Thalassiosira pseudonana CCMP1335 chromosome 8, 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 CM000644.\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##
phosphoenolpyruvate/phosphate translocator precursor (Tpt1) gene, contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site; see also next gene model downstream: Protein ID 7341
triose or hexose phosphate/phosphate translocator
Has EST support. 4344272:1 supports longer 3' untranslated transcript
based on sequence similarity, EST support from Phaeodactylum tricornutum, and predicted transmembrane domains
This gene was most similar to putative and unknown proteins from A. thaliana. It contains InterPro domain #003662, which is characteristic of general substrate transporters. It also has reasonable similarity to Pfam model #00083 for sugar (and other) transporters.
This enzyme catalyses the biosynthesis of glutathione. It was identified based on sequence similarity.
Reaction catalyzed:dTDP-glucose = dTDP-4-dehydro-6-deoxy-D-glucose + H2O. Note, requires NAD.; putative; thymidine diphosphoglucose oxidoreductase
Involved in respiratory ATP synthesis, inner membrane proteinNote: mt-encoded in many plants an algae, inferred from the surrounding genes it is nuclear encoded in T. pseudonana.
protein shows homology to eukaryotic Ankyrin proteins. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a largenumber of functionally diverse proteins mainly from eukaryotes. Many ankyrin repeat regions are known to function as protein-protein interaction domains.; hypothetical protein with ankyrin repeats
Putative trypsin-like serine protease; extensive EST support
I got to this gene by going down the list of genes involved in alanine and aspartate metabolism listed by KEGG. There is high similarity (76%) and identity (62%) to ASL in another stramenopile, Phytophthora infestans.
HSF7, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF7, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
Nuclear encoded promotor- recognising subunit of plastid encoded RNA polymerase. Note: there are several sigma factors recognising different promotors. This ons is most similar to a nucleomorph homologue indicating secondary gene transfer.
Contains regions of strong similarity to carbamoyl phosphate synthase L-chain domain and biotin-carboxylase C-terminal domain. Also shows some similarity with biotin carboxylase A (a subunit of acetyl-CoA carboxylase), pyruvate carboxylase, and propionyl CoA carboxylase. Strongest agreement occurs with pyruvate carboxylase.; uncertain carboxylase
beta subunit acetyl/propionyl-CoA carboxylase
Supported by Sequence Similarity only.no EST data
Good similarity to known MaoC family protein sequences, but identification is based upon very few hits.
Good similarity to the few known beta chain sequences that showed up as hits.
No EST data. Supported by sequence similarity only; hypothetical protein similar to anion exchangers
Putative protein of unknown function containing leucine-rich repeats; similar to gi|5734642|dbj|BAA83373.1| (AP000391) ESTs C22657(S0014),C22656(S0014) correspond to a region of the predicted gene.; Similar to receptor protein kinase, ERECTA (AC004484) [Oryza sativa (japonica cultivar-group)] (model%: 90, hit%: 24, score: 441, %id: 38) [Oryza sativa (japonica cultivar-group)]; EST support; putative protein of unknown function containing leucine-rich repeats
Putative protein of unknown function, containing a metalloprotease domain (metallopeptidase), similar to dme:CG3953 metalloendopeptidase custom_KEGG (model%: 83, hit%: 25, score: 154, %id: 32) [Drosophila melanogaster]; putative protein of unknown function, containing a metalloprotease domain
ABC transporter, ATP binding protein. EST data.
RPC25,-like protein to dna-directed RNA polymerase III 25 kDa polypeptide
RPC25, homolog to DNA-directed RNA polymerase III 25 kDa polypeptide
based on sequence similarity, presence of urease protein G domain and hypB/ureG nucleotide binding domain necessary for Ni binding and ATP/GTP domain, and EST support from Phaeodactylum
sir2-like transcriptional regulatory protein found in-like protein
Silent Information Regulator Sir2 protein is one of several factors critical for silencing at least three loci in yeast.
