Thalassiosira pseudonana CCMP1335 chromosome 4, 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 CM000641.\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##
based on sequence similarity and presence of defining domain suggests protein involved in de novo biosynthesis of pyridine nucleotides.
good EST support; putative protein of unknown function
possible calcium-binding glycoprotein of the cell wall; homologous to FRU-alpha2 from Cylindrotheca fusiformis
supported by a Phaedactylum EST; putative protein with no similarity
ubiquitin-conjugating enzyme (UBC)(E2) GI:6996506 from [Leishmania major];supported by full-length cDNA: Ceres:19071. (model%: 92, hit%: 95, score: 580, %id: 75) [Arabidopsis thaliana]
alpha carbonic anhydrase of nostoc-like protein
similar to partial active site of Alpha CA. Complete active site not present in gene model
Hypothetical protein with some similarity to 3' fragment of Alpha CA (fragment of active site).; hypothetical protein with similarity to a fragment of alpha
presence of ATP synthase gamma subunit, sequence similarity and strong EST support
putative violaxanthin de-epoxidase, putative bipartite chloroplast targeting presequence at N-terminus
Homology to putative serine/threonine kinase of cyanobacteria and ATP binding domain; hypothetcial protein
Catalyzes the reaction: L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate
Possible amino transporter/polyamine transporter family II.
supported by Thalassiosira cDNAs; putative protein similarity to unknown peptides
supported by Thalassiosira cDNAs; putative protein containing similarity to unknown peptides
similar human rev-interacting protein rip-1; hypothetical protein similar to yeast cell division and spore germination proteins
pre-mrna splicing factor splicing factor hprp17-like protein
EST support.Imidazoleglycerol-phosphate dehydratase is the enzyme that catalyzes the seventhstep in the biosynthesis of histidine in bacteria, fungi and plants. In most organisms it is amonofunctional protein of about 22 to 29 kD. In some bacteria such as Escherichia coli, it is theC-terminal domain of a bifunctional protein that include a histidinol-phosphatase domain.
U5 small nuclear ribonucleoprotein, RNA helicase
Presumably hydrolyzes 1,4-linked N-acetyl-beta-glucosamine residues.; hypothetical protein with similarity to chitinase
contains a zinc finger domain; supported by a Thalassiosira cDNA; putative protein with no similarity
Identification based on reasonable homology to known sequences. Complete cDNA support, although cDNA actually extends well beyond model (see Grail model).
supported by a Phaeodactylum EST; putative protein containing similarity to unknown peptides
This protein was listed in KEGG as a Beta-N-acetylhexosaminidase, which is involved in N-glycan degradation. However, the protein page reveals that the best hits are to a gene called periaxin, which has been found in myelinating Schwann cells of mice. The alignments of this gene to either Beta-N-acetylhexosaminidase or periaxin are poor (4% and 26% respectively).; unknown protein
involved in intracellular vesicle traffic;subunit of protein complex that coats golgi vesicles; beta2COP
Catalyzes the reaction: allantoate + H2O = (-)-ureidoglycolate + urea; supporting EST data from Phaeodactylum tricornutum. Weak alignment with other organisms (39% amino acid identity)
supported by a Phaeodactylum EST; similar to unknown peptides
Protein of unknown function cointaining a MA3 domain; associated with cell death or apoptosis; EST support; protein of unknown function cointaining a MA3 domain; associated with cell death or apoptosis
Reaction catalyzed:dTDP-glucose = dTDP-4-dehydro-6-deoxy-D-glucose + H2O. Note, requires NAD.; putative; thymidine diphosphoglucose oxidoreductase
membrane spanning protein of the nonaspanin family
putative multispanning membrane protein based on presence of nonaspanin domain, sequence similiarity and EST support
Fair similarity to known sequences. Transports Mg2+
Putative ubiquitin activating enzyme 2 (UBA2) identical to gi:1703477 (model%: 77, hit%: 79, score: 893, %id: 26) [Arabidopsis thaliana]; strong domain similarities; E1
Putative pseudouridylate synthase (pseudouridine synthase) (uracil hydrolase), similar to gi|21398100|ref|NP_654085.1| (NC_003995) PseudoU_synth_1, tRNA pseudouridine synthase (model%: 85, hit%: 85, score: 190, %id: 20) [Bacillus anthracis str. A2012]; EST support
