UniProtKB - P16456 (SELD_ECOLI)

>sp|P16456|SELD_ECOLI Selenide, water dikinase OS=Escherichia coli (strain K12) OX=83333 GN=selD PE=1 SV=1
MSENSIRLTQYSHGAGCGCKISPKVLETILHSEQAKFVDPNLLVGNETRDDAAVYDLGNG
TSVISTTDFFMPIVDNPFDFGRIAATNAISDIFAMGGKPIMAIAILGWPINKLSPEIARE
VTEGGRYACRQAGIALAGGHSIDAPEPIFGLAVTGIVPTERVKKNSTAQAGCKLFLTKPL
GIGVLTTAEKKSLLKPEHQGLATEVMCRMNIAGASFANIEGVKAMTDVTGFGLLGHLSEM
CQGAGVQARVDYEAIPKLPGVEEYIKLGAVPGGTERNFASYGHLMGEMPREVRDLLCDPQ
TSGGLLLAVMPEAENEVKATAAEFGIELTAIGELVPARGGRAMVEIR

Entry version 166 (02 Dec 2020)
Sequence version 1 (01 Aug 1990)
Previous versions | rss

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Protein

Selenide, water dikinase

Gene

selD

Organism

Escherichia coli (strain K12)

Status

Reviewed-Annotation score: -Experimental evidence at protein levelⁱ

Functionⁱ

Synthesizes selenophosphate from selenide and ATP.UniRule annotation2 Publications

Catalytic activityⁱ

ATP
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Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+
H₂O
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Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+
hydrogenselenide
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Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
=
AMP
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Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+ 2
H⁺
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See the description of this molecule in ChEBI.
+
phosphate
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Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+
selenophosphate
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
UniRule annotation
Manual assertion according to rulesⁱ
- HAMAP-Rule:MF_00625
2 Publications
Manual assertion based on experiment inⁱ
- Ref.1
  "In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA): involvement and characterization of the selD gene product."
  Leinfelder W., Forchhammer K., Veprek B., Zehelein E., Boeck A.
  Proc. Natl. Acad. Sci. U.S.A. 87:543-547(1990) [PubMed] [Europe PMC] [Abstract]
  Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY.
- Ref.8
  "Structural insights into the catalytic mechanism of Escherichia coli selenophosphate synthetase."
  Noinaj N., Wattanasak R., Lee D.Y., Wally J.L., Piszczek G., Chock P.B., Stadtman T.C., Buchanan S.K.
  J. Bacteriol. 194:499-508(2012) [PubMed] [Europe PMC] [Abstract]
  Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF MUTANT SER-17 IN COMPLEX WITH MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF ASP-51; ASP-68; ASN-87; ASP-91 AND ASP-227.
EC:
2.7.9.3
- Search proteins in UniProtKB for this EC number.
- See the description of this EC number in ENZYME.
UniRule annotation
Manual assertion according to rulesⁱ
- HAMAP-Rule:MF_00625
2 Publications
Manual assertion based on experiment inⁱ
- Ref.1
  "In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA): involvement and characterization of the selD gene product."
  Leinfelder W., Forchhammer K., Veprek B., Zehelein E., Boeck A.
  Proc. Natl. Acad. Sci. U.S.A. 87:543-547(1990) [PubMed] [Europe PMC] [Abstract]
  Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY.
- Ref.8
  "Structural insights into the catalytic mechanism of Escherichia coli selenophosphate synthetase."
  Noinaj N., Wattanasak R., Lee D.Y., Wally J.L., Piszczek G., Chock P.B., Stadtman T.C., Buchanan S.K.
  J. Bacteriol. 194:499-508(2012) [PubMed] [Europe PMC] [Abstract]
  Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF MUTANT SER-17 IN COMPLEX WITH MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF ASP-51; ASP-68; ASN-87; ASP-91 AND ASP-227.
Source:
Rhea
Search for this reaction in UniProtKB.
See the description of this reaction in Rhea.
. Show »« Hide
ATP
+
H₂O
+
hydrogenselenide
zoom
=
AMP
+
2
H⁺
+
phosphate
zoom
+
selenophosphate
zoom

Cofactorⁱ

Mg²⁺UniRule annotation1 PublicationNote: Binds 1 Mg²⁺ ion per monomer.UniRule annotation1 Publication

Sites

Feature key	Position(s)	DescriptionActions	Length
Active siteⁱ	17	UniRule annotation	1
Binding siteⁱ	20	ATPUniRule annotationBy similarity	1
Siteⁱ	20	Important for catalytic activityUniRule annotation1 Publication	1
Metal bindingⁱ	51	MagnesiumUniRule annotationCombined sources1 Publication	1
Binding siteⁱ	68	ATPUniRule annotationBy similarity	1
Metal bindingⁱ	91	MagnesiumUniRule annotationCombined sources1 Publication	1
Binding siteⁱ	91	ATPUniRule annotationBy similarity	1
Metal bindingⁱ	227	MagnesiumUniRule annotationCombined sources1 Publication	1

Regions

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Nucleotide bindingⁱ	48 – 50	ATPUniRule annotationBy similarity		3
Nucleotide bindingⁱ	139 – 141	ATP; shared with dimeric partnerUniRule annotationBy similarity		3

GO - Molecular functionⁱ

Complete GO annotation on QuickGO ...

