Micromonas commoda chromosome 2, 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 CP001323.\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##
contains LpqC domain in entirety, these are poly(3-hydroxybutyrate) depolymerases [Secondary metabolites biosynthesis, transport, and catabolism]
alpha-2 macroglobulin family-like protein
This protein contains A2M_N, A2M_N_2, A2M, A2M_2 and A2M_recep domains. These domains, include expected N term and C term domains of the alpha-2 macroglobulin family
contains UbiE domain, Methylase involved in ubiquinone/menaquinone biosynthesis; in general highly conserved with other putative methytransferases
Vps52 / Sac2 family (vacuolar protein sorting family 52)
splicing factor PWI domain-containing protein
nicotinamidase/pyrazinamidase domain-containing protein
High homology to CCMP1545 v2 Prot ID 50908; expressed; conserved uncharacterized protein
Predicted member of the Structural Maintenance of Chromosome (SMC) superfamily and a member of the cohesin complex protein sub-family; predicted homolog of Saccharomyces cerevisiae SMC1. ChromDB ID: CPC20103; SMC protein group
SMT1 is the Sterol methyltransferase C-terminal domain. This domain is found to the C-terminus of a methyltransferase domain (pfam08241) in fungal and plant sterol methyltransferases
has a portion of CumB domain which harbors Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]; conserved predicted protein, with CumB domain
Predicted chromatin remodeling protein similar to the SMARCA3 class of proteins in the SNF2 superfamily of ATP dependent helicases. ChromDB ID: CHR20123; Snf2, Ris1, Rad26 superclasses
Phosphoglycerate mutase family. Y019_MYCTU and YK23_YEAST are not included in the Prosite entry. However these sequences are significantly similar and contain identical active site residues. expressed
chloroplast envelope protein translocase family
outer chloroplast membrane translocase (import) GTP-binding protein Toc(IAP)34
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs
Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine
amine oxidases are enzymes that catalyze the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines.
Multidrug/Oligosaccharidyl-lipid/Polysaccharide flippase
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: CHR20114; Snf2, Ris1, Rad26 superclasses
putative uncharacterized contains run domain
This FBPase is part of a long open reading frame (orf) that extends about 2000 bases upstream of this model and includes a conserved protein at the 5prime end (DUF89 domain).
distantly related to protein O-linked N-acetylglucosamine transferase
Argininosuccinate lyase (argininosuccinase, ASAL). This group contains proteins similar to ASAL, a member of the Lyase class I family
putative phosphoenolpyruvate carboxylase. No signal peptide (ChloroP, TargetP, SignalP). Reaction: phosphate + oxaloacetate = H2O + phosphoenolpyruvate + CO2
a bacterial enzyme which catalyzes the reduction of D-lactate to pyruvate.
expressed ef-hand domain-containing protein
IPR002048 EF_hand_Ca_bd Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand
Predicted member of the JmjN_JmjC protein family. ChromDB ID: JMJ20101
Encodes a putative member of the Calossin/Pushover family of proteins with hydroxyproline-rich glycoprotein (HRGP) motifs
Predicted homolog of Saccharomyces cerevisiae RPT4; Proteasomal ATPases are proposed to link Ubiquitylation of Histone H2B to Methylation of Histone H3. ChromDB ID: PATPA20101
TLD is a domain of unknown function, restricted to eukaryotes, and commonly found in TBC and LysM domain containing proteins. TLD domain containing expressed protein
cupC9, conserved uncharacterized protein
Predicted chromatin remodeling protein similar to Saccharomyces cerevisiae RING finger protein RIS1 protein which is involved in proteolytic control of sumoylated substrates. ChromDB ID: CHR20124; Snf2, Ris1, Rad26 superclasses
cytosine/purines/uracil/thiamine/allantoin; NCS1
Predicted histone H3 lysine 4 methyltransferase. ChromDB ID: SDG20125
inner chloroplast membrane translocase (import) Tic55
putative TCP-1 Chaperonin, theta subunit - involved in productive folding of proteins; cpn60, GroL like.
Possesses MaoC_dehydratas domain. The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase
Predicted Argonaute-type protein ChromDB ID: AGO20101
chloroplast outer membrane translocon subunit Toc64
axoneme central apparatus protein-like protein
Protein of unknown function (DUF2008). This is a family of eukaryotic proteins whose function has not been characterised.