supported by Thalassiosira and Phaeodactylum ESTs
CRM1) (Chromosome region maintenance 1) (XPO1
RS20, ribosomal protein 20 40S small ribosomal subunit
RS20, ribosomal protein 20, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
Putative ubiE; ubiquinone/menaquinone biosynthesis methyltransferase, supported by cDNA
Reaction catalyzed:alpha-D-glucose-1-phosphate = alpha-D-glucose-6-phosphate. Enzyme can also interconvert the 1- and 6-phosphates of other alpha-D-aldoses. For example:alpha-D-ribose-1-phosphate = alpha-D-ribose-6-phosphate.; putative
Possibly catalyzes the reaction: UTP + alpha-D-glucose 1-phosphate = diphosphate + UDP-glucose.; hypothetical protein with high similarity to UTP--glucose-1-phosphate uridylyltransferase
Putative phospholipase (lysophospholipase), similar to gi|16945402|emb|CAC10084.2| (AL442164) related to lysophospholipase [Neurospora crassa] (model%: 75, hit%: 90, score: 351, %id: 40) [Neurospora crassa]
Contains conserved serine threonine protein kinase domains (IPR002290); strong supporting EST data. Strong alignment with other organisms (up to 54% identity of 850 amino acids)
v-snare protein, Vti1 C-terminal half-like protein
in region of overlap with best hits it has >50% identities, but it is a very short peptide
ribonucleotide reductase large chain subunit
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
Presence of Na+/H+ exchanger domain but best sequence similarity to potassium transporters.; sodium/hydrogen antiporter
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.
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. This protein also contains domains typical of transcription factors.
Putative protein of unknown function, containing a region similar to pseudouridylate synthase; similarities to gi|22831200|dbj|BAC16058.1| (AP004378) hypothetical protein; similar to Arabidopsis thaliana chromosome 4, At4g21770 [Oryza sativa (japonica cultivar-group)] (model%: 51, hit%: 44, score: 277, %id: 31) [Oryza sativa (japonica cultivar-group)]; strong EST support; putative protein of unknown function, containing a region similar to pseudouridylate synthase
RS10, ribosomal protein 10 40S small ribosomal subunit
RS10, ribosomal protein 10, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
Amino Acid Metabolism; Urea cycle and metabolism of amino groups. Catalyzes the deacylation of N-acylated L-amino acids except L-aspartic acid. Part of Urea cycle
Likely amino acid transporter, possible for aromatic amino acids.
Probable dihydroorotase, similar to gi_2121272_gb_AF000146.1_ATAF000146 (model%: 95, hit%: 89, score: 962, %id: 55) [Arabidopsis thaliana]; full length EST support
dolichyl-phosphate beta-mannosyltransferase
This enzyme catalyzes the reversible conversion between glycine and serine. Coupled with the glycine cleavage system it is also part of the photorespiratory pathway. Multicopy.
ABC cassette containing protein, possible elongation factor. Has EST support.
Putative protein of unknown function with similarities to exopolyphosphatases, similar to sce:YHR201C PPX1; exopolyphosphatase [SP:PPX1_YEAST] custom_KEGG (model%: 92, hit%: 82, score: 210, %id: 27) [Saccharomyces cerevisiae]; putative protein of unknown function with similarity to exopolyphosphatases
Catalyzes the reaction: ATP + xanthosine 5'-phosphate + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate; Strong supporting EST data; 59% amino acid identity to other organisms.
Adenylate cyclases catalyze the formation of cyclic AMP(cAMP) from ATP. cAMP is a common second messenger.
mannosyloligosaccharid alpha-mannosidase
involved in processing N-glycan moieties in the endoplasmic reticulum
mannosyl-oligosaccharide 1,2-alpha-mannosidase
Hydrolyzes alpha-1,2-mannopyranosyl residues during processing of nascent N-glycans in the endoplasmic reticulum.; putative
eukaryotic translation initiation factor 3, subunit 10
cold-shock DNA-binding domain-containing protein
Contains InterPro domain #IPR002059 which is a cold-shock DNA-binding domain. Contains strong similarity to Pfam model #PF00313 for cold-shock DNA-binding domain (CSD). This protein has EST support. It had quite a few hits to higher plant glycine-rich proteins belonging to the CSD family and higher plant cold shock proteins.
polyribonucleotide nucleotidyltransferase
Catalyzes the reaction: RNAn+1 + phosphate = RNAn + a nucleoside diphosphate; Has supporting EST data; 47% amino acid identity to other organisms.