GO - Biological processⁱ

Complete GO annotation on QuickGO ...

Keywordsⁱ

Molecular function	Kinase, Transferase
Ligand	ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Selenium

Enzyme and pathway databases

BioCycⁱ	EcoCyc:EG10943-MONOMER MetaCyc:EG10943-MONOMER
BRENDAⁱ	2.7.9.3, 2026

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: Selenide, water dikinaseUniRule annotation (EC:2.7.9.3UniRule annotation2 Publications) Alternative name(s): Selenium donor proteinUniRule annotation Selenophosphate synthaseUniRule annotation
Gene namesⁱ	Name:selDUniRule annotation Synonyms:fdhB Ordered Locus Names:b1764, JW1753
Organismⁱ	Escherichia coli (strain K12)
Taxonomic identifierⁱ	83333 [NCBI]
Taxonomic lineageⁱ	cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › Escherichia coli
Proteomesⁱ	UP000000318 Componentⁱ: Chromosome UP000000625 Componentⁱ: Chromosome

Subcellular locationⁱ

GO - Cellular componentⁱ

Complete GO annotation on QuickGO ...

Pathology & Biotechⁱ

Mutagenesis

Feature key	Position(s)	DescriptionActions	Length
Mutagenesisⁱ	13	H → N: No loss of activity. 1 Publication	1
Mutagenesisⁱ	17	C → S: Complete loss of activity. 2 Publications	1
Mutagenesisⁱ	18	G → V: Partial loss of activity. 1 Publication	1
Mutagenesisⁱ	19	C → S: No loss of activity. 1 Publication	1
Mutagenesisⁱ	20	K → Q: Complete loss of activity. 1 Publication	1
Mutagenesisⁱ	20	K → R: Marked loss of activity. 1 Publication	1
Mutagenesisⁱ	51	D → A: Complete loss of activity. 1 Publication	1
Mutagenesisⁱ	68	D → A: Complete loss of activity. 1 Publication	1
Mutagenesisⁱ	87	N → A: Complete loss of activity. 1 Publication	1
Mutagenesisⁱ	91	D → A: Complete loss of activity. 1 Publication	1
Mutagenesisⁱ	227	D → A: Complete loss of activity. 1 Publication	1

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
ChainⁱPRO_0000127620	1 – 347	Selenide, water dikinaseAdd BLAST		347

Proteomic databases

jPOSTⁱ	P16456
PaxDbⁱ	P16456
PRIDEⁱ	P16456

Interactionⁱ

Subunit structureⁱ

Homodimer.

UniRule annotation1 Publication

GO - Molecular functionⁱ

identical protein binding
Source: UniProtKB
Inferred from physical interactionⁱ
- Ref.8
  "Structural insights into the catalytic mechanism of Escherichia coli selenophosphate synthetase."
  Noinaj N., Wattanasak R., Lee D.Y., Wally J.L., Piszczek G., Chock P.B., Stadtman T.C., Buchanan S.K.
  J. Bacteriol. 194:499-508(2012) [PubMed] [Europe PMC] [Abstract]
  Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF MUTANT SER-17 IN COMPLEX WITH MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF ASP-51; ASP-68; ASN-87; ASP-91 AND ASP-227.

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

BioGRIDⁱ	4259138, 21 interactors
Database of interacting proteins More...DIPⁱ	DIP-10849N
IntActⁱ	P16456, 11 interactors
STRINGⁱ	511145.b1764

Structureⁱ

Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area

Feature key	Position(s)	DescriptionActions	Length
Beta strandⁱ	22 – 27	Combined sources	6
Beta strandⁱ	41 – 43	Combined sources	3
Beta strandⁱ	51 – 56	Combined sources	6
Beta strandⁱ	60 – 71	Combined sources	12
Helixⁱ	77 – 94	Combined sources	18
Beta strandⁱ	98 – 108	Combined sources	11
Turnⁱ	110 – 112	Combined sources	3
Helixⁱ	115 – 131	Combined sources	17
Beta strandⁱ	136 – 143	Combined sources	8
Beta strandⁱ	148 – 158	Combined sources	11
Helixⁱ	159 – 161	Combined sources	3
Beta strandⁱ	173 – 178	Combined sources	6
Helixⁱ	182 – 190	Combined sources	9
Helixⁱ	196 – 198	Combined sources	3
Helixⁱ	201 – 207	Combined sources	7
Helixⁱ	212 – 216	Combined sources	5
Beta strandⁱ	222 – 227	Combined sources	6
Helixⁱ	232 – 244	Combined sources	13
Beta strandⁱ	246 – 251	Combined sources	6
Turnⁱ	252 – 254	Combined sources	3
Helixⁱ	261 – 265	Combined sources	5
Helixⁱ	272 – 281	Combined sources	10
Helixⁱ	282 – 284	Combined sources	3
Helixⁱ	290 – 296	Combined sources	7
Beta strandⁱ	305 – 309	Combined sources	5
Helixⁱ	311 – 323	Combined sources	13
Beta strandⁱ	332 – 336	Combined sources	5
Beta strandⁱ	341 – 345	Combined sources	5

