P2CS-Web

Two-component systems, rebuilt for exploration

Documentation / Help

Explore P2CS-Web from genomes, genes, clusters, external identifiers, or protein sequences.

P2CS-Web is a public resource for prokaryotic two-component systems. Each result page has a shareable URL, and all listed functions operate without a user account.

Getting started

Choose the entry point that matches your biological question.

  • Home summarizes the current catalogue and links to the main exploration routes.
  • Browse is best for guided inspection of catalogued genomes, genes, or clusters.
  • Search is best when you already have an accession, locus tag, cluster identifier, taxonomy term, or external accession.
  • Use the cart to retain selected records while moving between pages, then compare compatible genome or cluster selections.

Genome exploration

Assembly, taxonomy, TCS census, and genome-scale context.

  • Search genomes by accession, organism name, strain, isolate, lineage, and assembly level, including complete genomes, scaffold, and contig assemblies.
  • Genome pages combine taxonomy, assembly metadata, a TCS census, family distributions, and gene lists.
  • When local annotation files are available, the circular map and linear views display the genomic distribution of P2CS genes and contexts.
  • Genome result lists can be exported as TSV or Excel using the documented summary columns.

Gene pages

Connect a P2CS protein to its domains, context, cluster, and references.

  • Gene detail pages report class, type, domain signature, PFAM-derived annotation, TMPRED signal peptide or transmembrane predictions when available, and genomic coordinates.
  • Genome neighborhood centers the current locus and shows the configured number of upstream and downstream genes from local GFF annotations.
  • The Protein sequence panel opens on demand and displays the local amino-acid record as FASTA. It can be copied or downloaded when a matching local .faa file is available.
  • External references link to RefSeq, UniProt, and MIST4 when the corresponding identifiers are available.

Incomplete HK refinement

Supplementary HisKA profiles for HK records marked as incomplete.

  • For HK proteins with complete=No, the gene page can add a derived HisKA_LIKE* profile from the IHK catalogue without changing the primary gene database.
  • The profile name, amino-acid coordinates, E-value, and IHKOC cluster are shown in Domain signature and in the native or Biotite-like domain graphics.
  • When an incomplete HK belongs to an IHKOC cluster, the gene page uses that IHKOC membership as its active cluster and reuses the standard cluster panels for PFAM architecture, taxonomy Sankey, and paginated members.
  • Complete HK proteins are not processed by this refinement layer.
  • On the incomplete-HK search page, Search by protein sequence is collapsed by default and can be opened when needed.
  • Example: GCF_040545925#ABID56_RS04515 displays HisKA_LIKE9 at positions 331-397 aa and cluster IHKOC_451327.

Cluster exploration

Inspect representative homologues and their domain architectures.

  • Browse or search HKOC and RROC clusters by identifier, representative gene, type, identity, or coverage threshold.
  • Cluster pages provide member counts, the representative, PFAM architectures, domain and architecture statistics, taxonomy distributions, and paginated member lists.
  • When enabled, an on-demand MSA retrieves related representative clusters with MMseqs2 and aligns them with MAFFT.
  • MSA taxonomy and sequence-logo panels describe the selected representative set; the displayed distance tree is exploratory and is not a phylogenetic reconstruction.

Search

Resolve identifiers directly or inspect a paginated list of matches.

  • Genome, gene, and cluster search fields are configurable by the resource administrator and are reflected in the visible form.
  • External-mapping search accepts RefSeq, UniProt, GI, and Gene Ontology identifiers. It initially restricts results to P2CS-associated proteins and can be expanded when required.
  • Protein search accepts one protein sequence or one FASTA record and searches the local HK or RR representative databases.
  • Protein MSA places a submitted FASTA sequence among matched representatives after on-demand alignment; submitted sequences are query inputs, not new P2CS annotations.

Cart, comparison, and export

Keep a reproducible selection while exploring the catalogue.

  • Select entries from result tables with the common checkboxes, then use Add to cart to retain them by data type.
  • The cart separates genomes, clusters, genes, and protein-search hits so that compatible selections can be compared.
  • Summary exports provide TSV and Excel output. Excel workbooks use one sheet per cart data type; TSV includes a data-type column.
  • Available export columns are configured by the resource administrator and may vary between list types.

Structures and limitations

Optional panels are displayed only when their source data are available.

  • Cluster and gene pages can display locally available MassiveFold or public UniProt CIF structures, with domain-colored three-dimensional views and optional two-dimensional domain maps.
  • Structure panels are informational: only public or appropriately deposited structure files should be interpreted or cited.
  • Some genome neighborhoods, protein sequences, TMPRED predictions, PFAM annotations, and structures depend on local source files. The page reports when a matching source is unavailable.
  • Use the production URL and the resource citation information when referring to P2CS-Web in publications.

Protein search engines

All searches run against the local HK and RR cluster databases configured for this P2CS-Web release.

MMseqs2 is the recommended interactive default for large local datasets. blastp provides the classical BLAST workflow; blastp-fast is the interactive default when similar proteins are expected. DIAMOND is available as a fast protein-protein alternative.

blastp-short is intended for peptide-like queries shorter than 30 amino acids and is not the right default for full-length HK or RR proteins.

Data access and support

Use stable identifiers and report any issue with its full URL.

The versioned API under /api/v1 serves the same public catalogue used by the interface. The resource, downloadable summaries, and external-source links should be used with their recorded release date and provenance. When reporting a problem, include the complete page URL, the identifier, and the observed message so that it can be reproduced.

The API documentation provides endpoint groups, request examples, and links to the live OpenAPI schema. For scientific questions, data corrections, or technical support, contact P2CS Contact at philippe.ortet@cea.fr.