Thalassiosira pseudonana CCMP1335 chromosome 5, 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 CM000642.\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##
Putative protein of unknown function containing leucine-rich repeats, with some similarities to gi|20143576|gb|AAM12333.1|AC091680_34 (AC091680) putative disease resistance protein [Oryza sativa (japonica cultivar-group)] (model%: 100, hit%: 15, score: 187, %id: 37) [Oryza sativa (japonica cultivar-group)]; putative protein of unknown function containing leucine-rich repeats
contains conserved inositol monophosphatase domain (IPR000760); enzymes of the inositol phosphate second messenger signalling pathway; may act by enhancing the synthesis or degradation of phosphorylated messenger molecules
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
Has highest similarity to unknown proteins of Arabidopsis and Drosophila. Minimal EST support.; unknown protein
Catalysis of the reaction: a nitrile + H2O = a carboxylate + NH3. Acts on a wide range of aromatic nitriles including (indole-3-yl)-acetonitrile and some aliphatic nitriles, and on the corresponding acid amides; similar to gi|9910460|ref|NP_064587.1| (NM_020202) Nit protein 2 [Homo sapiens] (model%: 77, hit%: 97, score: 679, %id: 48) [Homo sapiens]; strong EST support
5, 10-methylenetetrahydrofolate dehydrogenase
based on sequence homology, presence of defining domains, and EST support from Phaeodactylum
Good hits to other ABC transporters and domain libraries.
identified by trying to verify KEGG nitrogen metab cycle
Has some similarity to various helicases. Partial cDNA support.; unknown protein
possible calcium-binding gycoprotein of the cell wall; homologous to FRU-alpha1 from Cylindrotheca fusiformis; hypothetical frustulin gene
RS11, ribosomal protein 11 40S small ribosomal subunit
RS11, ribosomal protein 11, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
similar to human U6 snRNA-associated sm-like protein LSm6
Involved in the synthesis of GDP-L-fucose, catalyzes the reaction: GDP-D-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H2O.; putative; guanosine 5'-diphosphate-D-mannose oxidoreductase
RPB5, homolog to RNA polymerase I, II and III 24.3 kDa subunit protein
The RING-finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'.; hypothetical protein contains zinc finger,C3HC4 type, motif
sedlin has been implicated in the skeletal disorder spondyloepiphyseal dysplasia tarda and is proposed to play a role in endoplasmic reticulum (ER)-to-Golgi vesicular transport; putative protein with homology to sedlin
similar to expressed protein in arabidopsis
involved in fatty acids biosynthesis. N-terminus contains putative ER signal peptide predicted by SignalP (probability 0.964; cleavage site between pos. 22 and 23: VTA-FS) followed by putative chloroplast transit peptide predicted by TargetP and ChloroP. Putatively chloroplast targeted.; FabB/FabF; yjaY
GAF domains are present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; hypothetical protein containing GAF domain
This could be involved in phytochrome chromophore biosysnthesis.
Has some similarity to enoyl-CoA hydratase and delta 3.5 delta 2,4-dienoyl-CoA isomerase, mitochondrial precursor. Complete cDNA support.; unknown protein
Possible amino acid/polyamine transporter family II. Not supported by EST data.
TPS_101032 is homologous to inversion proteins in vertebrates. Also, the protein is predicted to contain an ankyrin repeat, which consists of tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. Many ankyrin repeat regions are known to function as protein-protein interaction domains.
putative protein of unknown function with similarities to cullin; Ceres:101723. (model%: 100, hit%: 54, score: 804, %id: 42) [Arabidopsis thaliana]; putative protein of unknown function with similarity to cullins
Contains conserved HSP70 domain (IPR001023). 51% amino acid identity to HSP70 in other organisms. Little is known of the function of hsp70 proteins. Some evidence suggests that the constitutive members have a role in the disassembly of clathrin cages, and may also participate in the post-translational transmembrane targetting of proteins to cellular organelles. No specific activities or associations have been found for the inducible members, although it has been suggested that they may accept incoming precursor proteins, keep them unfolded, then pass them on to the hsp60/hsp10 (cpn60/cpn10) complex for folding and assembly. Strong supporting EST data.
