Gene detail

AAAU22_RS06000

Response regulator, PleD_VieA family

[Clostridium] symbiosum · GCF_040095205

Open genome Open selected cluster RefSeq UniProt

ClassRRTypePleD_VieALength860 aaTM0ValidatedNoCompleteYesContexttriad

Gene IDGCF_040095205#AAAU22_RS06000Stable P2CS identifier used across views.

GenomeGCF_040095205Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae; Lachnoclostridium

Selected clusterRROC_0012214Run 7 · 15 sequences · id 100% · cov 80%

External referencesWP_156684466.1 · A0A6N3BWE0 · MIST4 AAAU22_RS06000RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regGGDEFEAL

Protein length860 aaLength used to scale native and Biotite-like views.

Annotated domains55 with usable coordinates.

Domain coverage694 / 860 aa (80.7%)Merged over positioned domains only.

Domain description2 Response_reg,2 GGDEF,1 EALSummary 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

Domain view

Native Biotite-like

Native P2CS viewFrontend rendering from the parsed domain string and TMPRED protein features.

1 aa860 aa

Domain-by-domain annotation5 items

1 Response_reg#1

7-120 aa · 114 aa · 13.3% of protein

Raw tokenResponse_reg:7:1.45e-27:120:115:111

2 GGDEF#2

137-225 aa · 89 aa · 10.3% of protein

Raw tokenGGDEF:137:0.00000000000000182:225:91:160

3 EAL#3

309-539 aa · 231 aa · 26.9% of protein

Raw tokenEAL:309:9.42e-70:539:231:235

4 Response_reg#4

575-685 aa · 111 aa · 12.9% of protein

Raw tokenResponse_reg:575:0.00000000000286:685:113:111

5 GGDEF#5

705-853 aa · 149 aa · 17.3% of protein

Raw tokenGGDEF:705:1.52e-32:853:160:160

Raw architecture: Response_reg:7:1.45e-27:120:115:111#GGDEF:137:0.00000000000000182:225:91:160#EAL:309:9.42e-70:539:231:235#Response_reg:575:0.00000000000286:685:113:111#GGDEF:705:1.52e-32:853:160:160
Domain description: 2 Response_reg,2 GGDEF,1 EAL
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_040095205::NZ_JBBNGG010000012.1::G00011

Group size33 locus tags listed below.

HK / RR2 / 1Counts resolved for the local TCS neighborhood.

Context span13343-22686Genomic interval covered by the local TCS group.

Identifiers

Old locus tagAAAU22_05985RefSeq proteinWP_156684466.1

Context group IDGCF_040095205::NZ_JBBNGG010000012.1::G00011

Context members

AAAU22_RS06000AAAU22_RS06005AAAU22_RS06010

Partner locus tags

AAAU22_RS06000AAAU22_RS06005AAAU22_RS06010

Partner old locus tags

AAAU22_05985AAAU22_05990AAAU22_05995

Partner protein IDs

WP_156684466.1 WP_150028465.1 WP_150028428.1

External references

Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table

RefSeqWP_156684466.1Primary protein accession used for annex mappings.

UniProt accessionA0A6N3BWE0Primary UniProt accession resolved in the annex database.

UniProt IDA0A6N3BWE0_CLOSYDisplay identifier provided by UniProt.

GO / PubMed2 / 0Unique GO terms and literature references available below.

Reference hubs

Open RefSeq Open UniProt accession

GO terms

GO:0071111 GO:0000160

Genomic coordinates

Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table

Current locus tagAAAU22_RS06000Primary locus identifier stored in the genes table.

Old locus tagAAAU22_05985Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_JBBNGG010000012.1Sequence record reported by the local genomic context database.

Genomic interval13 343-15 925 nt2 583 nt · Forward (+)

StrandForward (+)Strand sign follows the local context database convention.

Local TCS group span13 343-22 686 ntGCF_040095205::NZ_JBBNGG010000012.1::G00011

Quick actions

Open genome Search genes in genome

Local neighborhood

Graphical neighborhood resolved from the local TCS context group on the current contig

GCF_040095205::NZ_JBBNGG010000012.1::G00011

Graphic view

Compact Biotite-like

Zoom

Full window Focus gene

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_JBBNGG010000012.1All displayed genes belong to this local TCS context.

Neighborhood span13 343-22 686 nt9 344 nt

Members31 current focus gene

Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.

13 343 nt22 686 nt

+-AAAU22_RS06000 AAAU22_RS06005 AAAU22_RS06010

Neighborhood gene cards

3 genes in the current local neighborhood.

AAAU22_RS06000GCF_040095205#AAAU22_RS06000

RRPleD_VieACurrent focus

13 343-15 925 nt · Forward (+)

Old locus AAAU22_05985RefSeq WP_156684466.1

Open current gene

AAAU22_RS06005GCF_040095205#AAAU22_RS06005

HKHybrid

15 931-19 512 nt · Forward (+)

Old locus AAAU22_05990RefSeq WP_150028465.1

Open gene

AAAU22_RS06010GCF_040095205#AAAU22_RS06010

HKHybrid

19 525-22 686 nt · Forward (+)

Old locus AAAU22_05995RefSeq WP_150028428.1

Open gene

Clusters

CD-HIT memberships and selected cluster details for the current gene class

Available memberships1 cluster

RROC_0012214RR

Run 715 sequencesid 100%cov 80%

PFAM Response_reg + GGDEF + EAL + Response_reg + GGDEF

Representative GCF_015560355#I2I31_RS02810

Selected clusterRROC_0012214Run 7 · RR · 15 sequences

Representative sequenceGCF_015560355#I2I31_RS02810Use this link to inspect the representative gene detail.

PFAM architectureResponse_reg + GGDEF + EAL + Response_reg + GGDEF5 domains in the representative PFAM annotation.

Open in cluster search Open representative gene

PFAM architecture for RROC_0012214

Simplified PFAM architecture for RROC_0012214

PFAM domain coverage: 747 / 860 aa (86.9%)

1 aa860 aa

Response_regGGDEFEALResponse_regGGDEF

Simplified architecture: Response_reg + GGDEF + EAL + Response_reg + GGDEF
Raw architecture: Response_reg[7-119] | GGDEF[136-278] | EAL[307-539] | Response_reg[575-685] | GGDEF[706-852]
Domain count: 5
Matched identifier: RROC_0012214
Positioned domains: Response_reg 7-119 ; GGDEF 136-278 ; EAL 307-539 ; Response_reg 575-685 ; GGDEF 706-852

Cluster members and taxonomy

Representative gene: GCF_015560355#I2I31_RS02810

Sankey plot built from the taxonomy of all members in the selected cluster.

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 1 512 · GCF_040095205

AssemblyASM4009520v1 · Contighaploid

Genome composition5 046 588 bp · 47,5% GC[Clostridium] symbiosum

Signal transduction countsGenes 124 · HK 61 · RR 59CheA 1 · PP 4

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderLachnospiralesFamilyLachnospiraceaeGenusLachnoclostridium

Lineage path7 lineage nodes

1Bacteria2Bacillati3Bacillota4Clostridia5Lachnospirales6Lachnospiraceae7Lachnoclostridium

Open genome Search genes in genome Search RR genes NCBI assembly files

Related genes

Preview from the same derived genome key