1 Response_reg#1
5-114 aa · 110 aa · 48.7% of protein
Raw token
Response_reg:5:3.31e-22:114:111:111P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
HMPREF0220_RS12060
Response regulator OmpR family
Clostridioides difficile NAP08 · GCF_000164175
ClassRRTypeOmpRLength226 aaTM0ValidatedNoCompleteYesContexttriad
Gene IDGCF_000164175#HMPREF0220_RS12060Stable P2CS identifier used across views.
GenomeGCF_000164175Bacteria; Bacillati; Bacillota; Clostridia; Peptostreptococcales; Peptostreptococcaceae; Clostridioides
Domain signature
Compact overview inferred from the domain field
Response_regTrans_reg_C
Protein length226 aaLength used to scale native and Biotite-like views.
Annotated domains22 with usable coordinates.
Domain coverage184 / 226 aa (81.4%)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
150-223 aa · 74 aa · 32.7% of protein
Raw token
Trans_reg_C:150:2.34e-22:223:75:77- Raw architecture: Response_reg:5:3.31e-22:114:111:111#Trans_reg_C:150:2.34e-22:223:75:77
- 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 labeltriadGCF_000164175::NZ_GG770711.1::G00028
Group size33 locus tags listed below.
HK / RR1 / 2Counts resolved for the local TCS neighborhood.
Context span132989-136483Genomic interval covered by the local TCS group.
Identifiers
Old locus tagHMPREF0220_2901RefSeq proteinWP_003417207.1
Context group ID
GCF_000164175::NZ_GG770711.1::G00028Context members
HMPREF0220_RS12070HMPREF0220_RS12065HMPREF0220_RS12060
Partner locus tags
HMPREF0220_RS12070HMPREF0220_RS12065HMPREF0220_RS12060
Partner old locus tags
HMPREF0220_2899HMPREF0220_2900HMPREF0220_2901
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_003417207.1Primary protein accession used for annex mappings.
UniProt accessionD5Q7L7Primary UniProt accession resolved in the annex database.
UniProt IDD5Q7L7_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 tagHMPREF0220_RS12060Primary locus identifier stored in the genes table.
Old locus tagHMPREF0220_2901Legacy locus tag recovered from the local context mapping.
Contig / repliconNZ_GG770711.1Sequence record reported by the local genomic context database.
Genomic interval135 803-136 483 nt681 nt · Forward (+)
StrandForward (+)Strand sign follows the local context database convention.
Local TCS group span132 989-136 483 ntGCF_000164175::NZ_GG770711.1::G00028
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_000164175::NZ_GG770711.1::G00028Graphic view
Compact keeps a quick overview. Biotite-like switches to a coordinate-aware biological layout with strand and zoom.
Context labeltriadNeighborhood members are ordered by genomic coordinates.
Contig / repliconNZ_GG770711.1All displayed genes belong to this local TCS context.
Neighborhood span132 989-136 483 nt3 495 nt
Members31 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
132 989 nt136 483 nt
Neighborhood gene cards
3 genes in the current local neighborhood.
HMPREF0220_RS12070GCF_000164175#HMPREF0220_RS12070
RROmpR
132 989-133 666 nt · Forward (+)
HMPREF0220_RS12065GCF_000164175#HMPREF0220_RS12065
HKClassic
133 738-135 753 nt · Forward (+)
HMPREF0220_RS12060GCF_000164175#HMPREF0220_RS12060
RROmpRCurrent focus
135 803-136 483 nt · Forward (+)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000155065#QAE_RS0216025Use this link to inspect the representative gene detail.
PFAM architectureResponse_reg + Trans_reg_C2 domains in the representative PFAM annotation.
PFAM architecture for RROC_1408495
Simplified PFAM architecture for RROC_1408495
PFAM domain coverage: 183 / 226 aa (81.0%)
1 aa226 aa
Response_regTrans_reg_C
- Simplified architecture: Response_reg + Trans_reg_C
- Raw architecture: Response_reg[5-113] | Trans_reg_C[150-223]
- Domain count: 2
- Matched identifier: RROC_1408495
- Positioned domains: Response_reg 5-113 ; Response_reg 5-113 ; Trans_reg_C 150-223 ; Trans_reg_C 150-223
Cluster members and taxonomy
Representative gene: GCF_000155065#QAE_RS0216025
Sankey plot built from the taxonomy of all members in the selected cluster.
Genome taxonomy
Unknown
Taxonomy recordUnknownTaxon ID 525 259 · GCF_000164175
AssemblyASM16417v1 · Scaffoldhaploid
Genome composition4 078 686 bp · 29,0% GCClostridioides difficile NAP08
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