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Entry version 104 (02 Jun 2021)
Sequence version 2 (28 Jul 2009)
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Protein

Ribonuclease YxiD

Gene

yxiD

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

Toxic component of a type II toxin-antitoxin (TA) system. The C-terminus (residues 409-569) has RNase activity, and inhibits growth upon expression in E.coli. In vitro RNase activity and in vivo growth inhibition are neutralized by cognate antitoxin YxxD, but not by antitoxins specific to other toxins with the LXG domain.

1 Publication

<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

<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 functionHydrolase, Nuclease
Biological processToxin-antitoxin system

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU39300-MONOMER

<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:
Ribonuclease YxiD (EC:3.1.-.-)
Alternative name(s):
RNase YxiD
Toxin YxiD
<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:yxiD
Synonyms:J3D
Ordered Locus Names:BSU39300
<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 disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi548H → A: Loss of RNase activity, loss of E.coli growth inhibition. 1 Publication1

<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_00000500231 – 569Ribonuclease YxiDAdd BLAST569

Proteomic databases

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

More...
PaxDbi
P42296

PRoteomics IDEntifications database

More...
PRIDEi
P42296

<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

Probably interacts with cognate antitoxin YxxD but not with non-cognate antitoxins. The interaction inhibits the toxic activity of YxxD (Probable).

Curated

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224308.BSU39300

<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

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SMRi
P42296

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

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>Domaini1 – 235LXGPROSITE-ProRule annotationAdd BLAST235

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>Regioni548 – 569DisorderedSequence analysisAdd BLAST22

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and domains' section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili8 – 91Sequence analysisAdd BLAST84

Keywords - Domaini

Coiled coil

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG5444, Bacteria

Identification of Orthologs from Complete Genome Data

More...
OMAi
SPMEMML

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00085, HNHc, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003615, HNH_nuc
IPR006829, LXG_dom
IPR027797, PT-TG_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF04740, LXG, 1 hit
PF14449, PT-TG, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51756, LXG, 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.

P42296-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKTLDVHALH EGIQHTIEKL DKQKQQLEKL EKSVEHLAGM KDALKGKGGD
60 70 80 90 100
AIRTFYEECH KPFLLFFGIF IDEYKKVLKQ TQHAISSVES NSHGMIAEAF
110 120 130 140 150
LSHDARHGVK HAREVTEQLT DAVNRQTSAI DHIVSLPTVN DSFFRMETEQ
160 170 180 190 200
AERLISDTLN KLFQFDGQQT QALEAAKSDF QTMKKYIDQL ETMYTGPKIE
210 220 230 240 250
ITGYKSGSIL KSQEEENINQ IFGAINPQMK QADDSPMEMM LKKLAENEKS
260 270 280 290 300
KVDSVVKTGD SKKVSKNIIV INGKVYNTSE HREHIKTDFS NAEVKQVVYN
310 320 330 340 350
DTLYNVYISG NDMKLEPVVS LSDIKVDENG YVKILETAVE LTGVYDLFKA
360 370 380 390 400
ATGRDPVSGE KVTGKDRVVA SINSVPFAKI AKLEKLIDIN KLINNGKKAK
410 420 430 440 450
KASEVKNVAK DKGKIANDVS GSANKINSDL IKKYARDIEQ RTGRELPKNQ
460 470 480 490 500
IDKLKEALRN KEYKKMSPIE TAKHRTKFDK VKNKVIKEWE ENTGQKWPVY
510 520 530 540 550
KENVVSEKTG KIIRKKGDKY DAHHIIENTF GGEHEWWNMH PAKFPNEHQA
560
GIHGTGSPAN ELFKGGKKK
Length:569
Mass (Da):64,326
Last modified:July 28, 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:iE97E4F3E910D260E
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 conflicti176A → G in BAA06649 (PubMed:7704263).Curated1
Sequence conflicti287T → P in BAA06649 (PubMed:7704263).Curated1
Sequence conflicti397K → E in BAA06649 (PubMed:7704263).Curated1
Sequence conflicti533E → K in BAA06649 (PubMed:7704263).Curated1

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
D31856 Genomic DNA Translation: BAA06649.1
AL009126 Genomic DNA Translation: CAB15966.2

Protein sequence database of the Protein Information Resource

More...
PIRi
H70076

NCBI Reference Sequences

More...
RefSeqi
NP_391809.2, NC_000964.3
WP_003244234.1, NZ_JNCM01000034.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB15966; CAB15966; BSU_39300

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
937523

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU39300

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.4254

<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
D31856 Genomic DNA Translation: BAA06649.1
AL009126 Genomic DNA Translation: CAB15966.2
PIRiH70076
RefSeqiNP_391809.2, NC_000964.3
WP_003244234.1, NZ_JNCM01000034.1

3D structure databases

SMRiP42296
ModBaseiSearch...

Protein-protein interaction databases

STRINGi224308.BSU39300

Proteomic databases

PaxDbiP42296
PRIDEiP42296

Genome annotation databases

EnsemblBacteriaiCAB15966; CAB15966; BSU_39300
GeneIDi937523
KEGGibsu:BSU39300
PATRICifig|224308.179.peg.4254

Phylogenomic databases

eggNOGiCOG5444, Bacteria
OMAiSPMEMML

Enzyme and pathway databases

BioCyciBSUB:BSU39300-MONOMER

Family and domain databases

CDDicd00085, HNHc, 1 hit
InterProiView protein in InterPro
IPR003615, HNH_nuc
IPR006829, LXG_dom
IPR027797, PT-TG_dom
PfamiView protein in Pfam
PF04740, LXG, 1 hit
PF14449, PT-TG, 1 hit
PROSITEiView protein in PROSITE
PS51756, LXG, 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 nameiYXID_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: P42296
<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: November 1, 1995
Last sequence update: July 28, 2009
Last modified: June 2, 2021
This is version 104 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

Reference proteome
UniProt is an ELIXIR core data resource
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