2024-01-04
definition
IAO:0000233
external
term_tracker_item
true
true
term_tracker_item
term tracker item
IAO:0000700
external
has_ontology_root_term
true
true
has_ontology_root_term
has ontology root term
term replaced by
Rhea list of ChEBI terms representing the major species at pH 7.3.
Term not to be used for direct annotation
Term not to be used for direct manual annotation
AGR slim
Aspergillus GO slim
Candida GO slim
ChEMBL protein targets summary
Drosophila GO slim
FlyBase Drosophila GO ribbon slim
Generic GO slim
Metagenomics GO slim
Mouse GO slim
PIR GO slim
Plant GO slim
Fission yeast GO slim
GO subset for prokaryotes
synapse GO slim
Yeast GO slim
label approved by the SynGO project
Systematic synonym
subset_property
synonym_type_property
consider
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_scope
has_synonym_type
in_subset
shorthand
BFO:0000050
external
part_of
part_of
part of
BFO:0000051
external
has_part
has_part
has part
BFO:0000066
external
occurs_in
occurs_in
occurs in
RO:0002091
external
starts_during
starts_during
starts during
RO:0002092
external
happens_during
happens_during
happens during
RO:0002093
external
ends_during
ends_during
ends during
RO:0002211
external
regulates
regulates
regulates
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
RO:0002213
external
positively_regulates
positively_regulates
positively regulates
A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.
enolase complex
cellular_component
GO:0000015
phosphopyruvate hydratase complex
A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.
GOC:jl
ISBN:0198506732
Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.
https://github.com/geneontology/go-ontology/issues/20964
Reactome:R-HSA-912458
recombinase activity
strand transferase
molecular_function
RecA-family recombinase activity
strand exchange activity
GO:0000150
Note that this term represents activities that do not break or form phosphodiester bonds, and is therefore not a parent of 'site-specific recombinase activity ; GO:0009009'.
DNA strand exchange activity
Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.
GOC:elh
Reactome:R-HSA-912458
Formation of meiotic heteroduplex
A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
histidyl-aspartyl phosphorelay
biological_process
GO:0000160
phosphorelay signal transduction system
A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
PMID:9191038
Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
molecular_function
GO:0000166
nucleotide binding
Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
GOC:mah
ISBN:0198547684
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
GO:0005554
molecular function
molecular_function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
GOC:pdt
Binding to a nucleic acid.
GO:0000496
base pairing
molecular_function
GO:0003676
nucleic acid binding
Binding to a nucleic acid.
GOC:jl
A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
https://github.com/geneontology/go-ontology/issues/15704
https://github.com/geneontology/go-ontology/issues/16534
https://github.com/geneontology/go-ontology/issues/20253
krc
2010-10-21T04:37:54Z
GO:0000130
GO:0001071
GO:0001130
GO:0001131
GO:0001151
GO:0001199
GO:0001204
nucleic acid binding transcription factor activity
transcription factor activity
DNA binding transcription factor activity
gene-specific transcription factor activity
sequence-specific DNA binding transcription factor activity
bacterial-type DNA binding transcription factor activity
bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity
bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity
bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding
bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding
metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity
metal ion regulated sequence-specific DNA binding transcription factor activity
sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity
transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding
transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding
transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding
transcription factor activity, metal ion regulated sequence-specific DNA binding
molecular_function
GO:0003700
Usage guidance: Most DNA-binding transcription factors do not have enzymatic activity. The presence of specific DNA-binding domains known to be present in DNA-binding transcription factors (HOX, GATA etc) should be used to help decide whether a protein is a DNA binding transcription factor or a coregulator. If a protein has an enzymatic activity (for example, ubiquitin ligase, histone acetyl transferase) and no known DNA binding domain, consider annotating to GO:0003712 transcription coregulator activity. Special care should be taken with proteins containing zinc fingers, Myb/SANT and ARID domains, since only a subset of proteins containing these domains directly and selectively bind to regulatory DNA motifs in cis-regulatory regions.
DNA-binding transcription factor activity
A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
GOC:txnOH-2018
The action of a molecule that contributes to the structural integrity of the ribosome.
GO:0003736
GO:0003737
GO:0003738
GO:0003739
GO:0003740
GO:0003741
GO:0003742
ribosomal protein
molecular_function
ribosomal RNA
GO:0003735
Note that this term may be used to annotate ribosomal RNAs as well as ribosomal proteins.
structural constituent of ribosome
The action of a molecule that contributes to the structural integrity of the ribosome.
GOC:mah
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Wikipedia:Enzyme
enzyme activity
molecular_function
GO:0003824
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GOC:vw
ISBN:0198506732
enzyme activity
GOC:dph
GOC:tb
Catalysis of the reaction: a donor + a peroxide = an oxidized donor + 2 H2O.
https://github.com/geneontology/go-ontology/issues/23121
https://github.com/geneontology/go-ontology/issues/25776
GO:0016685
GO:0016686
GO:0016687
GO:0016693
EC:1.11.1.-
KEGG_REACTION:R03532
Reactome:R-HSA-1222346
Reactome:R-HSA-140359
Reactome:R-HSA-209815
Reactome:R-HSA-209840
Reactome:R-HSA-209925
Reactome:R-HSA-209973
Reactome:R-HSA-2309773
Reactome:R-HSA-2559639
Reactome:R-HSA-3341296
Reactome:R-HSA-350901
Reactome:R-HSA-5631885
Reactome:R-HSA-6789031
Reactome:R-HSA-6789126
Reactome:R-HSA-8855490
Reactome:R-HSA-8933635
Wikipedia:Peroxidase
peroxidase reaction
bacterial catalase-peroxidase activity
eosinophil peroxidase activity
extensin peroxidase
guaiacol peroxidase
heme peroxidase
horseradish peroxidase (HRP)
japanese radish peroxidase
lactoperoxidase activity
myeloperoxidase activity
protoheme peroxidase
pyrocatechol peroxidase
scopoletin peroxidase
secretory plant peroxidase activity
thiocyanate peroxidase
verdoperoxidase
molecular_function
MPO
donor:hydrogen-peroxide oxidoreductase activity
oxyperoxidase activity
GO:0004601
peroxidase activity
Catalysis of the reaction: a donor + a peroxide = an oxidized donor + 2 H2O.
