1 Response_reg#1
7-111 aa · 105 aa · 8.4% of protein
Raw token
Response_reg:7:2.49e-22:111:106:111P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
HMPREF9474_RS20090
Response regulator, RpfG family
[Clostridium] symbiosum WAL-14163 · GCF_000189595
ClassRRTypeRpfGLength1250 aaTM0ValidatedNoCompleteYesContextorphan
Gene IDGCF_000189595#HMPREF9474_RS20090Stable P2CS identifier used across views.
GenomeGCF_000189595Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae; Lachnoclostridium
Domain signature
Compact overview inferred from the domain field
Response_regHDPAS_3GGDEF
Protein length1250 aaLength used to scale native and Biotite-like views.
Annotated domains55 with usable coordinates.
Domain coverage533 / 1250 aa (42.6%)Merged over positioned domains only.
Domain description1 Response_reg,1 HD,2 PAS_3,1 GGDEFSummary 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 aa1250 aa
Domain-by-domain annotation5 items
2 HD#2
202-299 aa · 98 aa · 7.8% of protein
Raw token
HD:202:0.000000000000442:299:98:1103 PAS_3#3
540-623 aa · 84 aa · 6.7% of protein
Raw token
PAS_3:540:8.03e-18:623:84:894 PAS_3#4
669-757 aa · 89 aa · 7.1% of protein
Raw token
PAS_3:669:0.00000000000209:757:91:895 GGDEF#5
774-930 aa · 157 aa · 12.6% of protein
Raw token
GGDEF:774:6.35e-41:930:161:160- Raw architecture: Response_reg:7:2.49e-22:111:106:111#HD:202:0.000000000000442:299:98:110#PAS_3:540:8.03e-18:623:84:89#PAS_3:669:0.00000000000209:757:91:89#GGDEF:774:6.35e-41:930:161:160
- Domain description: 1 Response_reg,1 HD,2 PAS_3,1 GGDEF
- 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 labelorphanGCF_000189595::NZ_GL834317.1::G00055
Group size11 locus tag listed below.
HK / RR0 / 1Counts resolved for the local TCS neighborhood.
Context span109025-112777Genomic interval covered by the local TCS group.
Identifiers
Old locus tagHMPREF9474_03900RefSeq proteinWP_003503857.1
Context group ID
GCF_000189595::NZ_GL834317.1::G00055Context members
HMPREF9474_RS20090
Partner locus tags
HMPREF9474_RS20090
Partner old locus tags
HMPREF9474_03900
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_003503857.1Primary protein accession used for annex mappings.
UniProt accessionE7GSK5Primary UniProt accession resolved in the annex database.
UniProt IDE7GSK5_CLOS6Display identifier provided by UniProt.
GO / PubMed1 / 0Unique GO terms and literature references available below.
Reference hubs
GO terms
Genomic coordinates
Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table
Current locus tagHMPREF9474_RS20090Primary locus identifier stored in the genes table.
Old locus tagHMPREF9474_03900Legacy locus tag recovered from the local context mapping.
Contig / repliconNZ_GL834317.1Sequence record reported by the local genomic context database.
Genomic interval109 025-112 777 nt3 753 nt · Reverse (-)
StrandReverse (-)Strand sign follows the local context database convention.
Local TCS group span109 025-112 777 ntGCF_000189595::NZ_GL834317.1::G00055
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_000189595::NZ_GL834317.1::G00055Graphic view
Compact keeps a quick overview. Biotite-like switches to a coordinate-aware biological layout with strand and zoom.
Context labelorphanNeighborhood members are ordered by genomic coordinates.
Contig / repliconNZ_GL834317.1All displayed genes belong to this local TCS context.
Neighborhood span109 025-112 777 nt3 753 nt
Members11 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
109 025 nt112 777 nt
Neighborhood gene cards
1 gene in the current local neighborhood.
HMPREF9474_RS20090GCF_000189595#HMPREF9474_RS20090
RRRpfGCurrent focus
109 025-112 777 nt · Reverse (-)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000189595#HMPREF9474_RS20090The current gene is the representative for this cluster.
PFAM architectureResponse_reg + HD_5 + PAS_3 + PAS_3 + GGDEF5 domains in the representative PFAM annotation.
PFAM architecture for RROC_0006038
Simplified PFAM architecture for RROC_0006038
PFAM domain coverage: 569 / 1250 aa (45.5%)
1 aa1250 aa
Response_regHD_5PAS_3PAS_3GGDEF
- Simplified architecture: Response_reg + HD_5 + PAS_3 + PAS_3 + GGDEF
- Raw architecture: Response_reg[7-118] | HD_5[190-318] | PAS_3[541-623] | PAS_3[669-757] | GGDEF[775-930]
- Domain count: 5
- Matched identifier: RROC_0006038
- Positioned domains: Response_reg 7-118 ; Response_reg 7-118 ; HD_5 190-318 ; HD_5 190-318 ; PAS_3 541-623 ; PAS_3 541-623 ; PAS_3 669-757 ; PAS_3 669-757 ; GGDEF 775-930 ; GGDEF 775-930
Cluster members and taxonomy
Representative gene: GCF_000189595#HMPREF9474_RS20090
Sankey plot built from the taxonomy of all members in the selected cluster.
Genome taxonomy
Unknown
Taxonomy recordUnknownTaxon ID 742 740 · GCF_000189595
AssemblyClos_symb_WAL_14163_V1 · Scaffoldhaploid
Genome composition5 352 498 bp · 47,5% GC[Clostridium] symbiosum WAL-14163
Signal transduction countsGenes 111 · HK 54 · RR 54CheA 0 · PP 3
Ranked taxonomy7 ranked levels available
SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderLachnospiralesFamilyLachnospiraceaeGenusLachnoclostridium
Lineage path7 lineage nodes
1Bacteria2Bacillati3Bacillota4Clostridia5Lachnospirales6Lachnospiraceae7Lachnoclostridium
Related genes
Preview from the same derived genome key