Gene detail

Detailed information of BRAKERKREP00000023121.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:1284557...1286536
NR annotation: WP_028356328.1, MULTISPECIES: acetate--CoA ligase [Bordetella]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000023121

ATGTCCAATACCCTGCAATCCGTATTAGTAGAGACCCGTGTATTTCCCCCCTTGGCACGCGCCGTAGAAGGGGCGGCTATTGCCAGCATGTCATCCTATCGAACCTTGTGCGCAGAGGCCGCGAGCGATTTTGCCGGATTTTGGGAACGGTTAGCCCGTGAAAATCTGTGTTGGGCCAAGCCGTTTACCCAAGTCTTGGATGAGTCCAATCCGCCGTTTTATCGTTGGTTTAGCGATGGCGAGCTCAATGTGTCGGTCAACTGTTTGGACGTGCACGTCAACAACGGCAAGGCCAACAAAACCGCTTTTATCTTTGAGACGGATGACGGCCGCGTAGACCGCGTGAGCTATGGCGAATTGTTGGCGCGCGTCTGTCGCTTCGCCAATGGCTTGAAGTCGTTAGGCTATAAAAAAGGCGACTGCGCCATCATTTACATGCCTATGTCGATTGAGGCGGTAGTGGCCATGCAAGCTTGCGTACGCTTAGGCCTCACGCATTCTGTGGTCTTTGGCGGCTTTTCGGCTAAAAGCTTACAGCAGCGCTTGGTCGATGTTGGCGCTTCGTTGGTCATCACTGCAGACGAGCAAGTGCGTGGGGGCAAGACCCTACCGCTCAAAGCCGCTGTGGAGGAAGCCTACGCCATGGGCGGCTGCGACCCAGTGCGTCAGGTGGTGGTGTATCGCCGTACCGGCGGGGCTGTGCCGTGGAATGCAGACCGCGACGTGTGGTTGCATGAACTCGAAGTCGGCCAAGCCGACCGCTGTGATCCCGTGCCAGTGGAGGCCGAACATCCCTTATGCATCCTATATACCTCTGGTTCAACCGGCAAACCTAAAGGTGTGCAACATGCCTCGGCGGGCTATTTGTTGTGGGCACTGCTCACTATGAAATGGACCTTCGATGCGCGTCCGGAAGATATTTTTTGGTGTACGGCCGACGTGGGTTGGATCACTGGTCATACTTATGTGGCGTACGGTCCGCTGGCGGCAGGATTGACGCAAGTGATGTTCGAGGGTGTGCCAACTTATCCGCACGCTGGTCGCTTTTGGGACATGATCGCGCGCCATCAAGTGACGATTTTTTATACGGCGCCTACTGCCATTCGCTCACTTATCAAGGCGGCCGCGGCTGCGCCCTCTACCCATCCCTCAAACTACAACTTAGATAGTCTACGTATTATTGGTACGGTGGGTGAGCCCATCAATCCTGAGGCGTGGATGTGGTGTCACCAGCATGTAGCGCGTGCACGCTGTCCTATTGTGGATACATGGTGGCAGACGGAAACGGGCGGTCATATGATCGCCCCCTTGCCTGGCGCAACTGCGCTTAAACCAGGATCCTGCACCCTGCCGCTGCCCGGCATTGTTGCCGCCATTGTGGACGAAACAGGCGCTGAGGTAGAGCAAGGTCAAGGTGGCTTCCTGGTTATTCAGCGGCCCTGGCCCGCCATGATACGCAACATATGGGGTGATCCAGAACGCTTTAAAAAGACGTATTTCCCGCCTGAATTTTGCGGTTATTACCTGGCGGGAGACGGGGCGCACCGGGACGCTGACGGGTATTTTTGGATCATGGGCCGCATCGACGACGTTCTGAATGTGTCGGGCCATAGGTTGGGTACGATGGAGGTGGAATCGGCCCTTGTTGCGCACGCGTTGGTAGCGGAGGCGGCAGCGGTGGGCCGTCCCGATGATACGACGGGGGAGGCGCTGGTAGCCTTTGTAGTGCTCAAGCGCGTGCGGCCTGAAGGTAAAGAAGCGCAGGCTATCGCCCAGCAACTGCGCGATTGGGTGGCCAAGCAAATTGGTCCCATCGCCAAGCCCAAGGCTATTTACTTTGGCGACAATCTGCCTAAGACGCGTTCAGGAAAAATTATGCGTCGCTTGTTGCGCGCCGTCGCTAAGGGTGATACCTCAGCGCAGGACGTTTCCACCCTGGAGAATCCGGACATTCTTACGCAATTTTCTGATGCAGTATAA

Transcript

BRAKERKRET00000023121

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q39EK2	Acetyl-coenzyme A synthetase OS=Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383) OX=482957 GN=acsA PE=3 SV=1
Q46Z41	Acetyl-coenzyme A synthetase OS=Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) OX=264198 GN=acsA PE=3 SV=1
P31638	Acetyl-coenzyme A synthetase OS=Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337) OX=381666 GN=acsA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000990 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00501 all species →	AMP-binding	AMP-binding enzyme	Family	Interproscan
PF16177 all species →	ACAS_N	Acetyl-coenzyme A synthetase N-terminus	Family	Interproscan
PF13193 all species →	AMP-binding_C	AMP-binding enzyme C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR020845 all species →	Conserved_site	AMP-binding, conserved site	Interproscan
IPR045851 all species →	Homologous_superfamily	AMP-binding enzyme, C-terminal domain superfamily	Interproscan
IPR000873 all species →	Domain	AMP-dependent synthetase/ligase domain	Interproscan
IPR011904 all species →	Family	Acetate-CoA ligase	Interproscan
IPR032387 all species →	Domain	Acetyl-coenzyme A synthetase, N-terminal domain	Interproscan
IPR025110 all species →	Domain	AMP-binding enzyme, C-terminal domain	Interproscan
IPR042099 all species →	Homologous_superfamily	ANL, N-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24095 all species →	ACETYL-COENZYME A SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003987 all species →	Molecular Function	acetate-CoA ligase activity	Interproscan
GO:0016208 all species →	Molecular Function	AMP binding	Interproscan
GO:0019427 all species →	Biological Process	acetyl-CoA biosynthetic process from acetate	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006085 all species →	Biological Process	acetyl-CoA biosynthetic process	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
K01895	ACSS1_2, acs; acetyl-CoA synthetase	EC:6.2.1.1	Lipid biosynthesis proteins	ko01004	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000023121.1 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

5TPM > 0

7Conditions

4.8Max TPM

0.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	0	0.00	0.00
Whole	6	4	2.86	4.79
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	3.00	3.00
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	TPM
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
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
SRR21134056	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
SRR21134060	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
SRR21134064	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	4.79
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	4.34
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	4.27
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	3.75
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.00
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	3.00
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.00
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.00
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	0.00
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.