GOC:curators
Reactome:R-HSA-1222346
AhpC reduces H2O2
Reactome:R-HSA-140359
PGG2 is reduced to PGH2 by PTGS1
Reactome:R-HSA-209815
Tyrosine is monoiodinated
Reactome:R-HSA-209840
Two DITs combine to form thyroxine
Reactome:R-HSA-209925
DIT and MIT combine to form triiodothyronine
Reactome:R-HSA-209973
Tyrosine is diiodinated
Reactome:R-HSA-2309773
PGG2 is reduced to PGH2 by PTGS2
Reactome:R-HSA-2559639
Collagen type IV sulfilimine cross-linking by peroxidasin
Reactome:R-HSA-3341296
GPX7,8 catalyze peroxidation of P4HB (PDI)
Reactome:R-HSA-350901
Iodide is organified
Reactome:R-HSA-5631885
PRDX1 overoxidizes
Reactome:R-HSA-6789031
Membrane-bound myeloperoxidase (MPO) produces hypochlorous acid (HOCl)
Reactome:R-HSA-6789126
Myeloperoxidase (MPO) produces hypochlorous acid (HOCl)
Reactome:R-HSA-8855490
Lactoperoxidase (LPO) produces OSCN-
Reactome:R-HSA-8933635
Myeloperoxidase (MPO) catalyzes oxidation of nitrite to nitrogen dioxide
Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element.
GO:0004804
P-element encoded transposase activity
molecular_function
GO:0004803
transposase activity
Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element.
GOC:bm
ISBN:0198506732
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
GO:0005478
molecular_function
carrier
GO:0005215
Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
transporter activity
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
GOC:ai
GOC:dgf
Binding to a protein.
GO:0001948
GO:0045308
protein amino acid binding
glycoprotein binding
molecular_function
GO:0005515
protein binding
Binding to a protein.
GOC:go_curators
A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).
https://github.com/geneontology/go-ontology/issues/17729
GO:0008372
NIF_Subcellular:sao1337158144
cell or subcellular entity
cellular component
cellular_component
subcellular entity
GO:0005575
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
cellular_component
A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).
GOC:pdt
subcellular entity
NIF_Subcellular:nlx_subcell_100315
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
Wikipedia:Extracellular
extracellular
cellular_component
GO:0005576
Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
extracellular region
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GOC:go_curators
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
https://github.com/geneontology/go-ontology/issues/21669
Wikipedia:Cell_wall
cellular_component
GO:0005618
Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).
cell wall
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
GOC:giardia
ISBN:0198547684
PMID:15134259
Wikipedia:Microbial_cyst
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
https://github.com/geneontology/go-ontology/issues/17776
Wikipedia:Intracellular
internal to cell
intracellular
protoplasm
cellular_component
nucleocytoplasm
protoplast
GO:0005622
intracellular anatomical structure
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
ISBN:0198506732
nucleocytoplasm
GOC:mah
protoplast
GOC:mah
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
NIF_Subcellular:sao1702920020
Wikipedia:Cell_nucleus
cell nucleus
horsetail nucleus
cellular_component
GO:0005634
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GOC:go_curators
horsetail nucleus
GOC:al
GOC:mah
GOC:vw
PMID:15030757
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
Wikipedia:Chromosome
interphase chromosome
prophase chromosome
cellular_component
chromatid
GO:0005694
Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
chromosome
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
ISBN:0198547684
Circular DNA structures that are not part of a chromosome.
cellular_component
GO:0005727
extrachromosomal circular DNA
Circular DNA structures that are not part of a chromosome.
GOC:ai
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
https://github.com/geneontology/go-ontology/issues/23023
Wikipedia:Cytoplasm
cellular_component
GO:0005737
cytoplasm
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
ISBN:0198547684
A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.
GO:0000503
macropain
20S core complex
20S proteasome
PA28gamma-20S proteasome
cellular_component
GO:0005839
proteasome core complex
A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.
GOC:rb
PMID:10806206
20S proteasome
GOC:cjk
PA28gamma-20S proteasome
CORUM:194
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
GO:0033279
NIF_Subcellular:sao1429207766
Wikipedia:Ribosome
free ribosome
membrane bound ribosome
cellular_component
ribosomal RNA
GO:0005840
ribosome
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
ISBN:0198506732
free ribosome
NIF_Subcellular:sao1139385046
membrane bound ribosome
NIF_Subcellular:sao1291545653
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
NIF_Subcellular:sao1846835077
Wikipedia:Microtubule
microtubuli
microtubulus
neurotubule
cellular_component
GO:0005874
microtubule
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
ISBN:0879693568
neurotubule
NIF_Subcellular:sao248349196
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0005887
GO:0005904
juxtamembrane
NIF_Subcellular:sao1663586795
Wikipedia:Cell_membrane
cell membrane
cellular membrane
cytoplasmic membrane
plasmalemma
bacterial inner membrane
inner endospore membrane
integral component of plasma membrane
integral to plasma membrane
plasma membrane lipid bilayer
cellular_component
GO:0005886
plasma membrane
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
ISBN:0716731363
cellular membrane
NIF_Subcellular:sao6433132645
plasma membrane lipid bilayer
GOC:mah
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
https://github.com/geneontology/go-ontology/issues/22880
jl
2012-10-23T15:40:34Z
GO:0044261
GO:0044723
Wikipedia:Carbohydrate_metabolism
carbohydrate metabolism
biological_process
GO:0005975
carbohydrate metabolic process
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GOC:mah
ISBN:0198506732
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
energy pathways
biological_process
intermediary metabolism
metabolic energy generation
GO:0006091
generation of precursor metabolites and energy
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
GOC:jl
intermediary metabolism
GOC:mah
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
GO:0055132
DNA metabolism
cellular DNA metabolism
biological_process
GO:0006259
DNA metabolic process
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
ISBN:0198506732
Any process that modulates the frequency, rate or extent of DNA repair.
biological_process
GO:0006282
regulation of DNA repair
Any process that modulates the frequency, rate or extent of DNA repair.
