Thalassiosira pseudonana CCMP1335 chromosome 2, 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 CM000639.\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##
Possible Amino acid/polyamine transporter from family II
contains conserved protein tyrosine phosphatase catalytic domain (IPR003595); myotubularin family members have high similarity to dual specific protein phosphatase; similar to myotubularin; putative protein phosphatase
Putative protein of unknown function containing leucine-rich repeats, with some similarities to gi|18676566|dbj|BAB84935.1| (AK074109) FLJ00180 protein [Homo sapiens] (model%: 99, hit%: 58, score: 295, %id: 28) [Homo sapiens]; putative protein of unknown function containing leucine-rich repeats
RL38, ribosomal protein 38 60S large ribosomal subunit
RL38, ribosomal protein 38, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
Reasonable hits to other low molecular weight heat shock proteins. The best hit was to Funaria hygrometrica with an e value of 2.7e-09. It also conatins similarity to Pfam model #PF00011, which is a model for members of the HSP20 family. Most similar to higher plants. Probably cytoplasmic.
RS18, ribosomal protein 18 40S small ribosomal subunit
RS18, ribosomal protein 18, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
based on sequence similarity to hypothetical proteins in fungi and presence of domain found in other hypothetical proteins; hypothetical protein of unknown function
Putative lipoic acid synthetase (lipoate synthase), similar to gi|23821835|sp|Q99M04|LIAS_MOUSE Lipoic acid synthetase, mitochondrial precursor (Lip-syn) (Lipoate synthase) (mLIP1) (model%: 100, hit%: 78, score: 955, %id: 61) [Mus musculus]
N-terminus contains putative ER signal peptide predicted by SignalP (probability 1.000; cleavage site between pos. 25 and 26: THA-AQ). Chloroplast transit peptide has not been found by prediction programs. Possibly chloroplast targeted.; similar to DNAJ domain protein, putative
Glucanases are a family of glucan-degrading hydrolytic enzymes.; hypothetical protein with similarity to glucanase enzymes
most similar to a brown algal (Fucus) homologue, i.e. clearly different from the other 4 H3 genes present in Thaps which more resemble animal and plant homologues, P.tricornutum EST support
Putative protein of unknown function, similar to hypersensitive response-induced protein; At1g69840-68300.m06983 T17F3.13 unknown protein similar to hypothetical protein GB:CAA10289 [Cicer arietinum] (model%: 98, hit%: 96, score: 728, %id: 50) [Arabidopsis thaliana]; EST support; putative protein of unknown function, similar to hypersensitive response-induced protein
MYB DNA binding protein/ transcription factor-like protein
Member of MYB DNA binding protein/ transcription factor family.
TPS_102219 shows homology to other eukaryotic animal sphingosine kinase proteins. Also, the model contains a predited diacylglycerol kinase, catalytic domain.Diacylglycerol kinase phosphorylates diacylglycerol (DAG) to yield phosphatidic acid. This enzyme initiates resynthesis of phosphoinositides consumed by phospholipase C during cellular signal transduction. Mammalian DGK consists of nine isozymes encoded by separate genes.
contains a TypeI antifreeze protein domain; supported by Phaeodactylum ESTs; protein of unknown function, similar to unknown proteins NM_016403 and At3g13200-68298.m01413
Putative peptide methionine sulfoxide reductase (methionine sulfoxide protein reductase) (methionine sulfoxide peptide reductase) (protein methionine sulfoxide reductase) (MetO-peptide reductase) (peptide methionine sulfoxide reductase) (protein-L-methionine:oxidized-thioredoxin S-oxidoreductase; similar to gi|21593143|gb|AAM65092.1| (AY087550) protein-methionine-S-oxide reductase [Arabidopsis thaliana] (model%: 98, hit%: 55, score: 261, %id: 39) [Arabidopsis thaliana]
contains a ribosomal protein L19 domain; amino terminus supported by a Phaeodactylum EST
supported by cDNAs; hypothetical protein with no known similarity
transcription initiation protein spt4-like protein
supported by a Phaeodactylum EST; suppressor of ty 4 homolog
putative RNA helicase. DEAD/DEAH family protein, supported by cDNA
based on sequence similarity to hypothetical proteins and presence of domain found in other hypothetical proteins; putative protein of unknown function
4-diphosphocytidyl-2c-methyl-d-erythritol kinase
based on sequence similarity and presence of defining domains. may be involved in terpenoid biosynthesis
spindle assembly checkpoint serine/threonine-protein kinase
TPS_102263 shows significant homology over a very short section of about 100 amino acids to animal like eukaryotic spindle assembly checkpoint serine/threonine-protein kinases.
