AP3 (APD3), fragment
syntaxin, t-snare coiled-coil domain family
eukaryotic translation initiation factor 6
This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologues. Eukaryotic translation initiation factor 6 (eIF6) binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit. The Saccharomyces cerevisiae gene that encodes the 245-amino-acid eIF6 (calculated Mr 25,550), designated TIF6, has been cloned and expressed in Escherichia coli. The purified recombinant protein prevents association between 40S and 60S ribosomal subunits to form 80S ribosomes.
RK17, ribosomal protein 17 50S large ribosomal subunit, chloroplast
RK17, ribosomal protein 17, 50S large ribosomal subunit, chloroplast, nuclear encoded, translation, protein biosynthesis
This protein is up regulated by copper toxicity based on ESTs obtained from a subtraction library. The best hit in the browser comes up as dentin phosphoryn from Homo sapiens, however, this is only to a region containing a stretch of serine residues. When this region is masked out, the best hit (E=0.003) is to ebiP6832 from the Anopheles gambiae genome sequence. ebiP6832 was a direct submission and there seems to be no other information available about it.; unknown EST protein
HSF15, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF15, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
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. 49% amino acid identity to STE20/MAP4K family. Has a partial MAP kinase signature sequence, WMAPEV; putative protein kinase, simliar to STE20
Supported by partial cDNA.; hypothetical unknown gene
based on sequence similarity to conserved hypotheticals from bacteria; hypothetical protein
involved in intracellular vesicle traffic; subunit of protein complex that coats golgi vesicles
based on sequence similarity to hypothetical fungal proteins. Contains sprT domain which suggests may play a role in translation elogation; putative protein of unknown function
HSF16, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF16, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
hypothetical protein with thioredoxin type domains
Has ABC transporter like motifs but in the untranslated region???; unknown function
HSF13,Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF13, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
based on sequence similarity and presence of defining domains. Likely catalyzes the transfer of an intact diphosphate (PP) group from ATP to ribose-5-phosphate (R-5-P), which results in the formation of AMP and 5-phospho-D-ribosyl--1-diphosphate (PRPP).
RS8, ribosomal protein 8, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
Contains SNF2-related domain, and helicase C-terminal and DEAD/DEAH box domains.; hypothetical protein similar to putative DNA dependent ATPase and helicase
alpha subunit of tetrameric clathrin adaptor complex AP1
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.
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); GEF, GEP, GDP/GTP exchange protein
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
based on sequence similarity to fungal proteins; putative protein with sequence similarity to glucanase
Protein biosynthesis; Ligase; ATP-binding; needed for porphryin biosynthesis
This gene model does not have any EST support. It contains the conserved domain for prolyl 4-hydroxylase alpha subunit. It is most similar to putative prolyl 4-hydroxylase, alpha subunits in Arabidopsis thaliana.; hypothetical protein similar to the prolyl 4-hydroxylase alpha subunit
The best hit to this gene (e value = 5.6e-17) was to ZP_00018131 a hypothetical protein from Chloroflexus aurantiacus. It also had some similarity (e value = 9.2e-11) to NP_625702 a putative integral membrane protein from Streptomyces coelicolor and to NP_243797 a permease (major facilitator superfamily) from Bacillus halodurans with an e value of 2.8e-8.; hypothetical protein similar to ZP_00018131 hypothetical protein
Function unknown but is possibly involved in the acetylation of D-glucosamine 6-phosphate or the hydrolysis of acetate from N-acetyl-D-glucosamine 6-phosphate.; hypothetical protein sharing some sequence similarity with a putative n-acetylglucosamine-6-phosphate deacetylase
monogalactosyldiacylglycerol synthase i a-like protein
supported by EST data; putative protein of unknown function
Putatively targeted to mitochondrion; NDI
Possible calcium transporting atp-ase, cation transport
Limited sequence similarity to other proteins. No EST support. Presence of leucine-rich repeats; putative protein of unknown function, presence of leucine-rich repeats
similar to ubiquitin-protein ligase 1, putative similar to GB:AAF36454 from [Arabidopsis thaliana] (model%: 98, hit%: 9, score: 627, %id: 40) [Arabidopsis thaliana]; EST support
May catalyse the carboxyl-end addition of 2 carbons to long chain fatty acids. Microsomal membrane bound.