GOC:go_curators
The synthesis of an RNA transcript from a DNA template.
https://github.com/geneontology/go-ontology/issues/14854
https://github.com/geneontology/go-ontology/issues/16737
https://github.com/geneontology/go-ontology/issues/22258
https://github.com/geneontology/go-ontology/issues/22555
GO:0001121
GO:0006350
GO:0061018
GO:0061022
cellular transcription
transcription
Wikipedia:Transcription_(genetics)
DNA-dependent transcription
transcription, DNA-dependent
transcription, DNA-templated
bacterial transcription
transcription from bacterial-type RNA polymerase promoter
biological_process
GO:0006351
DNA-templated transcription
The synthesis of an RNA transcript from a DNA template.
GOC:jl
GOC:txnOH
transcription, DNA-dependent
GOC:txnOH
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GO:0006416
GO:0006453
GO:0043037
Wikipedia:Translation_(genetics)
protein anabolism
protein biosynthesis
protein biosynthetic process
protein formation
protein synthesis
protein translation
biological_process
GO:0006412
translation
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GOC:go_curators
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
https://github.com/geneontology/go-ontology/issues/25673
GO:0007022
GO:0007024
GO:0007025
Wikipedia:Protein_folding
alpha-tubulin folding
beta-tubulin folding
chaperonin-mediated tubulin folding
biological_process
chaperone activity
chaperonin ATPase activity
co-chaperone activity
co-chaperonin activity
glycoprotein-specific chaperone activity
non-chaperonin molecular chaperone ATPase activity
protein complex assembly, multichaperone pathway
GO:0006457
protein folding
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
GOC:go_curators
GOC:rb
alpha-tubulin folding
GOC:mah
beta-tubulin folding
GOC:mah
chaperonin-mediated tubulin folding
GOC:mah
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
Wikipedia:Proteolysis
peptidolysis
ATP-dependent proteolysis
biological_process
GO:0006508
This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein processing.
proteolysis
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
GOC:bf
GOC:mah
ATP-dependent proteolysis
GOC:mah
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
Wikipedia:Lipid_metabolism
lipid metabolism
biological_process
GO:0006629
lipid metabolic process
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
GOC:ma
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
nitrogen compound metabolism
biological_process
GO:0006807
nitrogen compound metabolic process
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
GOC:jl
ISBN:0198506732
Any process that modulates the frequency, rate or extent of nitrogen utilization.
biological_process
GO:0006808
regulation of nitrogen utilization
Any process that modulates the frequency, rate or extent of nitrogen utilization.
GOC:go_curators
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
https://github.com/geneontology/go-ontology/issues/20292
jl
2012-12-13T16:25:32Z
GO:0015457
GO:0015460
GO:0044765
biological_process
single-organism transport
GO:0006810
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
transport
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
GOC:dos
GOC:dph
GOC:jl
GOC:mah
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
biological_process
response to abiotic stress
response to biotic stress
GO:0006950
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to stress
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
GOC:mah
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
dos
2014-04-15T15:59:10Z
GO:0098602
Wikipedia:Cell_adhesion
biological_process
cell adhesion molecule activity
single organism cell adhesion
GO:0007155
cell adhesion
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
GOC:hb
GOC:pf
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
GO:0023014
GO:0023015
GO:0023016
GO:0023033
GO:0023045
Wikipedia:Signal_transduction
signal transduction by cis-phosphorylation
signal transduction by conformational transition
signal transduction by protein phosphorylation
signal transduction by trans-phosphorylation
signaling cascade
signalling cascade
biological_process
signaling pathway
signalling pathway
GO:0007165
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
signal transduction
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
GOC:go_curators
GOC:mtg_signaling_feb11
signalling pathway
GOC:mah
Binding to a transcription factor, a protein required to initiate or regulate transcription.
https://github.com/geneontology/go-ontology/issues/19354
TF binding
molecular_function
transcription regulator binding
GO:0008134
Note that this term should not be used for direct annotation. Please consier one of the more specific descendants, GO:0140297 ; DNA-binding transcription factor binding, GO:0140296 ; general transcription initiation factor binding or GO:0001221 ; transcription coregulator binding.
transcription factor binding
Binding to a transcription factor, a protein required to initiate or regulate transcription.
ISBN:0198506732
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
https://github.com/geneontology/go-ontology/issues/24968
jl
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
jl
2012-10-17T15:46:40Z
GO:0044236
GO:0044710
Wikipedia:Metabolism
metabolism
metabolic process resulting in cell growth
metabolism resulting in cell growth
multicellular organism metabolic process
biological_process
single-organism metabolic process
GO:0008152
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
metabolic process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
GOC:go_curators
ISBN:0198547684
The production of light by certain enzyme-catalyzed reactions in cells.
Wikipedia:Bioluminescence
biological_process
GO:0008218
bioluminescence
The production of light by certain enzyme-catalyzed reactions in cells.
