Thalassiosira pseudonana CCMP1335 chromosome 1, 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 CM000638.\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##
adenosylmehtionine-8-amino-7-oxononanoate aminotransferase
based on sequence similarity and presence of defining domain. likely involved in biotin synthesis
N2,N2, dimethylguanosine tRNA methyltransferase
putative protein similar to extra spindle poles protein (
isopentenyl-dephosphate delta-isomerase-like protein
Contains conserved Isopentenyl-diphosphate delta-isomerase domain (IPR002667); catalyses the interconversion of isopentenyl diphosphate and dimethylallyl diphosphate. Dimethylallyl phosphate is the initial substrate for the biosynthesis of carotenoids and other long chain isoprenoids; some similarity to other organisms (52% amino acid identity); also contains a NUDIX hydrolase domain (IPR000086)
putative protein based on sequence similarity to hypothetical bacterial proteins; putative protein of unknown function
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. This gene appears to encode a cAMP-specific phosphodiesterase
suppressor of actin mutations protein-like protein
Has good homolgy to debiotin synthetase from Arabidopsis, biotin synthesis, vitamin synmthesis; putative protein
similar to Skp1 component of ubiquitin protein degradation pathway GI:4959710 from [Medicago sativa] (model%: 58, hit%: 70, score: 198, %id: 37) [Arabidopsis thaliana]; putative protein similar to SKP1 component of ubiquitin protein degradation pathway
similar fragment is encoded on the G.theta nucleomorph but this one is more similar to a homologue from Chlamydia. The first 300 aa are missing in the model; fragment of a hypothetical helicase
No reasonable similarity to any known sequences.; hypothetical gene
Function unknown.; hypothetical protein with similarity to carboxy half of dihydrolipoamide S-acetyltransferase
A group of enzymes removing the serine/threonine or tyrosine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes which have been phosphorylated under the action of a kinase. Dual specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle; contains conserved dual-specificity phosphatase domains.
dual specificity protein phosphatse, tyrosine/serine/threonine
High sequence similarity on one side of the gene; other region is dissimilar to varying degrees, suggesting lower level of conservation in this region.
based on sequence similarity to transporters from bacteria
based on sequence similarity to Arabidopsis protein of unknown function and EST support from Phaeodactylum; putative protein of unknown function
vascular plant like serine/threonine protein kinase
over a very short segment TPS_98679 is significanlty homolous to other vascular plant putative serine/threnine protein kinases
cytochrome c biogenesis protein precursor
Reasonable similarity between this gene and other cytochrome c biogenesis protein precursors. The best hit was to A. thaliana with an E value of 9.6e-38.
I got to this annotation as one of seven of the aspartate aminotransferases called by grail/genewise. There appears to be high similarity to other putative aspartate aminotransferases in Arabidopsis, but there is no EST support for this assignment.
ornithine carbamoyltransferase precursor. Metabolism; Amino Acid Metabolism; Urea cycle and metabolism of amino groups. Transfers the carbamoyl group of carbamoyl phosphate to ornithine.
contains a CRALBP/TRIO domain, present in several lipid-transfer proteins and proteins with diverse functions; phosphatidylinositol/phosphatidylcholine transfer protein) (PI/PC TP
ferric reductase-like transmembrane component
Ferric reductase (Frp1) protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. This family includes a common region in the transmembrane proteins mammalian cytochrome b-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress.This may be a family of flavocytochromes capable of moving electrons across the plasma membrane that include a potential FAD binding domain. Mutations in the sequence of cytochrome b-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterised by the absence of a functional plasma membrane associated NADPH oxidase.
based on sequence similarity and presence of glycerol 3-P domain
putative protein of unknown function containing a F-box domain; putative protein of unknown function containing a f-box domain
Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells however others are implicated in ion uptake. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.
sucrose non-fermenting (SNF-1) related serine threonine protein kinase
Strong similiarity to SNF-1 (51% amino acid identity). Contains conserved protein kinase, serine theronine kinase, and tyrosine kinase domains (IPR000719, IPR00290, and IPR001245). Supporting EST data. SNF-1 may have role in regulating haploid invasive growth in response to glucose starvation; has borad role in transcriptional and metabolic regulation in response to stress.
Monooxygenases are enzymes that reduce molecular oxygen by incorporating one oxygen atom into its substrate and the other one in water.
Putative protein containing a zinc metallopeptidase (metalloprotease) domain; similarities to Q9SRP6 (Q9SRP6) T21P5.16 protein (Hypothetical 21.8 kDa protein) (model%: 100, hit%: 89, score: 316, %id: 40) [Arabidopsis thaliana]; putative protein containing a zinc metallopeptidase domain
sequence similarity to other mcm6-like proteins and posssession of MCm domains; DNA replication licensing factor mis5, cdc21
This family of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyze the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, E. coli and Bacillus.
based on sequence similarity and presence of defining domain
SRP54, signal recognition particle 54 kDa protein 2-like protein
possible cell cycle protein; putative cell division cycle protein similar to CDC48 in SOTBN, supported by cDNA
Excellent hits to other ABC transporters and interpro domains. Location unknown. Could be mitochondrial.
translation elongation factor ef-1 alpha
based on sequence similarity and presence of ATP binding site motif and EST support from T. pseudonana exponentially growing culture
lysophosphatidic acid acyltransferase-like protein
L-histidinol-phosphate + 2-oxoglutarate <=> 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate[COFACTOR] PYRIDOXAL PHOSPHATE.[PATHWAY] Histidine biosynthesis; seventh step.[SIMILARITY] BELONGS TO CLASS-II OF PYRIDOXAL-PHOSPHATE-DEPENDENT AMINOTRANSFERASES.