TPS_102264 shows weak homology to MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASES from eukaryotic animalsdentin phosphoryn proteins from Homo Sapien.; unknown protein
26S proteasome ATPase regulatory subunit 6
26S proteasome AAA-ATPase subunit RPT6a; supported by cDNA: gi_13537114_dbj_AB044348.1_AB044348 (model%: 96, hit%: 93, score: 1567, %id: 78) [Arabidopsis thaliana]; RPN6
CATALYZES THE REMOVAL OF ELEMENTAL SULFUR FROM CYSTEINE TO PRODUCE ALANINE. IT SUPPLIES THE INORGANIC SULFUR FOR IRON-SULFUR (FE-S) CLUSTERS.
contains kinase, hormone receptor, and RPEL repeat domains; putative kinase with distant similarity to unknown proteins
thylakoid lumenal 17.4 kDa protein, chloroplast precursor
Involved in the oxygen evolving complex of Photosystem II.
NADPH NIR is the C-terminal half of nitrite reductase and shares sequence homology with bacterial NADPH-sulfire reductases, contains the binding for nitrite, two redox centers, a 4Fe-4S center and a siroheme.
similar to dynein light chains in the roadblock/LC7 family
supported by a cDNA; hypothetical protein with distant similarity to uknown proteins
Supported by sequence simularity only. No EST data
member of the inositol monophosphatase protein family
contains conserved inositol monophosphatase domain (IPR000760); may act by enhancing the synthesis or degradation of phosphorylated messenger molecules
contains a general substrate transporter domain; abundant cDNA support; protein of unknown function with no known similarity
contains Sec63, DnaJ N-terminal, and ribosomal protein S2 domains; supported by Thaps and Pt ESTs
PSBP, photosystem II oxygen-evolving complex 23K protein
Similar to photosystem II oxygen-evolving complex 23K protein.
Similar sequences were found in Arabidopsis, several cyanobacteria and on red algal and cryptophyte plastid genomes. Surprisingly the gene is not most similar to red algal or cryptophyte homologues indicating that it is not a former red algal plastid gene as to be expected from secondary endosymbiosis hypothesis. There is a second ycf 19 homologue in the T. pseudonana nuclear genome (genewise 62.211.1); hypothetical protein
contains Patched family, CAAX box (prenylation motif), and HMGCR/Patched 5TM box domains; copious cDNA support; protein of unknown function containing very distant similarity to proteins involved in cholesterol metabolism
Sequence most similar to that of the fungi Magnporthe grisea; Involved in the reaction converting acetyl-CoA to O-Acetylcarnithine
with sequence similarity to yeast actin binding protein ABP140; putative protein
Function unknown, but is possibly an amine or alcohol sulfotransferase.; hypothetical protein with sulfotransferase domain
heavy metal transporter putative zinc transporter
Abstract These ZIP zinc transporter proteins define a family of metal ion transporters that are found in plants, protozoa, fungi, invertebrates, and vertebrates, making it now possible to address questions of metal ion accumulation and homeostasis in diverse organisms
contains SEC7 domain (Arf-specific GEFs); GEF, GEP, GDP/GTP exchange protein
Zinc finger protein similarity, PHD motif, DNA binding, transcription factor; zinc finger protein similarity, PHD motif, DNA binding, transcription factor
HSF20, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF20, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
Abstract The PHO-4 family of transporters includes the phosphate-repressible phosphate permease (PHO-4) from Neurospora crassa which is probably a sodium-phosphate symporter. This family also includes the human leukemia virus receptor.
sedoheptulose-7-phosphate:D-glyceraldehyde-3- phosphate glycolaldehydetransferase, cytosolic pentose phosphate pathway, similar to gi|19774416|gb|AAL99094.1| (AC116425) hypothetical protein [Dictyostelium discoideum] (model%: 98, hit%: 98, score: 1884, %id: 57)
Reaction catalyzed:acetyl-CoA + dihydrolipoamide = CoA + S-acetyldihydrolipoamide. Note, a lipoyl-protein; component of the multienzyme pyruvate dehydrogenase complex.; putative
presence of defining domains, sequence similarity and phaeodactylum EST support suggest this is a v-type ATPase subunit C
RM34, ribosomal protein 34 mitochondrial large ribosomal subunit
RM34, ribosomal protein 34, mitochondrial large ribosomal subunit, nuclear encoded, translation, protein biosynthesis
RL12, ribosomal protein 11 60S large ribosomal subunit
RL12, ribosomal protein 11, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
putative protein, supported by EST data, function unknown - no good blast hits.; putative protein, supported by EST data
contains a CDP-alcohol phosphatidyltransferase domain; hypothetical protein of unknown function containing partial similarity to phosphatidylinositol synthase
putative protein of unknown function with 2 CBS domains that are found in IMP dehydrogenases; putative protein of unknown function with CBS domains
Reaction catalyzed:ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate. Note, dATP can also act as donor.; putative; ribose-phosphate diphosphokinase; ribose-phosphate pyrophosphokinase
supported by Phaeodactylum ESTs; hypothetical protein with distant similarity to unknown proteins
Putative protein of unknown function containing a haloacid dehalogenase domain; some imilarities to spo:SPAC24B11.05 putative haloacid dehalogenase-like hydrolase [SP:YAI5_SCHPO] custom_KEGG (model%: 69, hit%: 80, score: 226, %id: 31) [Schizosaccharomyces pombe]; EST support; putative protein of unknown function containing a haloacid dehalogenase domain
Similar to Arabidopsis diacylglycerol acyltransferase. Transferses acyl-CoA to sn-3 position of 1,2 diacylglyceride.