Not strong evidence for sugar transporter. EST data suggest real protein.; unknown function
HSF10, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF10, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
The aminoacyl-tRNA synthetases catalyse the attachment of an amino acid to itscognate transfer RNA molecule in a highly specific two-step reaction. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetase specific for histidine is a class-II synthetase.
similar to human ran binding protein 16 (RanBP16)
limited sequence similarity to invertebrate virus and EST support; putative protein of unknown function
sequence similarity and presence of insulinase domain suggests this is a putative protease
phosphatase of serine threonine protein phosphatase
Serine/threonine (S/T) phosphatases catalyse the dephosphorylation of phosphoserine and phosphothreonine residues; contains conserved serine/threonine protein phosphatase.
cold-shock DNA-binding domain-containing protein
Contains InterPro domain #IPR002059 which is a cold-shock DNA-binding domain. Contains strong similarity to Pfam model #PF00313 for cold-shock DNA-binding domain (CSD). This protein has EST support. The best hit was to a glycine-rich protein belonging to the CSD family from Arabidopsis.
Putative protein of unknown function with with strong similarity to hypersensitive response-induced protein; see gi|22758308|gb|AAN05512.1| (AC027038) putative hypersensitive-induced response protein [Oryza sativa (japonica cultivar-group)] (model%: 94, hit%: 97, score: 728, %id: 51) [Oryza sativa (japonica cultivar-group)]; strong EST support; putative protein of unknown function with with strong similarity to hypersensitive response-induced protein
supported by T. pseudonana and T. weissflogii ESTs; putative protein of unknown function
[FUNCTION] ABLE TO ISOMERIZE BOTH 3-CIS AND 3-TRANS DOUBLE BONDS INTO THE 2-TRANS FORM IN A RANGE OF ENOYL-COA SPECIES. [CATALYTIC ACTIVITY] 3-ENOYL-COA = 2-TRANS-ENOYL-COA. [PATHWAY] UNSATURATED FATTY ACID BETA-OXIDATION PATHWAY. [SIMILARITY] BELONGS TO THE ENOYL-COA HYDRATASE/ISOMERASE FAMILY. Supported by EST data.
ubiquinone/menaquinone biosynthesis methyltransferase-like protein
INVOLVED IN BOTH UBIQUINONE AND MENAQUINONE BIOSYNTHESIS
RS23, ribosomal protein 23 40S small ribosomal subunit
RS23, ribosomal protein 23, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
putative protein of unkown function that contains two CBS domains. Two of these domains can be found in IMP dehydrogenases. EST support from Phaeodactylum; putative protein of unknown function with CBS domains
TPS125552, possible siderophore binding protein homolog
based on sequence similarity to Nostoc protein with 2 component sensor domain; putative protein
RL37A, ribosomal protein 37A 60S large ribosomal subunit
RL37A, ribosomal protein 37A, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
Function unknown.; hypothetical protein with weak similarity to arylesterase/monoxygenase from deinococcus radiodurans and putative esterase
no supporting EST data, but sequence similiarity to other cpmA-like proteins, particularly in apparently conserved regions. Presence of ATP binding domain; circadian phase modifier
RNA binding protein of the pumilio family
presence of pumilio domains and EST support for role of protein in translational repression
RL4e, ribosomal protein 4e 60S large ribosomal subunit
RL4e, ribosomal protein 4e, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
26S proteasome regulatory subunit RPN1 2
26S proteasome regulatory subunit S2 contains an APC-complex (cyclosome) and proteasome component repeat (PS50248); supported by cDNA: gi_13430607_gb_AF360216.1_AF360216 (model%: 97, hit%: 97, score: 2027, %id: 46) [Arabidopsis thaliana]
triosephosphate isomerase/glyceraldehyde-3-phosphate dehydrogenase precursor
Precursor to enzymes that carry out both the following reactions:D-glyceraldehyde 3-phosphate + phosphate + NAD = 3-phospho-D-glyceroyl phosphate + NADH2D-glyceraldehyde 3-phosphate = glycerone phosphate. Presumably localized to the mitochondria.; putative
glyceraldehyde 3-phosphate dehydrogenase
Most similar to homologues from Odontella and Phaeodactylum. In these two diatoms the gapC3 gene is fused to TPI and imported into mitochondria as a fusion protein. It is unclear whether the same is true in Thalassiosira because there is a possible start codon present.