DNA directed RNA polymerase II, largest subunit
similar to diacylglycerol kinase catalytic domain
chelatase of mg-protoporphyrin IX chelatase
Along with subunits I(plastid-encoded) and D (nucleus-encoded), catalyzes the insertion of Mg into protoporphyrin IX. First committed step of chlorophyll biosynthesis. Belongs to cobN/chelatase family. Very good match with cyanobacterial ChlH.
Very well supported by EST data. Good homology to other hypothetical sequences.Potentially important in Beta-transducin (G-beta) which is one of the three subunits (alpha, beta, and gamma) of the guanine nucleotide-binding proteins (G proteins) which act as intermediaries in the transduction of signals generated by transmembrane receptors.
TPS_10167 is homologous to VSP-3 and WP6 which are cell wall proteins in Chlamydomonas' reinhardti andC. eugametos. VSP-3 and WP6 contain (SerPro)x epitopes are common toextensin-like cell wall proteins. This prteins also shows homology to part of the Orgyia pseudotsugata single capsid nuclear polyhedrosis virus and the Epiphyas postvittana nucleopolyhedrovirus.Also the protein is predicted to have a Proline-rich region. This can be a characteristic either structural proteins or metal-binding proteins.; hypothetical protein
Putative lipoic acid synthetase (lipoate synthase), similar to gi|23482377|gb|EAA18375.1| lipoic acid synthetase, putative [Plasmodium yoelii yoelii] (model%: 99, hit%: 59, score: 1118, %id: 65) [Plasmodium yoelii yoelii]
rubisco small subunit small subunit n-methyltransferase
Regulation of rubisco activity, clear best hit with Gtheta thus indicating secondary gene transfer, EST support from P.tricornutum
putative cullin-like protein; supported by diatom est XZ06727.x1, Phaeodactylum est's PTMM01952, PTMM06447
Putative pyrimidine-nucleoside phosphorylase, similar to Pyrimidine Nucleoside Phosphorylase (model%: 92, hit%: 97, score: 832, %id: 43) [Geobacillus stearothermophilus]
addition to TONYC annotation: Extended N-terminus contains putative ER signal peptide (SignalP 0.848) followed by p[utative chloroplast transit peptide (TargetP 0.905). Protein is putatively chloroplast targeted.; hypothetical protein with similarity to galactokinase
Function(s) unknown.; the amino portion is weakly similar to hypothetical proteins from rhodobacter sphaeroides, trichodesmium erythraeum, burkholderia fungorum; hypothetical protein; the carboxy portion is very similar to a hypothetical auxin-regulated protein from arabidopsis thaliana
Possible amino acid transporter based on blast analyses and interpro hits. Location unknown.
Putative signal peptidase; similar to gi|6225603|sp|P72660|LEP1_SYNY3 Probable signal peptidase I-1 (SPase I-1) (Leader peptidase I-1) (model%: 100, hit%: 83, score: 215, %id: 37) [Synechocystis sp. PCC 6803]
partial EST support; hypothetical protein containing weak similarity to unknown proteins
similar to alkaline phosphatase from Brucella melitensis. Supported by small piece of EST from Phaeodactylum.
Has distant similarity to peptide methionine sulfoxide reductase; unknown gene
hypothetical protein with similarity to meiosis-specific nuclear structural protein
guanine nucleotide binding protein beta subunit-like protein
very high sequence similarity to other guanine nucleotide binding proteins (73& identity over 320 amino acids); supported by EST data; contains G-protein beta WD-40 repeats (IPR001680)
Good EST evidence for 3' end. Hits to Pfam and hsp domains at 5' end.; hypothetical protein similar to NAD-dependent oxidoreductases, possibly nadph-dependent cytochrome P450
No EST evidence and little sequence matches but this may be due to the fact that the sequence is truncated.; hypothetical protein with similarity to pyruvate:ferredoxin oxidoreductase
contains MORN motifs; supported by a Thalassiosira cDNA; protein of unknown function containing similarity to phosphatidylinositol-4-phosphate 5-kinase
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. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).
Putative protein of unknown function containing an acid phosphatase domain; similar to gi|4501873|ref|NP_001602.1| (NM_001611) tartrate resistant acid phosphatase 5 precursor [Homo sapiens] (model%: 94, hit%: 97, score: 442, %id: 34) [Homo sapiens]; strong EST support; putative protein of unknown function containing an acid phosphatase domain
Putative membrane-localized steroid binding protein. Supported by EST.
Possible amino acid/polyamine transporter family II protein. No EST data.