involved in oranellar protein synthesis, putatively chloroplast targeted, dual targeting possible
based on sequence similarity and presence of alanine racemase domain
putative aminotransferase similar to that of Streptomyces and Arabadopsis
molecular motor involved in microtubule-based transport
PLC hydrolyses phosphatidylinositol 4,5-bisphosphate (PIP2), yielding soluble inositol 1,4,5-trisphosphate (IP3) and membrane-bound diacylglycerol (DAG). IP3 binds specific intracellular receptors to trigger Ca2+ mobilisation, while DAG mediates activation of a family of protein kinase C isozymes
This gene contains a ribonuclease II domain (IPR001900). It matches a ribonuclease from Schizosaccharomyces pombe with 37.75% identity over 543 amino acids.
beta subunit of clathrin adaptor complex AP2
RS9, ribosomal protein 9, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
conserved protein with similarity to actin filament associated protein
ankyrin repeat-rich vertebrate like protein
TPS_104534 shows very significant homology to other hyptothetic proteins in vertebrates thatalso contain ankyrin reapeat rich regions. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes.Many ankyrin repeat regions are known to function as protein-protein interaction domains.
Proton-pumping nicotinamide nucleotide transhydrogenase (Nnt) is a membrane-bound enzyme that catalyzes the reversible reduction of NADP(+) by NADH.Usually exists in prokaryotes and animal mitochondria. TPS NNT is of the class found in animal mitochondria.
Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are all members of this ancient protein superfamily
Putative protein with similarity to Enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1), induced by pathogens and UV radiation; e.g. gi|20137881|sp|Q945F0|EDS5_ARATH Enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1) (model%: 100, hit%: 68, score: 349, %id: 27) [Arabidopsis thaliana]; EST support; putative protein with similarity to enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1)
contains conserved ergosterol biosynthesis ERG4/ERG24 enzyme domain (IPR001171); catalyzes the reaction: cholesterol + NADP = cholesta-5,7-dien-3beta-ol + NADPH2
probable SOLUBLE pyridine nucleotide transhydrogenase
Oxidoreductase that acts on NADH or NADPH with NAD+ or NADP+ as acceptor.catakyzes NADPH2 + NAD = NADP + NADH2; NAD(+) transhydrogenase {B-SPECIFIC}
putative protein kinase containing a cyclic nucleotide-binding domain
Weak similarity to ABC transporter family.
Cyclin B C terminal fragment, one of 4 copies; cyclin B fragment
Protein is putatively chloroplast targeted, it contains putative ER signal peptide and chloroplast transit peptide; hypothetical protein similar to plant cyclin
calcium binding protein,component of the centrosome,can also be found as a subunit of flagellar dynein
High similarity to Narf (nuclear prelamin recognition factor). Shows similarity to iron hydrogenases (conserved hydrogenase domain (IPRO04108)). The function of Narf-like proteins in protists is unknown.
l glycerol 3-phosphate acyltransferase-like protein
portion of protein has similiarity to glycerol 3-phosphate acyltransferase and Dihydroxyacetone phosphate acyltransferase
Zinc finger protein similarity, PHD motif, DNA binding, transcription factor; zinc finger protein similarity, PHD motif, DNA binding, transcription factor
based on sequence similarity, presense of RNA binding domains and Phaeodactylum EST
Putatively involved in the synthesis of chitin, a polymer of 4-linked N-acetyl-beta-glucosamine. UDP-acetyl-glucosamine is presumably the GlcNAc donor.; hypothetical protein containing domain with similarity to chitin synthase
ATP:D-ribulose-5-phosphate 1-phosphotransferaseCarbon fixation, Calvin cyclesimilar to gi|6469450|emb|CAA69902.2| (Y08610) phosphoribulokinase [Odontella sinensis] (model%: 96, hit%: 97, score: 1428, %id: 72)
Putative reaction catalyzed:PPi + D-fructose 6-phosphate = Pi + D-fructose 1,6-bisphosphate. Note, the best match is with a pyrophosphate-dependent 6-phosphofructokinase from Mastigamoeba balamuthi; the putative reaction catalyzed is therefore distinct from the ATP-dependent 6-phosphofructokinase.; pyrophosphate--fructose-6-phosphate 1-phosphotransferase
Good similarity to known sequences. Partial Phaeodactylum cDNA support.
