Thalassiosira pseudonana CCMP1335 chromosome 12, 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 CM000647.\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##
26S proteasome ATPase regulatory subunit
26S proteasome AAA-ATPase subunit RPT4a (gb|AAF22524.1); supported by cDNA: gi_13937182_gb_AF372945.1_AF372945 (model%: 96, hit%: 93, score: 1422, %id: 71) [Arabidopsis thaliana]
A number of proteins involved in the transport of sulphate across a membrane as well as some yet uncharacterized proteins have been shown to be evolutionary related. These proteins are highly hydrophobic and seem to contain about 12 transmembrane domains.
RL32, ribosomal protein 32 60S large ribosomal subunit
RL32, ribosomal protein 32, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
5-methyltretrahydrofolate-homocysteine s-methyltransferase
Good cDNA support as well as high similarity to putative homologs. An enzyme in the methionine metabolism pathway
Excellent agreement with known sequences. Complete cDNA support.
glutamine-fructose 6 phosphae transaminase
was automatically annotated as glutamine-fructose 6 phospahte tranaminase but not supported by sequence homology data or models
conatins Glycoside hydrolase, family 18 domain; protein with unknown function, possible chitinase
protein 23 of the large ribosomal subunit
most similar to eucaryotic homologues from animals
Involved in arginine synthesis and the urea cycle.acetyl-CoA + L-glutamate = CoA + N-acetyl-L-glutamate
limited similarity to protein of unknown function from Arabidopsis. EST support from Phaeodactylum.; putative protein of unknown function, contains leucine rich repeats
molecular motor involved in microtubule-based transport
ABC transporter multi-drug efflux transporter-like protein
sodium phosphate cotransporter, Na/Pi cotransport system protein
sequence similarity and presence of two conserved domains of unknown function and ATP/GTP binding site motif A; putative protein of unknown function
mitochondrial carrier protein-like protein
Protein putatively targeted to chloroplast and/or mitochondrion. Dual targeting possible.
myo-inositol-1-phosphate synthase-like protein
contains conserved Myo-inositol-1-phosphate synthase domain (IPR002687); catalyzes the conversion of D-glucose 6-phosphate to 1L-myo-inositol-1-phosphate, the first committed step in the production of all inositol-containing compounds; very strong similarity to other MIPs in database (up to 68% sequence identity over 470 amino acids).
[FUNCTION] CATALYZES THE DESATURATION OF LONG CHAIN ACYL-COAS TO 2-TRANS-ENOYL-COAS (By similarity). [CATALYTIC ACTIVITY] Acyl-CoA + O(2) = trans-2,3-dehydroacyl-CoA + H(2)O(2). [COFACTOR] FAD (By similarity). [PATHWAY] fatty acid beta-oxidation system; first step.[SIMILARITY] BELONGS TO THE ACYL-COA OXIDASE FAMILY.
origin recognition complex subunit 1-like protein
based on sequence similarity to origin recognition complex from candida. Binds origing in ATP-dependent manner and putative protein has ATP binding motif; orc1
Distant similarity to various sequences for proteins of different function; unknown protein
Similarity ranges from poor to fair with regions of good, but this does not appear to be a highly conserved protein. Partial support by cDNA.
based on sequence similarity; putative protein of unknown function with sequence similarity to nostoc hypothetical protein
The yeast GCN5 (yGCN5) transcriptional coactivator functions as a histone acetyltransferase (HAT) to promote transcriptional activation. The crystal structure of the yeast histone acetyltransferase Hat1-acetyl coenzyme A (AcCoA) shows that Hat1 has an elongated, curved structure, and the AcCoA molecule is bound in a cleft on the concave surface of the protein, marking the active site of the enzyme. A channel of variable width and depth that runs across the protein is probably the binding site for the histone substrate. The central protein core associated with AcCoA binding that appears to be structurally conserved among a superfamily of N-acetyltransferases, including yeast histone acetyltransferase 1 and Serratia marcescens aminoglycoside 3-N-acetyltransferase.
Distant similarity to many various protein kinases; unknown protein
DNA directed RNA polymerase i, second largest subunit
translation factor elongation factor ef-tu
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.