Supported by EST data; conserved hypothetical protein
putative protein containing an inositol monophosphatase domain
Adenylate cyclases catalyze the formation of cyclic AMP(cAMP) from ATP. cAMP is a common second messenger.
contains conserved protein phosphatase 2C domain; hypothetical protein containing a protein phosphatase 2C domain (PP2C)
protein kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. There are a number of conserved regions in the catalytic domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a glycine-rich stretch of residues in the vicinity of a lysine residue, which has been shown to be involved in ATP binding. In the central part of the catalytic domain there is a conserved aspartic acid residue which is important for the catalytic activity of the enzyme.; hypothetical protein kinase
probably involved in chloroplast and/or mitochondrion division, dual targteting possible; similar to cell division protein ftsH protein in cyanobacteria, gamma-proteobacteria and a
Strong similarities to both peroxiredoxin (an antioxidant) as well as thioredoxin peroxidase.
based on sequence similarity to histidine triad proteins from metazoans
based ond sequence similarity to bacterial proteins and ROK domain
This protein contains the motif for the aldo/keto reductase family. There is no EST support yet for this gene.; hypothetical protein similar to aldo/keto reductases
putative V-ATPase E subunit with Phaeodactylum EST support
Function unkown.; hypothetical protein with weak similarity to beta-galactosidase
Rad 27 family, DNA repair, DNA replication, Cleaves 5' ends of flap structureContains the N and I domain, Exonuclease; fen1-like protein
putative inorganic pyrophosphatase protein involved in oxidative phosphorylation based on sequence similarity, EST support and presence of defining domains
Possible amino acid/polyamine transporter family II.
family of nucleoside phosphatases, purine metabolism
dual function enzyme: UDP-glucose 4-epimerase
Putative reaction catalyzed:UDP-glucose = UDP-galactose. Note, requires NAD, and may also act on UDP-2-deoxyglucose. The gene is very similar to putative dual epimerase/dehydratase genes of Arabidopsis thaliana and Oryza sativa, suggesting the model protein may also catalyze the following:dTDP-D-glucose = dTDP-4-dehydro-6-deoxy-D-glucose + H2O.
hypothetical protein containing response regulator receiver domain
hypothetical protein; similar to HSPC064 protein
Reaction catalyzed:2-phospho-D-glycerate = 3-phospho-D-glycerate; putative
This gene contains the motif for the esterase/lipase/thioesterase family active site. There is partial EST support for this gene.; putative protein similar to putative prolylcarboxypeptidases and dipeptidyl-peptidases
No EST evidence but a hit to another diatom cytochrome P450 and several Pfam and hsp hits.; similar to cytochrome P450 retinoic-acid metabolizing protein; EC_number=1.14.-.-
EST support. Shows nice homology to other general methyltransferases. A number of methyltransferases have been shown to share regions of similarities.Methyl-transferases are responsible for the transfer of methyl groups between two molecules.
putative NADH dehydrogenase 24 kD subunit based on sequence similarity and Phaeodactylum EST support
Light chain of multiple dynein motors including outer arm dynein and cytoplasmic dynein. Has also been found in association with other proteins like mammalian myosin V and some transcription factors like NRF-1
TPS_107235 is very weakly homologous to known protein kinases from a variety of eurkaryotic organisms includingvascular plants, yeasts, and vertebrates. The model is supported by cDNA data and includesmotifcs which are characteristic of eukaryotic protein kinases
based on sequence similarity to bacterial proteins; hypothetical protein with glutamine amidotransferase class II domain
Probable papain cysteine protease, similar to gi|7245728|pdb|1DEU|A Chain A, Crystal Structure Of Human Procathepsin X: A Cysteine Protease With The Proregion Covalently Linked To The Active Site Cysteine (model%: 93, hit%: 80, score: 411, %id: 40) [Homo sapiens]
Good similarity to known sequences. Partial cDNA and Phaeodactylum cDNA support.
[FUNCTION] Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate)to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). [CATALYTIC ACTIVITY] 3-carboxy-3-hydroxy-4-methylpentanoate + CoA = acetyl-CoA + 3-methyl-2-oxobutanoate + H(2)O. [PATHWAY] Leucine biosynthesis; first step. [SIMILARITY] BELONGS TO THE ALPHA-IPM SYNTHETASE / HOMOCITRATE SYNTHASE FAMILY. LEUA 1 SUBFAMILY. Similar to bacterial homologues putatively chloroplast targeted
salicylate biosynthesis isochorismate synthase-like protein
[FUNCTION] Involved in the synthesis of o-succinylbenzoic acid and 2,3-dihydroxybenzoic acid. (By similarity).[CATALYTIC ACTIVITY] Chorismate = isochorismate.[COFACTOR] Magnesium.[SUBCELLULAR LOCATION] Putatively chloroplast targeted. [SIMILARITY] BELONGS TO THE ISOCHORISMATE SYNTHASE FAMILY. N-terminus contains putative ER signal peptide predicted by SignalP (probability 0.948; cleavage site between pos. 24 and 25: SYG-FQ) and putative chloroplast transit peptide predicted by TargetP (probability 0.629; length 63 aa)
contains conserved G-protein WD-40 repeats (IPR001680).; similar to arabidopsis putative splicing factor, contains WD40 repeats
This protein contains a glycosyl transferase group 1 domain. Members of this family transfer activated sugars to a variety of substrates, including glycogen, Fructose-6-phosphate and lipopolysaccharides. Members of this family transfer UDP, ADP, GDP or CMP linked sugars.
