Thalassiosira pseudonana CCMP1335 chromosome 18, complete 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 CP001159.\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.\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)\nLinear chromosome missing portions of the telomeres.\nThe remaining chromosomes for this strain have been deposited under\nthe Whole Genome Shotgun project accession AAFD00000000.\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##\nCOMPLETENESS: full length.
Putative protein with similarities to Metacaspase (model%: 21, hit%: 28, score: 285, %id: 42) [Schizosaccharomyces pombe]; EST support
weak homology to the alpha-1,6-mannosyltransferaseOCH1 from S.pombe which is involved in the outer chain elongation of N-glycans
ABC transporter, unknown function. Interpro and Blast support.; ABC transporter, unknownn function
GAF domains are present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.
putative protein with integrin domains; cell adhesion
member of the clp superfamily, large regulatory subunit
Clp proteins are involved in protein degradation, heat shock response and chaperone function. The given one is most similar to alpha purple bacteria counterparts and thus may be mitochodrial. According to sequence similarity it may act as a chaperone.There are at least 6 more large clp subunits encoded in the T. pseudonana genome.
(AS) is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate; Argininosuccinate synthase
based on presence of defining domains and sequence similarity to bacterial uraci-DNA N-glycosylase likely involved in DNA repair
Good hits to ABC transporter. Interpro domains present as well. Location unknown.
Probable 26S proteasome regulatory subunit rpn5 (model%: 95, hit%: 98, score: 620, %id: 32) [Schizosaccharomyces pombe]; 20s proteasome
Putative protein of unknown function containing papain cystein protease domains, similar to gi|537437|gb|AAC35211.1| (U12637) cysteine proteinase [Hemerocallis hybrid cultivar] (model%: 84, hit%: 22, score: 174, %id: 44) [no tax name]; Putative protein of unknownn function containing papain cystein protease domains
Sir2- type regulatory transcription factor silent information regulator protein
Silent Information Regulator Sir2 protein is one of several factors critical for silencing at least three loci in yeast. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres. Sir2p interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes. Unlike Sir3p and Sir4p, for which no homologues are known, Sir2p is part of a multigene family in yeast (Homologues of Sir Two (HST) 1,2,3,4) that has highly conserved structural homologues in organisms ranging from bacteria to man. Proteins of this family have been proposed to play a role in silencing, chromosome stability and recombination. In addition, an in vitro ADP ribosyltransferase activity has been associated with E. coli and human members of this family. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity.; Sirtuin
The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others. All possess a similar structure, with a beta-alpha-beta fold characteristic of nucleotide binding proteins. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones.
Invloved in Histidine metabolism. Histidinol dehydrogenase (HDH) catalyzes the terminal step in the biosynthesis of histidine in bacteria, fungi, and plants`, the four-electron oxidation of L-histidinol to histidine.Catalyzes the reaction L-histidinol + 2 NAD = L-histidine + 2 NADH2.
Putative protein of unknown function containing a rhodanese domain, with some similarities to At1g09280-68300.m00888 T12M4.1 unknown protein; supported by cDNA: gi_15081790_gb_AY048288.1_ (model%: 49, hit%: 35, score: 354, %id: 39) [Arabidopsis thaliana]; EST support; Putative protein of unknownn function containing a rhodanese domain
aminopeptidase with a membrane alanine aminopeptidase domain
Putative aminopeptidase with a membrane alanine aminopeptidase domain (ALA-peptase), similar to(NM_119463) aminopeptidase- like protein; protein id: At4g33090.1, gi_17473510 [Arabidopsis thaliana] (model%: 98, hit%: 98, score: 1475, %id: 39) [Arabidopsis thaliana]; EST support
RL5, ribosomal protein 5, 60S large ribosomal subunit
RL5, ribosomal protein 5, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
based on sequence similarity. Predicted presence of transmembrane domains
supported by Phaeodactylum cDNAs, good alignments; VAMP, vesicle-associated membrane protein, v-SNARE component
Putative dCMP deaminase; similar to gi|21619349|gb|AAH31719.1| (BC031719) Similar to dCMP deaminase [Mus musculus] (model%: 100, hit%: 91, score: 580, %id: 62) [Mus musculus]; EST support
[function] implicated in mitochondrial protein import and macromolecular assembly; may facilitate the correct folding of imported proteins and promote the refolding and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix; [subcullular location] mitochondrial; [induction] by heat shock; [similarity] belongs to the chaperoning (HSP60) family; Putatively targeted to mitochondrion
glycine or serine hydroxymethyltransferase, serine methylase
function: Interconversion of serine and glycine. catalytic activity: 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine. pathway: Key enzyme in the biosynthesis of purines, lipids, hormones and other components.
