Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Entry version 119 (02 Jun 2021)
Sequence version 1 (01 Jan 1998)
Previous versions | rss
Add a publicationFeedback
Protein

Putative L,D-transpeptidase YkuD

Gene

ykuD

Organism
Bacillus subtilis (strain 168)
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

Probable enzyme that may play an important role in cell wall biology.

1 Publication

Miscellaneous

Regulated by SigK. Could also be negatively regulated by GerE. Transcribed by SigK RNA polymerase.
Inactivation of the ykuD gene does not affect vegetative growth, spore resistance to heat, chloroform and lysozyme, or spore germination in the presence of L-alanine.

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

<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 functionGlycosyltransferase, Hydrolase, Transferase
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis, Sporulation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU14040-MONOMER

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

More...
UniPathwayi
UPA00219

Protein family/group databases

Carbohydrate-Active enZymes

More...
CAZyi
CBM50, Carbohydrate-Binding Module Family 50

MEROPS protease database

More...
MEROPSi
C82.003

<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 L,D-transpeptidase YkuD (EC:2.-.-.-)
Alternative name(s):
Spore protein YkuD
<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:ykuD
Ordered Locus Names:BSU14040
<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

<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_00002276611 – 164Putative L,D-transpeptidase YkuDAdd BLAST164

Proteomic databases

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

More...
PaxDbi
O34816

<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 T4 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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Monomer.

1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224308.BSU14040

<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

1164
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Biological Magnetic Resonance Data Bank

More...
BMRBi
O34816

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

More...
SMRi
O34816

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
O34816

<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 – 45LysMPROSITE-ProRule annotationAdd BLAST44

<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

Belongs to the YkuD family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG1376, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
O34816

Identification of Orthologs from Complete Genome Data

More...
OMAi
KAVSKGC

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O34816

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00118, LysM, 1 hit
cd16913, YkuD_like, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.40.440.10, 1 hit
3.10.350.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR005490, LD_TPept_cat_dom
IPR018392, LysM_dom
IPR036779, LysM_dom_sf
IPR038063, Transpep_catalytic_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01476, LysM, 1 hit
PF03734, YkuD, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00257, LysM, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF141523, SSF141523, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51782, LYSM, 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%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.

O34816-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLTYQVKQGD TLNSIAADFR ISTAALLQAN PSLQAGLTAG QSIVIPGLPD
60 70 80 90 100
PYTIPYHIAV SIGAKTLTLS LNNRVMKTYP IAVGKILTQT PTGEFYIINR
110 120 130 140 150
QRNPGGPFGA YWLSLSKQHY GIHGTNNPAS IGKAVSKGCI RMHNKDVIEL
160
ASIVPNGTRV TINR
Length:164
Mass (Da):17,643
Last modified:January 1, 1998 - v1
<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:i6E13A750890E7F4C
GO

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
AJ222587 Genomic DNA Translation: CAA10867.1
AL009126 Genomic DNA Translation: CAB13277.1

Protein sequence database of the Protein Information Resource

More...
PIRi
A69865

NCBI Reference Sequences

More...
RefSeqi
NP_389287.1, NC_000964.3
WP_010886500.1, NZ_JNCM01000035.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB13277; CAB13277; BSU_14040

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
939216

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU14040

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.43.peg.1488

<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
AJ222587 Genomic DNA Translation: CAA10867.1
AL009126 Genomic DNA Translation: CAB13277.1
PIRiA69865
RefSeqiNP_389287.1, NC_000964.3
WP_010886500.1, NZ_JNCM01000035.1

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
1Y7MX-ray2.05A/B1-164[»]
2MTZNMR-A2-164[»]
3ZQDNMR-A2-164[»]
4A1IX-ray1.76A/B/C/D/E/F/G/H1-164[»]
4A1JX-ray2.20A/B1-164[»]
4A1KX-ray1.75A1-164[»]
4A52NMR-A2-164[»]
BMRBiO34816
SMRiO34816
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU14040

Protein family/group databases

CAZyiCBM50, Carbohydrate-Binding Module Family 50
MEROPSiC82.003

Proteomic databases

PaxDbiO34816

Genome annotation databases

EnsemblBacteriaiCAB13277; CAB13277; BSU_14040
GeneIDi939216
KEGGibsu:BSU14040
PATRICifig|224308.43.peg.1488

Phylogenomic databases

eggNOGiCOG1376, Bacteria
InParanoidiO34816
OMAiKAVSKGC
PhylomeDBiO34816

Enzyme and pathway databases

UniPathwayiUPA00219
BioCyciBSUB:BSU14040-MONOMER

Miscellaneous databases

EvolutionaryTraceiO34816

Family and domain databases

CDDicd00118, LysM, 1 hit
cd16913, YkuD_like, 1 hit
Gene3Di2.40.440.10, 1 hit
3.10.350.10, 1 hit
InterProiView protein in InterPro
IPR005490, LD_TPept_cat_dom
IPR018392, LysM_dom
IPR036779, LysM_dom_sf
IPR038063, Transpep_catalytic_dom
PfamiView protein in Pfam
PF01476, LysM, 1 hit
PF03734, YkuD, 1 hit
SMARTiView protein in SMART
SM00257, LysM, 1 hit
SUPFAMiSSF141523, SSF141523, 1 hit
PROSITEiView protein in PROSITE
PS51782, LYSM, 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 nameiYKUD_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: O34816
Secondary accession number(s): Q796K7
<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: January 1, 1998
Last modified: June 2, 2021
This is version 119 of the entry and version 1 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
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again