Gene detail

QAC_RS0202755

Response regulator, PleD family

Clostridioides difficile QCD-66c26 · GCF_000003215

Open genome Open selected cluster RefSeq UniProt

ClassRRTypePleDLength319 aaTM0ValidatedNoCompleteYesContextorphan

Gene IDGCF_000003215#QAC_RS0202755Stable P2CS identifier used across views.

GenomeGCF_000003215Unknown

Selected clusterRROC_0533501Run 7 · 344 sequences · id 100% · cov 80% · representative

External referencesWP_009892662.1 · A0AB74R736 · MIST4 QAC_RS0202755RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regGGDEF

Protein length319 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage267 / 319 aa (83.7%)Merged over positioned domains only.

Domain description1 Response_reg,1 GGDEFSummary string stored in the genes table.

Signal peptideUnavailableNo TMPRED prediction file matched this gene.

Transmembrane helicesUnavailableConfigure [protein_features] tmpred_root_dir to enable this annotation.

Complete domain annotations

Domain view

Native Biotite-like

Native P2CS viewFrontend rendering from the parsed domain string and TMPRED protein features.

1 aa319 aa

Domain-by-domain annotation2 items

1 Response_reg#1

9-120 aa · 112 aa · 35.1% of protein

Raw tokenResponse_reg:9:2.01e-28:120:112:111

2 GGDEF#2

153-307 aa · 155 aa · 48.6% of protein

Raw tokenGGDEF:153:6.15e-48:307:158:160

Raw architecture: Response_reg:9:2.01e-28:120:112:111#GGDEF:153:6.15e-48:307:158:160
Domain description: 1 Response_reg,1 GGDEF
TM description: N/A
TMPRED source: No TMPRED file loaded
TMPRED segments: N/A
Complete: Yes

Protein sequence

On-demand local amino-acid sequence in FASTA format

Context mapping

Resolved via p2cs_tcs_context.db when a locus tag match exists

Context labelorphanGCF_000003215::NZ_CM000441.1::G00010

Group size11 locus tag listed below.

HK / RR0 / 1Counts resolved for the local TCS neighborhood.

Context span513358-514317Genomic interval covered by the local TCS group.

Identifiers

RefSeq proteinWP_009892662.1

Context group IDGCF_000003215::NZ_CM000441.1::G00010

Context members

QAC_RS0202755

Partner locus tags

QAC_RS0202755

Partner protein IDs

WP_009892662.1

External references

Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table

RefSeqWP_009892662.1Primary protein accession used for annex mappings.

UniProt accessionA0AB74R736Primary UniProt accession resolved in the annex database.

UniProt IDA0AB74R736_CLODIDisplay identifier provided by UniProt.

GO / PubMed5 / 0Unique GO terms and literature references available below.

Reference hubs

Open RefSeq Open UniProt accession

GO terms

GO:0005886 GO:0052621 GO:0043709 GO:1902201 GO:0000160

Genomic coordinates

Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table

Current locus tagQAC_RS0202755Primary locus identifier stored in the genes table.

Old locus tagUnavailableNo previous locus tag available for this gene.

Contig / repliconNZ_CM000441.1Sequence record reported by the local genomic context database.

Genomic interval513 358-514 317 nt960 nt · Forward (+)

StrandForward (+)Strand sign follows the local context database convention.

Local TCS group span513 358-514 317 ntGCF_000003215::NZ_CM000441.1::G00010

Quick actions

Open genome Search genes in genome

Genome neighborhood

Gene-centered window parsed directly from the configured gzipped GFF annotation

GCF_000003215 · NZ_CM000441.1

Graphic view

Compact Biotite-like

Zoom

Full window Focus gene

Compact keeps a quick overview. Biotite-like switches to a coordinate-aware biological layout with strand and zoom.

Centered locusQAC_RS020275511 genes displayed around the current focus.

Configured flank5 upstream / downstreamWindow size loaded from config.ini.

Annotation sourceGCF_000003215.gff.gzResolved as <gff_root_dir>/<genome_id>/<genome_id>.gff.gz when available.

View modeGene-centered orderThis track keeps the current gene in the middle of the context window when possible.

Gene-centered contextFive upstream and five downstream genes can be shown when the configured flank count is set to 5.

Current geneHKRROther P2CSOutside P2CS

QAC_RS0202730QAC_RS0202730

2QAC_RS0202735QAC_RS0202735

QAC_RS0202740QAC_RS0202740

QAC_RS0202745QAC_RS0202745

QAC_RS0202750QAC_RS0202750

6QAC_RS0202755QAC_RS0202755

QAC_RS0202760QAC_RS0202760

8QAC_RS0202765QAC_RS0202765

QAC_RS0202770QAC_RS0202770

QAC_RS0202775QAC_RS0202775

QAC_RS0202780QAC_RS0202780

Neighborhood gene cards

11 genes in the current genome window.