KE4,-like protein to histidine-rich membrane protein
KE4, homolog to histidine-rich membrane protein, some related to catecholamine regulation
based on sequence similarity to hypothetical proteins from bacteria and EST support; hypothetical protein
supported by a cDNA; hypothetical protein of unknown function, similar to unknown proteins
based on sequence similarity to Drosophila protein and presence of defining domains
Reasonable hits to other MFS transporters (E = 1.8e-27).
supported by cDNAs; hypothetical protein with partial similarity to unknown proteins
contains AAA family of ATPase and ATP/GTP-binding site domains; tat-binding homolog 4
similar to heat shock protein in mycobacterium, gene GrpE, hsp-70 cofactor
probable malate dehydrogenase with mitochondrial or glyoxysomal precursor
Citric acid cycle enzyme. Identification is supported by cDNA and numerous similar gene hits. The cDNA is longer on the 3' end, but probably erroneously, as all similar gene hits were consistent in length with the putatively identified gene.
ORC2, origin recognition complex subunit 2
ORC2, origin recognition complex subunit 2, origin of replication
based on sequence similarity, EST support and presence of mitochondrial carrier protein domain; oxoglutarate/malate carrier protein
Similarity to known cysteine synthases ranges from low to very high. Supported by cDNA. An enzyme in cysteine metabolism.
Similarity to known genes ranges from low to high. An enzyme in the cysteine mestabolism pathway.
3 thaps ESTs cover a central region and C-terminus
based on sequence similarity, contains beta lactamase domain; putative protein displaying similarity to other conserved hypotheticalals
Good hits to other transporters and pfam model. Also contains InterPro domain #003662, which is a domain characteristic of general substrate transporters.
DNA repair, Double strand break repair, Rad54
Also shows good similarity to queuine tRNA-ribosyltransferase
glutamine phosphoribosylpyrophosphate amidotransferase
putative glutamine phosphoribosylpyrophosphate amidotransferase based on sequence similarity, presence of defining domains and EST support
may be involved in phenylalanine and tyrosine biosynthesis. Predicted chloroplast protein
hypothetical protein with similarity to peroxisome assembly proteins
Possible amino acid/polyamine transporter family II. EST data available.
Complete cDNA support, fair similarity to other proteins of unknown function; unknown protein
Interconverts the alpha and beta configurations of aldose sugars.
putative protein similar to spindle checkpoint protein
n-acetylglucosaminyl-phosphatidylinositol biosynthetic protein
hypothetical protein with no recognizable similarity but supported by a cDNA
Nucleoside diphosphate kinase (NDK) (NDPK) (NDP kinase), similar to gi|12055485|emb|CAC20613.1| (AJ297707) nucleoside diphosphate kinase [Leishmania infantum] (model%: 100, hit%: 99, score: 500, %id: 59) [Leishmania infantum]
high sequence similarity with PKA in other organisms (55% identity over 300 amino acids). contains conserved serine threonine tyrosine kinsase domains (IPR002290 and IPR001245).
similar to 26S proteasome regulatory complex subunit p30 GB:AAF08395 GI:6434966 from [Drosophila melanogaster]; supported by cDNA: gi_14532465_gb_AY039857.1_ (model%: 100, hit%: 75, score: 406, %id: 43) [Arabidopsis thaliana]
heat shock protein belonging to the HSP70 family
Contains InterPro domain #IPR001023 for HSP70 proteins. Good hits to other heat shock proteins including human HSP105 and mouse HSP70-related protein. This is probably of eukaryotic origin and is probably cytoplasmic.
FTR1 is a plasma membrane permease for high-affinity iron uptake. In yeast and in Chlamydomonas Ftr1 has been shown to be associated with a complex at the plasma membrane.The Fet3 gene product is thought to oxidize Fe(2+) to Fe(3+) which is then delivered toFtr1 for transport of F3(3+) into the cell.
Contains conserved ATP-sulfurylase domain (IPR002650). Strong alignment with hypothetical protein from Synechococcus sp. WH 8102 (64% amino acid identity). Supporting Phaeodactylum tricornutum EST data.; hypothetical protein with similarity to sulfate adenylytransferase
DNA directed RNA polymerase III, second largest subunit
Putative protein of unknown function containing a metalloprotease domain (metallopeptidase), with soem similarities to gi|14575528|emb|CAC42882.1| (AJ312398) leishmanolysin-like peptidase, variant 2 [Homo sapiens] (model%: 35, hit%: 40, score: 210, %id: 27) [Homo sapiens]; EST support; putative protein of unknown function containing a metalloprotease domain
presence of diphthine synthase domain and uroporphyrin domains and sequence similarity and EST support suggest methyltransferase
based on presence of argk domain land ATP binding domain and sequence similarity may function as a kinase with ATPase activity; similar to hypotheticalal protein from human; putative protein with argk and ATP binding domain
transporter belonging to the MFS superfamily
Some hits to phosphate and sugar transporters and to pfam transporter profile #00083. Also contains InterPro domain #003662, which is a domain common to general substrate transporters.
Reaction catalyzed:PPi + D-fructose 6-phosphate = Pi + D-fructose 1,6-bisphosphate; putative; pyrophosphate dependent 6-phosphofructose 1-kinase
3',5'-cyclic nucleotide phosphodiesterase
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.
based on sequence similarity and EST support from exponentially growing cells; involved in chromosome condensation
Reaction catalyzed:UDP-glucose + 2 NAD + H2O = UDP-glucuronate + 2 NADH2. Note, also acts on UDP-2-deoxyglucose.; putative
I got to this annotation as one of seven of the aspartate aminotransferases called by grail/genewise. There appears to be no signal peptide at the 5' end as checked by the online site SignalP. Gene symbol does NOT imply homology to the Arabidopsis AAT2 that is located in the cytosol. Sequence shows high similarity to other aspartate aminotransferases.