similar to TIM44, translocase of inner mitochondrial membrane
based on sequence similarity and EST support from Phaedactylum; putative protein of unknown function with sequence similarity to hypothetical protein from arabiodpsis
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.; hypothetical protein kinase
pathogenesis-related transcription factor
Putative pathogenesis-related transcription factor (AP2 domain); similar to gi|1351945|sp|P47927|AP2_ARATH Floral homeotic protein APETALA2 (model%: 98, hit%: 16, score: 97, %id: 33) [Arabidopsis thaliana], but also gi|23040109|gb|ZP_00071641.1| hypothetical protein [Trichodesmium erythraeum IMS101] (model%: 90, hit%: 40, score: 113, %id: 43) [Trichodesmium erythraeum IMS101]
Putative protein of unknown function containing an acid phosphatase domain; some similarities to gi|19570986|dbj|BAB86413.1| (AP003221) diphosphonucleotide phosphatase -like protein [Oryza sativa (japonica cultivar-group)] (model%: 76, hit%: 34, score: 374, %id: 39) [Oryza sativa (japonica cultivar-group)]; EST support; putative protein of unknown function containing an acid phosphatase domain
Reaction catalyzed:2-phospho-D-glycerate = 3-phospho-D-glycerate; putative
Search for nitrate listed this model description as NIA_LYCES Nitrate reductase [NADH; hypothetical protein of the cytochrome B5 family
This gene model has partial EST support. It contains the fungal chitin synthetase domain.
No reasonable similarity to any known sequences.; hypothetical gene
conatins glycoside hydrolase, family 18 domain; protein of unknown function, possible chitinase
eukaryotic peptide chain release factor subunit 1
supported by Thalassiosira and Phaeodactylum ESTs; eRF1) (Eukaryotic release factor 1
RL11A, ribosomal protein 11A 60S large ribosomal subunit
RL11A, ribosomal protein 11A, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
ubiquitin activating enzyme e1-like protein
putative protein transport protein SEC23A
Probable AMP deaminase, similar to ath:At2g38280 F16M14.21; putative AMP deaminase (model%: 100, hit%: 85, score: 1075, %id: 44) [Arabidopsis thaliana]; EST support
based on sequence similarity to hypothetical proteins from bacteria; putative protein of unknown function
Similarity to fungal SNF2/RAD54 helicase. Could be involved in transcription regulation and DNA recombination.; moderate similarity to SNF2/RAD54 helicase family; hypothetical protein
RS16, ribosomal protein 16 40S small ribosomal subunit
RS16, ribosomal protein 16, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
Serine/threonine (S/T) phosphatases catalyse the dephosphorylation of phosphoserine and phosphothreonine residues; contains conserved serine/threonine protein phosphatase.
Catalyzes the transamination of alpha-ketoglutarate with ornithine or N-acetylornithine, and of glutamate-5-semialdehyde with glutamate and alanine. Shows strong homology to metazoan vertebrates and heterotrophic bacteria.
putative protein containing tubulin tyrosine ligase domain that displays sequence similarity to other hypothetical proteins; putative protein with tubulin tyrosine ligase domain
Distant similarity to unknown protein from Methanococcus.; hypothetical gene
in addition to ANDY annotation: the gene is a fusion of small (CarA) and large (CarB) subunits of CPS. The protein is putatively targeted to mitochondrion, this supports that it is involved in urea cycle.
RL18a, ribosomal protein 18a 60S large ribosomal subunit
RL18a, ribosomal protein 18a, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
based on sequence similarity to Arabidopsis topoisomerase VI subunit B and presence of ATP binding domains
Reaction catalyzed:6-phospho-D-gluconate + NADP = D-ribulose 5-phosphate + CO2 + NADPH2; putative
This sequence has very high similarity to obtusifoliol 14-alpha demethylase, also known as cytochrome P450 51. There are no corresponding ESTs, but hits to cytochrome P450 from Pfam and to demethylases from hsp groupings support this annotation.; cytochrome P450 51, CYPL1
Belongs to signal peptidase family. Couldn't figure out an EC number and took default GO number.
based on sequence similarity to protein of unknown function from Arabidopsis; putative protein of unknown function containing forkhead associated domain
cell cycle regulation, most similar to higher plant homologues, one of three copies, ESt support
Reaction catalyzed:D-mannose 1-phosphate = D-mannose 6-phosphate.; putative; mannose phosphomutase
ubiquitin activating enzyme 2 (UBA2)(E1) identical to gi:1703477 (model%: 89, hit%: 84, score: 1033, %id: 32) [Arabidopsis thaliana]
Protein phosphatase 2C (PP2C) is one of the four major classes of mammalian serine/threonine specific protein phosphatases; shows broad substrate specificity and is dependent on divalent cations; contains conserved PP2C domain (IPR001932, IPR000222); putative protein phosphatase
Bet3 acts in conjunction with SNAREs to target ER-derived vesicles to cis-Golgi
May catalyze first step of tiacylglycerol catabolism.