based on sequence similarity to bacterial proteins and presence o smpB domain appears to be invovled in recognizing stalled ribosomes
Contains InterPro domain #IPR001023 for HSP70 proteins. Also has strong similarity to Pfam model #PF00012 for HSP70 proteins. Similarity to HSP70's from other organisms probably due to the HSP70 domain.
translation initiation factor sui1-like protein
contains a translation initiation factor domain; supported by a cDNA
based on sequence similarity to bacterial proteins; putative protein containing class II aldolase/adducin domain
strong cDNA support; protein of unknown function containing distant similarity to unknown serine-rich proteins
importin beta-3 subunit, ran-binding protein 5
in additon to Demarest annotation: this gene clearly is of red algal origin indicating secondary gene transfer
contains a zinc-binding region (zinc metallopeptidases domain); supported by cDNAs; protein of unknown function
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.
ABC transporter family. Includes good hits to ABC transporters and domains. Includes hit to potential non-transporter.
Putative RNA helicase, supported by cDNA
Excellent hits to ABC transporters and Interpro domains. Location unclear.
based on sequence similarity to hypothetical proteins from bacteria; hypothetical protein with amine oxidase domain
C-terminus is supported by a Thaps EST; hypothetical protein with distant similarity to unknown protein
Identified based on similarity to other MFS transporters. Also contains InterPro domain # IPR003662. This domain is characteristic of general substrate transporters.; putative MFS transporter of unknown substrate
based on sequence similarity to conserved hypothetical proteins from cyanobacteria; hypothetical protein
Homology to ATP binding domain of prokaryotic serine/threonine kinase; hypothetical protein
putative protein of unknown function, supported by EST data
Reaction catalyzed:ATP + D-glucose = ADP + D-glucose 6-phosphate; with sequence similarity to Synechocystis glucokinase)
fucoxanthin chlorophyll a/c light-harvesting protein
based on sequence similarity, presence of MOSC domains found in molybdenum cofactor sulfurase proteins, and EST support from T. pseudonana
based on presence of armadillo domains and sequence similarity to yeast vacuolar protein; putative protein with armadillo repeats that displays similarity to pombe vacuolar protein
This model contains the motifs for the short-chain dehydrogenase/reductase superfamily and for glucose/ribitol dehydrogenase. There is no EST support yet for this gene.; hypothetical protein similar to other putative dehydrogenase
based on sequence simiality and presence of the glucose inhibited division protein A domain and EST support from T. pseudonana and Phaeodactylum; putative protein of unknown function similar to bacterial glucose inhibited division protein
Very high similarity to known aldehyde dehydrogenase sequences. Partial cDNA support.
EST support from T. pseudonana and T. weissflogii and sequence similarity to conserved hypotheticals; putative protein with similarity to conserved hypotheticalals in bacteria
RT5, ribosomal protein 5, mitochondrial small ribosomal subunit, nuclear encoded, translation, protein biosynthesis
RT16, ribosomal protein 16 mitochondrial small ribosomal subunit
RT16, ribosomal protein 16, mitochondrial small ribosomal subunit, nuclear encoded, translation, protein biosynthesis
Putative protein of unknown function with similarities to ATPases (adenosine 5' triphosphatase), close match to gi|14043666|gb|AAH07803.1|AAH07803 (BC007803) Unknown (protein for MGC:14291) [Homo sapiens] (model%: 91, hit%: 89, score: 1379, %id: 52) [Homo sapiens]; putative protein of unknown function with similarity to ATPases (adenosine 5' triphosphatase)
mitochondriale tricarboxylate carrier protein
A variety of substrate carrier proteins that are involved in energy transfer are found in the inner mitochondrial membrane . Such proteins include: ADP,ATP carrier protein (ADP/ATP translocase); 2-oxoglutarate/malate carrier protein; phosphate carrier protein; tricarboxylate transport protein (or citrate transport protein); Graves disease carrier protein; yeast mito- chondrial proteins MRS3 and MRS4; yeast mitochondrial FAD carrier protein; and many others.
