Micromonas commoda chromosome 4, complete sequence.
Eukaryota; Viridiplantae; Chlorophyta; prasinophytes; Mamiellophyceae; Mamiellales; Mamiellaceae; Micromonas.
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas
Submitted (22-JUN-2017) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
Submitted (23-DEC-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 CP001325.\nURL -- http://www.jgi.doe.gov/MicromonasRCC299\nJGI Project ID: 4000189\nOrganism available from the Center for Culture of Marine\nPhytoplankton (CCMP) and the Roscoff Culture collection (RCC)\nContacts: Alexandra Z. Worden (azworden@mbari.org)\n Igor Grigoriev (IVGrigoriev@lbl.gov)\nAnnotation done by the Micromonas genome consortium as identified\nin the authorship as listed as reference 1 above.\nThis organism was isolated from South Pacific surface waters in\n1998 by S.Boulben. This strain was rendered clonal and axenic in\nthe Worden Lab through plating and a series of antibiotic\ntreatments. Subsequently, the axenic strain was deposited at the\nCCMP (CCMP2709) and RCC (RCC827). RCC299 is also referred to as\nstrain NOUM17.\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. We welcome collaborative interaction on the project.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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##
MutS homologs (MSH) are involved in mismatch repair and recombination. Eukaryotes contain several MSH
putative metacaspase involved in regulation of apoptosis
Encodes an expansin-homology domain-containing protein with hydroxyproline-rich glycoprotein (HRGP) motifs at N-terminus
Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. One of 11 found in RCC299.
Predicted Class II RPD3 type histone deacetylase protein. ChromDB ID: HDA20106; Rpd3/HDA1 superfamily
putative NADP dependent malic enzyme, cytosolic (also called malate dehydrogenase), deduced by similarity search. TargetP predicts a 26 aa mTP but low significance
H+-or Na+-translocating f-type, v-type and A-type ATPase superfamily
Encodes a protein with a winged-helix domain.
Encodes a chromodomain-containing protein with hydroxyproline-rich glycoprotein (HRGP) motifs
Encodes a protein with four LIM-type zinc finger domains.
coproporphyrinogen III oxidase chloroplast precursor
Encodes a SHAQYF-like Myb-family transcription factor with two Myb domains.
Predicted protein arginine N-methyltransferase similar to human PRMT7. ChromDB ID: PRMT20101
Exostosin-like glycosyltransferase; hypothetical protein
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs and a Shugoshin C-terminal domain
Predicted histone demethylases similar to AOF2/ LSD1 homologs. ChromDB ID: HDMA20102; AOF2/ LSD1 homolog
monovalent Cation:Proton antiporter-2 family
related to Dol-P-Man: a-mannosyltransferases
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs
carbohydrate-binding module family 20 protein
Encodes a lectin-like protein with hydroxyproline-rich glycoprotein (HRGP) motifs
Part of the isoprenoid biosynthetic pathway, eukaryotic farnesyl pyrophosphate synthetase (FPP synthetase)catalyzes the sequential condensation of isopentenyl pyrophosphate (IPP) with dimethylallyl pyrophosphate (DMAPP), and then with the resultant geranyl pyrophosphate to form farnesyl pyrophosphate
expressed; conserved uncharacterized protein
chloroplast membrane protein ALBINO3; Oxa1
Encodes a protein containing Fasciclin domain with hydroxyproline-rich glycoprotein (HRGP) motifs at N-terminus
Has two domains. At 3 prime has TPR repeatst at 5 prime has pfam Region found in RelA / SpoT proteins
mitochondrial protein translocase family
inner membrane translocase Tim10 (import)
chlorophyll a/b-binding protein-like protein, chloroplast precursor
Predicted homolog of Saccharomyces cerevisiae RPT6, Proteasomal ATPases are proposed to link Ubiquitylation of Histone H2B to Methylation of Histone H3. ChromDB ID: PATPB20101
Encodes a GATA-like transcription factor.
Predicted histone H3 lysine 4 methyltransferase. ChromDB ID: SDG20118
has domain for sugar_tr, which includes sugar and other transporters; expressed
Predicted chromatin remodeling protein similar to the RAD16 class of proteins in the SNF2 superfamily of ATP dependent helicases. ChromDB ID: CHR20120; Snf2, Ris1, Rad26 superclasses
Encodes a protein with multiple hydroxyproline-rich glycoprotein (HRGP) motifs
PF00856: SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. expressed
PF03486: HI0933-like protein; This family is a member of the FAD/NAD(P)-binding Rossmann fold Superfamily clan.
