1 Response_reg#1
7-120 aa · 114 aa · 16.4% of protein
Raw token
Response_reg:7:3.57e-27:120:115:111P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
HMPREF9474_RS06600
Response regulator, PleD family
[Clostridium] symbiosum WAL-14163 · GCF_000189595
ClassRRTypePleDLength694 aaTM0ValidatedNoCompleteYesContextorphan
Gene IDGCF_000189595#HMPREF9474_RS06600Stable P2CS identifier used across views.
GenomeGCF_000189595Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae; Lachnoclostridium
Domain signature
Compact overview inferred from the domain field
Response_regPAS_3GGDEF
Protein length694 aaLength used to scale native and Biotite-like views.
Annotated domains44 with usable coordinates.
Domain coverage417 / 694 aa (60.1%)Merged over positioned domains only.
Domain description1 Response_reg,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 aa694 aa
Domain-by-domain annotation4 items
2 PAS_3#2
163-253 aa · 91 aa · 13.1% of protein
Raw token
PAS_3:163:0.000000000000309:253:91:893 PAS_3#3
320-381 aa · 62 aa · 8.9% of protein
Raw token
PAS_3:320:0.000000115:381:63:894 GGDEF#4
534-683 aa · 150 aa · 21.6% of protein
Raw token
GGDEF:534:4.16e-39:683:156:160- Raw architecture: Response_reg:7:3.57e-27:120:115:111#PAS_3:163:0.000000000000309:253:91:89#PAS_3:320:0.000000115:381:63:89#GGDEF:534:4.16e-39:683:156:160
- Domain description: 1 Response_reg,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_GL834306.1::G00024
Group size11 locus tag listed below.
HK / RR0 / 1Counts resolved for the local TCS neighborhood.
Context span626714-628798Genomic interval covered by the local TCS group.
Identifiers
Old locus tagHMPREF9474_01280RefSeq proteinWP_003499591.1
Context group ID
GCF_000189595::NZ_GL834306.1::G00024Context members
HMPREF9474_RS06600
Partner locus tags
HMPREF9474_RS06600
Partner old locus tags
HMPREF9474_01280
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_003499591.1Primary protein accession used for annex mappings.
UniProt accessionE7GK35Primary UniProt accession resolved in the annex database.
UniProt IDE7GK35_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_RS06600Primary locus identifier stored in the genes table.
Old locus tagHMPREF9474_01280Legacy locus tag recovered from the local context mapping.
Contig / repliconNZ_GL834306.1Sequence record reported by the local genomic context database.
Genomic interval626 714-628 798 nt2 085 nt · Forward (+)
StrandForward (+)Strand sign follows the local context database convention.
Local TCS group span626 714-628 798 ntGCF_000189595::NZ_GL834306.1::G00024
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_000189595::NZ_GL834306.1::G00024Graphic 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_GL834306.1All displayed genes belong to this local TCS context.
Neighborhood span626 714-628 798 nt2 085 nt
Members11 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
626 714 nt628 798 nt
Neighborhood gene cards
1 gene in the current local neighborhood.
HMPREF9474_RS06600GCF_000189595#HMPREF9474_RS06600
RRPleDCurrent focus
626 714-628 798 nt · Forward (+)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000189595#HMPREF9474_RS06600The current gene is the representative for this cluster.
PFAM architectureResponse_reg + PAS_3 + PAS_9 + GGDEF4 domains in the representative PFAM annotation.
PFAM architecture for RROC_0030855
Simplified PFAM architecture for RROC_0030855
PFAM domain coverage: 403 / 694 aa (58.1%)
1 aa694 aa
Response_regPAS_3PAS_9GGDEF
- Simplified architecture: Response_reg + PAS_3 + PAS_9 + GGDEF
- Raw architecture: Response_reg[7-113] | PAS_3[164-245] | PAS_9[324-387] | GGDEF[534-683]
- Domain count: 4
- Matched identifier: RROC_0030855
- Positioned domains: Response_reg 7-113 ; Response_reg 7-113 ; PAS_3 164-245 ; PAS_3 164-245 ; PAS_9 324-387 ; PAS_9 324-387 ; GGDEF 534-683 ; GGDEF 534-683
Cluster members and taxonomy
Representative gene: GCF_000189595#HMPREF9474_RS06600
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