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Entry version 128 (07 Oct 2020)
Sequence version 2 (16 Jun 2009)
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Protein

Putative sporulation-specific glycosylase YdhD

Gene

ydhD

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>
-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

Miscellaneous

Transcription of ydhD is dependent on SigE.
Cells producing excessive ydhD do not show impaired spore resistance, but their germination properties change: spores show reduced response to L-alanine and some of them germinate even without germinants.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei212Proton donorPROSITE-ProRule annotation1

<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 functionGlycosidase, Hydrolase
Biological processCarbohydrate metabolism, Polysaccharide degradation, Sporulation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU05710-MONOMER

Protein family/group databases

Carbohydrate-Active enZymes

More...
CAZyi
CBM50, Carbohydrate-Binding Module Family 50
GH18, Glycoside Hydrolase Family 18

<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%5Fand%5Ftaxonomy%5Fsection">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:
Putative sporulation-specific glycosylase YdhD (EC:3.2.-.-)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:ydhD
Ordered Locus Names:BSU05710
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fmanual">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 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

  • Spore wall 1 Publication
  • Note: Probably localized either on the surface of the outer spore membrane and/or in the inner spore coat.

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

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

According to PubMed:11011148, cells show no effect vegetative growth, spore resistance to heat, chloroform and lysozyme, or spore germination in the presence of L-alanine. According to PubMed:12177332, cells have no detectable alteration in either dormant or germinating spore peptidoglycan, and germinate normally.2 Publications

<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_00002276601 – 420Putative sporulation-specific glycosylase YdhDAdd BLAST420

Proteomic databases

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

More...
PaxDbi
O05495

<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 provides information on the expression of the gene product at various stages of a cell, tissue or organism development. By default, the information is derived from experiments at the mRNA level, unless specified 'at the protein level'.<p><a href='/help/developmental_stage' target='_top'>More...</a></p>Developmental stagei

Expressed in the mother cell compartment from T2 of sporulation.

<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.BSU05710

<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

1420
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
O05495

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
O05495

<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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini2 – 45LysM 1PROSITE-ProRule annotationAdd BLAST44
Domaini48 – 92LysM 2PROSITE-ProRule annotationAdd BLAST45
Domaini100 – 420GH18PROSITE-ProRule annotationAdd BLAST321

<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

LysM domains are thought to be involved in peptidoglycan binding.

<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

Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG1388, Bacteria
COG3858, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
O05495

Identification of Orthologs from Complete Genome Data

More...
OMAi
TAMRYQS

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O05495

Family and domain databases

Conserved Domains Database

More...
CDDi
cd02874, GH18_CFLE_spore_hydrolase, 1 hit
cd00118, LysM, 2 hits

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.10.350.10, 2 hits
3.10.50.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR041704, CFLE_GH18
IPR011583, Chitinase_II
IPR029070, Chitinase_insertion_sf
IPR001223, Glyco_hydro18_cat
IPR017853, Glycoside_hydrolase_SF
IPR018392, LysM_dom
IPR036779, LysM_dom_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00704, Glyco_hydro_18, 1 hit
PF01476, LysM, 2 hits

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00636, Glyco_18, 1 hit
SM00257, LysM, 2 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51445, SSF51445, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51910, GH18_2, 1 hit
PS51782, LYSM, 2 hits

<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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

O05495-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MFIHIVGPGD SLFSIGRRYG ASVDQIRGVN GLDETNIVPG QALLIPLYVY
60 70 80 90 100
TVQPRDTLTA IAAKAFVPLE RLRAANPGIS PNALQAGAKI TIPSISNYIA
110 120 130 140 150
GTLSFYVLRN PDLDRELIND YAPYSSSISI FEYHIAPNGD IANQLNDAAA
160 170 180 190 200
IETTWQRRVT PLATITNLTS GGFSTEIVHQ VLNNPTARTN LVNNIYDLVS
210 220 230 240 250
TRGYGGVTID FEQVSAADRD LFTGFLRQLR DRLQAGGYVL TIAVPAKTSD
260 270 280 290 300
NIPWLRGYDY GGIGAVVNYM FIMAYDWHHA GSEPGPVAPI TEIRRTIEFT
310 320 330 340 350
IAQVPSRKII IGVPLYGYDW IIPYQPGTVA SAISNQNAIE RAMRYQAPIQ
360 370 380 390 400
YSAEYQSPFF RYSDQQGRTH EVWFEDVRSM SRKMQIVREY RLQAIGAWQL
410 420
TLGFTPGPWL LRKFFTIRKV
Length:420
Mass (Da):46,864
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:i792B87B1BA04C79D
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence BAA19695 differs from that shown. Reason: Frameshift.Curated

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
D88802 Genomic DNA Translation: BAA19695.1 Frameshift.
AL009126 Genomic DNA Translation: CAB12390.2

Protein sequence database of the Protein Information Resource

More...
PIRi
H69783

NCBI Reference Sequences

More...
RefSeqi
NP_388452.2, NC_000964.3
WP_003234126.1, NZ_JNCM01000031.1
WP_009966675.1, NZ_CM000487.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB12390; CAB12390; BSU05710

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
939885

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU05710

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.614

<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
D88802 Genomic DNA Translation: BAA19695.1 Frameshift.
AL009126 Genomic DNA Translation: CAB12390.2
PIRiH69783
RefSeqiNP_388452.2, NC_000964.3
WP_003234126.1, NZ_JNCM01000031.1
WP_009966675.1, NZ_CM000487.1

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
3CZ8X-ray2.20A/B96-402[»]
SMRiO05495
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU05710

Protein family/group databases

CAZyiCBM50, Carbohydrate-Binding Module Family 50
GH18, Glycoside Hydrolase Family 18

Proteomic databases

PaxDbiO05495

Protocols and materials databases

The DNASU plasmid repository

More...
DNASUi
939885

Genome annotation databases

EnsemblBacteriaiCAB12390; CAB12390; BSU05710
GeneIDi939885
KEGGibsu:BSU05710
PATRICifig|224308.179.peg.614

Phylogenomic databases

eggNOGiCOG1388, Bacteria
COG3858, Bacteria
InParanoidiO05495
OMAiTAMRYQS
PhylomeDBiO05495

Enzyme and pathway databases

BioCyciBSUB:BSU05710-MONOMER

Miscellaneous databases

EvolutionaryTraceiO05495

Family and domain databases

CDDicd02874, GH18_CFLE_spore_hydrolase, 1 hit
cd00118, LysM, 2 hits
Gene3Di3.10.350.10, 2 hits
3.10.50.10, 1 hit
InterProiView protein in InterPro
IPR041704, CFLE_GH18
IPR011583, Chitinase_II
IPR029070, Chitinase_insertion_sf
IPR001223, Glyco_hydro18_cat
IPR017853, Glycoside_hydrolase_SF
IPR018392, LysM_dom
IPR036779, LysM_dom_sf
PfamiView protein in Pfam
PF00704, Glyco_hydro_18, 1 hit
PF01476, LysM, 2 hits
SMARTiView protein in SMART
SM00636, Glyco_18, 1 hit
SM00257, LysM, 2 hits
SUPFAMiSSF51445, SSF51445, 1 hit
PROSITEiView protein in PROSITE
PS51910, GH18_2, 1 hit
PS51782, LYSM, 2 hits

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 nameiYDHD_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: O05495
Secondary accession number(s): Q797E8
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: June 16, 2009
Last modified: October 7, 2020
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

3D-structure, Reference proteome

Documents

  1. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  2. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families
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