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.
RL14, ribosomal protein 14 60S large ribosomal subunit
RL14, ribosomal protein 14, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
putative Rab Escort Protein; rab GTPase activator domain protein, very distant similarity to
probable phosphoribosyl-amp cyclohydrolase
Phosphoribosyl-ATP pyrophosphatase catalyses the second step in the histidine biosynthetic pathway: 5-phosphoribosyl-ATP + H2O = 5-phosphoribosyl-AMP + PPi
probable 3-oxoacyl-reductase domain containing protein
DESCRIPTION: [FUNCTION] CATALYZES THE CONDENSATION REACTION OF FATTY ACID SYNTHESIS BY THE ADDITION TO AN ACYL ACCEPTOR OF TWO CARBONS FROM MALONYL-ACP. HAS A PREFERENCE FOR SHORT CHAIN ACID SUBSTRATES. [CATALYTIC ACTIVITY] Acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO(2) + [acyl-carrier protein]. [PATHWAY] Fatty acid biosynthesis. [SUBUNIT] Homodimer. [SIMILARITY] BELONGS TO THE BETA-KETOACYL-ACP SYNTHASES FAMILY
based on sequence similarity to other guanylate kinases
hypothetical protein with similarity to dihydrodipicolinate synthase
vacuolar membrane proton pump, inorganic pyrophosphatase
D-ribose-5-phosphate ketol-isomerase, probable cytosolic pentose phosphate pathway, similar to gi|18654317|gb|AAL77589.1|L43068_1 (L43068) ribose-5-phosphate isomerase [Spinacia oleracea] (model%: 97, hit%: 79, score: 582, %id: 51)
n-acetyl-gamma-glutamyl-phosphate reductase, urea cycle
Urea cycle, amino acid synthesis. Identified by verification of proteins through Kegg-Thaps database.
may desaturase or hydroxylate acyl lipids
EST support.; putatitive protein of unknown function, with
niemann-pick C type protein-like protein
Contains InterPro domain IPR003392 which is characteristic of proteins belonging to the Patched family (Niemann-Pick C proteins belong to this family). The Niemann-Pick C type protein is an integral membrene protein and is most likely involved in cholesterol transport in other organisms. This gene may be involved in sterol transport in T.pseudonana. This gene also contains InterPro domain IPR000731 which is a sterol-sensing domain (SSD)
signal recognition particle 54 kDA subunit
putative chloroplast-localized pre-protein; SRP54
EST support.; putative protein of unknown function, with
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.
CONVERTS ZEAXANTHIN INTO ANTHERAXANTHIN AND SUBSEQUENTLY VIOLAXANTHIN. INVOLVED IN THE EPOXIDATION OF ZEAXANTHIN
based on sequence similarity to yeast nitrogen permease regulator; hypothetical protein
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
This model contains the motif for the aldo/keto reductase family. There is no EST support yet for this gene. It is most similar to sequences from bacteria.; hypothetical protein similar to aldo/keto reductases and oxidoreductases
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
plastidic xanthophyll de-epoxidase-related protein, contains bipartite chloroplast targeting presequence, signal- and transit-peptides predicted at N-terminus with phenylalanine at signal peptide cleavage site
Reasonable conservation in some other genomes but unknown function.; unknown protein
supported by Thalassiosira cDNAs; putative protein with no similarity
Serine/threonine (S/T) phosphatases catalyse the dephosphorylation of phosphoserine and phosphothreonine residues; contains conserved serine/threonine protein phosphatase.
RS7, ribosomal protein 7, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
putative IMP-GMP specific 5' nucleotidase based on sequence similarity and Phaeodactylum EST support; purine 5' nucleotidase
Good hits to other phosphate transport proteins. The best hit was to Sulfolobus solfataricus with 32.32% (128/396) identity. The scores will likely improve once the gene model is corrected. This gene conatins InterPro domain #IPR003662, which is characteristic of general substrate transporters. Also contains Pfam model #PF0083 which is consistent with sugar (and other) transporters.
