Micromonas commoda chromosome 3, 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 CP001324.\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##
molybdenum cofactor biosynthesis protein CNX1E
the Arabidopsis thaliana cDNA cnx1 encodes a multifunctional two-domain protein homologous to a mammalian neuroprotein, the insect protein Cinnamon and three Escherichia coli proteins
malate dehydrogenases (MDH) cytoplasmic and cytosolic; member of the family of NAD-dependent 2-hydroxycarboxylate dehydrogenases
Beta-1,4-galactosyltransferase, related to b-glycosidases; expressed
Has two domains - COG3897, Predicted methyltransferase and COG5285 - Protein involved in biosynthesis of mitomycin antibiotics/polyketide fumonisin
Antibiotic biosynthesis monooxygenase; This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species
Predicted SET domain containing protein. ChromDB ID: SDG20129
CUP C11; putative uncharacterized protein
cupC11, conserved uncharacterized protein
formaldehyde dehydrogenase/S-formylglutathione hydrolase
This protein contains two domains; putative esterase - This family contains Esterase D ESTD_HUMAN. However it is not clear if all members of the family have the same function
prasinophyte specific chlorophyll a/b-binding protein, chloroplast precursor
light harvesting antenna protein specific to prasinophytes, type needs to be determined with phylogenetic analysis; ChloroP predicts 21 aa cTP; dissimilar to other LHCPs, but more like this group than standard LHC genes.
photosystem I subunit N, chloroplast precursor
Also known as PSI N; ChloroP predict 46aa cTP- no result with TargeT
Two domains identified; At N term is Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor
C-terminal subunit of a glycosyltransferase
Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. Cholorplast transit peptide (29 aa) on N-TERMINUS.
Ribulose-phosphate 3-epimerase, chloroplast precursor; predicted (ChloroP & TargetP) TP 1st 36 AA
Cysteine-rich protein domains are also occuring in antifreeze proteins from insects
Predicted member of the Structural Maintenance of Chromosome (SMC) superfamily and a member of the condensin sub-family;predicted homolog of Saccharomyces cerevisiae SMC4. ChromDB ID: CPC20101; SMC protein group
aryl-alcohol dehydrogenase related protein
Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]
Protein of unknown function (DUF1077). This family consists of several hypothetical eukaryotic proteins of unknown function. expressed; conserved uncharacterized DUF1077 protein cupA54
COG2252 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; expressed
Has two complete cysteine hydrolase domains like Chlamydomonas; missing in CCMP1545
Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle
cytosine deaminase/metal dependent hydrolase
Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia
semiconserved uncharacterized protein cupA53
PcbC isopenicillin N synthase and related dioxygenases
has sugar_tr domain - sugar (and other) transporters
TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria
SANT domain includes SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
Has C2 domain. The C2 domain is a Ca2+-dependent membrane-targeting module found in many cellular proteins involved in signal transduction or membrane trafficking
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs
Encodes a protein with single ERF domain
potassium/sodium hyperpolarization-activated cyclic nucleotide-gated potassium ion channel
60 KD inner membrane protein OxaA homolog; Oxa1
pfam00294, PfkB, pfkB family carbohydrate kinase. This family includes a variety of carbohydrate and pyrimidine kinases.
pf 00149: Calcineurin-like phosphoesterase This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829
pf02409: Omt_N O-methyltransferase N-terminus This domain is found at the N-terminus of polyketide synthesis O-methyltransferase proteins.
pf00478 IMP dehydrogenase / GMP reductase domain This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure
pf06624: RAMP4 Ribosome associated membrane protein RAMP4 This family consists of several ribosome associated membrane protein RAMP4 (or SERP1) sequences
[3x] PFAM 00076: RPM_1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein
expressed; putative uncharacterized protein
mitochondrial protein translocase family
inner membrane translocase (import) Tim21
Glutathione peroxidase. Shows DB homology to both GPX and PHGPX, but more plant hits to GPX
Predicted member of the JmjN_JmjC protein family. ChromDB ID: JMJ20104
This gene contains a 3 prime TPP riboswitch (not in model but 3 prime of model)
Predicted Class I RPD3 type histone deacetylase protein. ChromDB ID: HDA20107; Rpd3/HDA1 superfamily
inner membrane translocase (import) Tim23
distantly related to b-glycosyltransferases
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs at C-terminus
putative pyruvate kinase. ChloroP predicts a 17 aa transit peptide, but with a low score. Reaction: ATP + pyruvate = ADP + phosphoenolpyruvate
phosphoglucomutase/phosphomannomutase family protein
translocon-associated complex trap beta subunit
This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins
expressed; conserved uncharacterized putative protein
related to Dol-P-Man: a-mannosyltransferases
Protein disulfide isomerase percursor. Catalyzes the rearrangement of -S-S- bonds in proteins. Contains a thioredoxin conserved domain
distantly related to glycosyltransferases
resistance-nodulation-cell division superfamily
Dispatched segment polarity protein (cholesterol release)
carbohydrate-binding module family 20 protein
contains two pfam domains for aminotransferase clase I and II PF00155.11
H+-or Na+-translocating f-type, v-type and A-type ATPase superfamily
Mer3 is a DNA helicase involved in class I (interference-sensitive) cross-overs
Ribose 5-phosphate isomerase [Carbohydrate transport and metabolism]
chloroplast envelope protein translocase family
inner chloroplast membrane translocase (import) Tic55
has two KH-1 domains and a antimicrobial formaecin family domain. The K homology (KH) domain is present in a wide variety of quite diverse nucleic acid-binding proteins and it has been shown to bind RNA; expressed
conserved, found in CCMP1545, CCE9901 and O. tauri, has the same arrangement in CCMP1545 being found adjacent to a KH domain containing protein. Has two ClpB domains whose function is uncertain, but they may form a protein binding site
expressed; conserved hypothetical protein
UDP-glucuronic acid/UDP-N-acetylgalactosamine:UDP antiporter
Multidrug/Oligosaccharidyl-lipid/Polysaccharide flippase
Synonym: Centrin Component of flagellar inner arm dyneins and basal body/centriole-associated structures.
