Thalassiosira pseudonana CCMP1335 chromosome 20, 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 CM000652.\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##
putative protein with integrin domains; putative protein with integrin domains
Identification supported by Phaeodactylum cDNA and in good agreement with considerable known sequences. Citric acid cycle enzyme.
Putative protein of unknown function with similarities to hydrolases; e.g. At1g13820-68300.m01401 F16A14.4 unknown protein contains similarity to 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase GI:2822275 from [Pseudomonas putida] (model%: 88, hit%: 73, score: 434, %id: 36) [Arabidopsis thaliana]; putative protein of unknown function with similarity to hydrolases
hypothetical protein with thioredoxin type domains
function: maintain high levels of reduced glutathione in the chloroplast. catalytic activity: 2 glutathione + NADP(+) = glutathione disulfide + NADPH. cofactor: FAD. subcelular localization: chloroplast and mitochondrion, the majority of proteins is usually found in chloroplast, with only 3% in plant mitochondria. Belongs to the pyridine nucleotide-disulfide uxidoreductases class 1. Putatively chloroplast targeted.
Putative protein similar to DNA-directed DNA polymerase; similar togi|11994141|dbj|BAB01162.1| (AP000410) contains similarity to DNA polymerase I; gene_id:K10D20.8 [Arabidopsis thaliana] (model%: 97, hit%: 72, score: 1663, %id: 46) [Arabidopsis thaliana]; putative protein similar to dna-directed DNA polymerase
ambiguous EST support, compare to putative splice variant Protein ID 270271
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.; putative protein kinase
Contains conserved Cdc45-like domain (IPR003874). Weak alignment with other Cdc45 (39% amino acid identity).
This sequence has domains consistent with an FAD or NAD(P)-dependent oxidoreductase. Best hits suggest this may be a cytochrome P450 reductase.
Contains a Sac domain (inositide polyphosphate Pase activity), but none of the other domains of typeII 5-Pases (eg. synaptojanins).
As in fungi the T.pseudonana tryptophane synthase gene is a gene fusion of trpA and trpB known as individual genes in bacteria. The genes are not fused in Plants.
similar to Skp1-like protein of ubiquitin protein degradation pathway (model%: 98, hit%: 87, score: 571, %id: 71) [unidentified]; EST support; putative protein similar to SKP1 component of ubiquitin protein degradation pathway
based on sequence similarity to Leishmania protein and presence of nuclear migration domain
sequence similarity, presence of Beta-Ig-H3/Fasciclin domain and EST data support.; putative extracellular protein
Second copy of the lipB gene (see genewise 6.1045.1 annotated by my). This one is also clearly most similar to Arabidopsis and cyanobacterial homologues, therefore again indicating a green algal host cell for the Diatom secondary endosymbiosis.
based on sequence similarity to hypothetical proteins from metazoans; hypothetical protein
similar to putative ubiquitin protein ligase C57A7.03C (model%: 97, hit%: 37, score: 588, %id: 35) [Schizosaccharomyces pombe]; putative protein with ubiquitin protein ligase domain (E3)
Contains InterPro domain #IPR002068 for HSP20 proteins. Also contains similarity to Pfam model #00011 for HSP20/alpha crystallin family. Some similary to HSP20's from higher plants. Probably cytoplasmic.; HSP20 family
Putative protein of unknown function containing an esterase/lipase domain; similarities to gi|21401218|ref|NP_657203.1| (NC_003995) abhydrolase, alpha/beta hydrolase fold [Bacillus anthracis A2012] [Bacillus anthracis str. A2012] (model%: 80, hit%: 84, score: 157, %id: 22) [Bacillus anthracis str. A2012]; EST support; putative protein of unknown function containing an esterase/lipase domain
based on sequence similarity and presesence of cytidylyltransferase domain
sequence similarity over entire protein. presence of defining domains. T. psuedonana EST support.; putative protein similar to elongation factor
supported by cDNAsContains at least 3 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.
RS3A, ribosomal protein 3A 40S small ribosomal subunit
RS3A, ribosomal protein 3A, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
U2 SnRNP auxillary factor, splicing factor
molecular motor involved in microtubule-based transport
Fucoxanthin chlorophyll a/c protein, member of LHC superfamily; FCP5
zinc finger like protein, CXXC motif, DNA binding/transcription factor
This gene is highly similar to both actin interacting protein 2 and probable D-lactate dehydrogenase in Saccharomyces cerevisiae.
Fucoxanthin chlorophyll a/c protein, member of LHC Superfamily. Two introns were found,even only one intron was indicated in this model.; FCP2
fucoxanthin chl a/c protein-deviant sequence
See comments on model quality. Should probably replace Lhcf2 as that sequence seems to have evaporated.
supprted by sequence simularity and EST data; protein
There is no EST data support for this gene model yet. It contains the succinylglutamate desuccinlyas/aspartoacylase domain. The putative function of this gene is to convert N-Acetyl-L-Aspartate to L-aspartate.
MYB DNA binding protein/ transcription factor-like protein
Member of MYB DNA binding protein/ transcription factor family
based on sequence similarity to hypothetical proteins from bacteria, EST support and zinc carboxypeptidase domain; putative protein of unknown function with zn carboxypeptidase domain
phosphatidate cytidylytransferase-like protein
Putative protein of unknown function, containing a metalloprotease domain (metallopeptidase), similar to dme:CG3953 metalloendopeptidase custom_KEGG (model%: 100, hit%: 13, score: 155, %id: 41) [Drosophila melanogaster]; putative protein of unknown function, containing a metalloprotease domain
contains some similarity to response regulator receiver domain of bacterial two componaent systems. Does not appear to contain all conserved motifs.; contains similarity to receiver domain of response regulator protein
based on presence of leucine-rich repeats and limited sequence similarity to other proteins with leucine-rich repeats; putative protein with leucine-rich repeats of the ribonuclease inhibitor family
thought to be a light chain subunit of a subset of outer arm dynein motor
possibly involved in polyamine biosynthesis; low similarity to spermidine synthase; hypothetical protein
shows 50% idenetity and overlaps well with hypothetical ATP binding proteins form animals, no EST support
No EST support, but strong hits to many other catalases and peroxidases.
Alternative oxidase is alternative to cytochrome oxidase in mitochondrial ETC. Not inhibited by cyanide. Another copy, named AOX2 is close by and in opposite orientation.
alternative to cytochrome oxidase, cyanide insensitive. AOX1 is close by, in the opposite orientation, suggesting a relatively recent duplication.
No close similarity to any known sequences. Some similarity to ribonuclease III.; hypothetical gene
one of 22 hits of a hypothetical DNA helicase from the Gtheta nucleomorph, EST support; fragment of putative DNA helicase