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Entry version 112 (07 Apr 2021)
Sequence version 3 (28 Jul 2009)
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Protein

ABC transporter permease protein YxdM

Gene

yxdM

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

Annotation score:2 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

Part of the ABC transporter complex YxdLM which could be involved in peptide resistance.

<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 - 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

Biological processTransport

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU39630-MONOMER

Protein family/group databases

Transport Classification Database

More...
TCDBi
3.A.1.134.6, the atp-binding cassette (abc) superfamily

<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:
ABC transporter permease protein YxdM
<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:yxdM
Ordered Locus Names:BSU39630
ORF Names:B65G
<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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei20 – 40HelicalSequence analysisAdd BLAST21
Transmembranei56 – 76HelicalSequence analysisAdd BLAST21
Transmembranei118 – 138HelicalSequence analysisAdd BLAST21
Transmembranei154 – 174HelicalSequence analysisAdd BLAST21
Transmembranei195 – 215HelicalSequence analysisAdd BLAST21
Transmembranei219 – 239HelicalSequence analysisAdd BLAST21
Transmembranei279 – 299HelicalSequence analysisAdd BLAST21
Transmembranei498 – 518HelicalSequence analysisAdd BLAST21
Transmembranei558 – 578HelicalSequence analysisAdd BLAST21
Transmembranei590 – 610HelicalSequence analysisAdd BLAST21

Keywords - Cellular componenti

Cell membrane, Membrane

<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_00000500111 – 622ABC transporter permease protein YxdMAdd BLAST622

Proteomic databases

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

More...
PaxDbi
P42424

<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

Transcriptionally regulated by YxdJ. Induced by the antibacterial protein LL-37, probably via YxdJ.2 Publications

<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

The complex is composed of two ATP-binding proteins (YxdL) and two transmembrane proteins (YxdM).

Curated

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224308.BSU39630

<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

<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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
COG0577, Bacteria

Identification of Orthologs from Complete Genome Data

More...
OMAi
SAFSIMI

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P42424

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003838, ABC3_permease_dom
IPR027022, ABC_permease_BceB-typ

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02687, FtsX, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF018968, ABC_permease_BceB, 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.

P42424-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTFLQFAYKN VTRNKRAYLA FFLSSAFSVL IFFTFAMFLF HPALKEGYLN
60 70 80 90 100
NIAKKGLTAA EWMIFVFSFL FVLYSVNAFL KSRNKEFGIL LMQGITPGQL
110 120 130 140 150
RKLITAENMI IGVMSIAAGI IGGFIFSKTF FTVGAYILEM DALPLYMPWK
160 170 180 190 200
ALGITACGFL LLFFFLSQFT ILFVRSNTVI KLIKGTGKVK PEPKPSVLLS
210 220 230 240 250
LFGIACLCGG YGMVLKGNVH GAEPFIILLL TVIGTYFFFS QSSIWILRAL
260 270 280 290 300
KKWKTFYLRG KNIIWVSDLV YRLKDNARLF FIVSIISAVA FTATGVLAMY
310 320 330 340 350
KSTVGAEESA YEMEYLSYSN NPKEQTHLKD IDHELKTHGF TYTKDKIDVS
360 370 380 390 400
YVRYQEGETV PPVYMISESD AAKYFHVKVN GLKEDEAVYF PGTYDRNFKN
410 420 430 440 450
EAPDQLKLLN QKGELSDQKL SVKEVKKPLI SLNAIIAVND QTFDQLKSLG
460 470 480 490 500
DKASLYGYSY DHWKDSLEIS QSLQNEIYGN YIDVHSDFAS KAGTYYDTVQ
510 520 530 540 550
LPSLSLFIGL FIAIVFFVAA ASFLYFRLFT DLDEDRERYR SLAKIGLSER
560 570 580 590 600
EMAQSVTIQL AILFFFPFVI AVMHTLFALR TLAVEGYSDV AGPLSLTIGG
610 620
FFIFQLLFFL AVRSSYLKKM NK
Length:622
Mass (Da):70,477
Last modified:July 28, 2009 - v3
<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:i193A215B831A1414
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 conflicti136Y → I in BAA08316 (PubMed:8867804).Curated1
Sequence conflicti136Y → I in BAA03303 (PubMed:19383706).Curated1
Sequence conflicti153G → R in BAA08316 (PubMed:8867804).Curated1
Sequence conflicti153G → R in BAA03303 (PubMed:19383706).Curated1
Sequence conflicti426K → Q in BAA08316 (PubMed:8867804).Curated1
Sequence conflicti513 – 524AIVFF…AASFL → GNCILCRGTSFS in BAA08316 (PubMed:8867804).CuratedAdd BLAST12

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
D45912 Genomic DNA Translation: BAA08316.1
AL009126 Genomic DNA Translation: CAB15999.2
D14399 Genomic DNA Translation: BAA03303.1

Protein sequence database of the Protein Information Resource

More...
PIRi
B70074

NCBI Reference Sequences

More...
RefSeqi
NP_391842.2, NC_000964.3
WP_003244410.1, NZ_JNCM01000034.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB15999; CAB15999; BSU_39630

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
937589

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU39630

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.4288

<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
D45912 Genomic DNA Translation: BAA08316.1
AL009126 Genomic DNA Translation: CAB15999.2
D14399 Genomic DNA Translation: BAA03303.1
PIRiB70074
RefSeqiNP_391842.2, NC_000964.3
WP_003244410.1, NZ_JNCM01000034.1

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

STRINGi224308.BSU39630

Protein family/group databases

TCDBi3.A.1.134.6, the atp-binding cassette (abc) superfamily

Proteomic databases

PaxDbiP42424

Genome annotation databases

EnsemblBacteriaiCAB15999; CAB15999; BSU_39630
GeneIDi937589
KEGGibsu:BSU39630
PATRICifig|224308.179.peg.4288

Phylogenomic databases

eggNOGiCOG0577, Bacteria
OMAiSAFSIMI
PhylomeDBiP42424

Enzyme and pathway databases

BioCyciBSUB:BSU39630-MONOMER

Family and domain databases

InterProiView protein in InterPro
IPR003838, ABC3_permease_dom
IPR027022, ABC_permease_BceB-typ
PfamiView protein in Pfam
PF02687, FtsX, 1 hit
PIRSFiPIRSF018968, ABC_permease_BceB, 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 nameiYXDM_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: P42424
<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: April 7, 2021
This is version 112 of the entry and version 3 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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