Partial Phaeodactylum cDNA support. Very distant similarity to leucyl/phenylalanyl tRNA transferase.; unknown protein
based on sequence similarity to bacterial proteins and EST support
[FUNCTION] THIS ENZYME CONVERTS PHYTOENE INTO ZETA-CAROTENE VIA THE INTERMEDIARY OF PHYTOFLUENE BY THE SYMMETRICAL INTRODUCTION OF TWO DOUBLE BONDS AT THE C-11 AND C-11' POSITIONS OF PHYTOENE. [COFACTOR] NAD, NADP, OR FAD (PROBABLE). [ENZYME REGULATION] INHIBITED BY THE HERBICIDES METFLURAZON, DIFUNONE, FLURIDONE AND DIFLUFENICAN. [PATHWAY] Carotenoid biosynthesis. [SUBCELLULAR LOCATION] Chloroplast; chromoplast. [DEVELOPMENTAL STAGE] RIPENING FRUIT. [SIMILARITY] BELONGS TO THE PHYTOENE DEHYDROGENASE FAMILY.
Putative protein of unknown function with similarities to cytidine deaminases; e.g. At5g28050-68299.m02882 F15F15.120 putative cytidine deaminase - like putative cytidine deaminase, Cicer arietinum, EMBL:AJ006764. (model%: 46, hit%: 61, score: 156, %id: 34) [Arabidopsis thaliana]; putative protein of unknown function with similarity to cytidine deaminases
Putative protein of unknown function containing leucine-rich repeats, with similarioties to gi|15528705|dbj|BAB64771.1| (AP003282) putative receptor protein kinase [Oryza sativa (japonica cultivar-group)] (model%: 77, hit%: 11, score: 239, %id: 35) [Oryza sativa (japonica cultivar-group)]; putative protein of unknown function containing leucine-rich repeats
possible unitrate reductaes-close homology to inducible nitrate reducatse from soybean, similar to nitrate reductase in Arabidopsis; hypothetical protein
chromosomal protein,like chromosomal protein xcap-e
Zinc-dependent alcohol dehydrogenase. Catalyzes the conversion of short-chain alcohols to carbonyl derivatives. Part of the ADH superfamily
glyceraldehyde-3-phosphate dehydrogenase precursor
In Addition to Tonyc's annotation: this gene is most similar to gabpd1 from the cryptomonade nucleus, thus indicating seondary gene transfer
sedoheptulose-7-phosphate:D-glyceraldehyde-3- phosphate + glycolaldehydetransferase, chloroplastic pentose phosphate pathway, similar to gi|22299413|ref|NP_682660.1| (NC_004113) transketolase [Thermosynechococcus elongatus BP-1] (model%: 92, hit%: 98, score: 1777, %id: 54)
Some mild homology evidence suggesting this gene is real.
Has EST support. ambiguous: 4350755:1 supports model, 4346039:1 contradicts model
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; hypothetical protein possible protein kinase
Lipid biosynthesis--may be chloroplast targeted, but not clear from sequence or Genbank.
based on sequence similarity and presence of endoribonuclease domain that may be invovled in regulating purine biosynthesis; putative protein with endoribonuclease domain
sequence similarity and presence of transcription factor Tfb2 domain
function of protein is unknown but contains the SCP/Tpx-1/Ag5/PR-1/Sc7 domain which is found in a family of eukaryotic proteins involved in such things as sperm maturation in rodents, pathogenesis-related proteins, venom allergens. Common feature of these proteins is extracellular localization. The diatom protein appears to be a member of a protein family.; putative protein of unknown function that contains a SCP/Tpx-1/Ag5/PR-1/Sc7 domain
based on sequence similarity to hypothetical proteins from archae and eubacteria; hypothetical protein
RS30, ribosomal protein 30 40S small ribosomal subunit
RS30, ribosomal protein 30, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
phosphatidylinositol 4-kinase-like protein
contains conserved Phosphatidylinositol 3- and 4-kinase domain (IPR000403). Phosphatidylinositol 4-kinase (PI4-kinase) is an enzyme that acts on phosphatidylinositol (PI) in the first committed step in the production of the secondary messenger inositol-1,4,5,-trisphosphate. EST data from Phaeodactylum tricornutum supports model.
similiar to 56.5 kDa protein in DYS1-PCL5 intergenic region in Yeast
based on sequence similarity and presence of aminotransferase class I domain
Catalyzes the reaction L-ornithine = L-proline + NH3. Involved in the urea cycle and in the metabolism of amino groups.
