Micromonas commoda chromosome 8, 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 (21-JAN-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, 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 CP001575.\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##
Putatively; HECT domain and RCC1-like domain-containing protein; expressed
Has Hydantoinase_A_N, _A and _B domains; the Hydantoinase_B family includes N-methylhydaintoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase (OPLA_RAT)which catalyses the formation of L-glutamate from 5-oxo-L-proline
isocitrate dehydrogenase/citrate hydrolyase
has three domains: Monomeric isocitrate dehydrogenase
cytoseine endopeptidase (CP), Eukaryotic thiol proteases, others in DB are catagorized as cathepsin or papain
Encodes a protein with LIM-type zinc finger domain.
Includes glutamyl-tRNA synthetaseand Prolyl-tRNA synthetase
non phosphorylating glyceraldehyde-3-phosphate dehydrogenase
carbohydrate-binding module family 20 protein
Histone H2B, core histone required for chromatin assembly and chromosome function. ChromDB ID: HTB20101
putative NAD-dependent malate dehydrogenase (MDH), mitochondrial precursor. The mitochondrial location is deduced by similarity search and TargetP
s-adenosylmethionine-dependent methyltransferase
candidate a-galactosidase or raffinose synthase or stachyose synthase
Predicted chromatin remodeling protein similar to Homo Sapiens CHD1L (chromodomain helicase DNA binding protein 1-like), a subgroup within the SNF2 superfamily of ATP dependent helicases. ChromDB ID: CHR20112; Snf2, Ris1, Rad26 superclasses
translocation protein Sec62 homolog; NSCC2
Predicted DNA methyltransferase similar to the mammalian DNMT2 methyltransferases. ChromDB ID: DMT20101
Predicted chromatin remodeling protein similar to chromodomain-members of the SNF2 superfamily of ATP dependent helicases. ChromDB ID: CHR20126; Snf2, Ris1, Rad26 superclasses
U4/U6 small nuclear ribonucleoprotein Prp3
Prp3 is Pre-mRNA-splicing factor 3 in mouse
malic oxidoreductase mitochondrial precursor
Model needs 5'editing. First initiator Met after STOP is upstream of modeled init. Met. Upstream region gives clear evidence of a presequence for targeting to the mitochondrion (TargetP and Mitoprot positive).
serine/threonine protein kinase with protein kinase domain, ubiquitin associated domain and kinase associated domain (Ka1)
putatively tRNA modification GTPase - trmE in cyanos; does have GTPase of unknown function domain; GTPase of unknown function
Part of the G-protein superfamily Has elongation factor Tu GTP binding domain 1 and 2, in addition to elongation factor G C-terminus (at C-terminus) as well as GTP-binding protein LepA C-terminus domain
DNA mismatch repair protein-MLH2/PMS1/Pms2 family
PMS1 is an homolog of the E.Coli MutL and of the yeast PMS1 genes. Post meiotic segregation
photosystem II 22 kDa protein, chloroplast precursor
PSBS also known as Photosystem II 22 kDa protein, chloroplast precursor (CP22); ChloroP and TargetP show 23 aa cTP
Multidrug/Oligosaccharidyl-lipid/Polysaccharide flippase
expressed; Alternative splicing variant 2
xanthine/uracil; NCS2; Alternative splicing variant 1
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs
Nterm probably too long - ChloroP and TargeT predict 61aa cTP
expressed; conserved hypothetical protein
protoporphyrinogen IX oxidase chloroplast precursor
distantly related to glycosyltransferases; unknown protein
expressed; Alternative splicing variant 1
preprotein translocase SecY; Alternative splicing variant 2
phosphoribulokinase chloroplast precursor
Phosphoribulokinase(PRK) is one of the enzymes specific to the Calvin's reductive pentose phosphate cycle which is the major route by which carbon dioxide is assimilated and reduced by autotrophic organisms. PRK catalyzes the ATP-dependent phosphorylation of ribulose 5-phosphate into ribulose 1,5-bisphosphate which is the substrate for RubisCO
mitochondrial protein translocase family