triose or hexose phosphate/phosphate translocator
based on EST support and sequence similarity to translocators from plasmodium and plants
contains inositol phosphate-related phosphatase domain plus the sole RhoGAP domain of the Thaps genome
contains conserved WD-40 repeats (IPR001680); prl1 functions as a receptor for protein kinase C. May regulate glucose signalling in mammals; wd-40 repeats; putative phosphatase PP1/PP2A; similar to arabidopsis pleiotropic regulator-like (prl1/prl2)
AAA family cell division control-like protein
TPS_107377 is significantly homologous to many archea bacteria cell division proteins.The model is also similar to ATPase family genes in yeats and spermatogenesis associatedproteins in Homo sapiens. The model also includes a predicted AAA ATPase central region.The large family of ATPases are proteins whose key feature is that they share aconserved region of about 220 amino acids that contains an ATP-binding site. This family is nowcalled AAA, for 'A'TPases 'A'ssociated with diverse cellular 'A'ctivities. The proteins that belong tothis family either contain one or two AAA domains. It is proposed that, in general, the AAA domains in these proteins act as ATP-dependent protein clamps.
Excellent sequence similarity with known genes.
Putative protein of unknown function with some similarities to hypersensitive response-induced proteins; see gi|15239547|ref|NP_200221.1| (NM_124790) putative protein; protein id: At5g54100.1, supported by cDNA: 205622. [Arabidopsis thaliana] (model%: 100, hit%: 68, score: 577, %id: 40) [Arabidopsis thaliana]; putative protein of unknown function with some similarity to hypersensitive response-induced proteins
Possible amino acid/polyamine transporter family II based on BLAST hits, Interpro domains.
ATP binding domain and similarity to ATP subunit of ABC transporters.
Member of LHC superfamily, Lhca clade-matches red algal and cryptophyte LHCs.
TPS_107429 is homologous to vertebrate elongation factor-2 kinases. Also,the model is predicted to have a characteristic kinase domain. Proteins containingthis domain consist of a novel group of eukaryotic protein kinase catalyticdomains, which have no detectable similarity to conventional kinases. Proteins include myosinheavy chain kinasesand Elongation Factor-2 kinase and a bifunctional ion channel.
RM12, ribosomal protein 12 mitochondrial large ribosomal subunit
RM12, ribosomal protein 12, mitochondrial large ribosomal subunit, nuclear encoded, translation, protein biosynthesis
Function unknown. Possible reaction:alpha-D-glucose = beta-D-glucose; hypothetical protein with similarity to aldose-1-epimerase
Distant similarity to myrosinase binding protein, endogluconase precursor, collegenase precursor, and various unknown sequences.; hypothetical gene
supported by a Thalassiosira cDNA; putative protein with no similarity
N-terminus contains putative ER signal peptide predicted by SignalP (probability 0.999; cleavage site between pos. 21 and 22: TDG-FT) followed by putative chloroplast transit peptide predicted by TargetP (probability 0.504; length 42 aa). Putatively chloroplast targeted.; similar to anthranilate synthase in brucella and nostoc
supported by a Thalassiosira cDNA and 24 Phaedactylum ESTs; putative protein with no similarity
44% amino acid identity to other MAPK. Contains conserved protein kinase, ser/thr kinase, and tyr kinase domains (IPR000719, IPR002290, IPR001245). Contains partial MAPK signature sequence, VVTRWYRAPEL. Whole sequence is TE/DYVxTRWYRAPEL.
D-amino acid dehydrogenase has broad substrate specificity, catalyzing the oxidative deamination of mostD-amino acids. The enzyme shows broad substrate specificity, catalyzes the oxidative deamination of most D-amino acidsand also plays a role in alanine metabolism. The enzyme is bound to a membrane element and activity isdependent on membrane integrity.
CATALYTIC ACTIVITY: A 3-sn-phosphatidate + H2O = a 1,2-diacyl-sn-glycerol + phosphate.
catalyses aminopropylation of putrescine
supported by Thalassiosira cDNAs; putative protein with similarity to hypothetical membrane protein AABL01000697
supported by a Thalassiosira cDNA and a Phaeodactylum EST; putative protein containing similarity to hypothetical protein AABL01001655
presence of kinase domains and sequence similarity to similar protein from plants
supported by a Thalassiosira cDNA; putative protein with distant similarity to unknown proteins
Ca2+-dependent membrane-binding protein annexin
Has some similarity to 3-hydroxyisobutarate dehydrogenase, gamma-hydroxybutarate dehydrogenase, and 2-hydroxy 3-oxopropionate reductase.; unknown protein
This protein has EST support. It contains the motif for the aldo/keto reductase family. It is most similar to a hypothetical protein from Magnetospirillum magnetotacticum.; similar to aldo/keto reductases, D-xylose reductase
contains G-protein beta WD-40 repeats; supported by a Thalassiosira cDNA; putative protein similar to unknown proteins
Reaction catalyzed:ATP + D-fructose 6-phosphate = ADP + D-fructose 2,6-bisphosphate; putative
RL7, ribosomal protein 7, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
putative protein of unknown function containing a E2F transcription factor domain; putative protein of unknown function containing a E2F transcription factor domain
cycloartenol synthase;-2,3-epoxysqualene mutase-like protein
Functions as an isomerase/intramolecular transferase (mutase). Catalyzes the reaction: (S)-2,3-epoxysqualene = cycloartenol; strong supporting EST evidence. Contains a conserved Prenyltransferase/squalene oxidase domain (IPR001330). similarity to other organisms (47% amino acid identity); 2,3-epoxysqualene cycloartenol-cyclase
based on sequence similarity to metazoan proteins; putative protein of unknown function
similar to PPF-1, a post-floral-specific gene expressed in short-day-grown G2 pea.