ISBN:0198506732
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
GO:0070010
GO:0070011
EC:3.4.-.-
Reactome:R-HSA-205112
Reactome:R-HSA-3000243
Reactome:R-HSA-3000263
Reactome:R-HSA-3065958
Reactome:R-HSA-3065959
Reactome:R-HSA-3139027
Reactome:R-HSA-376149
Reactome:R-HSA-4167501
Reactome:R-HSA-448678
Reactome:R-HSA-5655483
Reactome:R-HSA-5684864
Reactome:R-HSA-5685902
Reactome:R-HSA-6803060
hydrolase, acting on peptide bonds
peptide hydrolase activity
protease activity
peptidase activity, acting on D-amino acid peptides
peptidase activity, acting on L-amino acid peptides
proteinase activity
molecular_function
GO:0008233
peptidase activity
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
GOC:jl
ISBN:0815332181
Reactome:R-HSA-205112
gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6
Reactome:R-HSA-3000243
Unknown lysosomal protease degrades CBLIF:RCbl to release Cbl
Reactome:R-HSA-3000263
TCN2:RCbl is degraded to release RCbl
Reactome:R-HSA-3065958
An unknown protease degrades ACACA
Reactome:R-HSA-3065959
An unknown protease degrades hCBXs
Reactome:R-HSA-3139027
Maturation of HIV Virion
Reactome:R-HSA-376149
Proteolytic processing of SLIT
Reactome:R-HSA-4167501
An unknown protease degrades ACACB
Reactome:R-HSA-448678
CTSG cleaves CASP1(1-404)
Reactome:R-HSA-5655483
USP1 autocleavage
Reactome:R-HSA-5684864
NAPSA, CTSH, PGA3-5 cleave pro-SFTPB
Reactome:R-HSA-5685902
NAPSA, CTSH, PGA3-5 cleave pro-SFTPC
Reactome:R-HSA-6803060
DCD(63-110) is processed to DCD(63-109)
Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
molecular_function
GO:0008658
penicillin binding
Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
GOC:ai
A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
https://github.com/geneontology/go-ontology/issues/21334
https://github.com/geneontology/go-ontology/issues/26572
GO:0009053
GO:0009054
Reactome:R-HSA-169260
Reactome:R-HSA-2564826
electron acceptor activity
electron donor activity
molecular_function
electron carrier
electron transporter activity
GO:0009055
electron transfer activity
A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
Wikipedia:Electron_transfer
Reactome:R-HSA-169260
Reducing equivalents from beta-oxidation of fatty acids transfer to ETF
Reactome:R-HSA-2564826
4Fe-4S cluster assembles on NUBP2:NUBP1 scaffold
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
jl
2012-10-17T15:52:18Z
GO:0044274
GO:0044711
formation
Wikipedia:Anabolism
anabolism
biosynthesis
synthesis
multicellular organismal biosynthetic process
biological_process
single-organism biosynthetic process
GO:0009058
biosynthetic process
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
GOC:curators
ISBN:0198547684
The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
1-2nm peptidoglycan-based cell wall
cell wall inner membrane
cellular_component
GO:0009276
Gram-negative-bacterium-type cell wall
The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
GOC:mlg
ISBN:0815108893
A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
flagellin-based flagellum
cellular_component
GO:0009288
bacterial-type flagellum
A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
GOC:cilia
GOC:jh2
GOC:krc
GOC:mtg_sensu
PMID:7787060
http:en.wikipedia.org/wiki/Flagellum#Bacterial
A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex.
ACCase complex
cellular_component
GO:0009317
acetyl-CoA carboxylase complex
A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex.
GOC:jl
GOC:mah
PMID:12121720
A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.
cellular_component
GO:0009341
beta-galactosidase complex
A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.
PMID:15950161
Citrate lyase is a multienzyme complex with three constituents: the alpha subunit, citrate-ACP transferase; the beta subunit, citryl-ACP lyase; and the gamma subunit, an acyl-carrier protein which also carries the prosthetic group components. All three subunits are required for citrate lyase enzyme activity. This enzyme has only been found in bacteria.
https://github.com/geneontology/go-ontology/issues/21028
citrate lyase complex
citrate synthase complex
MetaCyc:ACECITLY-CPLX
cellular_component
GO:0009346
Note that this complex has only been found in bacteria. For eukaryotic cytrate lyases, consider GO:0140615 ; ATP-dependent citrate lyase complex.
ATP-independent citrate lyase complex
Citrate lyase is a multienzyme complex with three constituents: the alpha subunit, citrate-ACP transferase; the beta subunit, citryl-ACP lyase; and the gamma subunit, an acyl-carrier protein which also carries the prosthetic group components. All three subunits are required for citrate lyase enzyme activity. This enzyme has only been found in bacteria.
PMID:32302313
An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine.
cellular_component
GO:0009349
riboflavin synthase complex
An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine.
PMID:18298940
The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
https://github.com/geneontology/go-ontology/issues/17730
https://github.com/geneontology/go-ontology/issues/18018
https://github.com/geneontology/go-ontology/issues/18061
GO:0010699
GO:0060247
Wikipedia:Quorum_sensing
quorum sensing system
biological_process
cell-cell signaling involved in quorum sensing
detection of cell density by secreted molecule
GO:0009372
quorum sensing
The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
GOC:krc
GOC:mlg
PMID:10607620
PMID:15716452
PMID:16497924
PMID:16630813
PMID:8288518
The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
toxin anabolism
toxin biosynthesis
toxin formation
toxin synthesis
biological_process
GO:0009403
toxin biosynthetic process
The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
GOC:go_curators
A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
https://github.com/geneontology/go-ontology/issues/13958
Wikipedia:Thylakoid
cellular_component
photosynthetic membrane
GO:0009579
A thylakoid is not considered an organelle, but some thylakoids are part of organelles.
thylakoid
A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
GOC:ds
GOC:mtg_sensu
ISBN:0198506732
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.
response to biotic stress
biological_process
GO:0009607
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to biotic stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.
GOC:hb
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
https://github.com/geneontology/go-ontology/issues/16572
response to abiotic stress
biological_process
GO:0009628
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to abiotic stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
GOC:hb
The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
UM-BBD_pathwayID:meth
Wikipedia:Methanogenesis
methane biosynthesis
methane biosynthetic process
biological_process
GO:0015948
methanogenesis
The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
GOC:ai
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
Wikipedia:Photosynthesis
biological_process
GO:0015979
photosynthesis
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
ISBN:0198547684
A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
2014-03-06T11:37:54Z
GO:0016021
GO:0098589
GO:0098805
Wikipedia:Biological_membrane
Wikipedia:Transmembrane_protein
integral component of membrane
integral to membrane
membrane region
region of membrane
whole membrane
cellular_component
transmembrane
GO:0016020
membrane
A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GOC:dos
GOC:mah
ISBN:0815316194
transmembrane
GOC:mah
A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
GO:0022415
Wikipedia:Viral_life_cycle
virus process
biological_process
viral infection
virulence
GO:0016032
See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.
viral process
A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
GOC:bf
GOC:jl
GOC:mah
virus process
GOC:bf
GOC:jl
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
RNA metabolism
biological_process
GO:0016070
RNA metabolic process
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
ISBN:0198506732
Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
molecular_function
GO:0016209
antioxidant activity
Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
ISBN:0198506732
The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
iron-sulphur cluster assembly
biological_process
iron-sulfur cluster biosynthesis
GO:0016226
iron-sulfur cluster assembly
The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
GOC:jl
GOC:mah
GOC:pde
GOC:vw
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
molecular_function
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
Wikipedia:Phosphorylation
biological_process
GO:0016310
phosphorylation
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
ISBN:0198506732
A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane. The complex comprises a membrane sector (F0, V0, or A0) that carries out proton transport and a cytoplasmic compartment sector (F1, V1, or A1) that catalyzes ATP synthesis or hydrolysis. Two major types have been characterized: V-type ATPases couple ATP hydrolysis to the transport of protons across a concentration gradient, whereas F-type ATPases, also known as ATP synthases, normally run in the reverse direction to utilize energy from a proton concentration or electrochemical gradient to synthesize ATP. A third type, A-type ATPases have been found in archaea, and are closely related to eukaryotic V-type ATPases but are reversible.
