1 Response_reg#1
5-112 aa · 108 aa · 48.0% of protein
Raw token
Response_reg:5:7.65e-26:112:109:111P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
BER39_RS16850
Response regulator OmpR family
Clostridioides difficile · GCF_001971905
ClassRRTypeOmpRLength225 aaTM0ValidatedNoCompleteYesContextpentad
Gene IDGCF_001971905#BER39_RS16850Stable P2CS identifier used across views.
GenomeGCF_001971905Bacteria; Bacillati; Bacillota; Clostridia; Peptostreptococcales; Peptostreptococcaceae; Clostridioides
Domain signature
Compact overview inferred from the domain field
Response_regTrans_reg_C
Protein length225 aaLength used to scale native and Biotite-like views.
Annotated domains22 with usable coordinates.
Domain coverage185 / 225 aa (82.2%)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
Native P2CS viewFrontend rendering from the parsed domain string and TMPRED protein features.
1 aa225 aa
Domain-by-domain annotation2 items
2 Trans_reg_C#2
147-223 aa · 77 aa · 34.2% of protein
Raw token
Trans_reg_C:147:7.45e-30:223:77:77- Raw architecture: Response_reg:5:7.65e-26:112:109:111#Trans_reg_C:147:7.45e-30:223:77:77
- 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
Context mapping
Resolved via p2cs_tcs_context.db when a locus tag match exists
Context labelpentadGCF_001971905::NZ_MTVV01000004.1::G00051
Group size55 locus tags listed below.
HK / RR2 / 3Counts resolved for the local TCS neighborhood.
Context span2552782-2558507Genomic interval covered by the local TCS group.
Identifiers
Old locus tagBER39_003314RefSeq proteinWP_003417201.1
Context group ID
GCF_001971905::NZ_MTVV01000004.1::G00051Context members
BER39_RS16830BER39_RS16835BER39_RS16840BER39_RS16845BER39_RS16850
Partner locus tags
BER39_RS16830BER39_RS16835BER39_RS16840BER39_RS16845BER39_RS16850
Partner old locus tags
BER39_003310BER39_003311BER39_003312BER39_003313BER39_003314
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_003417201.1Primary protein accession used for annex mappings.
UniProt accessionD5Q7L5Primary UniProt accession resolved in the annex database.
UniProt IDD5Q7L5_CLODIDisplay identifier provided by UniProt.
GO / PubMed5 / 0Unique GO terms and literature references available below.
Reference hubs
Genomic coordinates
Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table
Current locus tagBER39_RS16850Primary locus identifier stored in the genes table.
Old locus tagBER39_003314Legacy locus tag recovered from the local context mapping.
Contig / repliconNZ_MTVV01000004.1Sequence record reported by the local genomic context database.
Genomic interval2 557 830-2 558 507 nt678 nt · Reverse (-)
StrandReverse (-)Strand sign follows the local context database convention.
Local TCS group span2 552 782-2 558 507 ntGCF_001971905::NZ_MTVV01000004.1::G00051
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_001971905::NZ_MTVV01000004.1::G00051Graphic view
Compact keeps a quick overview. Biotite-like switches to a coordinate-aware biological layout with strand and zoom.
Context labelpentadNeighborhood members are ordered by genomic coordinates.
Contig / repliconNZ_MTVV01000004.1All displayed genes belong to this local TCS context.
Neighborhood span2 552 782-2 558 507 nt5 726 nt
Members51 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
2 552 782 nt2 558 507 nt
Neighborhood gene cards
5 genes in the current local neighborhood.
BER39_RS16830GCF_001971905#BER39_RS16830
HKClassic
2 552 782-2 553 897 nt · Reverse (-)
BER39_RS16835GCF_001971905#BER39_RS16835
RROmpR
2 553 933-2 554 631 nt · Reverse (-)
BER39_RS16840GCF_001971905#BER39_RS16840
RROmpR
2 555 013-2 555 693 nt · Reverse (-)
BER39_RS16845GCF_001971905#BER39_RS16845
HKClassic
2 555 743-2 557 758 nt · Reverse (-)
BER39_RS16850GCF_001971905#BER39_RS16850
RROmpRCurrent focus
2 557 830-2 558 507 nt · Reverse (-)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_012276925#GSQ42_RS10155Use this link to inspect the representative gene detail.
PFAM architectureResponse_reg + Trans_reg_C2 domains in the representative PFAM annotation.
PFAM architecture for RROC_1216755
Simplified PFAM architecture for RROC_1216755
PFAM domain coverage: 185 / 230 aa (80.4%)
1 aa230 aa
Response_regTrans_reg_C
- Simplified architecture: Response_reg + Trans_reg_C
- Raw architecture: Response_reg[10-117] | Trans_reg_C[152-228]
- Domain count: 2
- Matched identifier: RROC_1216755
- Positioned domains: Response_reg 10-117 ; Trans_reg_C 152-228
Cluster members and taxonomy
Representative gene: GCF_012276925#GSQ42_RS10155
Sankey plot built from the taxonomy of all members in the selected cluster.
Genome taxonomy
Unknown
Taxonomy recordUnknownTaxon ID 1 496 · GCF_001971905
AssemblyASM197190v1 · Contighaploid
Genome composition4 103 183 bp · 28,5% GCClostridioides difficile
Signal transduction countsGenes 98 · HK 47 · RR 51CheA 1 · PP 0
Ranked taxonomy7 ranked levels available
SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderPeptostreptococcalesFamilyPeptostreptococcaceaeGenusClostridioides
Lineage path7 lineage nodes
1Bacteria2Bacillati3Bacillota4Clostridia5Peptostreptococcales6Peptostreptococcaceae7Clostridioides
Related genes
Preview from the same derived genome key