Putative trypsin-like serine protease, similar to At5g40200-68299.m03687 MSN9.100 DegP protease contains similarity to DegP2 protease GI:13172275 from [Arabidopsis thaliana] (model%: 82, hit%: 76, score: 903, %id: 40) [Arabidopsis thaliana]
based on sequence similarity to T. weissflogii sig1 protein; sexually induced protein 1, EGF domains
Somewhat tentative identification based on moderate database hit similarities. Enzyme of the citric acid cycle.; putative partial isocitrate dehydrogenase
Function unknown, but is possibly involved in the interconversion of N-acetyl-D-glucosamine 1-phosphate and N-acetyl-D-glucosamine 6-phosphate.; hypothetical protein sharing some sequence similarity with phosphoacetylglucosamine mutase
HAS A ROLE IN POSTREPLICATION REPAIR. ALSO INVOLVED IN THE RNA DEGRADOSOME, A MULTI-ENZYME COMPLEX IMPORTANT IN RNA PROCESSING AND MESSENGER RNA DEGRADATION. BELONGS TO DEAD HELICASE FAMILY. Supported by cDNA.
20S proteasome beta subunit (beta5) [SP:_YEAST] custom_KEGG (model%: 92, hit%: 66, score: 549, %id: 54) [Saccharomyces cerevisiae](proteasome epsilon chain precursor) identical to GB:O23717;supported by full-length cDNA: Ceres:33591. (model%: 98, hit%: 73, score: 510, %id: 49) [Arabidopsis thaliana] Best Hit (KEGG): sce:YPR103W PRE2; 26S proteasome
Putative protein of unknown function containing a rhodanese domain; such domains are found in plant senescence proteins; similarities to gi|21292419|gb|EAA04564.1| (AAAB01008807) agCP3860 [Anopheles gambiae str. PEST] (model%: 81, hit%: 66, score: 179, %id: 42) [Anopheles gambiae str. PEST] and also to HSP 67Bb protein; putative protein of unknown function containing a rhodanese domain
Putative protein of unknown function containing a rhodanese domain; such domains are associated with senescence proteins in plants; similarities to At5g66040-68299.m06645 K2A18.11 senescence-associated protein almost identical to ketoconazole resistant protein GI:928938 from [Arabidopsis thaliana]; (model%: 69, hit%: 70, score: 81, %id: 29) [Arabidopsis thaliana] and also to HSP 67Bb proteins; EST support; putative protein of unknown function containing a rhodanese domain
supported by a Thalassiosira cDNA; putative protein containing similarity to unknown proteins
based on sequence similarity to hypothetical proteins from bacteria; hypothetical protein
supported by a Thalassiosira cDNA; putative protein containing similarity to unknown peptides
adenine nucleotide translocator; ATP/ADP translocase
Location unknown; ADP, ATP carrier protein
hypothetical protein with similarity to transporter ATPase
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
Unidentified and of questionable authenticity; unknown sequence identified by grail and genewise
This protein has EST support. It contains an InterPro domain #IPR001404, which is characterisitic of proteins belonging to the heat shock hsp90 protein family. It also has excellent similarity to Pfam model #PF00183, which is a model for HSP90 proteins. This gene has low similarity to Pfam model #PF02518 which represents a family consisting of the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
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%: 92, hit%: 87, score: 404, %id: 25) [Arabidopsis thaliana]; putative protein with similarity to enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1)
Na+/H+ exchange protein also known as sodium:hydrogen antiporter
based on presence of Na+/H+ exchange protein domain. There is good EST support for this gene model, but limited sequence homology
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%: 75, score: 469, %id: 30) [Arabidopsis thaliana]; putative protein with similarity to enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1)
flagellar protofilament ribbon like protein
TPS_101906 is significantly homologous to protofilament ribbon proteins in a variety of eukaryotes.
Proteasome subunit alpha type 7-1 (20S proteasome alpha subunit D1) (TAS-G64) (model%: 97, hit%: 92, score: 686, %id: 62) [Arabidopsis thaliana]
Similar to putative ubiquitin-protein ligase C57A7.03C (model%: 34, hit%: 37, score: 689, %id: 37) [Schizosaccharomyces pombe]; EST support; putative protein with similarity to ubiquitin protein ligase domain (E3)
Similarity to known proteins ranges from low to very high. An enzyme in the cysteine metabolism pathway.
26S proteasome ATPase regulatory subunit 4
26S proteasome subunit 4; supported by full-length cDNA: Ceres:36815. (model%: 99, hit%: 99, score: 1715, %id: 74) [Arabidopsis thaliana]; RPT2
This gene has EST support and shows some similarity to various transporters and permeases. For example, it was 23% identical (e value = 3e-32) to NC_003869 Permeases of the major facilitator superfamily from Thermoanaerobacter tengcongensis.; unknown function
A number of eukaryotic and prokaryotic proteins have been characterized on the basis of their structural similarity. They all seem to be involved in ATP-dependent, nucleic-acid unwinding.
N-fixation protein but more likley some other cellular function
Function unknown, but is possibly a glycosyl transferase.; hypothetical protein with glycosyl transferase family 20 domain
contains similarity to Sec14-like cytosolic factors; hypothetical protein containing a CRAL/TRIO domain
supported by Thalassiosira cDNAs; putative protein with no similarity
lies within the coding region of a 'real gene; no gene
putative protein with sequence similarity to hypothetical human protein that contains G-protein beta WD-40 repeats; putative protein of unknown function with G-protein beta wd-40 repeats
good EST support and presence of WW domain; putative protein of unknown function containing WW
Part of the valine/leucine/isoleucine biosynthesis pathway. Identified by high similarity to known sequences. Nearly complete cDNA support.