Fucoxanthin chlorophyll a/c protein, member of LHC superfamily. One intron.; FCP8
Putative protein similar to metacaspase-like protein [Plasmodium falciparum 3D7] (model%: 50, hit%: 9, score: 105, %id: 26) [Plasmodium falciparum 3D7]; EST support; putative protein with similarity to metacaspases
C-terminal part shows low similarity to sil-1 gene from C. fusiformis; serine-lysine rich protein of unknown function
Putative Phosphoenolpyruvate carboxykinase
probable beta subunit of type II geranylgeranyl transferase
probably catalizes cys prenylation of CAAX C-terminus of small GTPases
Reaction catalyzed:UDP-glucose = UDP-galactose. Note, requires NAD; also acts on UDP-2-deoxyglucose.; putative
may be involved in 40S ribosomal subunit synthesis; with sequence similarity to yeast nucleolar protein NOP5
based on sequence similarity to bacterial proteins and presence of hemolysin III domain and predicted transmembrane domains
involved in cytochrome oxidase assembly; putatively targeted to mitochonbdrion
malonyl coa-acyl carrier protein transacylase
[CATALYTIC ACTIVITY] Malonyl-CoA + [acyl-carrier protein] = CoA + malonyl-[acyl-carrier protein]. [PATHWAY] Fatty acid biosynthesis. [SIMILARITY] SIGNIFICANT, TO SEVERAL OTHER PROTEINS WITH TRANSACYLASE ACTIVITY
dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase
possibly involved in N-glycan biosynthesis or GPI-anchor biosynthesis
62 kDa nucleoporin; hypothetical protein, similar to nuclear pore glycoprotein p62
Strong hits to ABC transporters and Interpro domains.
Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism; B56 family member; contains conserved protein phosphatase 2A regulatory subunit; putative protein phosphatase 2A (B56 family), serine threonine
This protein contains the motifs for the short-chain dehydrogenase/reductase (SDR) superfamily, for glucose/ribitol dehydrogenase, and for aminoacyl-transfer RNA synthetases class-I. There is no EST data yet for this gene. It is most similar to other expressed genes in Arabidopsis thaliana.; hypothetical protein similar to other expressed and hypothetical proteins
transporter belonging to the MFS superfamily
34.12% (145/425) identical to hypothetical protein FLJ14153 from Homo sapiens, which is weakly similar to multidrug resistance protein 2. This gene contains InterPro domain #IPR003662 which is found in general substrate transporters.
putative aminotransferase similar to Arabdopsis and Synechocystis and cysteine beta conjugate-lyase similar to Takifugu rubripes.
This gene contains the vitamin K-dependent carboxylation/gamma-carboxyglutamin (GLA) domain. It is partially supported by EST.
nucleotide excision repair protein ERCC2
RL44, ribosomal protein 44 60S large ribosomal subunit
RL44, ribosomal protein 44, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
DNA Repair, Recombination, Double Starand break repair, ATP binding
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.
Putative protein probably associated with ubiquitin mediated proteolysis, containing CDC20 and WD40 domains; EST support; putative protein probably associated with ubiquitin mediated proteolysis, containing CDC20 and WD40 domains
based on sequence similarity and defining domain of protein involved in cell division
Hits to putative tetracycline transporters and pfam transporter model#00083. Also contains InterPro domain #003662, which is a domain common to general substrate transporters.; putative transporter of unknown substrate
Stress enhanced protein-like, similar to the Sep proteins of Arabidopsis thaliana (two transmembrane helices), contains bipartite plastid targeting presequence, signal- and transit-peptides predicted at N-terminus with phenylalanine at signal peptide cleavage site
High light induced protein 1, 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
mitochondrial manganese superoxide dismutase
Superoxide dismutase that belongs to the Mn/Fe binding superoxide dismutase family. Superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen.
Contains homology to SNF domains and DEAD/DEAH box helicase
fucoxanthin chl a/c light-harvesting protein
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.
based on T. pseudonana EST support; putative protein of unknown function
Putative RNA helicase DEAD/DEAH family, supported by cDNA. involved in RNA processing
High homology to dimethyladenosine transferase proteins and Ribosomal RNA adenine dimethylase
Contains high homology to peptidyl dipeptidase from a variety of organsims.