Partial Phaeodactylum cDNA support. Similar to mutator protein sequences, 7,8-dihydro-8-oxoguanine triphosphatase.; unknown protein
Removes ammonia from serine to create pyruvate. Possibly hydroxypyruvate.
Cyclins are eukaryotic proteins which play an active role in controlling nuclear cell division cycles [1, 2, 3], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. A
conserved hypothetical protein with GTP binding domain and similarity of elongation factor tu; conserved hypothetical protein
Moderately confident alignments with other malate hydrogenase proteins as well as some sulfolactate reductase, hypothetical oxidoreductase, and ureidoglycolate reductase hits. Strongest alignments occur with the malanate hydrogenases. Apparent member of the Malate/L-lactate dehydrogenase family (PF02615)
supported by EST data; conserved hypothetical protein
no EST data; conserved hypothetical protein
Putative protein of unknown function containing leucine-rich repeats, with some similarity to gi|7489084|pir||T10515 disease resistance protein Cf-2.2 - currant tomato (model%: 90, hit%: 48, score: 606, %id: 27) [Lycopersicon pimpinellifolium]; putative protein of unknown function containing leucine-rich repeats
RL34, ribosomal protein 34 60S large ribosomal subunit
RL34, ribosomal protein 34, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
RL36, ribosomal protein 36 60S large ribosomal subunit
RL36, ribosomal protein 36, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
Acetyl-coenzyme A synthetase, contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
Supported by EST data likely to be cytostolic
RS21, ribosomal protein 21 40S small ribosomal subunit
RS21,ribosomal protein 21, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
A number of eukaryotic and prokaryotic proteins involved in ATP-dependent, nucleic-acid unwinding have been characterized on the basis of their structural similarity. All these proteins share a number of conserved sequence motifs. Some of them are specific to this family while others are shared by other ATP-binding proteins or by proteins belonging to the helicases 'superfamily' .Proteins containing this domain include the DEAD and DEAH box helicases. The DExH/D-box proteins are a large family of ATPases that have been proposed to mediate RNA structural rearrangements in a variety of cellular processes, including nuclear pre-mRNA splicing, ribosome assembly, protein synthesis, nuclear transport, and RNA degradati
Hits to other cationic amino acid transporters. However specificity not clear.; cationic
Good sequence homology. Partially supported by cDNA. An enzyme involved in valine/leucine/isoleucine degradation.
microsomal membrane bound condensing enzyme involved in fatty acid elongation.
20S proteasome subunit beta type 6 precursor
20S Proteasome subunit beta type 6 precursor (Proteasome delta chain) (Macropain delta chain) (Multicatalytic endopeptidase complex delta chain) (Proteasome subunit Y) (model%: 100, hit%: 89, score: 585, %id: 51) [Mus musculus] multicatalytic endopeptidase complex, proteasome precursor, beta subunit [Arabidopsis thaliana] (model%: 91, hit%: 87, score: 577, %id: 56) [Arabidopsis thaliana]
based on sequence similarity and presence of topoisomerase I domains and ATP binding domains
similar to long-chain fatty-acid-CoA ligase
Guanine nucleotide binding proteins (G-proteins) are a family of membrane-associated proteins that couple extracellularly-activated integral-membrane receptors to intracellular effectors, such as ion channels and enzymes that vary the concentration of second messenger molecules. G-proteins are composed of 3 subunits (alpha, beta and gamma) which, in the resting state, associate as a trimer at the inner face of the plasma membrane. This family consists of the G protein alpha subunit which binds guanyl nucleotide and is a weak GTPase. Beat subunit binds a gamma subunit.
displays sequence similarity to nucleotide binding protein from plants. Also has ATP binding domain; putative protein of unknown function that displays sequence similarity to nucleotide-binding protein
based on similarity to conserved hypotheticals from metazoans and EST support; putative protein
based on presence of glycosyl hydrolase domain, chitinase family 18 and 2 domain, and EST support
low similarity to proline-rich region of frustulins (FRU-genes); no supporting data that this is a gene.
