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Protein

Probable murein peptide carboxypeptidase

Gene

ykfA

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 transcript 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

May be involved in the degradation of peptidoglycan by catalyzing the cleavage of the terminal D-alanine residue from cytoplasmic murein peptides.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: peptidoglycan degradation

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ 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 sitei116NucleophileBy similarity1
Active sitei214Charge relay systemBy similarity1
Active sitei284Charge relay systemBy 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 functionCarboxypeptidase, Hydrolase, Protease, Serine protease
Biological processCell wall biogenesis/degradation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

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BioCyci
BSUB:BSU12970-MONOMER

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

More...
UniPathwayi
UPA00549

Protein family/group databases

MEROPS protease database

More...
MEROPSi
S66.001

<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 murein peptide carboxypeptidase (EC:3.4.16.-)
Alternative name(s):
LD-carboxypeptidase
<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:ykfA
Ordered Locus Names:BSU12970
<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 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

Keywords - Cellular componenti

Cytoplasm

<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_00001728411 – 319Probable murein peptide carboxypeptidaseAdd BLAST319

Proteomic databases

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

More...
PaxDbi
O34851

PRoteomics IDEntifications database

More...
PRIDEi
O34851

<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

Repressed by AbrB, a transcription factor that negatively controls biofilm formation.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

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224308.Bsubs1_010100007191

<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

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...
ProteinModelPortali
O34851

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

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SMRi
O34851

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
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

<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 peptidase S66 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105EBE Bacteria
COG1619 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000025480

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
O34851

KEGG Orthology (KO)

More...
KOi
K01297

Identification of Orthologs from Complete Genome Data

More...
OMAi
MLTQWRL

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O34851

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.50.10740, 1 hit
3.50.30.60, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR027461 Carboxypeptidase_A_C_sf
IPR029062 Class_I_gatase-like
IPR027478 LdcA_N
IPR003507 S66_fam

The PANTHER Classification System

More...
PANTHERi
PTHR30237 PTHR30237, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF028757 LD-carboxypeptidase, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF141986 SSF141986, 1 hit
SSF52317 SSF52317, 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>.<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.

O34851-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKGVFSLNYK PKALNKGDTV GVIAPASPPD PKKLDTALLF LEELGLQVKL
60 70 80 90 100
GKALKNQHGY LAGQDDERLA DLHEMFRDDE VKAVLCACGG FGTGRIAAGI
110 120 130 140 150
DFSLIRKHPK IFWGYSDITF LHTAIHQNTG LVTFHGPMLS TDIGLDDVHP
160 170 180 190 200
LTKASYKQLF QETEFTYTEE LSPLTELVPG KAEGELVGGN LSLLTSTLGT
210 220 230 240 250
PFEIDTRGKL LFIEDIDEEP YQIDRMLNQL KMGGKLTDAA GILVCDFHNC
260 270 280 290 300
VPVKREKSLS LEQVLEDYII SAGRPALRGF KIGHCSPSIA VPIGAKAAMN
310
TAEKTAVIEA GVSEGALKT
Length:319
Mass (Da):34,596
Last modified:May 26, 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:i1E328AA2BC5077EE
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 CAA05577 differs from that shown. Reason: Frameshift at positions 71 and 88.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AJ002571 Genomic DNA Translation: CAA05577.1 Frameshift.
AL009126 Genomic DNA Translation: CAB13154.2

Protein sequence database of the Protein Information Resource

More...
PIRi
G69855

NCBI Reference Sequences

More...
RefSeqi
NP_389180.2, NC_000964.3
WP_009967072.1, NZ_JNCM01000035.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB13154; CAB13154; BSU12970

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
938175

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU12970

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.1409

<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
AJ002571 Genomic DNA Translation: CAA05577.1 Frameshift.
AL009126 Genomic DNA Translation: CAB13154.2
PIRiG69855
RefSeqiNP_389180.2, NC_000964.3
WP_009967072.1, NZ_JNCM01000035.1

3D structure databases

ProteinModelPortaliO34851
SMRiO34851
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100007191

Protein family/group databases

MEROPSiS66.001

Proteomic databases

PaxDbiO34851
PRIDEiO34851

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13154; CAB13154; BSU12970
GeneIDi938175
KEGGibsu:BSU12970
PATRICifig|224308.179.peg.1409

Phylogenomic databases

eggNOGiENOG4105EBE Bacteria
COG1619 LUCA
HOGENOMiHOG000025480
InParanoidiO34851
KOiK01297
OMAiMLTQWRL
PhylomeDBiO34851

Enzyme and pathway databases

UniPathwayi
UPA00549

BioCyciBSUB:BSU12970-MONOMER

Family and domain databases

Gene3Di3.40.50.10740, 1 hit
3.50.30.60, 1 hit
InterProiView protein in InterPro
IPR027461 Carboxypeptidase_A_C_sf
IPR029062 Class_I_gatase-like
IPR027478 LdcA_N
IPR003507 S66_fam
PANTHERiPTHR30237 PTHR30237, 1 hit
PIRSFiPIRSF028757 LD-carboxypeptidase, 1 hit
SUPFAMiSSF141986 SSF141986, 1 hit
SSF52317 SSF52317, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
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 nameiLDC_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: O34851
<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: May 30, 2000
Last sequence update: May 26, 2009
Last modified: December 5, 2018
This is version 106 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. Peptidase families
    Classification of peptidase families and list of entries
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
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