Most similar to fungal and plant homologues
putative V-type H-ATPase based on presence of defining domain and sequence similarity; 116 kD subunit
Contains homology to hypothetical proteins from various organisms, including a possible capillary morphogenesis protein from humans
limited similarity to BRARe Vaculolar protein sorting 18 but none of the expected conserved domains. EST support from T. weissflogii for presence of a gene.; hypothetical protein of unknown function
putative thiamin pyrophosphokinase, similar to Schizosaccharomyces pombe and Arabadopsis.
Putative protein of unknown function containing a zinc finger (RING finger) domain; similar to At1g05120-68300.m08264 T7A14.1 YUP8H12.27 predicted protein (model%: 78, hit%: 84, score: 1538, %id: 45) [Arabidopsis thaliana]; EST support; putative protein of unknown function containing a zinc finger domain
Contains homology to phosphate binding periplasmic ABC transporter protein from several prokaryotes
sequence similarity to hypothetical protein from humans; putative protein of unknown function with simiarity to other hypothetical proteins
hypothetical protein with nucleotide binding motif
Subunit of RPA, required for interaction with other proteins during nucleatide excisions repair; Rfa2, Rpa2
Putative HAL3 halotolerance protein, similar to gi|13124308|sp|P94063|HL3B_ARATH Halotolerance protein Hal3b (model%: 100, hit%: 88, score: 373, %id: 43) [Arabidopsis thaliana]
based on presence of defining domain and limited sequence similarity; cyclin, G1
TPS_98601 is homologous to VSP-3 and WP6 which are cell wall proteins in Chlamydomonas' reinhardti and C. eugametos. VSP-3 and WP6 contain (SerPro)x epitopes are common to extensin-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
Glycoside hydrolase, family 18; protein of unknown origin, putative chitinase based on glycoside hydrolase domain
Probable aspartyl aminopeptidase (asp-apase) (aspartate aminopeptidase) similar to At5g60160-68299.m05969 F15L12.1 aspartyl aminopeptidase - like protein aspartyl aminopeptidase, Homo sapiens, EMBL:AF005050. (model%: 95, hit%: 96, score: 1091, %id: 46) [Arabidopsis thaliana]
Probable dUTP pyrophosphatase; similar to gi|15232681|ref|NP_190278.1| (NM_114561) dUTP pyrophosphatase-like protein; protein id: At3g46940.1,(model%: 100, hit%: 86, score: 453, %id: 65) [Arabidopsis thaliana]
silicic acid transporter, silicon transport
Silicic acid transporter (SIT), similar to SITs in the diatom Cylindrotheca fusiformis. One of three copies in T. pseudonana
proteasome subunit beta type 5 precursor
PSB5_SPIOL Proteasome subunit beta type 5 precursor (20S proteasome subunit E) (Proteasome epsilon chain)SCORE: 743 EVALUE: 0Alignment Length: 239 IDENTITIES: 59.83% (143/239) SIMILARITIES: 73.64% (176/239)
presence of MCm domains and sequence similarity
requires confirmation upon model rearrangement
phosphatidylinositol 4-kinase-like protein
Poor alignment with other organism, but does contain conserved Phosphatidylinositol 3- and 4-kinase domain (IPR000403).
putative protein of unknown function containing a TB2/DP1 domain; putative protein of unknown function containing a TB2/DP1 domain
RL26, ribosomal protein 26 60S large ribosomal subunit
RL26, ribosomal protein 26, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
fucoxanthin chlorophyll a/c light-harvesting protein
unknown protein with similarity to kinesin light chains
Function unknown; may transfer sulfate groups from phosphoadenosine phosphosulfate to substrate molecules.; hypothetical protein with sulfotransferase domain
selenocysteine-specific elongation factor SelB
TRANSLATION FACTOR NECESSARY FOR THE INCORPORATION OF SELENOCYSTEINE INTO PROTEINS. IT REPLACES EF-1alpha FOR THE INSERTION OF SELENOCYSTEINE DIRECTED BY THE UGA CODON.
only support is presence of multiple fibronectin III domains and limited sequence similarity to titin; putative protein of unknown function that contains fibronectinIII domains
probable bifunctional purine synthesis protein
Probable bifunctional purine synthesis protein (Phosphoribosylaminoimidazolecarboxamide formyltransferase) (AICAR transformylase) (IMP cyclohydrolase) (Inosinicase) (IMP synthetase) (ATIC), similar to gi|1709915|sp|P38009|PU92_YEAST Bifunctional purine biosynthesis protein ADE17 [Includes: Phosphoribosylaminoimidazolecarboxamide formyltransferase (AICAR transformylase); IMP cyclohydrolase (Inosinicase) (IMP synthetase) (ATIC)] (model%: 96, hit%: 98, score: 1407, %id: 49) [Saccharomyces cerevisiae]
may be involved in cobalamine sysnthesis; conserved hypothetical protein
glyceraldehyde-3-phosphate dehydrogenase
D-glyceraldehyde 3-phosphate + phosphate + NAD = 3-phospho-D-glyceroyl phosphate + NADH2; putative
nuclear copy of photosystem II protein psbW
Comoponent of Photosystem IINote: there is a second copy of psbW present in the plastid genome (contig 169). Both copies are most similar to the Odontella homologue, however, the nuclear copy is only 68% similar whereas the plastid copy is more than 80 % similar. This clearly indicates an ongoing gene transfer from the plastid genome to the nuclear genome and a higher degree of conservation in the plastid genome. There is no EST evidence for the nuclear copy and no obvious transit peptid indicating that the gene was not yet activated.; also found on ct genome
The protein contains putative ER signal peptide at the N-terminus predicted by SignalP (probability 0.949; probable cleavage site between pos. 26 and 27: IVG-NV) followed by putative chloroplast transit peptide predicted by TargetP (probability 0.665; length 51 aa - NVGTSNRSCTMAALFGFQIASSSHSPSPLPRVHNSTAFANAELTEDEKAAE). Putatively chloroplast targeted
Eukaryotic protein kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. There are a number of conserved regions in the catalytic domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a glycine-rich stretch of residues in the vicinity of a lysine residue, which has been shown to be involved in ATP binding. In the central part of the catalytic domain there is a conserved aspartic acid residue which is important for the catalytic activity of the enzyme.
cyclic nucleotide and voltage-activated ion channel
Contains putative domains for cyclic nucleotide binding, cation channel, and calcium binding
serine or glycine-rich protein with nucleotide binding motif
Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented.
High identity to thioredoxin proteins. Supported by InterPro domains.
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants, and also to animals. Their functions in higher animals likely include the regulation of cell volume, control of electrical excitability and trans-epithelial transport.The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata, and subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits, and they have varying tissue distributions and functional properties. To date, CLC-0, CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments, rather than of the plasma membrane. However, they are all thought to have a similar transmembrane (TM) topology, initial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains . Recently, the postulated TM topology has been revised, and it now seems likely that the CLCs have 10 (or possibly 12) TM domains, with both N- and C-termini residing in the cytoplasm.
This profile covers the active site serine of a wide variety of enzymes including esterases, lipases, pepitdases etc. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes. They include a wide range of peptidase activity.
displays sequence similarity to SLA/LP which has been hypothesized to function as a serine hydroxymethyltransferase; putative protein that displays sequence similarity to soluble liver antigen/liver pancreas antigen (SLA/LP)
Reaction catalyzed:2-phospho-D-glycerate = 3-phospho-D-glycerate; putative
2 phosphoglycerate dehydratase; 2-phospho-D-glycerate hydro-lyase
I got to this gene by going down the list of gene involved in alanine and aspartate metabolism under KEGG. There is very high identity (51%) and similarity (66%) to the same gene in Arabidopsis thaliana.
Reaction catalyzed:ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA
putative V-type H-ATPase subunit H based on Phaeodactylum EST support and presence of defining domain
fucoxanthin chlorophyll a/c protein, LI818 clade
Has EST support. present: 1 || present: 1
Member of LHC superfamily. Assigned to LI818 clade on basis of matches to Chlamydomonas LI818 and Isochrysis galbana.No intron.
This gene is listed as one of the genes involved in Lysine degradation by KEGG. There is good EST support for this gene and there are many hits in SwissPROT Blastx and Arabidopsis Blastx.