Show more details

3D structure databases

SMRⁱ	P16456
ModBaseⁱ	Search...
PDBe-KBⁱ	Search...

Family & Domainsⁱ

Sequence similaritiesⁱ

Belongs to the selenophosphate synthase 1 family. Class I subfamily.UniRule annotationCurated

Phylogenomic databases

eggNOGⁱ	COG0709, Bacteria
InParanoidⁱ	P16456
PhylomeDBⁱ	P16456

Family and domain databases

Conserved Domains Database More...CDDⁱ	cd02195, SelD, 1 hit
Gene3Dⁱ	3.30.1330.10, 1 hit 3.90.650.10, 1 hit
HAMAPⁱ	MF_00625, SelD, 1 hit
InterProⁱ	View protein in InterPro IPR010918, PurM-like_C_dom IPR036676, PurM-like_C_sf IPR016188, PurM-like_N IPR036921, PurM-like_N_sf IPR023061, SelD_I IPR004536, SPS/SelD
PANTHERⁱ	PTHR10256, PTHR10256, 1 hit
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF00586, AIRS, 1 hit PF02769, AIRS_C, 1 hit
PIRSFⁱ	PIRSF036407, Selenphspht_syn, 1 hit
SUPFAMⁱ	SSF55326, SSF55326, 1 hit SSF56042, SSF56042, 1 hit
TIGRFAMsⁱ	TIGR00476, selD, 1 hit

Sequenceⁱ

Sequence statusⁱ: Complete.

P16456-1 [UniParc]FASTA Add to basket

« Hide

        10         20         30         40         50
MSENSIRLTQ YSHGAGCGCK ISPKVLETIL HSEQAKFVDP NLLVGNETRD 
        60         70         80         90        100
DAAVYDLGNG TSVISTTDFF MPIVDNPFDF GRIAATNAIS DIFAMGGKPI 
       110        120        130        140        150
MAIAILGWPI NKLSPEIARE VTEGGRYACR QAGIALAGGH SIDAPEPIFG 
       160        170        180        190        200
LAVTGIVPTE RVKKNSTAQA GCKLFLTKPL GIGVLTTAEK KSLLKPEHQG 
       210        220        230        240        250
LATEVMCRMN IAGASFANIE GVKAMTDVTG FGLLGHLSEM CQGAGVQARV 
       260        270        280        290        300
DYEAIPKLPG VEEYIKLGAV PGGTERNFAS YGHLMGEMPR EVRDLLCDPQ 
       310        320        330        340 
TSGGLLLAVM PEAENEVKAT AAEFGIELTA IGELVPARGG RAMVEIR

Length:347

Mass (Da):36,687

Last modified:August 1, 1990 - v1

Checksum:ⁱ595E5EC9F7B1370F

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	M30184 Genomic DNA Translation: AAA74748.1 U00096 Genomic DNA Translation: AAC74834.1 AP009048 Genomic DNA Translation: BAA15552.1 J05076 Genomic DNA Translation: AAA83922.1
PIRⁱ	JW0033
NCBI Reference Sequences More...RefSeqⁱ	NP_416278.1, NC_000913.3 WP_001295485.1, NZ_SSZK01000001.1

Genome annotation databases

EnsemblBacteriaⁱ	AAC74834; AAC74834; b1764 BAA15552; BAA15552; BAA15552
GeneIDⁱ	45114337 946768
KEGGⁱ	ecj:JW1753 eco:b1764
PATRICⁱ	fig\|1411691.4.peg.490

Protein	Similar proteins		Species	Score	Length	Source
P16456	Selenide, water dikinase		ECOHS		347	UniRef100_A8A0V7
Selenide, water dikinase		ECOLX		349
Selenide, water dikinase		Escherichia coli MS 198-1		349
Selenide, water dikinase		Escherichia coli MS 69-1		349
Selenide, water dikinase		Escherichia coli H386		349
+58