Putative protein of unknown function, containing leucine-rich repeats, with some similarity to disease resistance proteins; e.g. gi|7488988|pir||T30553 disease resistance protein Hcr2-5D - tomato (model%: 98, hit%: 18, score: 298, %id: 38) [Lycopersicon esculentum]; putative protein of unknown function, containing leucine-rich repeats, with some similarity to disease resistance proteins
based on sequence similarity to bacterial proteins; putative protein with inosine-uridine preferring nucleoside hydrolase domain
Retinal 3',5'-cGMP phosphodiesterase (PDE) is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion.; putative protein with some similarity to cyclic nucleotide phosphodiesterases
putative protein similar to kinesin light chains
Possibly multidrug efflux ABC transporter but high hit to non-transporter ABC family member as well.See Loomis review when published.
High similarity to known sequences, complete cDNA support (in combination with Phaeodactylum cDNA). Member of the valine/leucine/isoleucine biosynthesis pathway.
Excellent Phaeodactylum cDNA support, high sequence similarity with other enzyme genes, particularly in the central gene region. An enzyme of the citric acid cycle.
sequence similarity to conserved proteins of unknown function. Contains domain suggesting involved in regulation of purine biosynthesis; putative protein likely involved in regulation of purine biosynthesis
aminotransferase family, amino acid metabolism
Protein phosphatase 2C (PP2C) is one of the four major classes of mammalian serine/threonine specific protein phosphatases; shows broad substrate specificity and is dependent on divalent cations; putative protein phosphatase
good EST support and limited sequence similarity to other hypothetical proteins from Arabidopsis and presence of PPR domain; putative protein of unknown function with similarity to other hypothetical proteins
N-terminus and C-terminus supported by ESTs; RanBP7) (Importin7
MYB DNA binding protein/ transcription factor-like protein
member of MYB DNA binding protein/ transcription factor family
phosphatidylinositol-4-phosphate 5 kinase (PIP5K)-like protein
based on sequence similarity and presence of defining domains, including glucose/ribitol dehydrogenase domain; short chain dehydrogenase/ reductase
putative ATP-dependent RNA helicase, involved in RNA processing. supported by cDNA.
involved in intracellular vesicle traffic;subunit of protein complex that coats golgi vesicles; beta1COP
based on sequence similarity, presence of AMP-dependent synthetase and ligase domain and EST support from T. pseudonana and Phaeodactylum
Putative protein of unknown function containing a prolyl aminopeptidase domain, similar to (NC_002678) proline iminopeptidase [Mesorhizobium loti] (model%: 84, hit%: 89, score: 170, %id: 26) [Mesorhizobium loti]; putative protein of unknown function containing a prolyl aminopeptidase domain
based on sequence similarity. contains heme binding site domain; putative protein of unknown function
HSF2, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF2, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
weak homology to proteins of unknown function from Anopheles gambiae and Drosophila;noe EST support; function unknown
based on presence of defining domains and sequence similarity
Probably methionine aminopeptidase, similar to methionine aminopeptidase I (MAP1), putative; protein id: At1g13270.1: gi_11320955 [Arabidopsis thaliana] (model%: 98, hit%: 64, score: 613, %id: 47) [Arabidopsis thaliana]; EST support
Involved in DNA replication, most similar to green plant homologues, less similar to G.theta nucleomorph gene, thus originating from the host cell and not from the former red algal nucleus
Putative protein of unknown function containing a lipase domain, similar to gi|22299525|ref|NP_682772.1| (NC_004113) ORF_ID:tlr1982; probable lipase [Thermosynechococcus elongatus BP-1] (model%: 99, hit%: 97, score: 303, %id: 33) [Thermosynechococcus elongatus BP-1]; putative protein of unknown function, probable lipase
TPS_106843 is significantly homologous to calmdulin like genes in a variety of eukaryotic organisms; mostly protistst but some vascular plants. The model is alsosimilar to dynein light chain from the outer arm of Chlamydomonas flagella; this light chain is a novel member of the calmodulin superfamily of Ca2+ binding regulatory proteins.The model also contains a calcium bindign EF-hand. Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both side by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration.
contains histidine kinase homology; hypothetical protein
hypothetical methyltransferase, similar to Synechococcus PCC7942, supported by cDNA
Good hits to ABC transporters and interpro domains.Location unclear.
