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Entry version 120 (02 Jun 2021)
Sequence version 2 (15 Jun 2010)
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Protein

Outer membrane porin F

Gene

ompF

Organism
Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / CCUG 14189 / LMG 1036 / NCIMB 9965 / AN6)
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>
-Protein inferred from homologyi <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

Forms pores that allow passive diffusion of small molecules across the outer membrane.

By similarity

<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 functionPorin
Biological processIon transport, Transport

Protein family/group databases

Transport Classification Database

More...
TCDBi
1.B.1.1.6, the general bacterial porin (gbp) family

<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:
Outer membrane porin F
Alternative name(s):
Outer membrane protein F
Outer membrane protein OpnP
Porin OmpF
<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:ompF
Synonyms:opnP
Ordered Locus Names:XNC1_1586
<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>OrganismiXenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / CCUG 14189 / LMG 1036 / NCIMB 9965 / AN6)
<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 identifieri406817 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesMorganellaceaeXenorhabdus
<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
  • UP000008075 <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>Transmembranei22 – 27Beta strandedBy similarity6
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the subcellular compartment where each non-membrane region of a membrane-spanning protein is found.<p><a href='/help/topo_dom' target='_top'>More...</a></p>Topological domaini28PeriplasmicBy similarity1
Transmembranei29 – 44Beta strandedBy similarityAdd BLAST16
Topological domaini45 – 55ExtracellularBy similarityAdd BLAST11
Transmembranei56 – 68Beta strandedBy similarityAdd BLAST13
Topological domaini69 – 70PeriplasmicBy similarity2
Transmembranei71 – 83Beta strandedBy similarityAdd BLAST13
Topological domaini84 – 97ExtracellularBy similarityAdd BLAST14
Transmembranei98 – 106Beta strandedBy similarity9
Topological domaini107 – 108PeriplasmicBy similarity2
Transmembranei109 – 115Beta strandedBy similarity7
Topological domaini116 – 150ExtracellularBy similarityAdd BLAST35
Transmembranei151 – 157Beta strandedBy similarity7
Topological domaini158 – 165PeriplasmicBy similarity8
Transmembranei166 – 177Beta strandedBy similarityAdd BLAST12
Topological domaini178 – 193ExtracellularBy similarityAdd BLAST16
Transmembranei194 – 204Beta strandedBy similarityAdd BLAST11
Topological domaini205 – 206PeriplasmicBy similarity2
Transmembranei207 – 219Beta strandedBy similarityAdd BLAST13
Topological domaini220 – 234ExtracellularBy similarityAdd BLAST15
Transmembranei235 – 246Beta strandedBy similarityAdd BLAST12
Topological domaini247PeriplasmicBy similarity1
Transmembranei248 – 259Beta strandedBy similarityAdd BLAST12
Topological domaini260 – 278ExtracellularBy similarityAdd BLAST19
Transmembranei279 – 291Beta strandedBy similarityAdd BLAST13
Topological domaini292 – 294PeriplasmicBy similarity3
Transmembranei295 – 308Beta strandedBy similarityAdd BLAST14
Topological domaini309 – 320ExtracellularBy similarityAdd BLAST12
Transmembranei321 – 332Beta strandedBy similarityAdd BLAST12
Topological domaini333 – 334PeriplasmicBy similarity2
Transmembranei335 – 344Beta strandedBy similarity10
Topological domaini345 – 359ExtracellularBy similarityAdd BLAST15
Transmembranei360 – 369Beta strandedBy similarity10

Keywords - Cellular componenti

Cell outer 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 denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 21By similarityAdd BLAST21
<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_000002524022 – 369Outer membrane porin FAdd BLAST348

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q56828

<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

Homotrimer.