EST support, presence of defining domains and sequence similiarity indicate putative V-type H-ATPase D subunit
supported by Thalassiosira and Phaeodactylum ESTs; putative protein similar to unknown proteins
[FUNCTION] CYTOCHROMES P450 ARE A GROUP OF HEME-THIOLATE MONOOXYGENASES. IN MICROSOMES, THIS ENZYME IS INVOLVED IN AN NADPH-DEPENDENT ELECTRON TRANSPORT PATHWAY. IT OXIDIZES A VARIETY OF STRUCTURALLY UNRELATED COMPOUNDS, INCLUDING STEROIDS, FATTY ACIDS, AND XENOBIOTICS. [FUNCTION] THE P-450 SYSTEM IS RATHER SPECIALIZED FOR THE OMEGA-HYDROXYLATION OF FATTY ACIDS. P450-KA1 AND P450-KA2 CATALYZE THE OMEGA-HYDROXYLATION OF VARIOUS FATTY ACIDS AND HYDROXYLATE PROSTAGLANDIN A1 AND A2 SOLELY AT THE OMEGA-POSITION. [CATALYTIC ACTIVITY] Octane + reduced rubredoxin + O(2) = 1-octanol + oxidized rubredoxin + H(2)O. [SUBCELLULAR LOCATION] Membrane-bound. Endoplasmic reticulum. [SIMILARITY] BELONGS TO THE CYTOCHROME P450 FAMILY.
supported by cDNAs; protein containing similarity to transcription factors and DNA.binding peptides
supported by Thalassiosira cDNAs; putative protein with similarity to hypothetical proteins
supported by Thalassiosira cDNAs; putative protein with distant similarity to DNA-binding proteins and unknown peptides
(OMTs) have important roles in secondary metabolite biosynthesis. Methyl-transferases are responsible for the transfer of methyl groups between two molecules.
similar to ubiquitin protein ligase GI:2827198 from [Mus musculus] (model%: 97, hit%: 9, score: 483, %id: 35) [Arabidopsis thaliana]
Putative protein of unknown function, containing leucine-rich repeat domains; similar to gi|24216020|ref|NP_713501.1| Leucine-rich repeat containing protein [Leptospira interrogans serovar lai str. 56601] (model%: 100, hit%: 57, score: 250, %id: 24) [Leptospira interrogans serovar lai str. 56601]; putative protein of unknown function, containing leucine-rich repeat domains
Putative serine carboxypeptidase, similar to At3g10410-68298.m01075 F13M14.32 putative serine carboxypeptidase precursor identical to serine carboxypeptidase precursor GB:P32826 [Arabidopsis thaliana] up to residue 514 (model%: 73, hit%: 73, score: 396, %id: 30) [Arabidopsis thaliana]; EST support
I got to this gene by going down the list of genes involved in alanine and aspartate metabolism under KEGG. High similarity (69%)and identity (49%)to aspartate-tRNA ligase-like protein in both Drosophila melanogaster and Arabidopsis thaliana.
No reasonable similarity to any known sequences. Complete cDNA support; unknown protein
Matches to ESTs from diatoms. Good alignments with threonine synthase genes from yeasts.
based on sequence similarity to hypothetical proteins from metazoans and EST support from Phaeodactylum tricornutum; putative protein of unknown function
contains the chaperonin TCP1 domains. EST data supports gene model
Serine/threonine (S/T) phosphatases catalyse the dephosphorylation of phosphoserine and phosphothreonine residues; contains conserved serine/threonine protein phosphatase; PP2A CAN MODULATE THE ACTIVITY OF PHOSPHORYLASE B KINASE CASEIN KINASE 2, MITOGEN-STIMULATED S6 KINASE, AND MAP-2 KINASE; PP2A catalytic subunit
TPS_101757 shows significant homology over a segment ofabout 140 amino acids to receptor protein kinase-like proteins in vasular plants. The model also contains a predicted leucine-rich repeat. Leucine-rich repeats (LRRs) are 20-29-residue sequence motifs present in tandem arrays a number of proteins with diverse functions, such as hormone receptor interactions, enzyme inhibition, cell adhesion and cellular trafficking. A number of recent studies revealed the involvement of LRR proteins in early mammalian development, neural development, cell polarization, regulation of gene expression and apoptosis signalling.
Putative protein of unknown function with similarities to pseudouridylate synthase, e.g. gi|15924483|ref|NP_372017.1| (NC_002758) ribosomal large subunit pseudouridine synthase B (model%: 70, hit%: 54, score: 177, %id: 33) [Staphylococcus aureus subsp. aureus Mu50]; putative protein of unknown function with similarity to pseudouridylate synthase
FUNCTION: ACTIVATION OF LONG-CHAIN FATTY ACIDS FOR BOTH SYNTHESIS OF CELLULAR LIPIDS, AND DEGRADATION VIA BETA-OXIDATION. PREFERENTIALLY USES ARACHIDONATE AND EICOSAPENTAENOATE AS SUBSTRATES (by similarity) CATALYTIC ACTIVITY: ATP + a long-chain carboxylic acid + CoA = AMP + diphosphate + an acyl-CoA. COFACTOR: MAGNESIUM (BY SIMILARITY).
