Gene detail

Detailed information of BRAKERKREP00000022683.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: WP_053243957.1, aminomethyl-transferring glycine dehydrogenase [Achromobacter sp. DMS1]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000022683

ATGTTGCGCGCTCTAGATGCCCATACCGATTTCATTGCCCGTCACATCGGCCCCTCTGTAGCGGATCAAGCCGCCATGCTCGCCGTGATCGGCAGTCCCAGCCTTGACGCGCTTATCAATGAGGTAGTGCCGCCCCGCATACATAGCGAGGCGCCGCTCGCGCTGCCTCCTGCGCGCAGCGAGACGAATGTGTTGGCTGAACTGAAGGAAATCGCCGGCCGCAATAAGCTCTACCGTAATTACATCGGCCAAGGGTATTACGGTACCGAGACGCCTCATGTCGTGCTGCGCAACGTGCTTGAAAACCCCGCTTGGTATACCGCTTATACGCCTTATCAGCCGGAAATTTCTCAGGGACGTCTGGAGGCGTTGTTGAACTATCAAACCATGGTGGCTGATCTCACGGGCCTGGGTATCGCCAACGCTTCGCTGCTAGACGAGAGCACTGCCGCCGCCGAAGCTATGGCATTGGCCCAGCGCAGCGCGCAGTCGCCGAGTCGCGTTTTTTTTGTGTCGCGCCATTGCCATCCACAAACTATCGAGGTGGTGCGCACGCGCGCCGAGGGGCTAGGGATCGAACTCGTGGTGGGAGAGGAAGCGGACGGCTTGCCGCAATGCTTTGGCGTACTACTGCAATACCCACACAGCTTAGGCGCGATTGCCGATTACCGCGCCCTGGCCGCGGACGCGCACGCGCAGGGCGCGATAGTGGCGTGCGCCACCGATTTGCTGGCATTAGCCCTGTTGGCCCCGCCGGGTGCATGGGGTGCGGATATCGCTATCGGTTCGGCGCAGCGTTTTGGTGTGCCTTTTGGTTTTGGGGGTCCGCATGCTGGCTTCATCGCTTGCAAGGAGACCTTCAAGCGCCACCTGCCGGGCCGCCTGGTTGGGGTTTCCAAGGACGCTCAGGGTCAGCCGGCCTTAAGGCTGGCATTGCAGACACGCGAGCAGCATATTCGCCGTGAGAAGGCGACTTCTAATATTTGTACCGCGCAGGTTTTGTTGGCGGTCATTGCGGGCATGTATGCCGTGTGGCATGGGCCGCAAGGCCTACGCCGCATTGCTGATCGGGTGCAGCGCTACACCGCCGTATTGCGCTTGGCGCTGCAAGCGCTGGGCGTGAGGGTAGTTAACCCTACTTTTTTTGATACCCTGTTTTTAGACACTGGTGCGGCGACACCGGCTATCTTGCGTGCCGCCGACAGTGCCCACATTAATTTGCGCCACGTTGATGACACCCATCTGGCGCTCTCGCTAGACGAGACGGTAACAGCCGCTGATTTGCAGGAATTGCTTAAGGTCTTTAGCGCCGGCCTGGCCAAGCATGCGATGACGCTAGACATCGACGCACTTGATATGCGCGCGCCCGGGGGGATTCCGCCTTCGATGCAGCGCCACGGCGCCATTCTGTCGCATCCGGTGTTTTCTAGCATCCAGTCAGAGACCGACATGTTGCGCTATCTGCGTAAGTTATCCGACAAAGACTTGGCGTTGGACCGCAGCATGATTCCGCTGGGCTCGTGCACCATGAAGCTGAATGCCACGGCCGAGATGATTCCCATCACCTGGCCCGAATTCGCGCTTATGCACCCGTACGCACCGCCTGCGCAAAGCGTTGGCTATCACGAACTGATTGCGCGGTTGTCGGCCGCTTTGTGCGAGATTACTGGTTATGACGACATTTGCCTGCAGCCTAATTCTGGCGCACAGGGCGAGTATGCGGGCCTGTTAGCCATACGCGCCTACCACCAGGCCAATGGCCAAGAACAACGTAAGGTCTGCTTGATTCCATCGTCTGCCCACGGTACGAACCCAGCGTCGGCGCAAATGGCGGGTATGGAAGTTGTGATCGTCGAGTCTGACGCTAAGGGTAACGTGGACATCAATGACTTGCGCGCGAAGGTAGCTCAAGTGGGCGATCGGTTGGCGGCCTTGATGCTGACCTATCCTTCGACGCATGGGGTGTTTGAAGAAGGGGTCATAGAAATTTGTGTCCTCATCCACCAGGCAGGAGGGCAAGTTTACTTGGATGGGGCCAATATGAACGCCATGGTGGGCATTGCCAAACCGGGCAAATTCGGCGCCGATGTGTCGCACCTAAATTTGCATAAGACCTTTTGCATACCTCACGGCGGTGGTGGGCCTGGTGTCGGTCCAGTGGCCGTGCGGTCGCACTTAGCGCCTTATTTGCCAGGCGTGCTGAACAACCAAGGCAAGCTGTCCGGGCAGATCAAGGTGGGGCCGGTGGCGGCTGCGCCTTTTGGTTCAGCCGGCATTTTGCCGATTCCCTATGCCTATATTGCGATGATGGGAGCCGAGGGCCTACAGCGGGCTACCGAAGTGGCGATACTTAACGCTAATTACTTGGCTATTCGCTTGCGAGAGCATTATTCCGTACTGTATGCAGGTCGTCATGGCCGCGTGGCGCACGAATGCATTTTGGATGTGCGTCCACTCAAAGAAAGCAGCGGCGTTACGGCGGAAGATATCGCCAAACGCCTCATAGACTACGGCTTTCATGCGCCGACCATGAGCTTCCCTGTAGCGGGTACGCTAATGGTCGAGCCTACCGAATCGGAAGGGCGGGCTGAGCTGGATCGCTTTGTAGAAGCCATGATCGCGATTCGTGTTGAAATCGCTCGCATCGAAACAGGTGAGTGGGACCGCAACGACAATGTGCTGAAGAACGCGCCTCATACGGCGCACATGTTATTGGCCCAAGAGTGGCATCACGACTATACGCGCGAGCAAGCAGCCTATCCGTTACCGGGTTTGCGGGATAACAAATATTGGGCACCGGTTGCGCGCGTAGATAATGCTTATGGTGATCGTAATTTGATCTGCTCCTGCTTGCCGGTTGAGGCCTACGCCTAA

