1 Response_reg#1
5-114 aa · 110 aa · 47.4% of protein
Raw token
Response_reg:5:1.37e-36:114:111:111P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
BER28_RS16870
Response regulator OmpR family
Clostridioides difficile · GCF_001971835
ClassRRTypeOmpRLength232 aaTM0ValidatedNoCompleteYesContextpentad
Gene IDGCF_001971835#BER28_RS16870Stable P2CS identifier used across views.
GenomeGCF_001971835Bacteria; Bacillati; Bacillota; Clostridia; Peptostreptococcales; Peptostreptococcaceae; Clostridioides
Domain signature
Compact overview inferred from the domain field
Response_regTrans_reg_C
Protein length232 aaLength used to scale native and Biotite-like views.
Annotated domains22 with usable coordinates.
Domain coverage188 / 232 aa (81.0%)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
155-232 aa · 78 aa · 33.6% of protein
Raw token
Trans_reg_C:155:4.07e-28:232:78:77- Raw architecture: Response_reg:5:1.37e-36:114:111:111#Trans_reg_C:155:4.07e-28:232:78:77
- 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_001971835::NZ_MTVP01000005.1::G00053
Group size55 locus tags listed below.
HK / RR2 / 3Counts resolved for the local TCS neighborhood.
Context span666302-672027Genomic interval covered by the local TCS group.
Identifiers
Old locus tagBER28_003314RefSeq proteinWP_009891729.1
Context group ID
GCF_001971835::NZ_MTVP01000005.1::G00053Context members
BER28_RS16865BER28_RS16870BER28_RS16875BER28_RS16880BER28_RS16885
Partner locus tags
BER28_RS16865BER28_RS16870BER28_RS16875BER28_RS16880BER28_RS16885
Partner old locus tags
BER28_003313BER28_003314BER28_003315BER28_003316BER28_003317
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_009891729.1Primary protein accession used for annex mappings.
UniProt accessionA0A0H3N7P0Primary UniProt accession resolved in the annex database.
UniProt IDA0A0H3N7P0_CLODCDisplay identifier provided by UniProt.
GO / PubMed5 / 1Unique GO terms and literature references available below.
Reference hubs
PubMed
Genomic coordinates
Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table
Current locus tagBER28_RS16870Primary locus identifier stored in the genes table.
Old locus tagBER28_003314Legacy locus tag recovered from the local context mapping.
Contig / repliconNZ_MTVP01000005.1Sequence record reported by the local genomic context database.
Genomic interval667 453-668 151 nt699 nt · Reverse (-)
StrandReverse (-)Strand sign follows the local context database convention.
Local TCS group span666 302-672 027 ntGCF_001971835::NZ_MTVP01000005.1::G00053
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_001971835::NZ_MTVP01000005.1::G00053Graphic 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_MTVP01000005.1All displayed genes belong to this local TCS context.
Neighborhood span666 302-672 027 nt5 726 nt
Members51 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
666 302 nt672 027 nt
Neighborhood gene cards
5 genes in the current local neighborhood.
BER28_RS16865GCF_001971835#BER28_RS16865
HKClassic
666 302-667 417 nt · Reverse (-)
BER28_RS16870GCF_001971835#BER28_RS16870
RROmpRCurrent focus
667 453-668 151 nt · Reverse (-)
BER28_RS16875GCF_001971835#BER28_RS16875
RROmpR
668 533-669 213 nt · Reverse (-)
BER28_RS16880GCF_001971835#BER28_RS16880
HKClassic
669 263-671 278 nt · Reverse (-)
BER28_RS16885GCF_001971835#BER28_RS16885
RROmpR
671 350-672 027 nt · Reverse (-)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000003215#QAC_RS0216520Use this link to inspect the representative gene detail.
PFAM architectureResponse_reg + Trans_reg_C2 domains in the representative PFAM annotation.
PFAM architecture for RROC_1119294
Simplified PFAM architecture for RROC_1119294
PFAM domain coverage: 187 / 232 aa (80.6%)
1 aa232 aa
Response_regTrans_reg_C
- Simplified architecture: Response_reg + Trans_reg_C
- Raw architecture: Response_reg[5-114] | Trans_reg_C[155-231]
- Domain count: 2
- Matched identifier: RROC_1119294
- Positioned domains: Response_reg 5-114 ; Response_reg 5-114 ; Trans_reg_C 155-231 ; Trans_reg_C 155-231
Cluster members and taxonomy
Representative gene: GCF_000003215#QAC_RS0216520
Sankey plot built from the taxonomy of all members in the selected cluster.
Genome taxonomy
Unknown
Taxonomy recordUnknownTaxon ID 1 496 · GCF_001971835
AssemblyASM197183v1 · Contighaploid
Genome composition4 189 946 bp · 29,0% GCClostridioides difficile
Signal transduction countsGenes 106 · HK 50 · RR 56CheA 1 · PP 0
Ranked taxonomy7 ranked levels available
SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderPeptostreptococcalesFamilyPeptostreptococcaceaeGenusClostridioides
Lineage path7 lineage nodes
1Bacteria2Bacillati3Bacillota4Clostridia5Peptostreptococcales6Peptostreptococcaceae7Clostridioides
Related genes
Preview from the same derived genome key