Type II DNA topoisomerase 6 is composed of subunits A and B. Subunit A forms double-strand DNA breaks and sub-unit B contains the ATP-binding site
inward rectifier K+ channel family transporter
Encodes a Micromonas-specific homeobox protein with two homeobox domains.
Encodes a Squamosa-promoter-binding protein (SBP).
putative malate dehydrogenase. A similarity search suggests that the enzyme is glyoxysomal, but ChloroP and TargetP predict a chloroplast localization
transferase hexapeptide repeat-containing protein
Encodes a protein with a conserved proline-rich motif.
Intraflagellar Transport or IFT refers to the cellular process essential for the formation and maintenance of eukaryotic cilia and flagella
glutamine synthetase, catalytic domain protein
Glutamine synthetase (GS) [1] is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine: Glutamate + ATP + NH3 ->
glutamine synthetase, catalytic domain protein protein
Glycolate oxidase, peroxisomal. A PTS1-type peroxisomal targeting motif is present at the carboxy-terminus.
serine-pyruvate aminotransferase and/or alanine glyoxylate transaminase
Putative alanine glyoxylate aminotransferase domain; however, strong alignment with putative serine-pyruvate aminotransferase, an enzyme in the photorespiratory pathway that catalyzes the conversion of serine to hydroxypyruvate
glycine cleavage system H-protein, one of four subunits of the glycine cleavage system (aka glycine decarboxylase)
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.
Predicted homolog of Saccharomyces cerevisiae SWD2, a subunit of the COMPASS (Set1C) complex ChromDB ID: SWDC20101
This model contains a C-5 cytosine-specific DNA methylase domain and a PWWP domain. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The function of the domain is currently unknown. putative protein
This model contains a Metallophos domain (also known as STphosphatase and Calcineurin-like phosphoesteras)
mRNA cleavage and polyadenylation factor complex
This model contains a Clp1 domain. The pre-mRNA cleavage complex II protein Clp1 family consists of several pre-mRNA cleavage complex II Clp1 (or HeaB) proteins
This model contains a Abhydrolase_1 domain indicative of a alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes.
This model contains Cyclin, C-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs).
Putative protein; this model contains multiple C2 domains
ferredoxin-NADP oxidoreductase chloroplast precursor
ChloroP predict 22aa cTP and targeT 19aa sTP
chlorophyll a/b-binding protein, psi-associated, chloroplast precursor
This model contains a WD domain, G-beta repeat
This predicted protein has weak homology to XRCC2 in Arabidopsis and humans. XRCC2 is a member of the Rad51 family of DNA repair/recombination proteins involved in homologous recombination
Putative cyclin D2 involved in the control of the cell division cycle
Encodes a protein with hydroxyproline-rich glycoprotein (HRGP) motifs; putative uncharacterized protein
This model contains a phosphopantetheine attachment site domain
This model contains HMG boxes. High mobility group (HMG) chromosomal proteins are a family of relatively low molecular weight non-histone components that bind DNA without sequence specificity; Alternative splicing variant 1
Predicted High-mobility group non-histone chromatin protein. ChromDB ID: HMGB20103; Alternative splicing variant 2
This model contains a PAP_fibrillin domain.This family identifies a conserved region found in a number of plastid lipid-associated proteins (PAPs), and in a number of putative fibrillin proteins. putative protein
This model contains a Chaperonin 10 Kd subunit. This family contains GroES and Gp31-like chaperonins
This model contains a OB-fold nucleic acid binding domain, also known as Aspartyl_tRNA_N and tRNA_anti.This family contains OB-fold domains that bind to nucleic acids
This model contains tetratricopeptide repeat domains.
This model contains a protein kinase domain.
ubiquinone/menaquinone biosynthesis methlytransferase
This model contains a Ubie_methyltran (also known as ubiE/COQ5 methyltransferase) domain and is a member of the Methyltransferase superfamily clan.
This model contains a protein kinase domain; putative protein kinase
Histone acetyltransferase in the MYST family; predicted homolog of yeast ESA1. ChromDB ID: HAM20101
Encodes a prasinophyte-specific homeobox protein.
Selenoprotein O, known as YdiU in bacteria. Both members of the SelO family. Blast hits are mainly YdiU, but blast to eukaryotes gives Sel O
HemF ChloroP predics 47aa cTP whereas targeT predicts 38aa cTP
2-methylcitrate dehydratase is used during propanoate metabolism in prokartyoes; all best hits (NOUM17) to prokaryotes although a homologous gene has been found in yeast.
ribulose bisphosphate carboxylase small chain 1, chloroplast
RuBisCo small subunit, chloroplast precursor
Predicted homolog of Saccharomyces cerevisiae SIR2 protein, an NADH dependent Histone Deacetylase. ChromDB ID: SRT20102