1 Response_reg#1
3-114 aa · 112 aa · 25.5% of protein
Raw token
Response_reg:3:5.13e-25:114:112:111P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
HMPREF1123_RS00885
Response regulator NtrC family
Clostridioides difficile 050-P50-2011 · GCF_000235925
ClassRRTypeNtrCLength440 aaTM0ValidatedNoCompleteYesContextpaired
Gene IDGCF_000235925#HMPREF1123_RS00885Stable P2CS identifier used across views.
GenomeGCF_000235925Bacteria; Bacillati; Bacillota; Clostridia; Peptostreptococcales; Peptostreptococcaceae; Clostridioides
Domain signature
Compact overview inferred from the domain field
Response_regAAA_5HTH_8
Protein length440 aaLength used to scale native and Biotite-like views.
Annotated domains33 with usable coordinates.
Domain coverage271 / 440 aa (61.6%)Merged over positioned domains only.
Domain description1 Response_reg,1 AAA_5,1 HTH_8Summary 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 annotation3 items
2 AAA_5#2
157-275 aa · 119 aa · 27.0% of protein
Raw token
AAA_5:157:0.00000000274:275:128:1353 HTH_8#3
398-437 aa · 40 aa · 9.1% of protein
Raw token
HTH_8:398:0.000000000176:437:40:40- Raw architecture: Response_reg:3:5.13e-25:114:112:111#AAA_5:157:0.00000000274:275:128:135#HTH_8:398:0.000000000176:437:40:40
- Domain description: 1 Response_reg,1 AAA_5,1 HTH_8
- 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_000235925::NZ_JH379225.1::G00055
Group size22 locus tags listed below.
HK / RR1 / 1Counts resolved for the local TCS neighborhood.
Context span87063-90379Genomic interval covered by the local TCS group.
Identifiers
Old locus tagHMPREF1123_03789RefSeq proteinWP_003430220.1
Context group ID
GCF_000235925::NZ_JH379225.1::G00055Context members
HMPREF1123_RS00885HMPREF1123_RS00880
Partner locus tags
HMPREF1123_RS00885HMPREF1123_RS00880
Partner old locus tags
HMPREF1123_03789HMPREF1123_03790
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_003430220.1Primary protein accession used for annex mappings.
UniProt accessionA0A9P3YNM6Primary UniProt accession resolved in the annex database.
UniProt IDA0A9P3YNM6_CLODIDisplay identifier provided by UniProt.
GO / PubMed4 / 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 tagHMPREF1123_RS00885Primary locus identifier stored in the genes table.
Old locus tagHMPREF1123_03789Legacy locus tag recovered from the local context mapping.
Contig / repliconNZ_JH379225.1Sequence record reported by the local genomic context database.
Genomic interval87 063-88 385 nt1 323 nt · Reverse (-)
StrandReverse (-)Strand sign follows the local context database convention.
Local TCS group span87 063-90 379 ntGCF_000235925::NZ_JH379225.1::G00055
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_000235925::NZ_JH379225.1::G00055Graphic 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_JH379225.1All displayed genes belong to this local TCS context.
Neighborhood span87 063-90 379 nt3 317 nt
Members21 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
87 063 nt90 379 nt
Neighborhood gene cards
2 genes in the current local neighborhood.
HMPREF1123_RS00885GCF_000235925#HMPREF1123_RS00885
RRNtrCCurrent focus
87 063-88 385 nt · Reverse (-)
HMPREF1123_RS00880GCF_000235925#HMPREF1123_RS00880
HKClassic
88 385-90 379 nt · Reverse (-)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000210395#CDM68_RS09115Use this link to inspect the representative gene detail.
PFAM architectureResponse_reg + Sigma54_activat + AAA_lid_14 + HTH_84 domains in the representative PFAM annotation.
PFAM architecture for RROC_0333954
Simplified PFAM architecture for RROC_0333954
PFAM domain coverage: 386 / 440 aa (87.7%)
1 aa440 aa
Response_regSigma54_activatAAA_lid_14HTH_8
- Simplified architecture: Response_reg + Sigma54_activat + AAA_lid_14 + HTH_8
- Raw architecture: Response_reg[3-113] | Sigma54_activat[137-300] | AAA_lid_14[306-375] | HTH_8[397-437]
- Domain count: 4
- Matched identifier: RROC_0333954
- Positioned domains: Response_reg 3-113 ; Response_reg 3-113 ; Sigma54_activat 137-300 ; Sigma54_activat 137-300 ; AAA_lid_14 306-375 ; AAA_lid_14 306-375 ; HTH_8 397-437 ; HTH_8 397-437
Cluster members and taxonomy
Representative gene: GCF_000210395#CDM68_RS09115
Displayed with 5 columns and 10 rows per page from the local display config.
Showing members 1 to 50 over 274 total members. Page 1 / 6.
GCF_000210395#CDM68_RS09115 (representative) | ||||
Genome taxonomy
Unknown
Taxonomy recordUnknownTaxon ID 997 828 · GCF_000235925
AssemblyASM23592v1 · Scaffoldhaploid
Genome composition4 227 225 bp · 28,5% GCClostridioides difficile 050-P50-2011
Signal transduction countsGenes 104 · HK 50 · RR 54CheA 1 · PP 0
Ranked taxonomy7 ranked levels available
SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderPeptostreptococcalesFamilyPeptostreptococcaceaeGenusClostridioides
Lineage path7 lineage nodes
1Bacteria2Bacillati3Bacillota4Clostridia5Peptostreptococcales6Peptostreptococcaceae7Clostridioides
Related genes
Preview from the same derived genome key