PF 02353 Cyclopropane-fatty-acyl-phospholipid synthase This family consist of Cyclopropane-fatty-acyl-phospholipid synthase or CFA synthasethis enzyme catalyse the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid
Endonuclease that cleaves the 5' overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5' end of a downstream Okazaki fragment. Also possesses 5' to 3' double-stranded DNA exonuclease activity.
plant intracellular channel protein DHAR1 homolog (glutathione dehydrogenase/dehydroascorbate reductase)
2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Phosphoglyceromutase, also known as BPG-independent PGAM; Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. Pathway carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5
CPS; CARB; Carbamoyl-phosphate synthase large chain
protein kinase FA2, flagellar associated
The FA2 gene of Chlamydomonas encodes a NIMA family kinase with roles in cell cycle progression and microtubule severing during deflagellation
inner membrane translocase (import) Tim40
Protein of unknown function (DUF1336). This family represents the C-terminus (approximately 250 residues) of a number of hypothetical plant proteins of unknown function. expressed; conserved uncharacterized DUF1336 protein
Predicted histone H3 lysine 4 methyltransferase. ChromDB ID: SDG20124
Histone acetyltransferase in the GNAT/MYST superfamily; pedicted homolog of yeast GCN5. ChromDB ID: HAG20102
Histone H2B, core histone required for chromatin assembly and chromosome function. ChromDB ID: HTB20102
Histone H2A, core histone required for chromatin assembly and chromosome function. ChromDB ID: HTA20104
RNA14 family, Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification] and Suppressor of forked protein (Suf)
RecA/Rad51/DMC1 proteins are involved in homology searching and strand exchange in homologous recombination. This appears to be a Rad51A homolog
Encodes a small protein with hydroxyproline-rich glycoprotein (HRGP) motifs
(5x repeat) pfam05249: UPF0187. Uncharacterised protein family (UPF0187). This family of proteins is functionally uncharacterised.
cleft lip and palate transmembrane protein 1
pfam 05602 Cleft lip and palate transmembrane protein 1 (CLPTM1) This family consists of several eukaryotic cleft lip and palate transmembrane protein 1 sequences
pfam01331: mRNA capping enzyme, catalytic domain. This family represents the ATP binding catalytic domain of the mRNA capping enzyme; expressed
pfam 03992: ABM Antibiotic biosynthesis monooxygenase. This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species
MraW methylase/RNA recognition motif protein
pfam 01975: MraW methylase family Members of this family are probably SAM dependent methyltransferases based on Swiss:P18595 [1]. This family appears to be related to Methyltransf_3 [pfam 01596]
pfam 00226: DnaJ domain DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction
pfam08325: WLM domain. This is a predicted metallopeptidase domain called WLM (Wss1p-like metalloproteases)
carbohydrate-binding module family 45 protein
candidate a-glucan, water dikinase; expressed
monovalent Cation:Proton antiporter-1 family
Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]
growth arrest and dna-damage-inducible protein 45 alpha
Predicted Growth arrest and DNA-damage-inducible protein 45 alpha. ChromDB ID: GAD20101
SNF2 family DNA-dependent ATPase similar to transcription-coupled repair nucleotide excision repair proteins like Saccharomyces cerevisiae RAD26 CHR20101 In progress. ChromDB ID: CHR20101; Snf2, Ris1, Rad26 superclasses
magnesium-chelatase subunit chlH chloroplast precursor
involved in nitrogen assimilation catalyzes :2 L-glutamate + NADP+ = L-glutamine + 2-oxoglutarate + NADPH + H+
possibly phospho-N-acetylmuramoyl-pentapeptide- transferase
hydrolase, alpha/beta fold family-like protein
This model contains an alpha/beta hydrolase fold domain, which is found in a very wide range of enzymes.
This model contains an ATP-dependent protease La (LON) domain, a Lon protease (S16) C-terminal proteolytic domain, and a AAA domain
photosystem I subunit III, chloroplast precursor
This model contains adenylate kinase domains.
Hits RSP10 and 1 in Chlamy, has MORN repeats as do both these proteins so not sure which it is but as far as length goes is more like RSP10
This model contains ribosomal protein L6 domains.
