1 Response_reg#1
4-112 aa · 109 aa · 47.4% of protein
Raw token
Response_reg:4:5.52e-33:112:111:111P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
BER34_RS16220
Response regulator OmpR family
Clostridioides difficile · GCF_001972115
ClassRRTypeOmpRLength230 aaTM0ValidatedNoCompleteYesContextpaired
Gene IDGCF_001972115#BER34_RS16220Stable P2CS identifier used across views.
GenomeGCF_001972115Bacteria; Bacillati; Bacillota; Clostridia; Peptostreptococcales; Peptostreptococcaceae; Clostridioides
Domain signature
Compact overview inferred from the domain field
Response_regTrans_reg_C
Protein length230 aaLength used to scale native and Biotite-like views.
Annotated domains22 with usable coordinates.
Domain coverage186 / 230 aa (80.9%)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
Biotite-like viewServer-side Python rendering inspired by the Biotite sigma-domain example.
Domain-by-domain annotation2 items
2 Trans_reg_C#2
151-227 aa · 77 aa · 33.5% of protein
Raw token
Trans_reg_C:151:4.48e-28:227:77:77- Raw architecture: Response_reg:4:5.52e-33:112:111:111#Trans_reg_C:151:4.48e-28:227:77:77
- 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 labelpairedGCF_001972115::NZ_MTVX01000003.1::G00044
Group size22 locus tags listed below.
HK / RR1 / 1Counts resolved for the local TCS neighborhood.
Context span407698-409833Genomic interval covered by the local TCS group.
Identifiers
Old locus tagBER34_003196RefSeq proteinWP_003417590.1
Context group ID
GCF_001972115::NZ_MTVX01000003.1::G00044Context members
BER34_RS16220BER34_RS16225
Partner locus tags
BER34_RS16220BER34_RS16225
Partner old locus tags
BER34_003196BER34_003197
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_003417590.1Primary protein accession used for annex mappings.
UniProt accessionD5Q046Primary UniProt accession resolved in the annex database.
UniProt IDD5Q046_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 tagBER34_RS16220Primary locus identifier stored in the genes table.
Old locus tagBER34_003196Legacy locus tag recovered from the local context mapping.
Contig / repliconNZ_MTVX01000003.1Sequence record reported by the local genomic context database.
Genomic interval407 698-408 390 nt693 nt · Forward (+)
StrandForward (+)Strand sign follows the local context database convention.
Local TCS group span407 698-409 833 ntGCF_001972115::NZ_MTVX01000003.1::G00044
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_001972115::NZ_MTVX01000003.1::G00044Graphic view
Compact keeps a quick overview. Biotite-like switches to a coordinate-aware biological layout with strand and zoom.
Context labelpairedNeighborhood members are ordered by genomic coordinates.
Contig / repliconNZ_MTVX01000003.1All displayed genes belong to this local TCS context.
Neighborhood span407 698-409 833 nt2 136 nt
Members21 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
407 698 nt409 833 nt
Neighborhood gene cards
2 genes in the current local neighborhood.
BER34_RS16220GCF_001972115#BER34_RS16220
RROmpRCurrent focus
407 698-408 390 nt · Forward (+)
BER34_RS16225GCF_001972115#BER34_RS16225
HKClassic
408 526-409 833 nt · Forward (+)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000155065#QAE_RS0202390Use this link to inspect the representative gene detail.
PFAM architectureResponse_reg + Trans_reg_C2 domains in the representative PFAM annotation.
PFAM architecture for RROC_1200138
Simplified PFAM architecture for RROC_1200138
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[4-112] | Trans_reg_C[151-226]
- Domain count: 2
- Matched identifier: RROC_1200138
- Positioned domains: Response_reg 4-112 ; Response_reg 4-112 ; Trans_reg_C 151-226 ; Trans_reg_C 151-226
Cluster members and taxonomy
Representative gene: GCF_000155065#QAE_RS0202390
Sankey plot built from the taxonomy of all members in the selected cluster.
Genome taxonomy
Unknown
Taxonomy recordUnknownTaxon ID 1 496 · GCF_001972115
AssemblyASM197211v1 · Contighaploid
Genome composition4 010 693 bp · 28,5% GCClostridioides difficile
Signal transduction countsGenes 97 · HK 48 · RR 49CheA 1 · PP 0
Ranked taxonomy7 ranked levels available
SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderPeptostreptococcalesFamilyPeptostreptococcaceaeGenusClostridioides
Lineage path7 lineage nodes
1Bacteria2Bacillati3Bacillota4Clostridia5Peptostreptococcales6Peptostreptococcaceae7Clostridioides
Related genes
Preview from the same derived genome key