Predicted protein arginine N-methyltransferase similar to human PRMT7. ChromDB ID: PRMT20102
Encodes a RWP_RK transcription factor involved in nitrogen-related responses with two C-terminal Phox/Bem1 domains (IPR000270). NLP1
Encodes a protein containing GRF-interacting domain (SSXT)
carbohydrate-binding module family 1 protein
expressed; putative uncharacterized protein
related to a-N-acetylglucosaminyltransferases
ras-related gtp-binding rab2-like protein
transcription elongation-nucleosome displacement protein
Putatiave homolog of Saccharomyces cerevisiae SPT4. The yeast protein forms a complex with Spt5p and mediates both activation and inhibition of transcription elongation, and plays a role in pre-mRNA processing ChromDB ID: GTG20101; Spt4 homolog
Encodes a GATA-like transcription factor
endonuclease I/ribonuclease family protein
Endonuclease I. Bacterial periplasmic or secreted endonuclease IE. coli endonuclease I (EndoI) is a sequence independent endonuclease located in the periplasm
ABC transporter/cobalt transport family protein
Several domains, including Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota
Partial domain for AlaS - Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; expressed; conserved uncharacterized tRNA synthetase domain protein cupA56
Predicted homolog of Saccharomyces cerevisiae SWD2, a subunit of the COMPASS (Set1C) complex. ChromDB ID: SWDB20101
Predicted chromatin remodeling protein similar to Saccharomyces cerevisiae RDH54, a DNA-dependent ATPase which stimulates strand exchange by modifying the topology of double-stranded DNA. ChromDB ID: CHR20118; Snf2, Ris1, Rad26 superclasses
Glutathione peroxidase. Top hits in DB are GPXs. Number (GPX2) is for distinguishing between GPX's in NOUM17 only and has not been determined phylogenetically
Pedicted member of the JmjD1 Group in the JmjN_JmjC Protein Family. ChromDB ID: JMJ20109
Ubiquinone/menaquinone biosynthesis methyltransferase, bacterial-like protein
Catalysis of the transfer of a methyl group to an acceptor molecule.
sodium ion:calcium ion+potassium ion antiporter
elongation factor tu gtp-binding domain protein 2
Also known as: U5-116 kDa; and e.g. KIAA0031, SNRP116; These proteins with elongation factor Tu GTP binding domains belong to the G-protein super family
H+-or Na+-translocating f-type, v-type and A-type ATPase superfamily
Actin depolymerisation factor/cofilin -like domains; present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments. expressed
Encodes a protein containing two Pleckstrin-homology domains with hydroxyproline-rich glycoprotein (HRGP) motifs
Ribosomal protein L37e. This family includes ribosomal protein L37 from eukaryotes and archaebacteria. The family contains many conserved cysteines and histidines suggesting that this protein may bind to zinc. expressed
Protein phosphatase 2A regulatory B subunit (B56 family). Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism
ribulose bisphosphate carboxylase-like protein, large chain
ribulose bisphosphate carboxylase like; RuBisCo; closest to prokaryotic rbc; ChloroP and TargetP predict transit peptide of 22 AA; signalP did not indicate any.
translation initiation factor fusion with methylthioribose kinase
cytosolic glucose-6-phosphate dehydrogenase
Predicted protein similar to the DEMETER family of bifunctional DNA glycocylases. ChromDB ID: DNG20102
Serine/threonine phosphatase family protein
Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity
Cyclin dependant kinase regulatory subunit
SNF2 superfamily chromatin remodeling protein; predicted homolog of Saccharomyces cerevisiae SNF2, an essential abundant protein involved in regulation of transcription. ChromDB ID: CHR20115; Snf2, Ris1, Rad26 superclasses
Dephospho-coenzyme A kinasecatalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.
HIRA proteins are histone-interacting proteins which function in the nucleosome assembly pathway to facilitate the deposition of histones onto the DNA ChromDB ID: HIRA20101; Alternative splicing variant 1
Has WD40 repeat and TUP1-like enhancer of split domains. The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain pfam00400. expressed; Alternative splicing variant 2
has domain RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins
O-phosphoseryl-tRNA selenium transferase
Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis.
candidate GDP-Man: dolichyl-phosphate b-mannosyltransferase
catalytic LigB subunit OF aromatic ring-opening dioxygenase
Aromatic ring-opening dioxygenase, catalytic LigB subunit related enzyme [Amino acid transport and metabolism]
REJ domain. The REJ (Receptor for Egg Jelly) domain is found in PKD1, and the sperm receptor for egg jelly. The function of this domain is unknown
UDP-glucuronic acid/UDP-N-acetylgalactosamine
P-protein homolog (tyrosine transporter)
multispecific organic anion/multidrug (ABCC/MRP-type)
prasinophyte specific light harvesting complex protein, chloroplast precursor
light harvesting complex protein, chlorophyll a/b binding, specific to prasinophytes; ChloroP and TargetP predict 32 aa cTP
thylakoid lumenal 25.6kDa protein like, chloroplast precursor
PsbP related ChloroP and targeT predict 54 aa cTP
Predicted homolog of the ACF (ATP-dependent chromatin assembly factor) proteins BAZ1A (Homo sapiens) and Acf1 (Drosophila)
Contains a Zinc finger C-x8-C-x5-C-x3-H type. conserved, hypothetical protein
expressed; conserved hypothetical protein
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs; hypothetical uncharacterized protein
fkbp-type peptidyl-prolyl cis-trans isomerase
peptidylprolyl cis-trans isomerase-like protein
cyclophilin_ABH_like: Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain
prasinophyte specific chlorophyll a/b-binding protein
ChloroP and Target P did not predict cTP but signalP gave a 23 aa cTP; putitavely chloroplast precursor
prasinophyte specific chlorophyll a/b-binding protein, chloroplast precursor
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs and Calcium/lipid binding domain.
YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs(!). HMG-box like superfamily
Possesses a DUF618 domain. Protein of unknown function, DUF618 represents a conserved region found in a number of uncharacterised eukaryotic proteins. cupC23, conserved uncharacterized protein
dihydrouridine synthase-like family protein
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA
ras-related gtp-binding protein, alternative splice
This model contains a NifH/frxC family signatures and profile. putative protein
magnesium-protoporphyrin IX methyltransferase chloroplast precursor
ChloroP predicts 74aa cTP whereas targeT 22aa mTP...
candidate alpha-mannosidase; Likely glycosyl hydrolase family 47. Members of this family are alpha-mannosidases that catalyse the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2)
This model contains a CBM20 (carbohydrate binding type-20) domain profile. putative protein
This model contains a ribosome recycling factor (RRF / ribosome release factor), which dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth
sugar kinase and ribulose phosphate 3 epimerase, fused
Fusion of two proteins both involved in carbon metabolism:a sugar/xylulose kinase in the first half of the CDS and ribulose-phosphate 3 epimerase in the 3'half; RPE catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.
Has two conserved domains: Cathepsin propeptide inhibitor domain (I29). This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide
This model contains an ATP-binding cassette, ABC transporter-type, signature and profile; Alternative splicing variant 1
(Uup homolog/duplicated ATPase); Alternative splicing variant 2
(Uup homolog/duplicated ATPase); Alternative splicing variant 3
DUF1637; expressed; putative uncharacterized protein
Cytochrome c oxidase assembly protein CtaG / Cox11: Cytochrome c oxidase assembly protein is essential for the assembly of functional cytochrome oxidase protein
also identified as Glycerol Uptake (GUP) Family
Per1-like. PER1 is required for GPI-phospholipase A2 activity and is involved in lipid remodelling of GPI-anchored proteins.
glucose-1-phosphate adenylyltransferase chloroplast precursor
has NTP_transferase and glgC domains; ADP-glucose pyrophosphorylase small subunit; some of this models 5 prime UTR may be CDs but unknown at this point; chloroP predicts cTP
Encodes a conserved protein with hydroxyproline-rich glycoprotein (HRGP) motifs
This model has a GATA-type zinc finger domain signature and profile. expressed; putative protein
This model contains a Zinc finger ZZ-type signature and profile; putative uncharacterized protein
This model contains a DEAD-box RNA helicase Q motif profile, superfamilies 1 and 2 helicase domain profiles, and a Helicase conserved C-terminal domain
Vacuolar protein sorting-associated protein (Vps) 35 is one of around 50 proteins involved in protein trafficking
This model contains an alpha amylase, catalytic domain. Alpha amylase is classified as family 13 of the glycosyl hydrolases.
Has 3 domains, pfam01562: Pep_M12B_propep - Reprolysin family propeptide. This region is the propeptide for members of peptidase family M12B
This model contains a cyclophilin-type peptidyl-prolyl cis-trans isomerase signature & profile and a Myb-type HTH DNA-binding domain. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids
Enoyl-CoA hydratase/isomerase family. This family contains a diverse set of enzymes including: Enoyl-CoA hydratase. Napthoate synthase. Carnitate racemase. 3-hydoxybutyryl-CoA dehydratase
cytochrome b5-like Heme/Steroid binding fusion with acyl-coa dehydrogenase
Long chain acyl-CoA dehydrogenase (LCAD) is acyl-CoA dehydrogenases (ACAD), which is found in the mitochondria of eukaryotes and in some prokaryotes
light-dependent protochlorophyllide oxido-reductase chloroplast precursor
NADPH-protochlorophyllide oxidoreductase. ChloroP ant targeT predict 53aa cTP.