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs at N-terminus
elated to b-mannosidases / b-mannanases; glycosyl hydrolase
This model contains a WD domain, G-beta repeat region, a coatomer WD associated region, and a coatomer (COPI) alpha subunit C-terminus
This model contains Seryl-tRNA synthetase N-terminal, tRNA synthetase class II core, and Aminoacyl-transfer RNA synthetases class-II domains
Uncharacterised protein family (UPF0287). This is a family of uncharacterised proteins. conserved uncharacterized UPF0287 protein cupA52
Flavoprotein. This family contains diverse flavoprotein enzymes. This family includes epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein that binds FMN
Hydrolases Acting on carbon-nitrogen bonds, other than peptide bonds In linear amides; involved in sphingolipid metabolism
This model contains a CUE domain. CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to UBA and this has been confirmed by the structure of the domain
1-aminocyclopropane-1-carboxylate synthase
bacterial in origin judging by the BLAST hits.
putative fumarate hydratase class1-malate <=> fumarate + H(2)O
fumarate hydratase is an enzyme involved in the Tricarboxylic that catalyzes the hydration (addition of H2O across a double bond) of Fumarate to L-malate
glyceraldehyde-3-phosphate dehydrogenase
Glyceraldehyde-3-phosphate dehydrogenase, type I or GAP3, all hits are to prokaryotes although I annotated this in Otauri as well (apparently annotation/gene was not deposited)
lipoate-protein ligase b chloroplast precursor
TargetP predicts 46aa cTP; Also known as: Lipoyltransferase(Lipoyl-[acyl-carrier-protein]-protein-N- lipoyltransferase); Contains domain BPL_LipA_LipB which is found in biotin protein ligase, lipoate-protein ligase A and B
has Cupin_2 domain; putative uncharacterized protein
cytidine/deoxycytidylate deaminase family protein
Acetyltransferase (GNAT) family protein; The N-acetyltransferases (NAT)are enzymes that use acetyl coenzyme A (CoA) to transfer an acetyl group to a substrate, a reaction implicated in various functions from bacterial antibiotic resistance to mammalian circadian rhythm and chromatin remodeling
Has snf7 domain - This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells
ribulose bisphosphate carboxylase/oxygenase activase,chloroplast precursor
RuBisCO activase, TargetP predicts 41 aa cTP
The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins
hop2-mnd1 complex facilitates loading of Rad51 & DMC1
Meiosis-specific protein that localizes to chromosomes, preventing synapsis between nonhomologous chromosomes and ensuring synapsis between homologs; complexes with Mnd1p to promote homolog pairing and meiotic double-strand break repair.
YqeH. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication
Has domain for tRNA synthetases class I (I, L, M and V) Other tRNA synthetase sub-families are too dissimilar to be included in this pfam
belongs to small GTPase superfamily which are involved in intracellular cell signalling processes. The Ras family includes a large number of small GTPases, Members of Rab have been implicated in vesicle trafficking.
early light induced protein-like with fasciclin domain, chloroplast precursor
possible early light induced protein or carotenoid biosynthesis related, also has beta-Ig-H3/fasciclin domain which seems to be prokaryotic, may start late; chloroP predicts 48aa cTP. expressed
Has MutS I, III and V domains; The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins
related to UDP-sulfoquinovose:diacylglycerol sulfoquinovosyltransferases
intraflagellar transport protein IFT72/74
Intraflagellar Transport or IFT refers to the cellular process essential for the formation and maintenance of eukaryotic cilia and flagella
is member of the family of NAD-dependent 2-hydroxycarboxylate dehydrogenases
Katanin is a microtubule-severing AAA protein. It contains a 60 kDa ATPase subunit, which functions to sever microtubules. This subunit requires ATP and the presence of microtubules for activation
on HMMPFAM-pfam-v21 hit (PF08660.1: Alg14 Oligosaccharide biosynthesis protein Alg14 like),but with low blast score (50-80). Does not hit a pfam domain when blasted
photosystem I subunit VI, chloroplast precursor
ChloroP predicts 20aa cTP whereas TargeT 15aa SP
microtubule-severing protein katanin 60kDa subunit
putative pyruvate kinase, cytosolic. Localisation deduced by similarity search, no transit peptide predicted (ChloroP, TargetP, SignalP). Reaction: ATP + pyruvate = ADP + phosphoenolpyruvate
sialic-acid o-acetylesterase-like protein
Has DUF303: Domain of unknown function (DUF303). Distribution of this domain seems limited to prokaryotes and viruses, except here we see it in Micromonas.
arginase/agmatinase/formimionoglutamate hydrolase
semi-conserved uncharacterized protein cupA30
Hits Pfam domain ALG6, ALG8 glycosyltransferase family
CUP A5; expressed; conserved uncharacterized protein
magnesium-chelatase subunit chlh-like protein chloroplast precursor
Magnesium-chelatase subunit chlH-like protein, chloroplast precursor (Mg-protoporphyrin IX chelatase)