Thalassiosira pseudonana CCMP1335 chromosome 14, 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 CM000649.\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##
transcription factor IID, TATA box binding protein
TPS_106511 is sgnificantly homolous to Arabasopsis hypothetical proteins as well as hyptotheticalproteins in eukaryotic animals. Also the model shows similarity to cell cycle cwf25 proteins in yeast.; with sequence similarity to Arabidopsis hyopthetical protein; putative protein supported by cDNA
Function unknown, but possibly catalyzes the reaction:D-mannose 6-phosphate = D-fructose 6-phosphate; hypothetical protein with similarity to mannose-6-phosphate isomerase
Putative protein of unknown function containing leucine-rich repeats, some similarities to At3g56370-68298.m05379 T5P19.20 putative protein leucine-rich receptor-like protein kinase - Malus domestica, EMBL:AF053127 (model%: 23, hit%: 12, score: 213, %id: 40) [Arabidopsis thaliana]; strong EST support; putative protein of unknown function containing leucine-rich repeats
Probable trypsin-like serine protease; good EST support
EST evidence from Phaeodactylum. Good hits to other formyltetrahydrofolate deformylases including Synechocystis. This is the only good hit to an enzyme that catalyzes the formation of formate from N-formyl derivatives.
Putative protein with strong similarities to xylitol dehydrogenase (D-xyulose reductase) (erythritol dehydrogenase) (pentitol-DPN dehydrogenase); similar to gi|23096116|dbj|BAC16227.1| (AB091690) xylitol dehydrogenase [Gluconobacter oxydans] (model%: 95, hit%: 98, score: 617, %id: 48) [Gluconobacter oxydans]; EST support; putative protein with strong similarity to xylitol dehydrogenase
based on T. pseudonana and Phaeodactylum EST support; putative protein of unknown function
hypothetical protein with thioredoxin type domains
Identified by searching for nif genes-not in Kegg Tps annotation
Putative protein of unknown function containing leucine-rich repeats; somesimilarities to gi|18676566|dbj|BAB84935.1| (AK074109) FLJ00180 protein [Homo sapiens] (model%: 62, hit%: 80, score: 179, %id: 22) [Homo sapiens]; EST support; putative protein of unknown function containing leucine-rich repeats
eukaryotic translation initiation factor 4A
cDNA evidence for this protein in Arabidopsis; conserved unknown protein
hypothetical protein with similarity to peroxisomal membrane proteins
Identified based on sequence similarity and contains InterPro domain IPR004045. IPR004045 domain is a glutathione S-transferase, N-terminal domain (GST_N). GSTs catalyze the transfer of glutathione to a co-substrate containing a reactive electrophilic center to form a S-glutathionylated reaction product.
contains conserved protein kinase, serine threonine protein kinase, tyr kinase domain (IPR000719, IPR002290, IPR001245). Has a partial MAP kinase signature sequence, WMAPEV.; putative protein kinase
based on sequence similarity to sig3 protein from Thalassiosira weissflogii
Function unknown.; hypothetical protein with some sequence similarity to putative unknown proteins encoded by at_At5g52560-68299.m05097 and nr_18423407
Histone H3 is one of the four histones, along with H2A, H2B and H4, which forms the eukaryotic nucleosome octomer core; the nucleosome octamer winds 146 DNA base-pairs. It is a highly conserved protein of 135 amino acid residues.
RS29, ribosomal protein 29 40S small ribosomal subunit
RS29, ribosomal protein 29, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
RS5, ribosomal protein 5, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
contains an ATP/GTP binding domain; supported by cDNAs; protein of unknown function, contains similarity to unknown proteins
heterotrimeric G protein alpha subunit 1
Guanine nucleotide binding proteins (G-proteins) are a family of membrane-associated proteins that couple extracellularly-activated integral-membrane receptors to intracellular effectors, such as ion channels and enzymes that vary the concentration of second messenger molecules. G-proteins are composed of 3 subunits (alpha, beta and gamma) which, in the resting state, associate as a trimer at the inner face of the plasma membrane. This family consists of the G protein alpha subunit which binds guanyl nucleotide and is a weak GTPase.
gamma subunit of tetrameric clathrin adaptor complex AP2
APG2, AP2G1, CLAPG2, ADTG, gamma2-adaptin
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
Good hits to other phosphate transporters. The best hit was to a putative phosphate transporter from A. thaliana (At1g76430-68300.m07739) with an e value of 9e-43. Contains InterPro domain #IPR003662 which is characteristic of general substrate transporters.