ubiquitin-conjugating enzyme e2-16kda, ubiquitin protein ligase
26S proteasome regulatory subunit (RPN11), putative; protein id: At5g23540.1, supported by cDNA: 23276., supported by cDNA: gi_17979144, supported by cDNA: gi_20259104 [Arabidopsis thaliana] (model%: 97, hit%: 96, score: 1169, %id: 73) [Arabidopsis thaliana]Similar to 26S proteasome, non-ATPase subunit. (Y13071) [Oryza sativa (japonica cultivar-group)] (model%: 100, hit%: 100, score: 1170, %id: 71) [Oryza sativa (japonica cultivar-group)]
dnaj-like protein subfamily B member 1-like protein
contains DnaJ N-term only; Heat shock 40 kDa protein 1) (Heat shock protein 40) (HSP40
the t-complex beta chaperonin-like protein
Putative protein of unknown function with similarities to transport proteins; strong EST support; putative protein of unknown function with similarity to transport proteins
20S proteasome subunit PAC1 [SP:PSA4_ARATH] custom_KEGG (model%: 85, hit%: 84, score: 681, %id: 56) [Arabidopsis thaliana]
the actin binding protein cofilin-like protein
No significant homology with any known proteins.; hypothetical gene
Excellent hits to other ABC transporters and interpro domains.
based on sequence similarity to bacterial proteins and presence of carnitine dehydratase domain; putative protein of unknown function
presence of nonaspanin domain and phaeodactylum EST support suggests this is a membrane spanning protein
contains conserved importin-beta N terminal domain (IPR001494). stong sequence alignment with beta importin in Arabidopsis.
RL30, ribosomal protein 30 60S large ribosomal subunit
RL30, ribosomal protein 30, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
Displays high homology to known hydrase sequences. Partial cDNA support. Citric acid cycle enzyme.
DNA Repair, Base Excision repair, 8-oxo G, FAPY; 8-OXO g, FAPY
based on sequence similarity to chloroplast-localized translocators from plants and presence of 7 predicted transmembrane domain
Nuclear encoded promotor- recognising subunit of plastid encoded RNA polymerase. Note: there are several sigma factor that recognise different promotors. This one is most similar to cyanobacterial and nucleomorph homologues indicating secondary gene transfer.
putative rRNA methyltransferase, supported by cDNA
strong EST support; RanBP4) (importin beta 4 subunit) (karyopherin beta 4 subunit
Identified this gene by looking at arginine and proline metabolism in KEGG,hydrolyses carbon-nitrogen bonds
fucoxanthin chl a/c light-harvesting protein
fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type
RS13, ribosomal protein 13 40S small ribosomal subunit
RS13, ribosomal protein 13, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
RL13e, ribosomal protein 13e 60S large ribosomal subunit
RL13e, ribosomal protein 13e, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
hypothetical protein, similar to methyltransferase; hypothetical protein
riboflavin metabolism, viatmin b2, protein rb A that includes GTP cyclohydrolase II
riboflavin metabolism, Vitamin B12 synthesis, hydrolase; GTP cyclohydrolase II, possibly riboflavin biosyntheis protein ribA that includes GTP cyclohydrolase II and DHBP synthase)
This gene was identified based on sequence similarity to a putative beta-mannosidase from Gossypium hirsutum (upland cotton) (Alignment Length: 814 IDENTITIES: 21.25% SIMILARITIES: 30.59%). Beta-mannosidase is involved in the degradation of complex N-linked oligosaccharide chains in the lysosome. Specifically, it is responisble for the hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides (according to KEGG). This gene also contains IPR000169, which is a eukaryotic thiol (cysteine) protease active site.
probably chloroplast targeted; similar to DNA polymerase I in alphaproteobacteria
Probable prohibitin, an evolutionarily conserved protein that inhibits cell cycle progression; Q9P7H3 (Q9P7H3) Putative prohibitin (model%: 99, hit%: 98, score: 761, %id: 54) [Schizosaccharomyces pombe]; EST support; probable prohibitin, an evolutionarily conserved protein that inhibits cell cycle progression
RL13A, ribosomal protein 13A 60S large ribosomal subunit
RL13A, ribosomal protein 13A, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
contains SEC7 domain (Arf-specific GEFs); GEF, GEP, GDP/GTP exchange protein
based on sequence similarity to yeast protein