IFT proteins are part of a large complex that are transported along ciliary microtubules and are required for assembly of cilia.
based on sequence similarity to bacterial proteins; putative protein with NAD/NADP octopine/nopaline dehydrogenase domain
This gene was identified by sequence similarity and contains InterPro domain IPR000101. InterPro describes Gamma-glutamyltranspeptidase as catalyzing the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide, or water. It plays a key role in the gamma-glutamyl cycle, a pathway for the synthesis and degradation of glutathione and drug and xenobiotic detoxification. It is an enzyme that consists of two polypeptide chains processed from a single chain precursor.
structure specific recognition protein 1
based on sequence similarity, presence of HMG domains and EST support from T. pseudonana and T. weissflogii
Putative protein, similar to dihydroorate oxidase (DHOdehase) (dihydroorotate dehydrogenase) (dihydoorotic acid dehydrogenase) (DHO dehydrogenase) (4,5-L-dihydroorotate:oxygen oxidoreductase) (S-dihydroorotate:oxygen oxidoreductase); see gi|1709949|sp|P54321|PYDA_LACLC Dihydroorotate dehydrogenase A (Dihydroorotate oxidase A) (DHOdehase A) (DHODase A) (DHOD A) (model%: 83, hit%: 99, score: 602, %id: 43) [Lactococcus lactis subsp. cremoris]; putative protein
based on EST support from T. pseudonana, T. weissflogii, and Phaeodactylum; sequence similarity and the presence of defining domains
Function unknown but may catalyze the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-D-glucose + H2O.; protein similar to unknown protein from arabidopsis (At1g63000-68300.m06176 F16P17.17) and with substantial similarity to putative dtdp-glucose 4,6-dehydratase from arabidopsis ()
possibly involved in polyamine biosynthesis; low similarity to spermidine synthase; hypothetical protein
possibly involved in polyamine catabolism
sequence similarity to conserved hypotheticals from Drosophilla and Arabidopsis; putative protein of unknown function
RM47, ribosomal protein 47 mitochondrial large ribosomal subunit
RM47, ribosomal protein 47, mitochondrial large ribosomal subunit, nuclear encoded, translation, protein biosynthesis
eukaryotic translation initiation factor 4E
Putative protein of unknown function containing leucine-rich repeats; similarities eo gi|7489084|pir||T10515 disease resistance protein Cf-2.2 - currant tomato (model%: 74, hit%: 45, score: 511, %id: 27) [Lycopersicon pimpinellifolium]; putative protein of unknown function containing leucine-rich repeats
RM17, ribosomal protein 17 mitochondrial large ribosomal subunit
RM17, ribosomal protein 17, mitochondrial large ribosomal subunit, nuclear encoded, translation, protein biosynthesis
The enzyme catalyses the the first step in the pentose pathway, i.e. the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the presence of NADP, producing NADPH. The ubiquitous expression of the enzyme gives it a major role in the production of NADPH for the many NADPH-mediated reductive processes in all cells (description taken from Interpro).; G6PD, G6PC
possible calcium binding glycoprotein of the cell wall; homologous to FRU;alpha3 from Cylindrotheca fusiformis; hypothetical frustulin gene
Contains similarity to RNA polymerase I, II, and III; contains conserved RNA polymerase Rpb6 domain (IPR006110 and IPR006111); Strong alignment with other organisms (up 89% identity on amino acid level)
one of 22 hits of a hypotetical DNA helicase fron the Gtheta nucleomorph genome, no EST support; fragment of hypothetical DNA helicase
Putative signal peptidase; similar to O74800 (O74800) Hypothetical 17.3 kDa protein C2D10.07C in chromosome II (model%: 100, hit%: 75, score: 211, %id: 42) [Schizosaccharomyces pombe]
sigma subunit of clathrin adaptor complex AP4
Putative protein with similarities to ADP-ribose pyrophosphatase (ADP-ribose diphosphatase) (Adenosine diphosphoribose pyrophosphatase) (ADPR-PPase) (ADP-ribose phosphohydrolase); similar to gi|586919|sp|Q01976|ADPP_YEAST ADP-ribose pyrophosphatase(model%: 51, hit%: 50, score: 307, %id: 57) [Saccharomyces cerevisiae]; putative protein with similarity to adp-ribose pyrophosphatase
putative protein of unknown function containing a RabGAP/TBC domain
This gene contains the motif for the insulinase family (Peptidase family M16). There is no EST support yet for this gene. It has high similarity to putative metalloprotases in Arabidopsis thaliana.; metalloprotease/hypothetical hydrogenase
This enzyme catalyzes the formation of glycine from sarcosine as part of the urea cycle and glycine metabolism.
hypothetical protein containing a conserved serine threonine phosphatase domain
MYB DNA binding protein/ transcription factor-like protein
Member of MYB DNA binding protein/ transcription factor family.
spindle pole component spc97-like protein
Esterase/lipase/thioesterase family active site
high sequence similarity to protein in other organisms (48% over 1000 amino acids). Contains conserved SNF2 domain (IPR000330) and DEAD/DEAH box helicase domain (IPR001410). May play role in ATP dependent chromatin remodelling.; ISW2-like
I got to this gene by going down the list of genes involved in alanine and aspartate mebolism under KEGG.