26S proteasome AAA-ATPase subunit RPT3 (gb|AAF22523.1) (model%: 99, hit%: 81, score: 1350, %id: 76) [Arabidopsis thaliana]
actin related protein centractin-like protein
Homology to ATP binding domain of cyanobacterial serine/threonine kinase
In addition to berges annotation: This gene clearly is most similar to green plant homologues, less similar to animal ones and even less similar to a G theta nucleomorph copy. Therfore it indicates a chlorophytic origin of the diatom host cell.
tocopherol polyprenyltransferase-like protein
function: catalyzes condensation of homogentisic acid and phytyl diphosphate in tocopherol synthesis. note: there are other plant and cyanobacterial hypothetical proteins with higher similarity. Putatively chloroplast targeted.
hypothetical protein with thioredoxin type domains
phosphatidylinositol/phosphatidylcholine transfer protein
contains a CRALBP/TRIO domain, present in several lipid-transfer proteins and proteins with diverse functions; PI/PC TP
This protein contains InterPro domain #IPR000889, which is found in glutathione peroxidases. The top blast hits are to glutathione peroxidases, but the scores are low (155) and the gene does not have EST support.; putative protein containing glutathione peroxidase domain
Function unknown. The descriptions of the functions of the target proteins vary and are equivocal. The enzyme is possibly a type of isomerase, converting between different nucleotide sugars.; hypothetical protein with similarity to nucleotide sugar epimerases
RL35, ribosomal protein 35 60S large ribosomal subunit
RL35, ribosomal protein 35, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
based on sequence similarity to bacterial proteins and EST support; putative protein with Esterase/lipase/thioesterase domain
one of 22 hits of a hypothetical DNA helicase form the Gtheta nucleomorph, no EST support; fragment of hypothetical DNA helicase
glutamine-fructose-6-phosphate transaminase
enzyme in glutamate cycle, amino transferase family
based on sequence similarity and ATPase and ATP/GTP binding motif.
Homolog putative serine/threonine kinases of cyanobacteria
Nicotinate-nucleotide pyrophosphorylase, also known as quinolinate phosphoribosyltransferase (decarboxylating), catalyses the conversion of nicotinateD-ribonucleotide, pyrophosphate and carbon dioxide into pyridine-2,3-dicarboxylate and5-phospho-alpha-D-ribose 1-diphosphate in the de novo biosynthesis of NAD and NADP.
based on sequence similarity to bacterial proteins
Multidrug efflux transporters are integral membrane proteins that can mediate transport of toxic compounds over biological memebranes. This gene was identified based on sequence similarity and has some similarity to multidrug transporters. The best hit was to Bacillus subtilis with 29.76% (50/168) identity. This score will likely improve once the gene model is corrected.
putative protein of unknown function with sequence similarity to hypothetical protein and GTP pyrophosphokinases; putative protein of unknown function with sequence similar to hypothetical protein
Contains very high homology to ubiquitin domain
vascular plant-like receptor protein kinase
TPS_108807 is significanlty homologous to protein kinases in a variety of vascular plants.Most of these are receptor-like kinases and many are associated with disease resistanceand are transmembrane proteins.
Reasonable hits to sugar and multidrug-efflux transporters.
Contains high homology to ubiquitin carboxyl terminal hydrolase and carboxyl terminal proteinase-like proteins
cell division control protein 2-like protein
presense of kinase domains and sequence similarity to cdc2 from plants; cdc2-like
Contains homology to SNF motif and helicases
PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukarya. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein.
Putative subtilisin-like serine protease; first gene model has some similarities to At5g67090-68299.m06769 K21H1.5 subtilisin-like serine protease contains similarity to subtilisin-like protease ag12 GI:757522 from [Alnus glutinosa] (model%: 62, hit%: 16, score: 83, %id: 24) [Arabidopsis thaliana]; re-evaluate merged model
beta-glycan synthesis associated protein
putative protein with internal repeats and integrin domains; putative protein with integrin domains
hypothetical protein with formin homology
putative protein of unknown function with sequence similarity to neuropathy target esterase from humans. Presence of cyclic nucleotide-binding domains and patatin domain, which has been associated with cleavage of fatty acids from membranes; putative protein of unknown function
Possibly involved in urea metabolism, creatine metabolism; low homology to creatine kinase
The CHROMO (CHRromatin Organization MOdifier) domain is a conserved region of around 60 amino acids,originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin,a cytologically visible condition where gene expression is repressed. In one of these proteins,Polycomb,the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain,eg. Drosophila and human heterochromatin protein Su(var)205 (HP1); and mammalian modifier 1 and modifier 2. The second class includes proteins with a single chromo domain,eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigenand and several yeast and C. elegans hypothetical proteins. In the third class paired tandem chromo domains are found,eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.
putative protein containing wd-40 repeats
phosphatidylinositol 3-kinase (PI3K)-like protein
contains conserved Phosphatidylinositol 3- and 4-kinase domain (IPR000403), FAT and FATC domain (IPR003151, IPR003152), a domain present in the PIK-related kinases; Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways; alignment with other PI3K is okay (37% identity over 2500 amino acids), but no EST data available to support model.
This gene is up regulated in response to copper toxicity.