Protein	Similar proteins		Species	Score	Length	Source
P16456	Selenide, water dikinase		ECOHS		347	UniRef90_A8A0V7
Selenide, water dikinase		ECOLX		349
Selenide, water dikinase		Escherichia coli MS 198-1		349
Selenide, water dikinase		Escherichia coli MS 69-1		349
Selenide, water dikinase		Escherichia coli H386		349
+101

Protein	Similar proteins		Species	Score	Length	Source
P16456	Selenide, water dikinase		HAEIN		346	UniRef50_P43911
Selenide, water dikinase		HAEIG		347
Selenide, water dikinase		HAEI8		347
Selenide, water dikinase		COLP3		344
Selenide, water dikinase		PHOLL		347
+5330

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	M30184 Genomic DNA Translation: AAA74748.1 U00096 Genomic DNA Translation: AAC74834.1 AP009048 Genomic DNA Translation: BAA15552.1 J05076 Genomic DNA Translation: AAA83922.1
PIRⁱ	JW0033
RefSeqⁱ	NP_416278.1, NC_000913.3 WP_001295485.1, NZ_SSZK01000001.1

3D structure databases

Select the link destinations: Protein Data Bank Europe More...PDBeⁱ Protein Data Bank RCSB More...RCSB PDBⁱ Protein Data Bank Japan More...PDBjⁱ Links Updated	PDB entry	Method	Resolution (Å)	Chain	Positions	PDBsum
	3U0O	X-ray	2.25	A/B	1-347	[»]
SMRⁱ	P16456
ModBaseⁱ	Search...
PDBe-KBⁱ	Search...

Protein-protein interaction databases

BioGRIDⁱ	4259138, 21 interactors
DIPⁱ	DIP-10849N
IntActⁱ	P16456, 11 interactors
STRINGⁱ	511145.b1764

Proteomic databases

jPOSTⁱ	P16456
PaxDbⁱ	P16456
PRIDEⁱ	P16456

Protocols and materials databases

The DNASU plasmid repository More...DNASUⁱ	946768

DNASUⁱ

946768

Genome annotation databases

EnsemblBacteriaⁱ	AAC74834; AAC74834; b1764 BAA15552; BAA15552; BAA15552
GeneIDⁱ	45114337 946768
KEGGⁱ	ecj:JW1753 eco:b1764
PATRICⁱ	fig\|1411691.4.peg.490

Organism-specific databases

EchoBASEⁱ	EB0936

EchoBASEⁱ

EB0936

Phylogenomic databases

eggNOGⁱ	COG0709, Bacteria
InParanoidⁱ	P16456
PhylomeDBⁱ	P16456

Enzyme and pathway databases

BioCycⁱ	EcoCyc:EG10943-MONOMER MetaCyc:EG10943-MONOMER
BRENDAⁱ	2.7.9.3, 2026

Miscellaneous databases

Protein Ontology More...PROⁱ	PR:P16456

PROⁱ

PR:P16456

Family and domain databases

CDDⁱ	cd02195, SelD, 1 hit
Gene3Dⁱ	3.30.1330.10, 1 hit 3.90.650.10, 1 hit
HAMAPⁱ	MF_00625, SelD, 1 hit
InterProⁱ	View protein in InterPro IPR010918, PurM-like_C_dom IPR036676, PurM-like_C_sf IPR016188, PurM-like_N IPR036921, PurM-like_N_sf IPR023061, SelD_I IPR004536, SPS/SelD
PANTHERⁱ	PTHR10256, PTHR10256, 1 hit
Pfamⁱ	View protein in Pfam PF00586, AIRS, 1 hit PF02769, AIRS_C, 1 hit
PIRSFⁱ	PIRSF036407, Selenphspht_syn, 1 hit
SUPFAMⁱ	SSF55326, SSF55326, 1 hit SSF56042, SSF56042, 1 hit
TIGRFAMsⁱ	TIGR00476, selD, 1 hit
ProtoNetⁱ	Search...
MobiDBⁱ	Search...

Entry informationⁱ

Entry nameⁱ	SELD_ECOLI
Accessionⁱ	P16456Primary (citable) accession number: P16456 Secondary accession number(s): P78172
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
	Last sequence update:	August 1, 1990
	Last modified:	December 2, 2020
	This is version 166 of the entry and version 1 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Prokaryotic Protein Annotation Program

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UniProtKB - P16456 (SELD_ECOLI)

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Selenide, water dikinase

selD

Select a section on the left to see content.

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Regions

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

Enzyme and pathway databases

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Proteomic databases

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

GO - Molecular functioni

Protein-protein interaction databases

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

3D structure databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

Family and domain databases

Sequence databases

Genome annotation databases

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Miscellaneous databases

Family and domain databases

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Documents

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Functionⁱ

Catalytic activityⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

GO - Cellular componentⁱ

Pathology & Biotechⁱ

PTM / Processingⁱ

Interactionⁱ

GO - Molecular functionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