The majority of the gene is highly similar to known naphthoate synthase genes.
MYB DNA binding protein/ transcription factor-like protein
Member of MYB DNA binding protein/ transcription factor family.
DNA repair protein involved in Nucleotide excision repair but not in DNA repair, Interacts with several transcriptional activators; RP-A, HSSB, rf-a, Rfa1, Mup1
HSF27, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF27, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
based on presence of defining domain and sequence similarity to other UDP-galactose transporters and presence of 6 transmembrane domains and EST support from exponentially growing T. pseudonana culture
[FUNCTION] PROBABLY PLAYS A ROLE IN FACILITATING THE ASSEMBLY OF MULTIMERIC PROTEIN COMPLEXES INSIDE THE ER. [SUBCELLULAR LOCATION] ENDOPLASMIC RETICULUM LUMEN. [SIMILARITY] BELONGS TO THE HEAT SHOCK PROTEIN 70 FAMILY.
contains bipartite plastid targeting presequence with conserved motif at signal peptide cleavage site
Function unknown.; putative protein with some similarity to phosphoglycerate kinase
Plastidic diadinoxanthin de-epoxidase, contains bipartite chloroplast targeting presequence, signal- and transit-peptides predicted at N-terminus with conserved motif at signal peptide cleavage site
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.
Supported by EST data and sequence similarity.
Probable metalloprotease, containing a insulinase domain, similar to gi|15222238|ref|NP_172173.1| unknown protein; protein id: At1g06900.1 [Arabidopsis thaliana] (model%: 97, hit%: 93, score: 1161, %id: 30) [Arabidopsis thaliana]
glyceraldehyde-3-phosphate dehydrogenase
D-glyceraldehyde 3-phosphate + phosphate + NAD = 3-phospho-D-glyceroyl phosphate + NADH2; putative
Probable serine protease inhibitor, similar to gi|632203|pir||S45677 proteinase inhibitor - signal crayfish (model%: 54, hit%: 77, score: 270, %id: 27) [Pacifastacus leniusculus]; very strong EST suppport
Putative protein of unknown function containing a rhodanese domain, similar to gi|23111445|gb|ZP_00097094.1| (NZ_AABB01000054) hypothetical protein [Desulfitobacterium hafniense] (model%: 97, hit%: 93, score: 1215, %id: 45) [Desulfitobacterium hafniense]; EST support; putative protein of unknown function containing a rhodanese domain
This gene model has no EST support yet. It contains the conserved domain for prolyl 4-hydroxylase alpha subunit. It is most similar to putative prolyl 4-hydroxylase alpha subunits from Arabidopsis thaliana.; hypothetical protein similar to prolyl 4-hydroxylase alpha subunit
The SUR2-type hydroxylase/desaturase catalytic domain is present in a variety of proteins including C-4 methyl sterol oxidase, which is involved in cholesterol biosynthesis; beta-carotene hydroxylase, which catalyses the hydroxylation of beta-carotene to zeaxanthine; C-5 sterol desaturase, which introduces a C-5 double bond into the ring of ergosterol; and SUR2 (syringomycin response protein 2), which is involved in the response to syringomycin.; hypothetical protein similar to beta-carotene hydroxylase
CATALYTIC ACTIVITY] ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione. [PATHWAY] Glutathione biosynthesis; second step. [SUBCELLULAR LOCATION] Chloroplast (Potential). [SIMILARITY] BELONGS TO THE EUKARYOTIC GSH SYNTHASE FAMILY. Supported by EST data
putative RNA helicase, supported by cDNA, DEAD-box family
Similar to ubiquitin conjugating enzyme but does not align well. there is EST support
precursor of hydrogenase glutaryl-coa dehydrogenase
Has very high similarity to known gene sequences.