https://github.com/geneontology/go-ontology/issues/15936
hydrogen-transporting two-sector ATPase complex
cellular_component
vacuolar hydrogen-transporting ATPase
GO:0016469
proton-transporting two-sector ATPase complex
A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane. The complex comprises a membrane sector (F0, V0, or A0) that carries out proton transport and a cytoplasmic compartment sector (F1, V1, or A1) that catalyzes ATP synthesis or hydrolysis. Two major types have been characterized: V-type ATPases couple ATP hydrolysis to the transport of protons across a concentration gradient, whereas F-type ATPases, also known as ATP synthases, normally run in the reverse direction to utilize energy from a proton concentration or electrochemical gradient to synthesize ATP. A third type, A-type ATPases have been found in archaea, and are closely related to eukaryotic V-type ATPases but are reversible.
GOC:mah
ISBN:0716743663
PMID:16691483
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
EC:1.-.-.-
Reactome:R-HSA-1614362
Reactome:R-HSA-209921
Reactome:R-HSA-209960
Reactome:R-HSA-3095889
Reactome:R-HSA-390425
Reactome:R-HSA-390438
Reactome:R-HSA-5662660
Reactome:R-HSA-8878581
Reactome:R-HSA-8936442
Reactome:R-HSA-9020249
Reactome:R-HSA-9020260
Reactome:R-HSA-9024624
Reactome:R-HSA-9024630
Reactome:R-HSA-9025007
Reactome:R-HSA-9026001
Reactome:R-HSA-9026917
Reactome:R-HSA-9027033
Reactome:R-HSA-9693722
redox activity
oxidoreductase activity, acting on other substrates
molecular_function
GO:0016491
oxidoreductase activity
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GOC:go_curators
Reactome:R-HSA-1614362
SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases
Reactome:R-HSA-209921
Monoiodinated tyrosine can be deiodinated
Reactome:R-HSA-209960
Diiodinated tyrosine can be deiodinated
Reactome:R-HSA-3095889
MMACHC dealkylates RCbl
Reactome:R-HSA-390425
FAR1 reduces PalmCoA to HXOL
Reactome:R-HSA-390438
FAR2 reduces PalmCoA to HXOL
Reactome:R-HSA-5662660
Dopachrome is transformed to DHICA by DCT
Reactome:R-HSA-8878581
TYRP1 oxidises DHICA to IQCA
Reactome:R-HSA-8936442
MARC1,MARC2 reduce N-hydroxylated compounds
Reactome:R-HSA-9020249
Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6
Reactome:R-HSA-9020260
Hydroperoxy reducatse reduces 7(S)-Hp-17(S)-HDHA to RvD5
Reactome:R-HSA-9024624
Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6
Reactome:R-HSA-9024630
Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5
Reactome:R-HSA-9025007
Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1
Reactome:R-HSA-9026001
Hydroperoxy reductase reduces 7,17-diHp-DPAn-3 to RvD5n-3DPA
Reactome:R-HSA-9026917
Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA
Reactome:R-HSA-9027033
Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA
Reactome:R-HSA-9693722
Unknown sepiapterin synthase transforms PTHP to sepiapterin
Binding to an amino acid, organic acids containing one or more amino substituents.
molecular_function
GO:0016597
amino acid binding
Binding to an amino acid, organic acids containing one or more amino substituents.
GOC:ai
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
EC:2.-.-.-
Reactome:R-HSA-1483089
Reactome:R-HSA-1483186
Reactome:R-HSA-5668414
Reactome:R-HSA-8868783
molecular_function
GO:0016740
transferase activity
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
ISBN:0198506732
Reactome:R-HSA-1483089
PE is converted to PS by PTDSS2
Reactome:R-HSA-1483186
PC is converted to PS by PTDSS1
Reactome:R-HSA-5668414
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
Reactome:R-HSA-8868783
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
Catalysis of the transfer of a nucleotidyl group to a reactant.
EC:2.7.7.-
Reactome:R-HSA-6782434
molecular_function
GO:0016779
nucleotidyltransferase activity
Catalysis of the transfer of a nucleotidyl group to a reactant.
ISBN:0198506732
Reactome:R-HSA-6782434
THG1L transfers GMP to 5' end of tRNA(His)
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
EC:3.-.-.-
Reactome:R-HSA-1236938
Reactome:R-HSA-2029475
Reactome:R-HSA-5694583
Reactome:R-HSA-5695964
Reactome:R-HSA-6786190
Reactome:R-HSA-6788295
Reactome:R-HSA-8938314
Reactome:R-HSA-8952137
molecular_function
GO:0016787
hydrolase activity
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
ISBN:0198506732
Reactome:R-HSA-1236938
Partial proteolysis of antigen in phagolysosomes
Reactome:R-HSA-2029475
Production of AA by iPLA2 upon FCGR activation
Reactome:R-HSA-5694583
ABHD4 hydrolyses NAPE
Reactome:R-HSA-5695964
ABHD14B hydrolyses PNPB
Reactome:R-HSA-6786190
CMBL hydrolyses OM to OLMS
Reactome:R-HSA-6788295
HDHD1:Mg2+ dephosphorylates PURIDP
Reactome:R-HSA-8938314
ENPPs hydrolyse CoA-SH to PPANT, PAP
Reactome:R-HSA-8952137
Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate
Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
https://github.com/geneontology/go-ontology/issues/25755
GO:0003869
GO:0016302
EC:3.1.3.-
Reactome:R-HSA-4419986
Reactome:R-HSA-9636457
Reactome:R-HSA-9837419
phosphoric monoester hydrolase activity
molecular_function
phosphatase
GO:0016791
phosphatase activity
Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
GOC:curators
GOC:pg
Reactome:R-HSA-4419986
Unknown pPPP phosphatase dephosphorylates pPPP to pPNOL
Reactome:R-HSA-9636457
SapM dephosphorylates PI3P
Reactome:R-HSA-9837419
PANK4 hydrolyzes PPANT to pantetheine
Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
EC:4.-.-.-
Reactome:R-HSA-5696408
Reactome:R-HSA-6782895
molecular_function
GO:0016829
lyase activity
Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
ISBN:0198547684
Reactome:R-HSA-5696408
PXLP-K278-PHYKPL tetramer hydrolyses 5PHL
Reactome:R-HSA-6782895
TYW1:FMN:4Fe-4S transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) at nucleotide 37 of tRNA(Phe)
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
EC:5.-.-.-
Reactome:R-HSA-6787623
other isomerase activity
molecular_function
GO:0016853
isomerase activity
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
ISBN:0198506732
Reactome:R-HSA-6787623
TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal
Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.
https://github.com/geneontology/go-ontology/issues/19380
EC:6.-.-.-
synthetase activity
molecular_function
GO:0016874
ligase activity
Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.
GOC:mah
synthetase activity
GOC:jh2
The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
antibiotic anabolism
antibiotic biosynthesis
antibiotic formation
antibiotic synthesis
biological_process
GO:0017000
antibiotic biosynthetic process
The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
GOC:go_curators
The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
cytochrome biogenesis
biological_process
GO:0017004
cytochrome complex assembly
The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
GOC:jl
GOC:mah
Catalysis of the reaction: a ribonucleoside triphosphate + H2O = a ribonucleoside diphosphate + H+ + phosphate.
https://github.com/geneontology/go-ontology/issues/21232
https://github.com/geneontology/go-ontology/issues/23401
apyrase activity
nucleoside 5-triphosphatase activity
nucleoside triphosphatase activity
nucleoside triphosphate hydrolase activity
nucleoside triphosphate phosphatase activity
nucleoside-triphosphatase activity
EC:3.6.1.15
MetaCyc:NUCLEOSIDE-TRIPHOSPHATASE-RXN
RHEA:23680
Reactome:R-HSA-8850846
Reactome:R-HSA-8851089
Reactome:R-HSA-8851110
Reactome:R-HSA-8851234
Reactome:R-HSA-8851494
Reactome:R-HSA-8851538
NTPase activity
molecular_function
nucleoside triphosphate phosphohydrolase activity
nucleoside-5-triphosphate phosphohydrolase activity
GO:0017111
ribonucleoside triphosphate phosphatase activity
Catalysis of the reaction: a ribonucleoside triphosphate + H2O = a ribonucleoside diphosphate + H+ + phosphate.
RHEA:23680
nucleoside 5-triphosphatase activity
EC:3.6.1.15
Reactome:R-HSA-8850846
NTPDase1 hydrolyzes nucleoside triphosphates
Reactome:R-HSA-8851089
NTPDase2 hydrolyzes nucleoside triphosphates
Reactome:R-HSA-8851110
NTPDase3 hydrolyzes nucleoside triphosphates
Reactome:R-HSA-8851234
NTPDase4 hydrolyzes nucleoside triphosphates
Reactome:R-HSA-8851494
NTPDase7 hydrolyzes nucleoside triphosphates
Reactome:R-HSA-8851538
NTPDase8 hydrolyzes nucleoside triphosphates
A protein complex that possesses molybdopterin synthase activity. In E. coli, the complex is a heterotetramer consisting of two MoaD and two MoaE subunits.
GO:0019009
molybdopterin converting factor complex
cellular_component
GO:0019008
molybdopterin synthase complex
A protein complex that possesses molybdopterin synthase activity. In E. coli, the complex is a heterotetramer consisting of two MoaD and two MoaE subunits.
GOC:mah
PMID:12571227
PMID:15709772
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044246
regulation of metabolism
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
biological_process
GO:0019222
regulation of metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
regulation of organismal metabolic process
GOC:tb
Binding to a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
molecular_function
GO:0019842
vitamin binding
Binding to a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
GOC:ai
The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
cellular_component
GO:0019867
outer membrane
The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
GOC:go_curators
The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
GO:0030396
Wikipedia:Peripheral_membrane_protein
extrinsic to membrane
peripheral membrane protein
cellular_component
GO:0019898
Note that proteins extrinsic to membranes can be removed by treatments that do not disrupt the membrane, such as salt solutions.
extrinsic component of membrane
The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
GOC:dos
GOC:jl
GOC:mah
Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
molecular_function
GO:0030170
pyridoxal phosphate binding
Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
GOC:mah
ISBN:0198506732
Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
GO:0005529
sugar binding
molecular_function
selectin
GO:0030246
carbohydrate binding
Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
GOC:mah
A protein complex that possesses DNA helicase activity.
cellular_component
GO:0033202
DNA helicase complex
A protein complex that possesses DNA helicase activity.
GOC:mah
Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
bf
2011-08-01T02:45:27Z
GO:0004872
GO:0019041
receptor activity
receptor activity involved in signal transduction
signalling receptor activity
molecular_function
GO:0038023
signaling receptor activity
Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
GOC:bf
GOC:signaling
receptor activity involved in signal transduction
GOC:bf
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
response to chemical stimulus
response to chemical substance
biological_process
GO:0042221
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to chemical
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
GOC:jl
response to chemical stimulus
GOC:dos
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
cellular_component
GO:0042575
DNA polymerase complex
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
GOC:jl
PMID:12045093
The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
GO:0005620
periplasm
cellular_component
GO:0042597
periplasmic space
The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
GOC:go_curators
GOC:md
Enables the directed movement of a xenobiotic from one side of a membrane to the other. A xenobiotic is a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
https://github.com/geneontology/go-ontology/issues/19460
GO:0015238
GO:0015239
GO:0015559
GO:0015564
GO:0090484
Reactome:R-HSA-5625574
Reactome:R-HSA-597628
molecular_function
drug transmembrane transporter activity
drug transporter activity
multidrug efflux pump activity
multidrug transporter activity
multidrug, alkane resistant pump activity
xenobiotic transporter activity
GO:0042910
xenobiotic transmembrane transporter activity
Enables the directed movement of a xenobiotic from one side of a membrane to the other. A xenobiotic is a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
GOC:go_curators
GOC:krc
Reactome:R-HSA-5625574
Defective SLC22A18 does not exchange extracellular organic cations for cytosolic H+
Reactome:R-HSA-597628
SLC22A18 exchanges extracellular organic cations for cytosolic H+
Binding to an ion, a charged atoms or groups of atoms.
molecular_function
atom binding
GO:0043167
ion binding
Binding to an ion, a charged atoms or groups of atoms.
GOC:jl
A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
GO:0043191
GO:0043192
ABC-type efflux permease complex
ABC-type efflux porter complex
ABC-type uptake permease complex
mating pheromone exporter
cellular_component
GO:0043190
ATP-binding cassette (ABC) transporter complex
A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
GOC:jl
GOC:mtg_sensu
PMID:11421269
PMID:15111107
The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
Wikipedia:Spore
biological_process
GO:0043934
sporulation
The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
GOC:pamgo_curators
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
jl
2010-01-26T12:05:20Z
small molecule metabolism
biological_process
GO:0044281
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
small molecule metabolic process
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
GOC:curators
GOC:pde
GOC:vw
Any constituent part of a virion, a complete fully infectious extracellular virus particle.
GO:0019012
Wikipedia:Virus
virion part
cellular_component
complete virus particle
virion
GO:0044423
virion component
Any constituent part of a virion, a complete fully infectious extracellular virus particle.
GOC:jl
Any process that maintains the redox environment of a cell or compartment within a cell.
https://github.com/geneontology/go-ontology/issues/24135
GO:0030503
GO:0045867
GO:0045868
regulation of redox homeostasis
Wikipedia:Redox
biological_process
regulation of cell redox homeostasis
GO:0045454
cell redox homeostasis
Any process that maintains the redox environment of a cell or compartment within a cell.
GOC:ai
GOC:dph
GOC:tb
The process by which a symbiont breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the symbiont or its genome is released into the host cell.
https://github.com/geneontology/go-ontology/issues/26670
GO:0019063
VZ:936
entry of virus into host cell
phage translocation
viral entry into host cell
viral penetration
virion penetration
virion penetration into host cell
virus entry into host cell
biological_process
GO:0046718
Viral attachment to the host cell is not part of viral entry in GO because virus attachment does not always lead to viral entry: attachment can also result in the virion being carried by the host cell to another location.
symbiont entry into host cell
The process by which a symbiont breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the symbiont or its genome is released into the host cell.
GOC:jl
VZ:936
Virus entry
Binding to a metal ion.
metal binding
heavy metal binding
molecular_function
GO:0046872
metal ion binding
Binding to a metal ion.
GOC:ai
Binding to a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position.
porphyrin binding
molecular_function
GO:0046906
tetrapyrrole binding
Binding to a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position.
GOC:curators
ISBN:0198506732
A complex of protein and RNA which facilitates translocation of proteins across membranes.
Wikipedia:Signal_recognition_particle
cellular_component
GO:0048500
signal recognition particle
A complex of protein and RNA which facilitates translocation of proteins across membranes.
GOC:mlg
Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
Fe/S binding
iron sulfur cluster binding
iron sulphur cluster binding
iron-sulphur cluster binding
molecular_function
GO:0051536
iron-sulfur cluster binding
Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
GOC:ai
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
https://github.com/geneontology/go-ontology/issues/22580
GO:0006461
GO:0034622
GO:0043623
cellular protein complex assembly
biological_process
cellular macromolecule complex assembly
cellular protein-containing complex assembly
chaperone activity
macromolecular complex assembly
macromolecule complex assembly
protein complex assembly
protein complex formation
GO:0065003
protein-containing complex assembly
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
GOC:jl
A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule.
mah
2009-11-09T11:36:34Z
DNA conformation modification
biological_process
GO:0071103
DNA conformation change
A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule.
GOC:mah
DNA conformation modification
GOC:mah
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
mah
2010-09-10T01:39:16Z
GO:0071841
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
biological_process
GO:0071840
cellular component organization or biogenesis
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:mah
cellular component organisation or biogenesis
GOC:mah
cellular component organisation or biogenesis at cellular level
GOC:mah
Cell motility due to the motion of one or more bacterial-type flagella. A bacterial-type flagellum is a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
mah
2010-10-21T12:00:53Z
flagellin-based flagellar cell motility
biological_process
bacterial-type flagellar cell motility
GO:0071973
bacterial-type flagellum-dependent cell motility
Cell motility due to the motion of one or more bacterial-type flagella. A bacterial-type flagellum is a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
GOC:cilia
GOC:krc
GOC:mah
flagellin-based flagellar cell motility
GOC:mah
Any protein complex that is part of a membrane.
cellular_component
GO:0098796
membrane protein complex
Any protein complex that is part of a membrane.
GOC:dos
A protein complex which is capable of catalytic activity.
https://github.com/geneontology/go-ontology/issues/19980
bhm
2013-11-13T16:18:47Z
enzyme complex
cellular_component
GO:1902494
catalytic complex
A protein complex which is capable of catalytic activity.
GOC:TermGenie
GOC:bhm
PMID:8077207
enzyme complex
GOC:bhm
GOC:jl
Any protein complex that possesses oxidoreductase activity.
bhm
2013-10-07T08:24:47Z
oxidation-reduction complex
redox complex
cellular_component
GO:1990204
oxidoreductase complex
Any protein complex that possesses oxidoreductase activity.
GOC:bhm
PMID:18982432
BFO:0000062
external
preceded_by
preceded_by
preceded by
BFO:0000063
external
precedes
precedes
precedes
cjm
2012-03-14T10:35:44Z
GOREL:0000040
external
results_in
results_in
This relation is currently used to connect two regulation processes p1 and p2, such that if r1 regulates p1 and r2 regulates p2, and r1 results_in r2 then the regulation of p1 is required for the regulation of p2. For an example of use, see GO:0035958 'regulation of glyoxylate cycle by regulation of transcription from RNA polymerase II promoter'. Note that a precise definition of this relation is under discussion. After it has been formalized it will be added to RO, where it will have a RO ID. Note that the existing identifier and label are subject to change.
results in
GOREL:0001019
external
results_in_division_of
results_in_division_of
use occurs_in
results in division of
GOREL:0002003
external
results_in_distribution_of
results_in_distribution_of
results in distribution of
GOREL:0002004
external
results_in_fission_of
results_in_fission_of
results in fission of
GOREL:0012006
external
results_in_maintenance_of
results_in_maintenance_of
results in maintenance of
RO:0000053
external
bearer_of
bearer_of
bearer of
RO:0000056
external
participates_in
participates_in
participates in
RO:0000057
external
has_participant
has_participant
has participant
RO:0002007
external
bounding_layer_of
bounding_layer_of
bounding layer of
RO:0002008
external
coincident_with
coincident_with
coincident with
RO:0002013
external
has_regulatory_component_activity
has_regulatory_component_activity
has regulatory component activity
RO:0002014
external
has_negative_regulatory_component_activity
has_negative_regulatory_component_activity
has negative regulatory component activity
RO:0002016
external
has_necessary_component_activity
has_necessary_component_activity
has necessary component activity
RO:0002087
external
immediately_preceded_by
immediately_preceded_by
immediately preceded by
RO:0002090
external
immediately_precedes
immediately_precedes
immediately precedes
RO:0002131
external
overlaps
overlaps
overlaps
RO:0002180
external
has_component
has_component
has component
RO:0002215
external
capable_of
capable_of
capable of
RO:0002216
external
capable_of_part_of
capable_of_part_of
capable of part of
RO:0002220
external
adjacent_to
adjacent_to
adjacent to
RO:0002224
external
starts_with
starts_with
starts with
RO:0002230
external
ends_with
ends_with
ends with
RO:0002231
external
has_start_location
has_start_location
has start location
RO:0002232
external
has_end_location
has_end_location
has end location
RO:0002233
external
has_input
has_input
has input
RO:0002234
external
has_output
has_output
has output
RO:0002295
external
results_in_developmental_progression_of
results_in_developmental_progression_of
results in developmental progression of
RO:0002296
external
results_in_development_of
results_in_development_of
results in development of
RO:0002297
external
results_in_formation_of
results_in_formation_of
results in formation of
RO:0002298
external
results_in_morphogenesis_of
results_in_morphogenesis_of
results in morphogenesis of
RO:0002299
external
results_in_maturation_of
results_in_maturation_of
results in maturation of
RO:0002304
external
causally_upstream_of,_positive_effect
causally_upstream_of,_positive_effect
causally upstream of, positive effect
RO:0002305
external
causally_upstream_of,_negative_effect
causally_upstream_of,_negative_effect
causally upstream of, negative effect
RO:0002315
external
results_in_acquisition_of_features_of
results_in_acquisition_of_features_of
results in acquisition of features of
RO:0002332
external
regulates_levels_of
regulates_levels_of
regulates levels of
RO:0002334
external
regulated_by
regulated_by
regulated by
RO:0002335
external
negatively_regulated_by
negatively_regulated_by
negatively regulated by
RO:0002336
external
positively_regulated_by
positively_regulated_by
positively regulated by
RO:0002338
external
has_target_start_location
has_target_start_location
has target start location
RO:0002339
external
has_target_end_location
has_target_end_location
has target end location
RO:0002341
external
results_in_transport_along
results_in_transport_along
results in transport along
RO:0002342
external
results_in_transport_across
results_in_transport_across
results in transport across
RO:0002343
external
results_in_growth_of
results_in_growth_of
results in growth of
RO:0002344
external
results_in_transport_to_from_or_in
results_in_transport_to_from_or_in
results in transport to from or in
RO:0002348
external
results_in_commitment_to
results_in_commitment_to
results in commitment to
RO:0002349
external
results_in_determination_of
results_in_determination_of
results in determination of
RO:0002353
external
output_of
output_of
output of
RO:0002355
external
results_in_structural_organization_of
results_in_structural_organization_of
results in structural organization of
RO:0002356
external
results_in_specification_of
results_in_specification_of
results in specification of
RO:0002404
external
causally_downstream_of
causally_downstream_of
causally downstream of
RO:0002405
external
immediately_causally_downstream_of
immediately_causally_downstream_of
immediately causally downstream of
RO:0002411
external
causally_upstream_of
causally_upstream_of
causally upstream of
RO:0002412
external
immediately_causally_upstream_of
immediately_causally_upstream_of
immediately causally upstream of
RO:0002418
external
causally_upstream_of_or_within
causally_upstream_of_or_within
causally upstream of or within
RO:0002427
external
causally_downstream_of_or_within
causally_downstream_of_or_within
causally downstream of or within
RO:0002505
external
has_intermediate
has_intermediate
has intermediate
RO:0002565
external
results_in_movement_of
results_in_movement_of
results in movement of
RO:0002578
external
directly_regulates
directly_regulates
directly regulates
RO:0002588
external
results_in_assembly_of
results_in_assembly_of
results in assembly of
RO:0002590
external
results_in_disassembly_of
results_in_disassembly_of
results in disassembly of
RO:0002591
external
results_in_remodeling_of
results_in_remodeling_of
results in remodeling of
RO:0002592
external
results_in_organization_of
results_in_organization_of
results in organization of
RO:0002608
external
process_has_causal_agent
process_has_causal_agent
process has causal agent
RO:0002629
external
directly_positively_regulates
directly_positively_regulates
directly positively regulates
RO:0002630
external
directly_negatively_regulates
directly_negatively_regulates
directly negatively regulates
RO:0003000
external
produces
produces
produces
RO:0003001
external
produced_by
produced_by
produced by
RO:0004007
external
has_primary_input_or_output
has_primary_input_or_output
has primary input or output
RO:0004008
external
has_primary_output
has_primary_output
has primary output
RO:0004009
external
has_primary_input
has_primary_input
has primary input
RO:0012001
external
has_small_molecule_activator
has_small_molecule_activator
has small molecule activator
RO:0012003
external
acts_on_population_of
acts_on_population_of
acts on population of
RO:0012008
external
results_in_fusion_of
results_in_fusion_of
results in fusion of
RO:0019000
gene_ontology
regulates_characteristic
regulates_characteristic
regulates characteristic
RO:0019001
gene_ontology
positively_regulates_characteristic
positively_regulates_characteristic
positively regulates characteristic
RO:0019002
gene_ontology
negatively_regulates_characteristic
negatively_regulates_characteristic
negatively regulates characteristic
RO:0040036
external
results_in_changes_to_anatomical_or_cellular_structure
results_in_changes_to_anatomical_or_cellular_structure
results in changes to anatomical or cellular structure