This model contains a Zinc finger, C3HC4 type (Ring finger). The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs; expressed; putative uncharacterized protein
Predicted DNA methyltransferase similar to the mammalian DNMT2 methyltransferases. ChromDB ID: DMT20102
pfam 00225: Kinesin motor domain; PROFILE entry PS50067: Kinesin motor domain; Kinesin [1,2,3] is a microtubule-associated force-producing protein that may play a role in organelle transport
PROSITE entry PS50945: I/LWEQ domain; The I/LWEQ domain is a 250-residue actin-binding module that is found in the C-termini of functionally diverse proteins from yeast to mammals
pfam 01363: FYVE zinc finger; The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1
pfam 00069: Protein kinase domain PROFILE entry PS50011 Protein kinases signatures and profile: Eukaryotic protein kinases [1,2,3,4,5] are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common to both serine/threonine and tyrosine protein kinases. There are a number of conserved regions in the catalytic domain of protein kinases. We have selected two of these regions to build signature patterns. The first region, which is located in the N-terminal extremity of the catalytic domain, is a glycine-rich stretch of residues in the vicinity of a lysine residue, which has been shown to be involved in ATP binding. The second region, which is located in the central part of the catalytic domain, contains a conserved aspartic acid residue which is important for the catalytic activity of the enzyme [6]
Cyclin dependant kinase D (CDKD) or CAK (CDK activating kinase) with a NFTAIRE cyclin binding motif.
Predicted member of the nucleosome/chromatin assembly factor group C (RBBP4 and RBBP7 homologs); highly similar to human RbAp46 and RbAp48 (Retinoblastoma associated proteins) - a WD-40 domain containing protein found in several chromatin regulatory complexes
pfam00149: Metallophos Calcineurin-like phosphoesterase
carbohydrate-binding module family 48 protein
candidate a-glucan-binding protein; expressed
expressed; conserved uncharacterized protein cupA41
expressed; semiconserved uncharacterized protein cupA42
may be mitochondrially targeted; expressed
aminotransferase/S-adenosyl-L-homocysteine hydrolase
has two major domains: DegT/DnrJ/EryC1/StrS aminotransferase family and NAD_binding_4. The members of DegT.
transcription factor TFIID with WD40 repeat
TATA binding protein associated factor 5 protein
Predicted homolog of Saccharomyces cerevisiae TAF5, a subunit (90 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification. ChromDB ID: TAFV20101; Alternative splicing variant 2
has WD40 associated region in TFIID subunit. This region, possibly a domain is found in subunits of transcription factor TFIID. The function of this region is unknown; expressed; Alternative splicing variant 1
expressed; conserved uncharacterized protein cupA51
Profilin is an actin-binding protein involved in the dynamic turnover and restructuring of the actin cytoskeleton
distantly related to glycosyltransferases; unknown protein
E2F dimerisation partner. Control cell division cycle
Alpha-CA (plastidic). N-terminus is missing in the current model
candidate arabinosyltransferase; expressed; hypothetical protein
contains the syntaxin Pfam domain and the SNARE region typical of syntaxin
One of six ammonium transporters in NOUM17 genome
Putatiave homolog of Saccharomyces cerevisiae SPT5
related to a-glucosidases; unknown protein
putative glycerate kinase, involved in C2 cycle of photorespiration, chloroplast targeted if model is extended upstream to next initiator Met
Nuclear actin-related protein involved in chromatin remodeling; predicted homolog of Arabidopsis thaliana ARP7. ChromDB ID: ARP20103
Predicted DNA methyltransferase similar to the mammalian DNMT1 methyltransferases. ChromDB ID: DMT20107
dynein-1-alpha heavy chain, flagellar inner arm I1 complex
acetyltransferase-like/FAD linked oxidase
Has alpha/beta hydrolase fold - This catalytic domain is found in a very wide range of enzymes. Also has FAD N and C terms
Has two domains: 1.) pfkB family carbohydrate kinase - This family includes a variety of carbohydrate and pyrimidine kinases. It belongs to the Ribokinase-like superfamily
phosphoribosylglycinamide formyltransferase
Conserved region of Rad21 / Rec8 like protein This family represents a conserved region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families
4-diphosphocytidyl-2c-methyl-d-erythritol synthase
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs and integrins alpha chains
small conductance mechanosensitive ion channel family
small-conductance mechanosensitive ion channel
Predicted SET domain containing protein. ChromDB ID: SDG20130
n-ethylmaleimide sensitive fusion protein
putatively, has two AAA domains - ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes; expressed
Predicted bromodomain-containing protein. ChromDB ID: GTE20101
Predicted protein arginine N-methyltransferase similar to human CARM1 (PRMT4). ChromDB ID: PRMT20106
Cyclin dependant kinase A with a PSTAIRE cycling binding site; expressed
DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system.
Contains DUF938 domain This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown. putative uncharacterized protein
Contains the 2OG-FeII_Oxy domain The 2OG-Fe(II) oxygenase superfamily contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily PUBMED:11276424
radical SAM protein with TRAM and UPF0004 domains
3 detected domains: UPF0004, Radical SAM and TRAM. Uncharacterized protein family UPF0004 is the N terminal half of the Prosite family
Has CSP and CSD domains - in eukaryotes used to regulate translation
Contains a ubiquitin and a UBA domain Ubiquitin is a protein of seventy six amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates