Thalassiosira pseudonana CCMP1335 chromosome 23, 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 CM000654.\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##
Distant similarity to cysteinyl-tRNA synthetase; unknown protein
The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes.; putative protein with heat domain repeats with similarity to hypothetical protein predicted by genemark.hmm
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; putative protein kinase
Strong sequence similarity to alpha importin in other organisms (65% identity over 500 amino acids); strong EST supporting data; contains conserved armadillo repeats (IPR000225) and importin beta binding domain (IPR002652).
good supporting EST evidence; Protein tyrosine phosphatases dephosphorylate tyrosine residues.; with sequence similarity to Drosophila PRL-1 prenylated PTP; putative protein tyrosine phosphatase
based on sequence similarity to other glucosylceramidases from metazaons, a ricin domain and the glucosidase domain
CTP + phosphatidate = diphosphate + CDP-diacylglycerol; cytidine-5'-diphosphate-diacylglycerol synthase
The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue.; hypothetical protein with putative FYVE zn-finger, rabphilin/VPS27/FAB1 type-domain
supported by a Thalassiosira cDNA; putative protein containing similarity to unknown proteins
On the basis of sequence similarities a family of related ATP-binding proteins has been characterized. ABC transporters are transport systems which consist of three different proteins which function together to import metabolites into the cell. ABC stands for ATP-binding cassette. The three components are: 1) ATP-binding protein - resides in the cytoplasm, associated with the inner membrane, provides the energy for transport through hydrolysis of ATP. 2) permease - spans the inner membrane, makes the channel for the metabolite to pass through. 3) periplasmic substrate-binding protein - resides in the periplasm in gram negative organisms and is attached to the cytoplasmic membrane in gram positive organisms (and is therefore not called periplasmic), this protein binds the substrate with high affinity and initiates transport through the permease. The likely stoichiometry of these proteins in the cell is two permeases, two ATP-binding proteins and great excess of substrate binding protein per transport structure. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence or the 'P-loop' (see IPR001687).
On the basis of sequence similarities a family of related ATP-binding proteins has been characterized. ABC transporters are transport systems which consist of three different proteins which function together to import metabolites into the cell. ABC stands for ATP-binding cassette. The three components are: 1) ATP-binding protein - resides in the cytoplasm, associated with the inner membrane, provides the energy for transport through hydrolysis of ATP. 2) permease - spans the inner membrane, makes the channel for the metabolite to pass through. 3) periplasmic substrate-binding protein - resides in the periplasm in gram negative organisms and is attached to the cytoplasmic membrane in gram positive organisms (and is therefore not called periplasmic), this protein binds the substrate with high affinity and initiates transport through the permease. The likely stoichiometry of these proteins in the cell is two permeases, two ATP-binding proteins and great excess of substrate binding protein per transport structure.The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence or the 'P-loop' (see IPR001687).
I got to this annotation as one of seven of the aspartate aminotransferases called by grail/genewise. The 5' end of the amino acid sequence may contain a signal peptide. This model shows high sequence similarity to putative aspartate aminotransferase in Arabidopsis.
protoporphyrinogen IX oxidase usually abbreviated
Converts protoporphyrinogen IX to protoporphyrin IX; EST support
putative chitinase. Contains chitin binding domains also referred to as a peritophin-A domain common in animal and insect chitinases. This is an extracellular domain with six conserved cysteines. Also contains a o-glycosyl hydrolase domain suggesting that protein can hydrolyze chitin oligosaccharides. Also contains the chitinases family 18 active site.
Complex 1 electron transport, shows most similarity to operon identified in the bacteria Desulfovibrio fructosovorans. Supported by EST sequence.
A number of transport proteins which are involved in the uptake of xanthine or uracil are evolutionary related . They are proteins of from 430 to 595 residues that seem to contain 12 transmembrane domains.
One of small subunits associated with RNA polymerase RpoB.
based on sequence similarity to other conserved hypotheticals; putative protein of unknown function with sequence similarity to hypothetical protein
contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
Probable nucleoside disphosphate kinase (NDK) (NDPK) (NDP kinase) similar to gi|127984|sp|P19804|NDKB_RAT Nucleoside diphosphate kinase B (NDK B) (NDP kinase B) (P18) (model%: 86, hit%: 97, score: 520, %id: 66) [Rattus norvegicus]
putative aminotransferase similar to Deinococcus radiodurans
Possible amino acid transporter based on BLAST on interpro hits.
fucoxanthin chlorophyll a/c protein, LI818 clade
Member of LHC superfamily. Assigned to LI818 clade on basis of matches to Chlamydomonas LI818 and Isochrysis galbana (Swissprot FCP_ISOGA; gi535080, 535081)
Member of LHC superfamily. Assigned to LI818 clade on basis of matches to Chlamydomonas LI818 and Cyclotella cryptica.No intron.
Member of LHC superfamily. Assigned to LI818 clade on basis of matches to Chlamydomonas LI818.
Poor hits to most other sequences, but does align with an EST from Phaeodactylum.; hypothetical protein with domain similar to flavodoxin
Involved in arginine biosynthesis. Putatively chloroplast targeted
No reasonable similarity to any known sequences.; hypothetical gene