Mge1 homolog (motor component); Alternative splicing variant 1
contain pfam domains for PF00036.22: EF hand; expressed hypothetical protein
Superoxide dismutasecatalyzes the conversion of superoxide radicals to molecular oxygen. Superoxide radicals are damaging to many cell components including membranes, proteins and nucleic acids
Putatiave homolog of Saccharomyces cerevisiae CTR9, a RNA polymerase II-associated Paf1p complex protein
Inositol 1, 3, 4-trisphosphate 5/6-kinase. This family consists of several inositol 1, 3, 4-trisphosphate 5/6-kinase proteins
multispecific organic anion/multidrug (ABCC/MRP-type)
monovalent Cation:Proton antiporter-1 family
Predicted homolog of the human DEK protein, an abundant chromatin protein that is linked with cancers and autoimmune disease. ChromDB ID: DEK20101
conserved uncharacterized protein cup B007
H+-or Na+-translocating f-type, v-type and A-type ATPase superfamily
glutamate-gated ion channel neurotransmitter receptor family
Encodes an AP2 class protein with two ERF domain
Protein of unknown function (DUF1640) is a family consisting of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured. conserved uncharacterized DUF1640 protein
conserved uncharacterized DUF299 protein
All DB hits are inconsistent execpt excellent hits to an Ostreococcus unnamed protein. There is EST support for this protein however, including support for UTR regions and a Sec codon
Has both RRM and RRM1 motifs, RNA recognition motif; RNA recognition motif (RRM1): (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein
semiconserved uncharacterized protein cupA59
expressed; putative uncharacterized protein
Uncharacterised protein family UPF0066 This domain had been observed is a number of proteins of archaea and bacterial origin. The function of this domain is unknown. uncharacterized protein family UPF0066
conserved uncharacterized protein cupA60
cyclophilin-type peptidyl-prolyl cis-trans isomerase
FKBP-type peptidyl-prolyl cis-trans isomerase and cyclophilin_ABH_like domains: Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain
Cwf15/Cwc15 cell cycle control family protein
Cwf15/Cwc15 cell cycle control protein. This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues
This entry represents MYND-type zinc finger domains
distantly related to glycosyltransferases
inner membrane translocase (import) Tim44
early light induced protein-like protein
carotene biosynthesis related (CBR) or ELIP, ChloroP and TargetP predict 34 aa cTP
Predicted homolog of Saccharomyces cerevisiae RAD26, a DNA-dependent ATPase that stimulates strand exchange by modifying the topology of double-stranded DNA; involved in the recombinational repair of double-strand breaks in DNA. ChromDB ID: CHR20105
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs at N-terminus
conserved in Otauri, CCE9901 and NOUM17 and contains PF00398.10 Ribosomal RNA adenine dimethylase and PF08242.2 & PF08241.2 Methyltransferase; ribosomal RNA adenine dimethylase, predicted
contains two of pfam domain PF02319.11 E2F/DP family winged-helix DNA-binding protein
SNF2 superfamily chromatin remodeling protein; predicted homolog of Saccharomyces cerevisiae FUN30, a SWI/SNF2 family protein, over expression of the protein affects chromosome stability. ChromDB ID: CHR20117; Snf2, Ris1, Rad26 superclasses
resistance-nodulation-cell division superfamily
Niemann-Pick type C1 disease protein homolog
Hydroxy/Aromatic amino acid permease family
shows conservation to CCMP1545; uncharacterized protein
Peptidyl-prolyl cis-trans isomerase B precursor; signalP indicates 27 aa SP & TargetP indicates 27 aa signal peptide for secretory pathway; most like Cyclophilin B (as opposed to other cyclophilin types)
Both Dcp2 and Dcp2p domains; Dcp2, box A domain. This domain is always found to the amino terminal side of pfam00293
sodium ion:calcium ion+potassium ion antiporter
ribulose bisphosphate carboxylase-like protein
ribulose bisphosphate caboxylase-like; rbcL PFAM; probably could be considered rbcL