P-type (or E1-E2-type) ATPases constitute a superfamily of cation transport enzymes, present both in prokaryota and eukaryota, whose members mediate membrane flux of all common biologically relevant cations
Poor alignment with hits in other databases, but contains conserved phosphatidylinositol 3- and 4- kinase domain (IPR000403) and FAT domain (IPR003151), a domain present in the PIK-related kinases.; hypothetical protein containing a phosphatidylinositol 3-and 4-kinase domain and fat domain
No similarity to any known sequences. Partial cDNA support.; unknown protein
member of the clp superfamily, regulatory gamma subunit
Clp proteins are involved in protein degradation, chaperone function and heat shock response. The given gene by similarity seems to be involved in protein degradation. It is ost similar to various gamma subunits. At least 6 more regulative subunits are in the T. pseudonana genome.In higher plants the corresponding gene product is imported into the chloroplast. There is no targeting sequence obvious in T. pseudonana.
beta subunit of clathrin adaptor protein AP3
mannosyl-oligosaccharide alpha-mannosidase
involved in processing of N-glycan moieties in the endolplasmic reticulum
possibliy involved in biosilica formation
matches prokaryotic hypothetical proteins; hypothetical protein
contains similarity to receiver domain of response regulator from bacterial two-component systems. Missing some conserved residue motifs.; contains similarity to receiver domain of response regulator from bacterial two-component systems
contains homology to prokaryotic two component sensors and regulators; hypothetical protein
catalyzes the reaction L-ornithine = L-proline + NH3. Involved in the urea cycle and in arginine synthesis and in the metabolism of amino groups.
EST data.Strong hits to multiple same protein in multiple genomes.
based on sequence similarity and presence of biopterin domain and EST support from Phaeodactylum; putative protein with transmembrane domains with sequence similarity to hypothetical protein
IFT proteins are part of a large complex that are transported along ciliary microtubules and are required for assembly of cilia.
presence of Na+/H+ domain and cyclic nucleotide-binding domain suggests may be a nucleotide-gated ion channel; sodium/hyrogen antiporter, nucleotide-gated ion channel
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 red algal homologues indicating secondary gene transfer
RM11, ribosomal protein 11 mitochondrial large ribosomal subunit
RM11, ribosomal protein 11, mitochondrial large ribosomal subunit, nuclear encoded, translation, protein biosynthesis
Adenosylmethionine--8-amino-7-oxononanoate aminotransferase
found through KEGG site for Biotin metabolism
based on limited sequence similarity and presence of defining domains
Putative protein containing a U7 serine protease domain; also similar to gi|23468495|gb|ZP_00123830.1| hypothetical protein [Pseudomonas syringae pv. syringae B728a] (model%: 98, hit%: 51, score: 356, %id: 45) [Pseudomonas syringae pv. syringae B728a]; putative protein containing a U7 serine protease domain
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
presence of MCM domains and sequence similarity to other MCM5-like proteins; DNA replication licensing factor, CDC46
Function unknown, but presumably is a key enzyme for commitment toward lysine biosynthesis and represents a point in the pathway for feedback regulation by lysine.
RL20, ribosomal protein 20 60S large ribosomal subunit
RL20, ribosomal protein 20, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
Putative carboxyl-terminal protease similar to gi|17229992|ref|NP_486540.1| carboxyl-terminal protease [Nostoc sp. PCC 7120] (model%: 89, hit%: 80, score: 508, %id: 36) [Nostoc sp. PCC 7120]
[FUNCTION] CHAPERONE SUBUNIT OF A PROTEASOME-LIKE DEGRADATION COMPLEX (BY SIMILARITY). INHIBITS LEUKOTOXIN EXPRESSION.[SUBUNIT] Interacts with hslV (By similarity).[SUBCELLULAR LOCATION] probably mitochondrial(by putative import sequence). [SIMILARITY] BELONGS TO THE CLPX CHAPERONE FAMILY. HSLU
with sequence similarity to human Rab 22B (Rab 31, small GTPase)
Contains InterPro domain #IPR001023 for HSP70 proteins. This gene has EST support. It has similarity to HSP70 proteins from other organisms due to the HSP70 domains.
Good support from Phaeodactylum cDNA and similarity to other SCS genes. Enzyme of the citric acid cycle.
No reasonable similarity to any known sequences.
U5 small nuclear ribonucleoprotein, U5 snRNP
Putative protein of unknown function containing an esterase/lipase domain; similarities to At5g19850-68299.m02082 T29J13.270 putative protein predicted proteins - different species (model%: 92, hit%: 77, score: 393, %id: 32) [Arabidopsis thaliana]; EST support; putative protein of unknown function containing an esterase/lipase domain
Matches with diatom ESTs as well as strong matches to this gene from other organisms such as Arabidopsis. Contains appropriate domains such as anticodon binding domain.
Histone H2A is a small, highly conserved nuclear protein that, together with 2 molecules each of histones H2B, H3 and H4, forms the eukaryotic nucleosome core; the nucleosome octamer winds 146 DNA base-pairs.