involved in intracellular vesiclre traffic;subunit of protein complex that coats golgi vesicles
No similarity to any known sequences.; hypothetical gene
hemk-like sam-dependent methylase protein
based on sequence similarity to metazoan proteins and presence of defining domains
Function unknown.; hypothetical protein with some similarity to alpha-galactosidase
putative protein of unknown function based on presence of Ham domain. Sequence similarity to auxin regulated protein; putative protein of unknown function with Ham1 domain
Reaction catalyzed:sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate; putative
Putative metalloprotease (metallopeptidase); similar to gi|24412835|emb|CAD35289.1| metalloprotease, MEP1 [Microsporum canis] (model%: 100, hit%: 73, score: 645, %id: 34) [Microsporum canis]
No EST evidence but good hits to other aminotransferases. Good scores for Arabidopsis alanine:glyoxylate aminotransferases.
thioredoxin f, contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
hypothetical component of the thylakoid Delta-pH-dependent protein translocation pathway, Tat pathway.may be chloroplast-localized
2-dehydro-3-deoxyphosphoheptonate aldolase-like protein
addition to previous annotation: N-terminus contains putative ER signal peptide predicted by SignalP (probability 0.999; cleavage site between pos. 17 and 18: GAA-FI) followed by putative chloroplast transit peptide predicted by TargetP (probability 0.805; lebgth 13 aa). Putatively chloroplast targeted.
catalytic subunit of clp protein superfamily
clp proteins are involved in protein degradation, heat shock response and chaperone function. They consist of a regulatory subunit (clpABCX) and a catalytic subunit (clpP). The given gene is most similar to homologues from alpha purple bacteria indicating mitochondrial origin. There are at least 6 more clpP genes present in T. pseudonana.
bifunctional fatty acid oxidation enzyme
[CATALYTIC ACTIVITY] (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O. [CATALYTIC ACTIVITY] (S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH. [CATALYTIC ACTIVITY] 3-cis-dodecenoyl-CoA = 2-trans-dodecenoyl-CoA. [PATHWAY] CATALYZES THREE STEPS OF THE FATTY ACID BETA-OXIDATION CYCLE. [SIMILARITY] IN THE N-TERMINAL SECTION; BELONGS TO THE ENOYL-COA HYDRATASE/ISOMERASE FAMILY. [SIMILARITY] IN THE C-TERMINAL SECTION; BELONGS TO THE 3-HYDROXYACYL-COA DEHYDROGENASE FAMILY.; 3-hydroxyacyl-coa dehydrogenase); Enoyl-CoA hydratase; 3,2-trans-enoyl-CoA isomerase
based on sequence similarity to conserved hypotheticals from Arabidopsis and cyanobacteria and presence of ABC1 domain; putative protein of unknown function with sequence similarity to conserved hypotheticalals
RL39, ribosomal protein 39 60S large ribosomal subunit
RL39, ribosomal protein 39, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
DNA replication licensing factor, mcm8-like protein
High light induced protein 2, similar to the Ohp proteins of Arabidopsis thaliana (one transmembrane helix), contains bipartite plastid targeting presequence, signal- and transit-peptides predicted at N-terminus with conserved motif at signal peptide cleavage site
Contains GCS-type Zinc finger characteristic of Arf GAPs, plus a Pleckstrin Homology (PH) domain (phosphoinositide-binding) and one ankyrin repeat (protein-protein interaction); the GCS and PH domains are supported by Thalassiossira ESTs; with sequence similarity to human centaurin beta2
No EST data The tetratricopeptide repeat of typically 34 amino acids was first described in the yeast cell cycle regulator Cdc23p and later found to occur in a large number of proteins [1, 2, 3]. A function for this repeat seems to be protein-protein interaction, but common features in the interaction partners have not been defined. It has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes. Prominent examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase.; hypothetical protein, TPR containing
Putative protein very similar to bis(5'-adenosyl)-triphosphatase; also similar to fragile histidine triadgi|15237142|ref|NP_200632.1| (NM_125209) bis(5'-adenosyl)-triphosphatase-like; also similar to fragile histidine triad; protein id: At5g58240.1 [Arabidopsis thaliana] (model%: 100, hit%: 93, score: 363, %id: 46) [Arabidopsis thaliana]; also similar to fragile histidine triad; putative protein very similar to bis(5'-adenosyl)-triphosphatase
Contains homology to mitochondria/peroxisomal membrane carrier proteins
No EST evidence, but many hits to cytochrome P450 domains.; hypothetical protein with cytochrome P450 domains