Histone H2B is one of the four histones, along with H2A, H3 and H4, which forms the eukaryotic nucleosome core. Histone H2B is a small, highly conserved nuclear protein that, together with 2 molecules each of histones H2A, H3 and H4, forms the eukaryotic nucleosome core; the nucleosome octamer winds 146 DNA base-pairs.
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.
possibly involved in biosynthesis of glycoproteins or glycolipids; werak but significant homology to beta-1,4-galactosyltransferase from many different organisms
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
This gene model has not EST support yet. It contains the ShK toxin domain. It is most similar to hypothetical proteins from Caenorhaditis elegans; hypothetical protein
prolyl 4-hydroxylase alpha subunit-like protein
addition to previous annotation: when extended at the N-terminus (233 aa upstream), it contains putative ER signal peptide predicted by SignalP (probability 0.999, possible cleavage site between pos. 24 and 25: AVS-EE). Putatively ER targeted.
supported by Thalassiosira cDNAs; putative protein with no similarity
RS19, ribosomal protein 19 40S small ribosomal subunit
RS19, ribosomal protein 19, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
Protein contains chitin binding peritrophin-A domains (IPR002557).; putative protein with chitin binding peritrophin-a domains
Presumably hydrolyzes 1,4-linked N-acetyl-beta-glucosamine residues.; hypothetical protein with domain belonging to glycosyl hydrolase family 18 and with similarity to chitinase
TPS_106060 shows significant homology to an unknown protein that was cloned from cDNAconstructed from a Homo Sapien sleen sample. The protein has a Leucine-rich repeats (LRRs) which is a relatively short motifs (22-28 residues in length) that is found in a varietyof cytoplasmic, membrane and extracellular proteins. Although these proteins are associatedwith widely different functions, a common property involves protein-protein interaction. Little isknown about the 3D structure of LRRs, although it is believed that they can form amphipathicstructures with hydrophobic surfaces capable of interacting with membranes.; hypothetical unknown protein
Presumably hydrolyses 1,4-linked N-acetyl-beta-glucosamine residues.; hypothetical protein with domain belonging to glycosyl hydrolase family 18 and with similarity to chitinase
Matches to ESTs from diatom and Phaeodactylum libraries. Good alignments with this gene from various bacteria.
Putative protein of unknown function containing serine protease domains; some EST support; putative protein of unknown function containing serine protease domains
eukaryotic translation initiation factor 3 subunit 8
RL10, ribosomal protein 10 60S large ribosomal subunit
RL10, ribosomal protein 10, 60S large ribosomal subunit, nuclear, translation, protein biosynthesis
component II, glutamine amidotransferase
Poor sequence alignment with other organisms, but EST suggest this is a real gene. Contains conserved Indole-3-gycerol phosphate synthase domain, IGPS (IPR001468); function:atalyzes the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate; putative protein similar to antranilate synthase multifunctional protein
Putative presenilin, similar to Q9SIK7 (Q9SIK7) Putative presenilin (model%: 100, hit%: 91, score: 559, %id: 37) [Arabidopsis thaliana]
HSF24, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF24, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
DNA directed RNA polymerase II subunit, 8.2kDa, rpb10-like protein
Catalyzes the reaction: nucleoside triphosphate + RNAn = diphosphate + RNAn+1; contains conserved RNA polymerase N/8 kDa domain (IPR000268). 88% amino acid identity, but over a short region (64 amino acids)
function unknown; contains a CRAL/TRIO domain; supported by a Thalassiosira cDNA; putative protein containing similarity to sec14-like proteins
4th intron and C-term are supported by Pt cDNAs
Function unknown.; hypothetical protein with some similarity to putative short-chain dehydrogenase/reductase