one of 22 hits of a hypothetical DNA helicase from the Gtheta nulceomorph, ESt support; fragment of putative DNA helicase
The enzyme encoded by this gene likely catalyzed the synthesis of L-asparagine from L-aspartate. This form of the enzyme is ammonia-dependent rather than glutamine-dependent. There is high identity (52%) and similarity (66%) to a bacterial (Clostridium perfingens) sequence for this gene. There are no goods hits to Plasmodium, Synechocystis Anabaena, Thermosynechococcus, and Arabidopsis.; ammonia-dependent asparagine synthetase
Catalyzes a methylation reaction. S-adenosyl-L-methionine + cycloartenol = S-adenosyl-L-homocysteine + (24R)-24-methylcycloarta-8,25-dien-3beta-ol
chromosome condensation protein-like protein
RM24, ribosomal protein 24 mitochondrial large ribosomal subunit
RM24, ribosomal protein 24, mitochondrial large ribosomal subunit, nuclear encoded, translation, protein biosynthesis
Reaction catalyzed:UDP-glucose + 2 NAD + H2O = UDP-glucuronate + 2 NADH2. Note, also acts on UDP-2-deoxyglucose.; putative
No significant similarities to any blast hits. Good cDNA support.; unknown protein
This gene is supported by full-length EST.
Putative protein of unknown function, with similarities to IMP dehydrogenase (inosine monophosphate dehydrogenase), gi|16331252|ref|NP_441980.1| (NC_000911) IMP dehydrogenase [Synechocystis sp. PCC 6803] (model%: 68, hit%: 94, score: 141, %id: 25) [Synechocystis sp. PCC 6803]; putative protein of unknown function, with similarity to IMP dehydrogenase
similar to ORF543 from G. theta nucleomorph chromosome 1; hypothetical protein
presence of EGF domains and limited sequence similarity to sig3; putative protein with EGF domains
catalytic subunit of clp protein superfamily
clp proteins are involved in protein degradation, heat shock response and chaperone function. They consist of a regulatory subunit (clpABCX) and a catalytic subunit (clpP). The given gene is most similar to homologues from Guilliardia theta indicating gene transfer from the nucleomorph to the diatom host cell nucleus. There are at least 6 more clpP genes present in T. pseudonana.
Putative psedouridylate synthase (pseudouridine synthase) (uracil hydrolase), similar to pmu:PM1836 rsuA_2; ribosomal large subunit pseudouridine synthase A custom_KEGG (model%: 79, hit%: 94, score: 345, %id: 33) [Pasteurella multocida]; strong EST support
Unkown function, but has a putative phosphoglycerate mutase domain.; putative protein similar to translation product of arabidopsis gene
t-complex protein 1 alpha subunit chaperonin-like protein
Enzyme of the methionine metabolism pathway. Also shows good similarity to cystathionine gamma-lyase and cystathionine gamma synthase.
This model does not have EST support yet. It is most similar to other putative prolyl 4-hydroxylase alpha subunits in Arabidopsis thaliana.
based on presence of defining domains and sequence similarity
There is no EST support yet for this gene. It is similar to other probable microsomal signal peptidase amino acid sequences.; hypothetical protein similar to microsomal signal peptidase 22 kDa subunit
based on sequence similarity to bacterial hypothetical proteins; putative conserved hypothetical protein
dna-directed RNA polymerase I 40kDa polypeptide, rpo1-1-like protein
Contains RNA polymerase D/30 to 40kDa subunit domain (IPR001514); 49% amino acid identity to other organisms; strong supporting EST data.
molecular motor involved in actin-based transport
weak homology to core1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase from C. elegansgene model is supported by EST; function unknown
RS27, ribosomal protein 27 40S small ribosomal subunit
RS27, ribosomal protein 27, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
Putative protein of unknown function containing a metalloprotease domain, similar to gi|21301112|gb|EAA13257.1| ebiP3474 [Anopheles gambiae str. PEST] (model%: 100, hit%: 96, score: 1265, %id: 33) [Anopheles gambiae str. PEST]; EST support; putative protein of unknown function containing a metalloprotease domain
based on sequence similarity to conserved hypotheticals from Arabidopsis and cyanobacteria, and presence of ABC1 and kinase domains; putative protein with sequence similarity to conserved hypotheticalals
Putative protein containing CDC20 and WD40 domains, probably associated with ubiquitin-dpendent protein degradation; similar to putative cdc20 protein [Arabidopsis thaliana] (model%: 100, hit%: 69, score: 978, %id: 55) [Arabidopsis thaliana]; EST support; putative protein containing CDC20 and WD40 domains, probably associated with ubiquitin-dpendent protein degradation
Similar to proteins in Arabidposis and Humans; hypothetical protein
Probably leukotriene hydrolase (LKHA) (LTA) (aminopetidase) (metallopeptidase), similar to LKHA_HUMAN Leukotriene A-4 hydrolase (LTA-4 hydrolase) (Leukotriene A(4) hydrolase) (model%: 100, hit%: 91, score: 1227, %id: 45) [Homo sapiens]; EST support; hypothetical protein
phosphoadenosine-phosphosulphate reductase
Involved in sulfate assimilation (see annotation by Miroslav). The gene shows some interesting features: the aminoterminal 276 aa are colinear and most similar to PAPS reductase from the moss Physcomitrella. Attached to these, and separated by an intron, is a carboxyterminal domain showing similarity to higher plant-like APS reductases, enzymes that exclusively are known from higher plant chloroplasts. The correct identification of the intron is confirmed by a Phaedactylum EST.