Contains several WD40-repeat domains. 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.; putative protein with high similarity to human nuclear receptor co-repressor/HDAC3 complex subunit TBLR1 (TBL1-related protein 1)
Has similarity to putative helicases and anti-viral proteins. Partial cDNA support.; unknown protein
26S proteasome regulatory subunit (RPN9), putative; protein id: At5g45620.1, supported by cDNA: gi_20260473 [Arabidopsis thaliana] (model%: 93, hit%: 95, score: 521, %id: 32) [Arabidopsis thaliana]
lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme
Acts to some extent on all D-amino acids, except D-aspartate and D-glutamate.This gene is homologous to other 'hypothetical' gene in eukaryotes and only slightlysimilar to bacterial D-amino acid oxidorectases.
putative V-type H-ATPase based on EST support and sequence similarity
RL28, ribosomal protein 28 60S large ribosomal subunit
RL28, ribosomal protein 28, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
RL15, ribosomal protein 15 60S large ribosomal subunit
RL15, ribosomal protein 15, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
Putative protein of unknown function containing an esterase/lipase domain; some similarities togi|22955202|gb|ZP_00003003.1| (NZ_AAAY01000001) hypothetical protein [Nitrosomonas europaea] (model%: 52, hit%: 70, score: 251, %id: 31) [Nitrosomonas europaea]; EST support; putative protein of unknown function containing an esterase/lipase domain
Phospholipid:diacylglycerol acyltransferase
[FUNCTION] Triacylglycerol formation by an acyl-CoA independent pathway. The enzyme specifically transfers acyl groups from the sn-2 position of a phospholipid to diacylglycerol, thus forming an sn-1-lysophospholipid. [CATALYTIC ACTIVITY] Phospholipid + 1,2-diacylglycerol = lysophospholipid + triacylglycerol.
Strong support for ABC transporter.EST data as well.; mitochondrial
Fucoxanthin chlorophyll a/c protein, member of LHC superfamily. One intron.; FCP8
mevalonate disphosphate decarboxylase-like protein
Strong supporting EST data; similar to other organisms (49% amino acid identity); catalyzes the reaction: ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO2
good EST support from T. weissflogii and T. pseudonana; putative protein of unknown function similar to hypothetical arabidopsis protein
GTPase putatively involved in vesicle transport; ARF1
UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase
responsible for the synthesis of core1 structure of O-glycans;no EST support
26S proteasome regulatory particle chain rpt6-like protein
This protein is homologus to other hypthetical proteins of unknown function in cyanobacteriaand vascular plants. At the 5' end, it is homologous to calcium bindining kinases in Arabadosis and vertebrates.
Somewhat reasonable similarity to polypeptide deformylases
based on sequence similarity to elaC protein from E. coli and EST support; putative protein of unknown function with beta-lactamase domain
Methyl-transferases are responsible for the transfer of methyl groups between two molecules.
Similar to high affinity sulfate transporter in Aquifex aeolicus and to other sulfate transporters
Putative protein of unknown function containing a rhodanese domain; this domain is associated eith plant senescence proteins; similarities to At2g40760-68297.m04300 T7D17.1 rhodanese-like family protein (model%: 90, hit%: 68, score: 394, %id: 31) [Arabidopsis thaliana]; strong EST support; putative protein of unknown function containing a rhodanese domain
fucoxanthin chlorophyll a/c protein, LI818 clade
Member of LHC superfamily. LI818 clade based on sequence similarity to Chlamydomonas LI818. Has 3 introns.
putative vesicle transpor protein; contains similarity to synaptobrevin and Sec22p
Cation channels are transport proteins responsible for the movement of cations through the membrane. This family contains sodium, potassium and calcium ion channels. These proteins contain 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices. Proteins containing this domain are members of the non-ligand gated cation channel proteins, and are found in eukaryotes.
Proteasome subunit alpha type 3 (model%: 98, hit%: 97, score: 664, %id: 51) [Acanthamoeba castellanii] Best Hit (Arabidopsis): At2g27020-68297.m02763 T20P8.7 20S proteasome subunit C8 (PAG1/PRC8_ARATH) identical to GB:Y13693;supported by full-length cDNA: Ceres:8342. (model%: 100, hit%: 99, score: 647, %id: 49) [Arabidopsis thaliana]
possibly involved in polyamine biosynthesis; low similarity to spermidine synthase; hypothetical protein
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; putative protein phosphatase
This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification. Family M20 are E carboxypeptidases. Peptidase family M25 contains X-His dipeptidases.
No reasonable similarity to any known sequences. Complete cDNA support.; unknown protein
based on sequence similarity to drosophila protein, presence of mak16 domain and EST support from T. pseudonana.; putative protein of unknown function (mak16 related)
This gene had good hits (ie. e value = 0) to putative and hypothetical proteins from A. thaliana and Saccharomyces cerevisiae.; putative protein
coproporphyrinogen III oxidase, chloroplast targeted
converts coproporphyrinogen III to protoporphyrin IX. Closely related to Chlamydomonas enzyme.
One of 22 hits of a hypothetical DNA helicase from te Gtheta nulceomorph, no ESt support; fragment of hypothetical DNA helicase
Poor similarity to ABC or other transporters; unknown function
Putative protein with prolyl aminopeptidase domainsimilar to (NC_003272) proline iminopeptidase [Nostoc sp. PCC 7120] (model%: 83, hit%: 92, score: 370, %id: 30) [Nostoc sp. PCC 7120]; putative protein with prolyl aminopeptidase domain