Similarity to other 70 kDa heat shock proteins probably due to the presence of InterPro domain #IPR001023, which is characteristic of HSP70 family members. Has reasonable homology to pfam model #PF00012 for hsp70 proteins.
reductase of ferredoxin thioredoxin reductase
Ferredoxin thioredoxin reductase, beta subunit precursor contains N-terminal bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
Putative anaphase promoting complex subunit, similat to gi|16197625|gb|AAL13436.1| (AY052402) anaphase promoting complex subunit 11 [Arabidopsis thaliana] (model%: 97, hit%: 97, score: 269, %id: 48) [Arabidopsis thaliana]
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 protein phosphatase 2C-like domain (IPR001932).; putative protein phosphatase
HSF18, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF18, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
FUNCTION: ACTIVATION OF LONG-CHAIN FATTY ACIDS FOR BOTH SYNTHESIS OF CELLULAR LIPIDS, AND DEGRADATION VIA BETA-OXIDATION. PREFERENTIALLY USES ARACHIDONATE AND EICOSAPENTAENOATE AS SUBSTRATES (by similarity) CATALYTIC ACTIVITY: ATP + a long-chain carboxylic acid + CoA = AMP + diphosphate + an acyl-CoA. COFACTOR: MAGNESIUM (BY SIMILARITY).
This protein is up-regulated by copper toxicity. An EST fragment of this gene was obtained from a subtraction library that was enriched for genes up-regulated by copper toxicity. It is located within an inverted repeat and grail# 23.69.1 is almost identical to this gene (They differ by 3 amino acids out of 292 amino acids).; EST support.; unknown protein with
proline rich protein kinase like protein
TPS_102873 is significantly homologous to other protein kinase like genes over a very short segment of about 100 amino acids. Also, the protein is predicted to contain a proline-rich region.
putative ubiquinol cytochrome c reductase based on sequence similarity and presence of defining domain
There is no EST support yet for this gene. It contains the motifs for G-protein beta WD-40 repeats.; hypothetical protein similar to wd-repeat protein
similar to ubiquitin-protein ligase 1, putative similar to GB:AAF36454 from [Arabidopsis thaliana] (model%: 98, hit%: 9, score: 631, %id: 38) [Arabidopsis thaliana]; EST support
putative NADH dehydrogenase supported by sequence similiarity, presence of defining domains, and Phaeodactylum EST support; NADH:ubiquinone oxidoreductase
phosphatase 2A (PP2A) regulatory subunit B-like protein-like protein
dephosphorylates proteins. very short region similar to EF hand domain (IPR002048).
RL6, ribosomal protein 6, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
based on sequence similarity, EST support from Phaeodactylum, and presence of defining domains. Likely catalyzes conversion of O-phospho-L-homoserine and water into L-threonine and orthophosphate, using pyridoxal phosphate as a cofactor in threonine biosynthesis
dual specific tyrosine protein phosphatase
A group of enzymes removing the serine/threonine or tyrosine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes which have been phosphorylated under the action of a kinase. Dual specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle; contains conserved dual-specificity phosphatase domains
based on sequence similarity; putative protein of unknown function with sequence similarity to oryza protein of unknown function
Putative pseudouridylate synthase (pseudouridine synthase) (uracil hydrolase); similar to gi|15642221|ref|NP_231854.1| (NC_002505) pseudouridine synthase family 1 protein (model%: 82, hit%: 70, score: 332, %id: 34) [Vibrio cholerae]
Good hits to ABC transporters and domains
Probably nuclear-encoded chloroplast targeted. Potential Met and signal sequence about 120 amino acids upstream
ABC transporter, possibly for metal detoxification or drug efflux
signal recognition particle-like protein
HSF43, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF43, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
most closely related to fungal sequences
Nearly complete cDNA support. No similarity to any known sequences.; unknown protein
with sequence similarity to human Rab6GAP
putative membrane protein based on presence of Nonaspanin (TM9SF)domain and EST support.
receptor mediated endocytosis protein-like protein
In C. elegans, the homologous protein is endosome-associated and is required for endocytic recycling
cleavage and polyadenylation specificity factor
based on sequence similarity and presence of defining domains
Similarity to regions of hsp70 proteins from other organisms. Contains InterPro domain #IPR001023, which is found in heat shock protein (hsp70) family members.
2-oxoglutarate dehydrogenase E1 component
Component of the multienzyme 2-oxoglutarate dehydrogenase complex. CATALYTIC ACTIVITY:2-oxoglutarate + lipoamide <=>S-succinyldihydrolipoamide + CO(2. This step is part of the citric acid cycle.
No similarity to any known sequences. Partial cDNA support.; unknown protein