By similarity

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
406817.XNC1_1586

<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

More...
SMRi
Q56828

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

<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 Gram-negative porin family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane beta strand

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG3203, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_058202_0_0_6

Identification of Orthologs from Complete Genome Data

More...
OMAi
MYQNNDN

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00342, gram_neg_porins, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.40.160.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR033900, Gram_neg_porin_domain
IPR023614, Porin_dom_sf
IPR001897, Porin_gammaproteobac
IPR001702, Porin_Gram-ve
IPR013793, Porin_Gram-ve_CS

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00267, Porin_1, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00183, ECOLIPORIN
PR00182, ECOLNEIPORIN

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00576, GRAM_NEG_PORIN, 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.

<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 in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

Q56828-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKRNILAVVI PALLVAGTAN AAEIFNKDGN KLDLYGKVDV RHQFADKRSS
60 70 80 90 100
EDGDDSYARI GIKGETQISD QLTGFGRWEY NVKAKGTEAA VAESSTRLAF
110 120 130 140 150
AGLKFANYGS LDYGRNYGVN YDVNAWTDVL PIFGGDAMAQ TDNFMTGRST
160 170 180 190 200
GLLTYRNTDF FGLVDGLNFA LQYQGQNSDR TKNKGRDTER SNGDGYGLSS
210 220 230 240 250
TYDVGYGITV GGSYANSART ADQKEKVSDA YGKRAEAWNI GAKYDANNVY
260 270 280 290 300
LAAMYGETRN MTRYTRTIAD TDATLIANKT QNIELTAQYL FSDLGLKPSL
310 320 330 340 350
AYVQSKGKDL TEGKGFNGDL VKYVSVGTYY YFNKNLSTYV DYKINLLKKD
360
NELGVNARNV FGVGLTYQF
Length:369
Mass (Da):40,641
Last modified:June 15, 2010 - 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:i5B03C898AD8EA57C
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 conflicti118G → R in AAB41114 (PubMed:8817498).Curated1
Sequence conflicti137A → P in AAB41114 (PubMed:8817498).Curated1
Sequence conflicti170A → R in AAB41114 (PubMed:8817498).Curated1

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
L40919 Genomic DNA Translation: AAB41114.1
FN667742 Genomic DNA Translation: CBJ89649.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S70847

NCBI Reference Sequences

More...
RefSeqi
WP_013183934.1, NC_014228.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CBJ89649; CBJ89649; XNC1_1586

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
xne:XNC1_1586

<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
L40919 Genomic DNA Translation: AAB41114.1
FN667742 Genomic DNA Translation: CBJ89649.1
PIRiS70847
RefSeqiWP_013183934.1, NC_014228.1

3D structure databases

SMRiQ56828
ModBaseiSearch...

Protein-protein interaction databases

STRINGi406817.XNC1_1586

Protein family/group databases

TCDBi1.B.1.1.6, the general bacterial porin (gbp) family

Proteomic databases

PRIDEiQ56828

Genome annotation databases

EnsemblBacteriaiCBJ89649; CBJ89649; XNC1_1586
KEGGixne:XNC1_1586

Phylogenomic databases

eggNOGiCOG3203, Bacteria
HOGENOMiCLU_058202_0_0_6
OMAiMYQNNDN

Family and domain databases

CDDicd00342, gram_neg_porins, 1 hit
Gene3Di2.40.160.10, 1 hit
InterProiView protein in InterPro
IPR033900, Gram_neg_porin_domain
IPR023614, Porin_dom_sf
IPR001897, Porin_gammaproteobac
IPR001702, Porin_Gram-ve
IPR013793, Porin_Gram-ve_CS
PfamiView protein in Pfam
PF00267, Porin_1, 1 hit
PRINTSiPR00183, ECOLIPORIN
PR00182, ECOLNEIPORIN
PROSITEiView protein in PROSITE
PS00576, GRAM_NEG_PORIN, 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 nameiOMPF_XENNA
<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: Q56828
Secondary accession number(s): D3VBL0
<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: December 15, 1998
Last sequence update: June 15, 2010
Last modified: June 2, 2021
This is version 120 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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