Transcript

BRAKERKRET00000022683

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A9I7K9	Glycine dehydrogenase (decarboxylating) OS=Bordetella petrii (strain ATCC BAA-461 / DSM 12804 / CCUG 43448) OX=340100 GN=gcvP PE=3 SV=1
Q7WP29	Glycine dehydrogenase (decarboxylating) OS=Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) OX=257310 GN=gcvP PE=3 SV=1
Q7W1C4	Glycine dehydrogenase (decarboxylating) OS=Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253) OX=257311 GN=gcvP PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002709 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02347 all species →	GDC-P	Glycine cleavage system P-protein	Domain	Interproscan
PF21478 all species →	GcvP2_C	Glycine dehydrogenase, C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR049315 all species →	Domain	Glycine cleavage system P-protein, N-terminal domain	Interproscan
IPR003437 all species →	Family	Glycine dehydrogenase (decarboxylating)	Interproscan
IPR015422 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, small domain	Interproscan
IPR020581 all species →	Family	Glycine cleavage system P protein	Interproscan
IPR015424 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase	Interproscan
IPR015421 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, major domain	Interproscan
IPR049316 all species →	Domain	Glycine dehydrogenase, C-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11773 all species →	GLYCINE DEHYDROGENASE, DECARBOXYLATING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004375 all species →	Molecular Function	glycine dehydrogenase (decarboxylating) activity	Interproscan
GO:0006544 all species →	Biological Process	glycine metabolic process	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0005960 all species →	Cellular Component	glycine cleavage complex	Interproscan
GO:0006546 all species →	Biological Process	glycine catabolic process	Interproscan
GO:0016594 all species →	Molecular Function	glycine binding	Interproscan
GO:0019464 all species →	Biological Process	glycine decarboxylation via glycine cleavage system	Interproscan
GO:0030170 all species →	Molecular Function	pyridoxal phosphate binding	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
K00281	GLDC, gcvP; glycine cleavage system P protein (glycine dehydrogenase)	EC:1.4.4.2	Lipoic acid metabolism	ko00785	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000022683.1 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.