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Entry version 128 (08 May 2019)
Sequence version 2 (16 Jun 2009)
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Protein

Probable glucarate dehydratase

Gene

gudD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:3 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>
-Protein inferred from homologyi <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 glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).By similarity

<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

Mg2+By similarity

<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: D-glucarate degradation

This protein is involved in step 1 of the subpathway that synthesizes 2,5-dioxopentanoate from D-glucarate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Probable glucarate dehydratase (gudD)
  2. Probable 5-dehydro-4-deoxyglucarate dehydratase (ycbC)
This subpathway is part of the pathway D-glucarate 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 2,5-dioxopentanoate from D-glucarate, the pathway D-glucarate degradation and in Carbohydrate acid metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei42SubstrateBy similarity1
Binding sitei113SubstrateBy similarity1
Binding sitei160SubstrateBy similarity1
Binding sitei215SubstrateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei217Proton acceptorBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi245MagnesiumBy similarity1
Metal bindingi276MagnesiumBy similarity1
Metal bindingi299MagnesiumBy similarity1
Binding sitei299SubstrateBy similarity1
Active sitei349Proton acceptorBy similarity1
Binding sitei378SubstrateBy similarity1
Binding sitei431SubstrateBy similarity1

<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
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU02490-MONOMER

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

More...
UniPathwayi
UPA00564;UER00627

<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:
Probable glucarate dehydratase (EC:4.2.1.40)
Short name:
GDH
Short name:
GlucD
<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:gudD
Synonyms:ycbF
Ordered Locus Names:BSU02490
<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>OrganismiBacillus subtilis (strain 168)
<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 identifieri224308 [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 lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
<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
  • UP000001570 <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

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001712671 – 455Probable glucarate dehydrataseAdd BLAST455

Proteomic databases

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

More...
PaxDbi
P42238

PRoteomics IDEntifications database

More...
PRIDEi
P42238

<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

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224308.BSU02490

<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

3D structure databases

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

More...
SMRi
P42238

Database of comparative protein structure models

More...
ModBasei
Search...

<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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni245 – 247Substrate bindingBy similarity3
Regioni349 – 351Substrate bindingBy similarity3

<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

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105EQX Bacteria
COG4948 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000238021

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P42238

KEGG Orthology (KO)

More...
KOi
K01706

Identification of Orthologs from Complete Genome Data

More...
OMAi
RVAQMCN

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P42238

Family and domain databases

Conserved Domains Database

More...
CDDi
cd03323 D-glucarate_dehydratase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.20.20.120, 1 hit
3.30.390.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR036849 Enolase-like_C_sf
IPR029017 Enolase-like_N
IPR029065 Enolase_C-like
IPR017653 Glucarate_dehydratase
IPR034598 GlucD-like
IPR034593 Mandelate_racemase-like
IPR013342 Mandelate_racemase_C

The PANTHER Classification System

More...
PANTHERi
PTHR43287 PTHR43287, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF13378 MR_MLE_C, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00922 MR_MLE, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51604 SSF51604, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR03247 glucar-dehydr, 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.

P42238-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSSPIQEQVQ KEKRSNIPSI SEMKVIPVAG HDSMLLNLSG AHSPFFTRNI
60 70 80 90 100
VILTDSSGNQ GVGEVPGGEH IRRTLELSEP LVVGKSIGAY QAILQTVRKQ
110 120 130 140 150
FGDQDRGGRG NQTFDLRTTV HAVTALEAAL LDLLGKFLQE PVAALLGEGK
160 170 180 190 200
QRDEVKMLGY LFYIGDRNRT TLPYQSDEQS DCAWFRLRHE EALTPEAIVR
210 220 230 240 250
LAESAQERYG FQDFKLKGGV LRGEEEIEAV TALSKRFPEA RITLDPNGAW
260 270 280 290 300
SLEEAIALCK GKQDVLAYAE DPCGDENGYS AREVMAEFRR ATGLPTATNM
310 320 330 340 350
IATDWREMGH AIQLHAVDIP LADPHFWTMQ GSVRVAQMCH DWGLTWGSHS
360 370 380 390 400
NNHFDISLAM FTHVAAAAPG RITAIDTHWI WQDGQRLTKQ PFEISSGCVK
410 420 430 440 450
VPDKPGLGVD IDMEQVEKAH EIYRKMNLGA RNDAIPMQFL ISNWEFDRKR

PCLVR
Length:455
Mass (Da):50,749
Last modified:June 16, 2009 - 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:i075D81418A0A0483
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti133L → F in BAA06470 (PubMed:7704254).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
D30808 Genomic DNA Translation: BAA06470.1
AL009126 Genomic DNA Translation: CAB12043.2

Protein sequence database of the Protein Information Resource

More...
PIRi
A69753

NCBI Reference Sequences

More...
RefSeqi
NP_388131.2, NC_000964.3
WP_003234816.1, NZ_JNCM01000030.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB12043; CAB12043; BSU02490

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
938410

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU02490

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.256

<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
D30808 Genomic DNA Translation: BAA06470.1
AL009126 Genomic DNA Translation: CAB12043.2
PIRiA69753
RefSeqiNP_388131.2, NC_000964.3
WP_003234816.1, NZ_JNCM01000030.1

3D structure databases

SMRiP42238
ModBaseiSearch...

Protein-protein interaction databases

STRINGi224308.BSU02490

Proteomic databases

PaxDbiP42238
PRIDEiP42238

Genome annotation databases

EnsemblBacteriaiCAB12043; CAB12043; BSU02490
GeneIDi938410
KEGGibsu:BSU02490
PATRICifig|224308.179.peg.256

Phylogenomic databases

eggNOGiENOG4105EQX Bacteria
COG4948 LUCA
HOGENOMiHOG000238021
InParanoidiP42238
KOiK01706
OMAiRVAQMCN
PhylomeDBiP42238

Enzyme and pathway databases

UniPathwayiUPA00564;UER00627
BioCyciBSUB:BSU02490-MONOMER

Family and domain databases

CDDicd03323 D-glucarate_dehydratase, 1 hit
Gene3Di3.20.20.120, 1 hit
3.30.390.10, 1 hit
InterProiView protein in InterPro
IPR036849 Enolase-like_C_sf
IPR029017 Enolase-like_N
IPR029065 Enolase_C-like
IPR017653 Glucarate_dehydratase
IPR034598 GlucD-like
IPR034593 Mandelate_racemase-like
IPR013342 Mandelate_racemase_C
PANTHERiPTHR43287 PTHR43287, 1 hit
PfamiView protein in Pfam
PF13378 MR_MLE_C, 1 hit
SMARTiView protein in SMART
SM00922 MR_MLE, 1 hit
SUPFAMiSSF51604 SSF51604, 1 hit
TIGRFAMsiTIGR03247 glucar-dehydr, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

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 nameiGUDD_BACSU
<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: P42238
<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: November 1, 1995
Last sequence update: June 16, 2009
Last modified: May 8, 2019
This is version 128 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
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