QAC_RS0202730QAC_RS0202730

Outside P2CS

509 893-510 390 nt · 498 nt · Forward (+)

GyrI-like domain-containing protein

Protein WP_009888330.1

QAC_RS0202735QAC_RS0202735

RRCheY

511 134-511 496 nt · 363 nt · Forward (+)

response regulator

Protein WP_003425081.1Response regulator, CheY family

QAC_RS0202740QAC_RS0202740

Outside P2CS

511 595-512 179 nt · 585 nt · Forward (+)

chemotaxis protein CheC

Protein WP_225544781.1

QAC_RS0202745QAC_RS0202745

Outside P2CS

512 176-512 661 nt · 486 nt · Forward (+)

chemotaxis protein CheD

Protein WP_003425085.1

QAC_RS0202750QAC_RS0202750

Outside P2CS

512 704-513 222 nt · 519 nt · Forward (+)

chemotaxis protein CheW

Protein WP_009888332.1

QAC_RS0202755QAC_RS0202755

RRPleDCurrent focus

513 358-514 317 nt · 960 nt · Forward (+)

diguanylate cyclase

Protein WP_009892662.1Response regulator, PleD family

QAC_RS0202760QAC_RS0202760

Outside P2CS

514 343-516 046 nt · 1 704 nt · Forward (+)

HAMP domain-containing methyl-accepting chemotaxis protein

Protein WP_009888334.1

QAC_RS0202765QAC_RS0202765

HKCheA

516 303-518 405 nt · 2 103 nt · Forward (+)

chemotaxis protein CheA

Protein WP_021419288.1Histidine kinase, CheA

QAC_RS0202770QAC_RS0202770

Outside P2CS

518 418-518 858 nt · 441 nt · Forward (+)

chemotaxis protein CheW

Protein WP_003439104.1

QAC_RS0202775QAC_RS0202775

Outside P2CS

518 894-519 697 nt · 804 nt · Forward (+)

CheR family methyltransferase

Protein WP_009888336.1

QAC_RS0202780QAC_RS0202780

Outside P2CS

519 737-520 333 nt · 597 nt · Forward (+)

CheB methylesterase domain-containing protein

Protein WP_009888337.1

3D Structure

UniProt CIF structure root: /mnt/p2cs-s3/P2CS_WEB/DATAS/SP_CIF

Loading 3D structure...

Response_reg9-120 aa

GGDEF153-307 aa

Structure domain maps

The initial PFAM_pred3D-style renderer is shown by default, using domain positions stored in P2CS for this gene. The optional Biotite-like renderer can be enabled from config.ini.

GCF_000003215#QAC_RS0202755

Initial PFAM_pred3D-style view.

No CIF or PDB file was found for RROC_0533501 under /home/biam/MYTOOLS/p2cs-web/DATAS/MassiveFold/work/recovered_by_cluster_all_ranked/clusters.

Using the UniProt CIF structure for A0AB74R736.

Clusters

CD-HIT memberships and selected cluster details for the current gene class

Available memberships1 cluster

RROC_0533501RR

Run 7344 sequencesid 100%cov 80%

PFAM Response_reg + GGDEF

Current gene is the representative sequence.

Selected clusterRROC_0533501Run 7 · RR · 344 sequences

Representative sequenceGCF_000003215#QAC_RS0202755The current gene is the representative for this cluster.

PFAM architectureResponse_reg + GGDEF2 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for RROC_0533501

Simplified PFAM architecture for RROC_0533501

PFAM domain coverage: 266 / 319 aa (83.4%)

1 aa319 aa

Response_regGGDEF

Simplified architecture: Response_reg + GGDEF
Raw architecture: Response_reg[9-120] | GGDEF[153-306]
Domain count: 2
Matched identifier: RROC_0533501
Positioned domains: Response_reg 9-120 ; Response_reg 9-120 ; GGDEF 153-306 ; GGDEF 153-306

Cluster members and taxonomy

Representative gene: GCF_000003215#QAC_RS0202755

Sankey plot built from the taxonomy of all members in the selected cluster.

Genome taxonomy

Clostridioides difficile QCD-66c26

Taxonomy recordClostridioides difficile QCD-66c26Taxon ID 455 631 · GCF_000003215

AssemblyASM321v1 · Chromosomehaploid

Genome composition4 127 750 bp · 28,5% GCGenome size and GC content from the linked genome record.

Signal transduction countsGenes 106 · HK 50 · RR 56CheA 1 · PP 0

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderPeptostreptococcalesFamilyPeptostreptococcaceaeGenusClostridioides

Lineage path1 lineage nodes

1Unknown

Open genome Search genes in genome Search RR genes NCBI assembly files

Related genes

Preview from the same derived genome key