Involved (together with sec62 & 63) in protein transport across the ER. Membrane protein. Two copies present in the genome. Similar to secY involved in protein transport across the thylakoid membrane.
based on sequence similarity to other hypothetical proteins from metazoans.; hypothetical protein of unknownn function
DNA repair and recombination protein RecA, chloroplast precursor, contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
D-glyceraldehyde 3-phosphate = glycerone phosphate; putative
Presumably involved in transporting GDP-fucose from cytosol to ER-Golgi lumen.; with sequence similarity to human GDP-fucose transporter 1
NADP-dependent ferredoxin reductase and adrenodoxin reductase, fprA-like protein
Possibly part of the adrenodoxin complex of the mitochondrial P450 system. No EST evidence, some good hits to domains from Pfam and hsp groupings. Ok hits to adrenodoxin oxidoreductases and ferredoxin reductases from other organisms.
fucoxanthin chlorophyll a/c protein -LI818 clade
Member of LHC superfamily. Closest match to Cyclotella homologs of LI818.
Putative protein of unknown function containing a region similar to an aspartic protease domain; EST support; Putative protein of unknownn function containing a region similar to an aspartic protease domain
good est support and presence of conserved domain found in other proteins of unknown function; putative protein of unknownn function
Excellent sequence similarity to other putatuve aldehyde dehydrogenases
Contains homology to mitochondria/peroxisomal membrane carrier proteins
1-deoxy-D-xylulose 5-phosphate reductoisomerase
addition to previous annotation: Contains ER signal peptide and chloroplast transit peptide. Is putatively chloroplast targeted.
basic leucine zipper protein smilarity, DNA binding, transcription factor
possible amino acid/polyamine transporter family II protein
fucoxanthin chl a/c light-harvesting protein, major type
possible amino acid/polyamine transporter family II
Putative protein of unknown function with a prolyl aminopeptidase domain, similar to (NC_002505) conserved hypothetical protein [Vibrio cholerae] (model%: 100, hit%: 42, score: 200, %id: 39) [Vibrio cholerae]; EST support; Putative protein of unknownn function with a prolyl aminopeptidase domain
based on presence of defining domain and sequence similarity to mitochondrial carrier proteins; putative 2-oxoglutarate/malate carrier protein
one of 22 hits of a hypothetical DNA helicase from the Gtheta nucleomorph; fragment of a hypothetical DNA helicase
based on sequence similarity and presence of defining domains
Good similarity to known sequences. Partial cDNA and Phaeodactylum cDNA support. A member of the valine/leucine/isoleucine biosynthesis pathway.; valine-tRNA ligase
Putative protein of unknown function containing a Rhodanese domain (associated with plant senescence responses), with some similarities to phage shock proteins, e.g. gi|15600871|ref|NP_232501.1| (NC_002506) phage shock protein E [Vibrio cholerae] (model%: 49, hit%: 49, score: 106, %id: 34) [Vibrio cholerae]; EST support; Putative protein of unknownn function containing a rhodanese domain, with some similarity to phage shock proteins
fucoxanthin chlorophyll a/c light-harvesting protein
contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site