Fair similarity to known sequences, partial Phaeodactylum cDNA support. A member of the folate biosynthesis pathway.
basic leucine zipper protein smilarity, DNA binding, transcription factor; basic leucine zipper protein similarity, DNA binding, transcription factor
RS6, ribosomal protein 6, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
putative splicing factor related to human splicing factor 3B subunit 2 (Spliceosome associated protein 145) (SAP 145) (SF3b150) (Pre-mRNA splicing factor SF3b 145 kDa subunit)
No EST evidence but very strong hits to splicing proteins in humans. Also hits to hsp and Pfam domains. Some similarities to thioredoxins.
RL8, ribosomal protein 8, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
based on sequence similarity and presence of ABC1 domain; putative protein of unknown function with ABC1 domain
putative DNA Primase, involved in DNA processing, similar to 58kD large subunit
26S proteasome regulatory ATPase subunit
26S PROTEASE REGULATORY SUBUNIT 7 (26S PROTEASOME SUBUNIT 7) (model%: 97, hit%: 97, score: 1697, %id: 76) [Spinacia oleracea]; RPT1
Reasonable hits to DnaJ (HSP40)-like proteins. The best hit was to DnaJ (HSP40) homolog, subfamily B, member 5 from Mus musculus with an evalue of 8.3e-18. Contains InterPro domain #IPR001623, which is a DnaJ N-terminal domain. Also similar to Pfam model #PF00226, for a DnaJ domain.
Excellent sequence agreement with known genes. Enzyme of the methionine metabolism pathway.
contains tRNA methyltransferase domain; partial EST support; 5-methylaminomethyl-2-thiouridylate
The annexins are a structurally conserved family of proteins characterized by reversible Ca2+-dependent intracellular membrane binding. Membrane association is critical for their proposed functions which include vesicle trafficking, membrane fusion and ion channel formation.
Proteasome subunit alpha type 5-2 (20S proteasome alpha subunit E2) (model%: 100, hit%: 100, score: 824, %id: 68) [Arabidopsis thaliana]; 20S proteasome
RS25, ribosomal protein 25 40S small ribosomal subunit
RS25, ribosomal protein 25, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
putative DNA polymerase based on sequence similarity, polymerase domains, and EST support from T. weissflogii
contains a GCN5-related N-acetyltransferase domain; supported by cDNAs; protein of unknown function
This enzyme catalyzes the reversible conversion between glycine and serine. Coupled with the glycine cleavage system it is also part of the photorespiratory pathway. Multicopy. Support from Pfam, hsp groupings, ESTs, and high similarities to SHMT from other organisms.
succinate dehydrogenase flavoprotein subunit
CATALYTIC ACTIVITY: Succinate + ubiquinone = fumarate + ubiquinol. PATHWAY: Tricarboxylic acid cycle. SUBUNIT: Forms part of complex II containing four subunits: a 70 kDa flavoprotein (FP), a 27 kDa iron-sulfur protein (IP), a cytochrome B and a membrane-anchoring protein. SUBCELLULAR LOCATION: Mitochondrial inner membrane
possibly involved in polyamine biosynthesis; low similarity to spermidine synthase; hypothetical protein
UDP-N-acetylglucosamine: polypeptide-n-acetylglucosaminyl transferase
possibly involved in transfer of N-acetylglucosamin to Ser/Thr residues within a glycoproteincontains spy domain which is characteristic for O-GlcNAc transferases
Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA.
Histone H2A is a small, highly conserved nuclear protein that, together with 2 molecules each of histones H2B, H3 and H4, forms the eukaryotic nucleosome core; the nucleosome octamer winds 146 DNA base-pairs
Histone H2B is one of the four histones, along with H2A, H3 and H4, which forms the eukaryotic nucleosome core. Histone H2B is a small, highly conserved nuclear protein that, together with 2 molecules each of histones H2A, H3 and H4, forms the eukaryotic nucleosome core; the nucleosome octamer winds 146 DNA base-pairs.
Histone H4 is one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core. Along with H3, it plays a central role in nucleosome formation. The sequence of histone H4 has remained almost invariant in more then 2 billion years of evolution.
peroxisomal biogenesis factor 6, peroxisomal assembly factor w, Paf2, pex6-like protein
Some similirity to other organisms (50% amino acid idnentity); contains AAA ATPase domain (IPR003959 and IPR003593), AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes
mu subunit of tetrameric clathrin adaptor complex AP1
clathrin adaptor protein complex 1 is involved in protein sorting in the trans-Golgi network and endosomes; mu-adaptin, AP1M1, CLTNM
Potein show weak homology to receptor kinases in vascular plants
Homology to putative serine/threonine kinases of cyanobacteria and ATP binding domain
Homology to putative serine/threonine kinases of cyanobacteria and ATP binding domain; hypothetical protein