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Entry version 139 (29 Sep 2021)
Sequence version 2 (01 Nov 1995)
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Protein

Galactarate dehydratase (L-threo-forming)

Gene

garD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<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

Catalyzes the dehydration of galactarate to form 5-dehydro-4-deoxy-D-glucarate (5-KDG).

UniRule annotation2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Fe2+1 Publication

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 22 sec(-1).1 Publication
  1. KM=800 µM for galactarate1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: galactarate degradation

This protein is involved in step 1 of the subpathway that synthesizes D-glycerate from galactarate.UniRule annotation1 Publication This subpathway is part of the pathway galactarate degradation, which is itself part of Carbohydrate acid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glycerate from galactarate, the pathway galactarate degradation and in Carbohydrate acid metabolism.

<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

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionLyase
LigandIron, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:GALACTARDEHYDRA-MONOMER
MetaCyc:GALACTARDEHYDRA-MONOMER

SABIO-RK: Biochemical Reaction Kinetics Database

More...
SABIO-RKi
P39829

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00565;UER00629

<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 subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Galactarate dehydratase (L-threo-forming)1 PublicationUniRule annotation (EC:4.2.1.42UniRule annotation1 Publication)
Short name:
GalcD1 PublicationUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:garD1 PublicationUniRule annotation
Synonyms:yhaG
Ordered Locus Names:b3128, JW3097
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<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

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001722851 – 523Galactarate dehydratase (L-threo-forming)Add BLAST523

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P39829

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P39829

PRoteomics IDEntifications database

More...
PRIDEi
P39829

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Induced by galactarate, D-glucarate and D-glycerate.1 Publication

<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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4259485, 24 interactors
851954, 1 interactor

Protein interaction database and analysis system

More...
IntActi
P39829, 5 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b3128

<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

1523
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P39829

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P39829

<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 general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Consists of three domains. The N-terminal SAF domain, which forms a beta-clip fold, is likely involved in the substrate recognition. It is connected by a long unstructured linker to the second domain, which serves as a dimerization interface between two monomers. The C-terminal domain represents the catalytic core of the protein and probably contains the metal binding site.1 Publication

<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

Belongs to the UxaA family.UniRule annotationCurated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG2721, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_029189_0_0_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P39829

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P39829

Family and domain databases

Conserved Domains Database

More...
CDDi
cd11613, SAF_AH_GD, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_02031, Galactar_dehydrat, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR007392, Gal/Altron_deHydtase_C
IPR017654, GarD-like
IPR032893, GarD_Enterobacteriaceae
IPR013974, SAF
IPR044144, UxaA/GarD_SAF

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF04295, GD_AH_C, 1 hit
PF08666, SAF, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00858, SAF, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR03248, galactar-dH20, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P39829-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MANIEIRQET PTAFYIKVHD TDNVAIIVND NGLKAGTRFP DGLELIEHIP
60 70 80 90 100
QGHKVALLDI PANGEIIRYG EVIGYAVRAI PRGSWIDESM VVLPEAPPLH
110 120 130 140 150
TLPLATKVPE PLPPLEGYTF EGYRNADGSV GTKNLLGITT SVHCVAGVVD
160 170 180 190 200
YVVKIIERDL LPKYPNVDGV VGLNHLYGCG VAINAPAAVV PIRTIHNISL
210 220 230 240 250
NPNFGGEVMV IGLGCEKLQP ERLLTGTDDV QAIPVESASI VSLQDEKHVG
260 270 280 290 300
FQSMVEDILQ IAERHLQKLN QRQRETCPAS ELVVGMQCGG SDAFSGVTAN
310 320 330 340 350
PAVGYASDLL VRCGATVMFS EVTEVRDAIH LLTPRAVNEE VGKRLLEEME
360 370 380 390 400
WYDNYLNMGK TDRSANPSPG NKKGGLANVV EKALGSIAKS GKSAIVEVLS
410 420 430 440 450
PGQRPTKRGL IYAATPASDF VCGTQQVASG ITVQVFTTGR GTPYGLMAVP
460 470 480 490 500
VIKMATRTEL ANRWFDLMDI NAGTIATGEE TIEEVGWKLF HFILDVASGK
510 520
KKTFSDQWGL HNQLAVFNPA PVT
Length:523
Mass (Da):56,402
Last modified:November 1, 1995 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i919BCC8B49411BB0
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U18997 Genomic DNA Translation: AAA57931.1
U00096 Genomic DNA Translation: AAC76162.1
AP009048 Genomic DNA Translation: BAE77175.1
M30178 Genomic DNA No translation available.

Protein sequence database of the Protein Information Resource

More...
PIRi
D65102

NCBI Reference Sequences

More...
RefSeqi
NP_417597.1, NC_000913.3
WP_001273753.1, NZ_CP014272.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76162; AAC76162; b3128
BAE77175; BAE77175; BAE77175

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947641

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW3097
eco:b3128

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.3603

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<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

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA Translation: AAA57931.1
U00096 Genomic DNA Translation: AAC76162.1
AP009048 Genomic DNA Translation: BAE77175.1
M30178 Genomic DNA No translation available.
PIRiD65102
RefSeqiNP_417597.1, NC_000913.3
WP_001273753.1, NZ_CP014272.1

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 entryMethodResolution (Å)ChainPositionsPDBsum
3LAZX-ray1.92A/B1-96[»]
6U7LX-ray2.75A/B/C/D1-523[»]
SMRiP39829
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4259485, 24 interactors
851954, 1 interactor
IntActiP39829, 5 interactors
STRINGi511145.b3128

Proteomic databases

jPOSTiP39829
PaxDbiP39829
PRIDEiP39829

Genome annotation databases

EnsemblBacteriaiAAC76162; AAC76162; b3128
BAE77175; BAE77175; BAE77175
GeneIDi947641
KEGGiecj:JW3097
eco:b3128
PATRICifig|1411691.4.peg.3603

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB2413

Phylogenomic databases

eggNOGiCOG2721, Bacteria
HOGENOMiCLU_029189_0_0_6
InParanoidiP39829
PhylomeDBiP39829

Enzyme and pathway databases

UniPathwayiUPA00565;UER00629
BioCyciEcoCyc:GALACTARDEHYDRA-MONOMER
MetaCyc:GALACTARDEHYDRA-MONOMER
SABIO-RKiP39829

Miscellaneous databases

EvolutionaryTraceiP39829

Protein Ontology

More...
PROi
PR:P39829

Family and domain databases

CDDicd11613, SAF_AH_GD, 1 hit
HAMAPiMF_02031, Galactar_dehydrat, 1 hit
InterProiView protein in InterPro
IPR007392, Gal/Altron_deHydtase_C
IPR017654, GarD-like
IPR032893, GarD_Enterobacteriaceae
IPR013974, SAF
IPR044144, UxaA/GarD_SAF
PfamiView protein in Pfam
PF04295, GD_AH_C, 1 hit
PF08666, SAF, 1 hit
SMARTiView protein in SMART
SM00858, SAF, 1 hit
TIGRFAMsiTIGR03248, galactar-dH20, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<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 subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiGARD_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P39829
Secondary accession number(s): Q2M981
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: November 1, 1995
Last modified: September 29, 2021
This is version 139 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<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

3D-structure, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
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