homeobox protein similarity, DNA binding, transcription factor; homeobox protein similarity, DNA binding, transcription factor
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
fucoxanthin-chlorophyll a-c binding protein, plastid precursor
Fucoxanthin-chlorophyll a-c binding protein, contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
glycerate dehydrogenase and hydroxypyruvate reductase-like protein
in addition to previous annotation: looks like having mitochondrial leader sequence at the extension at the N-terminus
nitrogen metabolism, ammonium metabolsim, glutamate metabolism
based on sequence similarity to RNA pol II subunit from yeast; putative protein
A variety of isoprenoid compounds are synthesized by various organisms. For example in eukaryotes the isoprenoid biosynthetic pathway is responsible for the synthesis of a variety of end products including cholesterol, dolichol, ubiquinone or coenzyme Q. In bacteria this pathway leads to the synthesis of isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids. Among the enzymes that participate in that pathway, are a number of polyprenyl synthetase enzymes which catalyze a 1'4-condensation between 5 carbon isoprene units. It has been shown that all the above enzymes share some regions of sequence similarity. Two of these regions are rich in aspartic-acid residues and could be involved in the catalytic mechanism and/or the binding of the substrates.
atp-dependent RNA DEAD/DEAH box helicase
Was found by balsting with the Cyanidium caldarium plastid ycf 24 but is much more similar to hypothetical alpha purple bacterial sequences and, thus, probably of mitochondrial origin. However, it seems to only represent a domain of the homologue from bacteria; hypothetical protein
Putative presenilin; similar to Q9SIK7 (Q9SIK7) Putative presenilin (model%: 100, hit%: 81, score: 513, %id: 34) [Arabidopsis thaliana]
based on sequence similarity to glycotransferase from Dictyostelium
HSF8, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF8, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
Putative proline dehydrogenase (proline oxidase); similar to gi|15240986|ref|NP_198687.1| proline oxidase, mitochondrial precursor -like protein; protein id: At5g38710.1 [Arabidopsis thaliana] (model%: 99, hit%: 90, score: 546, %id: 26) [Arabidopsis thaliana]; weak EST support
probable mitochondrial translation initiation factor
Most similar to bacterial, i.e. (alpha) purple bacterial, homologues, thus likely involved in mitochondrial protein synthesis initiation
Putatively chloroplast targeted; plastid division protein
Putative protein of unknown function, containing leucine-rich repeat domains; IPI:IPI00112968.1|ENSEMBL:ENSMUSP00000035091 Tax_Id=10090 Ensembl_locations(Chr-bp):9-115099481 (model%: 100, hit%: 75, score: 384, %id: 30) [Homo sapiens]; putative protein of unknown function, containing leucine-rich repeat domains
RL19, ribosomal protein 19 60S large ribosomal subunit
RL19, ribosomal protein 19, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
Reaction catalyzed:pyruvate + lipoamide = S-acetyldihydrolipoamide + CO2; putative
Apparently an ORF but with very weak aligment scores, should not be considered as GFA; hypothetical protein; hypothetical protein
EST support.; putative protein of unknown function with
The tetratricopeptide repeat of typically 34 amino acids was first described in the yeast cell cycle regulator Cdc23p and later found to occur in a large number of proteins [1, 2, 3]. A function for this repeat seems to be protein-protein interaction, but common features in the interaction partners have not been defined. It has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes. Prominent examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase.; hypothetical protein with TPR repeat
RL9, ribosomal protein 9, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
EST support.; putative RNA binding motif protein of unknown function, with
I got to this annotation as one of seven of the aspartate aminotransferases called by grail/genewise. There is no good EST support for this assignment. There is high percent similarity to other known aspartate aminotransferases.
Identification based on fair sequence similarity to known sepiapterin reductases.
cyclophilin-type peptidyl-prolyl cis-trans isomerase
PPIases are enzymes that accelerate protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. These proteins commonly belong to a family of isozymes. Synonyms are cyclophillins, cyclosporing A-binding proteins. In vertebrates, cyclophilins bind to the imuunosuppressive drug cyclosporing A (CSA).
