Gene detail

Detailed information of BRAKERKREP00000022908.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:2078010...2079881
NR annotation: WP_066632726.1, protein translocase subunit SecD [Bordetella sp. H567]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P0AG91	Protein translocase subunit SecD OS=Escherichia coli O157:H7 OX=83334 GN=secD PE=3 SV=1
P0AG90	Protein translocase subunit SecD OS=Escherichia coli (strain K12) OX=83333 GN=secD PE=1 SV=1
P0AG92	Protein translocase subunit SecD OS=Shigella flexneri OX=623 GN=secD PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0012723 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07549 all species →	Sec_GG	SecD/SecF GG Motif	Motif	Interproscan
PF21760 all species →	SecD_1st	Protein translocase subunit SecDF, P1 domain, N-terminal	Domain	Interproscan
PF13721 all species →	SecD-TM1	SecD export protein N-terminal TM region	Family	Interproscan
PF02355 all species →	SecD_SecF	Protein export membrane protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR022645 all species →	Family	Protein-export membrane protein SecD/SecF, bacterial	Interproscan
IPR005791 all species →	Family	Protein translocase subunit SecD	Interproscan
IPR022646 all species →	Conserved_site	Protein-export membrane protein SecD/SecF/SecDF, conserved site	Interproscan
IPR022813 all species →	Family	Protein-export membrane protein SecD/SecF, archaeal and bacterial	Interproscan
IPR048631 all species →	Domain	Protein translocase subunit SecDF, P1 domain, N-terminal	Interproscan
IPR027398 all species →	Domain	SecD export protein N-terminal TM domain	Interproscan
IPR048634 all species →	Domain	Protein export membrane protein SecD/SecF, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30081 all species →	PROTEIN-EXPORT MEMBRANE PROTEIN SEC	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0015450 all species →	Molecular Function	protein-transporting ATPase activity	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0015031 all species →	Biological Process	protein transport	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K03072	secD; preprotein translocase subunit SecD	-	Secretion system	ko02044	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000022908.1 across 29 RNA-seq samples of Hydra viridissima. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

29Samples

14TPM > 0

7Conditions

42.6Max TPM

11.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	4	4.97	31.03
Whole	6	6	15.75	27.72
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	42.08	42.08
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	37.35	37.35
symbioic hydra M9 strain · symbioic hydra rep1	1	1	40.08	40.08
symbioic hydra M9 strain · symbioic hydra rep2	1	1	42.63	42.63
unannotated	1	0	0.00	0.00

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	31.03
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	25.83
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	22.85
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	9.73
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	27.72
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	25.49
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	12.86
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	12.64
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	11.37
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	4.44
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	42.08
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	37.35
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	40.08
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	42.63
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636	0.00

Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM, StringTie quantification over 29 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.