Gene detail

QAC_RS0204850

Response regulator OmpR family

Clostridioides difficile QCD-66c26 · GCF_000003215

Open genome Open selected cluster RefSeq UniProt

ClassRRTypeOmpRLength227 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_000003215#QAC_RS0204850Stable P2CS identifier used across views.

GenomeGCF_000003215Unknown

Selected clusterRROC_1353984Run 7 · 691 sequences · id 100% · cov 80% · representative

External referencesWP_003418728.1 · D5Q1G2 · MIST4 QAC_RS0204850RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regTrans_reg_C

Protein length227 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage186 / 227 aa (81.9%)Merged over positioned domains only.

Domain description1 Response_reg,1 Trans_reg_CSummary 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 aa227 aa

Domain-by-domain annotation2 items

1 Response_reg#1

4-113 aa · 110 aa · 48.5% of protein

Raw tokenResponse_reg:4:7.79e-32:113:111:111

2 Trans_reg_C#2

148-223 aa · 76 aa · 33.5% of protein

Raw tokenTrans_reg_C:148:1.42e-29:223:76:77

Raw architecture: Response_reg:4:7.79e-32:113:111:111#Trans_reg_C:148:1.42e-29:223:76:77
Domain description: 1 Response_reg,1 Trans_reg_C
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 labelpairedGCF_000003215::NZ_CM000441.1::G00016

Group size22 locus tags listed below.

HK / RR1 / 1Counts resolved for the local TCS neighborhood.

Context span1002238-1004173Genomic interval covered by the local TCS group.

Identifiers

RefSeq proteinWP_003418728.1

Context group IDGCF_000003215::NZ_CM000441.1::G00016

Context members

QAC_RS0204850QAC_RS0204855

Partner locus tags

QAC_RS0204850QAC_RS0204855

Partner protein IDs

WP_003418728.1 WP_009888761.1

External references

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

RefSeqWP_003418728.1Primary protein accession used for annex mappings.

UniProt accessionD5Q1G2Primary UniProt accession resolved in the annex database.

UniProt IDD5Q1G2_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:0005829 GO:0032993 GO:0000156 GO:0000976 GO:0006355

Genomic coordinates

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

Current locus tagQAC_RS0204850Primary 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 interval1 002 238-1 002 921 nt684 nt · Forward (+)

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

Local TCS group span1 002 238-1 004 173 ntGCF_000003215::NZ_CM000441.1::G00016

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_RS020485011 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_RS0204825ybaK

QAC_RS0204830QAC_RS0204830

QAC_RS0204835QAC_RS0204835

QAC_RS0204840QAC_RS0204840

QAC_RS0204845QAC_RS0204845

6QAC_RS0204850QAC_RS0204850

7QAC_RS0204855QAC_RS0204855

QAC_RS0204860QAC_RS0204860

QAC_RS0204865QAC_RS0204865

QAC_RS0204870QAC_RS0204870

QAC_RS0204875QAC_RS0204875

Neighborhood gene cards

11 genes in the current genome window.

QAC_RS0204825ybaK

Outside P2CS

997 959-998 432 nt · 474 nt · Forward (+)

Cys-tRNA(Pro) deacylase

Protein WP_003437064.1

QAC_RS0204830QAC_RS0204830

Outside P2CS

998 629-999 468 nt · 840 nt · Forward (+)

fumarate hydratase

Protein WP_003437062.1

QAC_RS0204835QAC_RS0204835

Outside P2CS

999 481-1 000 029 nt · 549 nt · Forward (+)

Fe-S-containing hydro-lyase

Protein WP_003437060.1

QAC_RS0204840QAC_RS0204840

Outside P2CS

1 000 095-1 001 276 nt · 1 182 nt · Forward (+)

NAD(P)-dependent malic enzyme

Protein WP_009888757.1

QAC_RS0204845QAC_RS0204845

Outside P2CS

1 001 449-1 001 712 nt · 264 nt · Forward (+)

zinc ribbon domain-containing protein

Protein WP_003418727.1

QAC_RS0204850QAC_RS0204850

RROmpRCurrent focus

1 002 238-1 002 921 nt · 684 nt · Forward (+)

response regulator transcription factor

Protein WP_003418728.1Response regulator OmpR family

QAC_RS0204855QAC_RS0204855

HKClassic

1 002 932-1 004 173 nt · 1 242 nt · Forward (+)

sensor histidine kinase

Protein WP_009888761.1Histidine kinase, Classic

QAC_RS0204860QAC_RS0204860

Outside P2CS

1 004 245-1 004 928 nt · 684 nt · Forward (+)

ABC transporter ATP-binding protein

Protein WP_009888764.1

QAC_RS0204865QAC_RS0204865

Outside P2CS

1 004 925-1 007 255 nt · 2 331 nt · Forward (+)

ABC transporter permease

Protein WP_009888766.1

QAC_RS0204870QAC_RS0204870

Outside P2CS

1 007 436-1 008 278 nt · 843 nt · Reverse (-)

S1 RNA-binding domain-containing protein

Protein WP_009888767.1

QAC_RS0204875QAC_RS0204875

Outside P2CS

1 008 573-1 009 307 nt · 735 nt · Forward (+)

GntR family transcriptional regulator

Protein WP_003437044.1

3D Structure

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

Loading 3D structure...

Response_reg4-113 aa

Trans_reg_C148-223 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_RS0204850

Initial PFAM_pred3D-style view.

No CIF or PDB file was found for RROC_1353984 under /home/biam/MYTOOLS/p2cs-web/DATAS/MassiveFold/work/recovered_by_cluster_all_ranked/clusters.

Using the UniProt CIF structure for D5Q1G2.

Clusters

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

Available memberships1 cluster

RROC_1353984RR

Run 7691 sequencesid 100%cov 80%

PFAM Response_reg + Trans_reg_C

Current gene is the representative sequence.

Selected clusterRROC_1353984Run 7 · RR · 691 sequences

Representative sequenceGCF_000003215#QAC_RS0204850The current gene is the representative for this cluster.

PFAM architectureResponse_reg + Trans_reg_C2 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for RROC_1353984

Simplified PFAM architecture for RROC_1353984

PFAM domain coverage: 185 / 227 aa (81.5%)

1 aa227 aa

Response_regTrans_reg_C

Simplified architecture: Response_reg + Trans_reg_C
Raw architecture: Response_reg[4-113] | Trans_reg_C[148-222]
Domain count: 2
Matched identifier: RROC_1353984
Positioned domains: Response_reg 4-113 ; Response_reg 4-113 ; Trans_reg_C 148-222 ; Trans_reg_C 148-222

Cluster members and taxonomy

Representative gene: GCF_000003215#QAC_RS0204850

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