An enzyme involved in valine/leucine/isoleucine degradation.
DNA repair, DNA Recombination, ATP binding motif,; RecA/Rad51?Dmc1-like protein; hypothetical protein
Probable cytidylate kinase (deoxycytidylate kinase) (deoxycytidylate kinase) (CMP kinase) (CTP:CMP phosphotransferase) (dCMP kinase) (deoxycytidine monophosphokinase) (UMP-CMP kinase) (ATP:UMP-CMP phosphotransferase) (pyrimidine nucleoside monophosphate kinase), similar to gi|137024|sp|P15700|UMPK_YEAST Uridylate kinase (model%: 83, hit%: 98, score: 500, %id: 49) [Saccharomyces cerevisiae]
This gene was identified based on sequence similarity and contains InterPro domain IPR004045. InterPro describes glutathione S-transferases(GSTs) as being soluble proteins composed of two polypeptide subunits. They catalyze the transfer of the tripeptide glutathione to a co-substrate containing a reactive electrophilic center to form a polar S-glutathionylated product. InterPro describes GSTs in eukaryotes as participating in the detoxification of reactive compounds by catalyzing their conjugation to glutatione.
Converts hydroxymethylbilane to uroporphyrinogen III in heme/chlorophyll biosynthetic pathway. Nuclear coded, chloroplast localized.
This enzyme is involved in the breakdown of glutathione. The reaction involves the hydrolysis of the 5-membered ring of 5-Oxoproline and requires the hydrolysis of ATP.This gene was identified by sequence similarity.; 5-oxo-L_prolinase)(5-opase
Sequence shows similarity to various unidentified and hypothetical proteins.; unknown protein
Function unknown.; hypothetical protein sharing some sequence similarity with cell division cycle protein 27
Putative protein with similarities to signal peptide peptidase, and gi|17232082|ref|NP_488630.1| protease IV [Nostoc sp. PCC 7120] (model%: 100, hit%: 75, score: 600, %id: 34) [Nostoc sp. PCC 7120]; putative protein with similarity to signal peptide peptidase
RS4, ribosomal protein 4, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
contains domain present in the G10 protein, which has an unknown function.; putative protein of unknown function (G10 protein)
vascular plant-like leucine rich repeat transmembrane-like protein kinase
TPS_107149 is homologous to protein kinases and disease resistance proteinsin vascular plants. Many of these proteins are receptor-like proteins. The model alsocontains a preicted leucine rich repeat region. Leucine-rich repeats (LRRs) are 20-29-residue sequence motifs present in tandem arrays anumber of proteins with diverse functions, such as hormone receptor interactions, enzymeinhibition, cell adhesion and cellular trafficking.
addition to berges annotation: This gene is clearly most similar to a higher plant homologue, as four other of the ubc genes
RL17A, ribosomal protein 27A 60S large ribosomal subunit
RL17A, ribosomal protein 27A, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
only support is presence of fibronectin type III domains; putative protein containing fibronectin type III domains
Putative protein of unknown function containing a rhodanese domain, such domains have been associated with plant senescence related proteins; similar to Molybdenum cofactor synthesis protein 3 (Molybdopterin synthase sulfurylase) (MPT synthase sulfurylase); see gi|22001817|sp|Q9ZNW0|MOC3_ARATH Molybdenum cofactor synthesis protein 3 (Molybdopterin synthase sulfurylase) (MPT synthase sulfurylase) (model%: 88, hit%: 86, score: 716, %id: 39) [Arabidopsis thaliana]; putative protein of unknown function containing a rhodanese domain, similar to molybdenum cofactor synthesis protein 3
Most similar to higher plant homologues, much less similar to animal, fungal and G theta nucleomorph homologues, indicating green ancestry of the diatom host cell
mu subunit of clathrin adaptor complex AP3
member of the Orn/Dap/Arg decarboxylase family 2;possibly involved in spermine biosynthesis
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.
eukaryotic translation initiation factor 4E
Matches to diatom and Phaeodactylum ESTs. Very good alignments to glycyl tRNA synthetase genes from bacteria.
No reasonable similarity to any known sequences; hypothetical gene
based on defining domain and sequence similarity to bacterial carbamate kinase appears to be involved in breakdown of carbamoyl phosphate to ADP, ammonia and CO2
wd-40 repeat protein with similarity to mitotic checkpoint protein
Ligase, ATP dependent DNA ligase, Discriminates between correctly paired and mispaired residues at the 3 prime end