Gene detail

Detailed information of BRAKERKREP00000022728.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: WP_257127924.1, fimbria/pilus outer membrane usher protein [Burkholderia sp. MSMB1835]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000022728

ATGCAAATTCGTTTTTTGCGGGCTGCGATCGGCTCGCTTTTATTTTTCCTGGGTAATACCCCCAGTCATGCGGCAGCGGCGCTGCAGCTACAGAGTTCGCTCGTCGTGGTCGATACCGCCGAACAGGAAGGCACCCTGAGCGTGCGTAACAGTGCCGACACGCCCTTGTTAATGATCACCAAAGTCGAACCCATTCCCGAAGATCCGCAGGATCTACTGTTGGTTAATCCGCCAATTACACGCGTTGAGCCGGGTGATACTCAAATCGTCCGGTTTCTGCTCAAACCCCGGGATGCAGGCCAGCCCAAAATCACCACCGAGCGTCTTATGCGGGTGAGCTTCGAAGGGATACCGCCTAAAGAGAACAATAAAGTAAACCTTTCCATTAGCCAGAATATCCCGGTCATCATCCATCCAAGTGGGCTACCTAAAGTGGACGCGCCATGGAAGTTACTGCTTTGGCAGCGCGAGGGTGACGGGTTGCTCATTAAAAACCCCACCCCTTATGTCATTCGCTTCATGCCAGAGCTCAGGCTGCTGCCTAGCAATACGCTGGTCACGCTGCCACGCACCTATATCCTGCCGAACGAATCGTTGCACGCTAGGGTTCAATCACCCAGCGAGTCGTTACGTGCAAGCGTAAAACCCCTGCCGGTCACTGACACCCAAGTGAAGATGCAGCCTGCCTCGCAATATGGCTATGTGGTAGACGCCTATGAGGCGCCGTTAACGGCTGCTGCAACATCGGCGGTGGTCGACTATTTCAGTCAGGCATCTCGGTTTGCACCTGGCGCTAATTATGTGGGGCTCTATGTCAATGGTGTCAAACTCGGTACTACCGCAGTCACCTTCGACGCCGAGGGCCAGTTATGTGTCGATCAGGCGCTCTTGGATCGAGCCGGCATCGCTTGGACCAAGGATAAGACGCAAACTTCAGCAACCAATACCTGTTTAGATCTGCATAAAGCTTGGCCCACCGCTACGGTGACGCTGCGTCCCCGCTTAAACCAGGTTGAGCTACTGGTACCACCGCAGGCTATCACCGCCACGGGAGCTGCCCCTGTGTATGTCAGCGGTGGGCGTGCGGCCATGCTCAATTACCGTTTGTTCGATATGCGCAATACGGGCTATGGCAGCGGCACTAACATGTTCTACGCTGACCTGGAATCAGGCTTAAATGTCGGCGACTGGATCTTGCGCAGCCATGATCTATATTCTAGCGACGACGGACGCAAAACGTTTCAACACGTTCAAGCCTATGCGCAAAAGACCTTCGTCCCTTATAAATCAACCTTCCAGCTGGGGCAACTCAACTTAAACAACGCTCTCTTTTCTGCGCCTTCCTTTACGGGTGTGCAAGCGTTTCCAGAAGGGGCGCTTGCGCCTGCCAATAGCGCTACGAGCGTCTCGGGTATTGCGCAAACGCCCGCACGGGTGGAAATTAGACAAAGCGCGGTCCTTATCTATTCCACCCTCGTGCCTGCTGGTCCCTTTACGATCAAGCAGGTGCCGCTGCTGAATTCAACAGCCGATTTGCAGGTGACAGTGGTTGAAAGCACCGGTGAGCAGCGCAGCTTCGTCGTACCAGCCACCTCATTTGCCAGCAACTTTGCCGCCGCCCAGAAAGGCGTGTCGTGGGCGATCGGTAAGCCTCGTTCGATCACGGGCGACGCCGATGCCTTGGGCAGTGCCTGGTTTATGAGCGCCACCGGCACGCTACCGGTGGGACACGCCAATGTGACCACCGGCTTAATGCTGGCTGATCGTTATCGCGCTATCGGCGCTGGGGTGGATGGTGCACCGGTGATCGGTACTCATGGCTACCTGCGCGGCGTCTACGCCCACGATGAGCGTATCGCCGAACAGGGTGAGCGGTTAGAGAGTGGATTAGATGTGCGGCTAGGCAAGAGCTGGTCAGTCAGTACCAGCGTGCGGCAACAAAGCGTGGGCTATCGCGACCTCACCGATACGCCTGATGACCGCCCAACCTATGACCCGCAAGACCCCTTCGCGCCGATTCTGGTTTGGGATCCCTCTCGCCTGCAGTTTAGCGCCAACCTCGGTTACGCCAACCCTAATCTTGGAAGCGTAAGCTTAGGGTTTAGCCAATCGCAGCAATTCCATAACGGCAGCACGCATAGTCTGAACGCTTCCTGGAGCCGCAGCTTTGGTAAGGTCACCCTATCGATCAACGGTGATATTTATAGCGGCTATGACAACGACCGGCGCATTTACGTTTCTCTTGGCATGCCTTTGGGTTCCGGCTCGGTCAGTGCCACCTTTACCCACGATGGCTCCCAGACCCAAAGCAGTCTGCGCTTAGACCAACAGGTCAACGACTATGTAGGCTATGGTGTCTCGGCTTCCACCCAGACGCCGTCGAACCAACAATCGTATACGGGTAATCTCTCTTTGCTGCCTAAATATACCCAGCTCGGTCTCGGCGTAGCTGTCAATGACGCACACTCGCGTTCTTATTCAGGTACCTTAAGCGGCGGGGTGGTGTTTGATGGCGGCGAACCGCTATTCTCACCGTATCAAATCCAAGACACCTATGCCGTAGTATCGGCCTCACAACTGCCGGGTGCCCGCATTCAAACGCCGGCTGGTCCTGCTTGGACCGACAGCGCTGGGCGCGCAGTGGCAGCCAGCATAATGCCCTATAGCGAGTCGCGCTTAGAGCTACAAACCAAGGGCTTGCCGCGTAATGTGGATGTCAAAAACGGCATACAAGCCGTGCAAGCCGGTCGAGGTTCAGTCAGCCACATTAACTTTACCGCCGTGCGCTTACGTCGTGTGCTGCTCACGGTGCGCGATACGCAAGGCAAACCTCTGTCAACGGGCCTGGGTGTGCTCGACAATAGCGACCACTATTTAAGCATCGTTGGTCCGGGCAGCCAGGTATTTGTCGATGCCGATCATCTGAAGACCGGTGTATTTGTGAAGCCAGAAACGGGTAAGCCGTGCCGGCTGGAGGCGACCTTAAATAAACAACCTAAAGATGTGCCATACGAAGAAGCACAGGCGTGTGCTACTGGCAGGTCTGGTCCATGCCGAGGAACCCGTGTGTCAAGCCACGCTCTCAAACTCGACGCTGGACTTTGGTCAATTCGGCAAATTTGGCGCCGGCACCAGTCACCCCAACGAGCCGCAAAGTGTGGGCAAGCAACTGACCACGCTACAAGTTCACTGCCTCAAGCCTACGCGCTTTGTGGTGCGGGTGCATGGACGACCTGCGCCAAATGCGCAGCACTTTGCCTTTGGCAAGCGAGGCGAGACGGTGTTGTCGGTGCAATCGGCGTTGCTAGACGGGCACACGGCGCAGGTAGGGCTTGCTGA

Transcript

BRAKERKRET00000022728

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P45420	Uncharacterized outer membrane usher protein YhcD OS=Escherichia coli (strain K12) OX=83333 GN=yhcD PE=3 SV=1
P28722	Uncharacterized fimbrial chaperone YhcA OS=Escherichia coli (strain K12) OX=83333 GN=yhcA PE=3 SV=2
P31527	Outer membrane usher protein PsaC OS=Yersinia pestis OX=632 GN=psaC PE=3 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0023558 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00577 all species →	Usher	Outer membrane usher protein	Family	Interproscan
PF00345 all species →	PapD_N	Pili and flagellar-assembly chaperone, PapD N-terminal domain	Domain	Interproscan
PF13954 all species →	PapC_N	PapC N-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR042186 all species →	Homologous_superfamily	Outer membrane usher protein FimD, plug domain	Interproscan
IPR008962 all species →	Homologous_superfamily	PapD-like superfamily	Interproscan
IPR037224 all species →	Homologous_superfamily	PapC, N-terminal domain superfamily	Interproscan
IPR000015 all species →	Family	Outer membrane usher protein	Interproscan
IPR016147 all species →	Domain	Pili assembly chaperone, N-terminal	Interproscan
IPR025885 all species →	Domain	PapC, N-terminal domain	Interproscan
IPR001829 all species →	Family	Pili assembly chaperone, bacterial	Interproscan
IPR036316 all species →	Homologous_superfamily	Pili assembly chaperone, C-terminal domain superfamily	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR043142 all species →	Homologous_superfamily	PapC-like, C-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30451 all species →	OUTER MEMBRANE USHER PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0009297 all species →	Biological Process	pilus assembly	Interproscan
GO:0015473 all species →	Molecular Function	fimbrial usher porin activity	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0030288 all species →	Cellular Component	outer membrane-bounded periplasmic space	Interproscan
GO:0071555 all species →	Biological Process	cell wall organization	Interproscan
GO:0043711 all species →	Biological Process	pilus organization	Interproscan
GO:0061077 all species →	Biological Process	chaperone-mediated protein folding	Interproscan
GO:0009279 all species →	Cellular Component	cell outer membrane	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

No KEGG orthology assignment for BRAKERKREP00000022728.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000022728.1 across 29 RNA-seq samples of Hydra viridissima. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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

0TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole body	18	0	0.00	0.00
Whole	6	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00	0.00
symbioic hydra M9 strain · symbioic hydra rep1	1	0	0.00	0.00
symbioic hydra M9 strain · symbioic hydra rep2	1	0	0.00	0.00
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
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636

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.