Synonym(s): Suvar3-9,Enhancer-of-zeste,Trithorax Several proteins that contribute to epigenetic mechanisms of gene regulation contain a characteristic 130 amino acid motif of unknown function called the SET domain. The SET domain genes are widely represented in the eukaryotic genomes,and proteins were initially distributed into four families,SU(VAR)3-9,E(Z),ASH1 and TRITHORAX based on the homology of their SET domains. Addtional proteins have now been identified which do not fit into this classification [PMID: 12039029]. The SET domain is mainly found in proteins with multi-cellular functions,although some exceptions to this are found in yeasts. It appears to be a protein-protein interaction domain,however histone-specific methylase activity has been associated with the SET-domain of SU(VAR)3-9 family members. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control. The SET domain containing Drosophila protein,enhancer of zeste,has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. This protein also contains a Zn finger domain.; putative set-domain transcriptional regulator contains set domain
based on sequence similarity and presence of defining domain likely encodes GcpE protein involved in isoprenoid biosynthesis
Gamma tubulins are a highly conserved subfamily within the tubulin family. They are localized at the microtubule organizing center (centrosome) of the cell
Probable trypsin-like serine protease, similar to gi|13898841|gb|AAK48894.1|AF357226_1 (AF357226) CUB-serine protease [Panulirus argus] (model%: 54, hit%: 48, score: 344, %id: 37) [Panulirus argus]; good EST support
Putative trypsin-like serine protease, similar to gi|136413|sp|P07478|TRY2_HUMAN Trypsin II precursor (Anionic trypsinogen) (model%: 47, hit%: 91, score: 341, %id: 35) [Homo sapiens]
Putative trypsin-like serine protease similar to dme:CG9564 Try29F; trypsin custom_KEGG (model%: 53, hit%: 84, score: 358, %id: 40) [Drosophila melanogaster]
Putative trypsin-like serine protease, similar to gi|13898841|gb|AAK48894.1|AF357226_1 (AF357226) CUB-serine protease [Panulirus argus] (model%: 74, hit%: 48, score: 300, %id: 33) [Panulirus argus]
based on sequence similarity to hypothetical protein from cyanobacteria; putative protein of unknown function
peptidyl-prolyl cis-trans isomerase; ppiase
Putative protein with some similarity to Enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1), and also to Q9SJU3 Expressed protein (model%: 100, hit%: 62, score: 375, %id: 32) [Arabidopsis thaliana]; putative protein with some similarity to enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1)
TPS_105367 is homologous over a short stretch of about100 amino acids to vertebrate elongation factor proteinkinases.
found as putative biotin synthesis protein, also contains SAM (and some other nucleotide) binding motif
Putative protein of unknown function with some similarity to Enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1), and also to Q9SJU3 (Q9SJU3) Expressed protein (model%: 100, hit%: 71, score: 382, %id: 30) [Arabidopsis thaliana]; EST support; putative protein of unknown function with some similarity to enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1)
homeobox protein similarity, DNA binding, transcription factor; homeobox protein similarity, DNA binding, transcription factor
based on sequence similarity, presence of DUF92 domain found in conserved hypotheticals, EST support from T. pseudonana and Phaeodactylum appears to encode a integral membrane protein; putative protein of unknown function with sequence similarity to hypothetical proteins with transmembrane domains
mitogen activated protein kinase-like protein
Strong alignment with other MAPKKK (54% amino acid identity). Contains conserved protein kinase, serine/threonine kinase, and tyrosine kinase domains (IPR000719, IPR002290, IPR001245). Also has signature MAPKKK sequence GTPEFMAPELY.
Probably involved in the formation of sulfolipids which requires conversion of UDP-glucose to UDP-sulfoquinovose [i.e., UDP-(6-deoxyglucose 6-sulfate)], followed by the transfer of sulfoquinovose to position sn-3 of diacylglycerol.; putative
sequence similarity to choline dehydrogenases and presence of glucose-methanol-choline oxidoreductase domain; putative protein with similarity to oxidoreductases of glucose-methanol-choline family
fucoxanthin chl a/c light-harvesting protein
based on sequence similarity to conserved hypothetical proteins from bacteria, and EST support from T. pseudonana; hypothetical protein