Thalassiosira pseudonana CCMP1335 chromosome 17, 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 CM000651.\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##
good supporting EST data. However, no strong hits in other databases, but gene does contain conserved eukaryotic protein kinase domain (IPR000719).; putative protein kinase
molecular motor involved in actin-based transport
based on sequence similarity to IGPS from cyanobacteria and presence of defining IGPS domain
Reasonable hits to permeases and MFS transporters. The best hit was to a putative permease from Thermotoga maritima with 33.11% (149/450) identity. The scores will probably be better after the gene model is corrected.
contains a domain found in other proteins of unknown function; putative protein of unknown function
glutamine fructose 6 phosphate transaminase
amino transferase family, (another gene with better sequence alignment etc in grail 105.5.1)
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.
Supported by sequence similarity and EST data
Putative protein with similarities to pseudouridylate synthase (pseudouridine synthase) (uracil hydrolase), e.g. gi|13431951|sp|Q9PJT0|TRUA_CHLMU tRNA pseudouridine synthase A (Pseudouridylate synthase I) (Pseudouridine synthase I) (Uracil hydrolyase) (model%: 70, hit%: 90, score: 248, %id: 28) [Chlamydia muridarum]; putative protein with similarity to pseudouridylate synthase
Contains conserved ser/thr protein kinas domain (IPR002290) and tyr kinase domain (IPR001245). Aligns with Yak1 homolog from yeast (43% identity over 385 amino acids); similar to yak1, yakA; putative protein kinase
based on sequence similarity to human hypothetical protein; putative protein of unknown function
Putative protein of unknown function, containing a presenilin protein peptidase domain; gi|21302687|gb|EAA14832.1| agCP4971 [Anopheles gambiae str. PEST] (model%: 100, hit%: 68, score: 633, %id: 45) [Anopheles gambiae str. PEST]; full-length EST support; putative protein of unknown function, containing a presenilin protein peptidase domain
in addition to previous annotation: N-terminus contains putative ER signal peptide. Putatively chloroplast targeted, dual targeting possible.
3-oxo-5-alpha-steroid 4-dehydrogenase 1-like protein
Contains conserved 3-oxo-5-alpha-steroid 4-dehydrogenase, C-terminal domain (IPR001104); catalyse the conversion of 3-oxo-5-alpha-steroid + acceptor to 3-oxo-delta(4)-steroid + reduced acceptor. The steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development; some similarity to other organisms (e.g. 41% amino acid identity to Rattus norvegicus; Steroid 5-alpha-reductase) (DET2
catalyzes formation of spermidine (from putrescine) or spermine (from spermidine); EST support
At1g79230-68300.m08039 YUP8H12R.17 mercaptopyruvate sulfurtransferase (Mst1/Rdh1) identical to Putative protein of unknown function containing a rhodanese domain (mercaptopyruvate sulfurtransferase) (thiosulfate sulfurtransferase); similar to mercaptopyruvate sulfurtransferase GI:6009981 and thiosulfate sulfurtransferase GI:5834508 from [Arabidopsis thaliana]. (model%: 90, hit%: 73, score: 328, %id: 31) [Arabidopsis thaliana]; putative protein of unknown function containing a rhodanese domain
Hits to peroxisomal targeting signal receptor
based on sequence similarity to bacterial hypothetical proteins; putative protein of unknown function
Predicted O-linked N-acetylglucosamine transferase (SPINDLY family); glycosylates serine/threonine residues of specific cytosolic and nuclear proteins
based on sequence similarity and presence of defining domains
Contains bery high homology to GTP binding proteins; hypothetical protein
Contains homology to Phospholipid and glycerol acyltransferase domains; hypothetical protein
Putative protein of unknown function containing an esterase/lipase domain; some similarities to At5g19850-68299.m02082 T29J13.270 putative protein predicted proteins - different species (model%: 95, hit%: 78, score: 461, %id: 37) [Arabidopsis thaliana]; putative protein of unknown function containing an esterase/lipase domain
Contains high homology to Mov34 proteins which act as the regulatory subunit of the 26 proteasome.; hypothetical protein
Contains homology to hypothetical proteins from a variety of organisms
26S proteasome regulatory subunit 3 (26S proteasome regulatory subunit S3) (Rpn3) (Proteasome subunit p58) (Transplantation antigen P91A) (Tum-P91A antigen) (model%: 99, hit%: 57, score: 713, %id: 45) [Mus musculus] putative similar to SP:P93768 from [Nicotiana tabacum];supported by full-length cDNA: Ceres:101030. (model%: 99, hit%: 62, score: 591, %id: 43) [Arabidopsis thaliana]
phosphoribosylformylglycinamidine synthase
putative FGAM synthase based on sequence similarity and EST support
Contains homology to mitochondrial carrier proteins
GTPase putatively involved in vesicle transport; ARF1
Putative protein of unknown function containing trypsin-like serine protease domains; putative protein of unknown function containing trypsin-like serine protease domains
similar to TIM10, translocase of inner mitochondrial membrane
Putative protein of unknown function containing an OTU-like cysteine protease domain, similar to gi|15240231|ref|NP_201518.1| (NM_126117) putative protein; protein id: At5g67170.1 [Arabidopsis thaliana] (model%: 97, hit%: 23, score: 163, %id: 41) [Arabidopsis thaliana]; putative protein of unknown function containing an otu-like cysteine protease domain
ABC-transporter like protein, ATP binding domains. May function as elongation factor.
Strong hits to multiple sugar transporters.Difficult to detect specificity.
in additon to ANDY annotation: looks like fusion of large and small subunits (LeuC and LeuD genes) typical for fungi. H-terminus contain putative ER signal peptide predicted by SignalP (probability 0.993; cleavage site between pos. 20 and 21: VES-FA) followed by sequence resembling chloroplast transit peptide (less than 20 aa) but not recognized by prediction programs. Protein is probably chloroplast targeted.
may be the phosphatase that regenerates dolichylphosphate from dolichyl pyrophosphateweak sequence homology (28,6% identity, 45,6% similarity)to DOLPP1 from mus musculus (Genbank accession number AB030189) contains a PAP2 phosphatase domainno EST data
Related to rRNA intron-encoded homing endonuclease of Oryza sativa (rice AF139989) and to an EST from Porphyra (gi|8587996|gb|AV432771.1)