Gene detail

Detailed information of BRAKERKREP00000023397.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:2160446...2166130
NR annotation: WP_066670890.1, bifunctional 2-methylcitrate dehydratase/aconitate hydratase [Bordetella bronchialis]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000023397

ATGTCTACCCATATCTCTAACGTCCGCCCGGAGCCCGATCAGGTCCTCGTTGACATTGCGGATTATGTGCTTAACTATAAAATCAATAGCAGTTTGGCTTATGAAACGGCACGTAATTGCCTTATCGATACCCTAGGCTGCGGACTCGAGGCGCTGGAATACCCTGCTTGCAAAAAGCTTTTAGGACCCATTGTGCCGGGCACGGTGGTGCCCAATGGCGCCAAGGTCCCTGGCACCCAATTTCAGTTAGACCCAATCCAAGCCGCTTTCAATATCGGCGCCATGATTCGTTGGCTGGATTTCAACGATACTTGGCTAGCGGCCGAATGGGGCCATCCTTCGGACAATTTAGGCGGCATACTCGCCACCGCCGATTGGCTTTCGCGCAATGCGATTGCAGCTGGCAAAAAGCCGTTATCCATGCGGGACGTGCTTACCGCAATGATTAAAGCGCACGAAATCCAAGGCTGCATTGCACTGGAAAACTCCTTTAACAAAGTGGGGCTAGACCATGTGGTACTGGTCAAAGTCGCCTCCACTGCCATCGTCGCGCAAATGCTAGGCTTAAACCGCGAAGAAATTATCAACGCGGTATCGCTCGCCTGGGTAGATGGCCAAAGTTTACGCACCTATCGCCATGCCCCTAATACGGGCAGCCGCAAAAGTTGGGCGGCGGGTGACGCGACCAGCCGGGCCGTTCGTCTCGCGCTAATGGCGCGCACCGGCGAAATGGGCTACCCATCGGTATTAACAGCCAAAACCTGGGGCTTTTACGACGTACTGTTTAAAGGCCGCCCCTTTACATTCCAGCGCCCTTACGGCAGCTACGTGATGGAGAATGTGCTGTTTAAGATTTCTTTCCCCGCCGAGTTTCATTCGCAAACGGCCGTAGAGTGCGCCATGGACCTTCATCAACAGCTTAAGATCGCCGGCAAGACCGCTGAGGATATTAAGCAGATTACCATCCGTACGCACGAAGCCTGCATCCGTATCATTGACAAAAAAGGCTCGCTCAACAACCCGGCTGACCGTGATCATTGCGTACAGTACATGGTAGCGGTGCCCTTGCTGTTCGGCCGCCTCACGGCTGCCGACTATGAAGACGACATCGCGCAAGACCCATGTATCGACGCCTTACGTGAGAAAATCGTTTGCATAGAAGACCCTGCTTTTACCAAGGATTATCACGATCCCGAAAAGCGCTCCATCGCTAACGCGCTTTGCGTAGAATTTCGCGATGGAACTCGCTTACCCGAAAAGGTGTGCGAATATCCTATTGGCCACAAGCGCCGCCGCCAAGAAGGTATACCGCTACTAGAAGCAAAGTTCCGTACCAACCTAGCGCGTATGTTCCCTGCTCGTCAGCAGCAAAAAATCCTAGATATTTCGCTGGACCAGCAAAAACTTGAAGCCATGCCCGTGCACGAGTATGTGGATCTTTATAGTACTGTTACGTTTCCTTCTACGCATCCGCGAGCAGGGAACGGCAATAGAAACGCCCTACCGCACAGCGTTGAAGTCACCATTAGTGACGCTTCGCGCGAGCTGCTGGAATTTGACGCAGAAATGCTCGAAGAATCCTTATTCTTACTCGTTGGCTACGTCGGCCCCATACCGAATAACGCTCAGATGAGCCTTAGTGACGCTCCACGAGAGCTGCTGGAGGTGGGACCGGACATGGCGGTCCTTCCCCTCAGCATACTGAAAGCAGGCACTTTTCCCCTGAGCGCGATTGAACAGTCCTTACTAGATTGTTTAAAGCAGGAAACGGAGGCCTTAAAGAAACTCGAGGCATCACTTGCAGCGGAAGCTGCCGTCATTAAGGCGGAAACCCAAGCCTTTACCGAGCAGCCCGTCGACCTGCAGAAACTGGAAGCGATTAGGGAAACACTGCCATTAATTAGCAGAAGGAAGATGAGTTTGACGATGTGGTTAGCCACACTTGGCGAAAGGCGTGACGCTTTGCTCGAAAAGCTAGGCCTGCCCAAAGGGAGTGAAGGCACGCGCCAGGCAGCGCAAGCCGCTAAACCTCCGCTCATCAAAGCTTGGAATAGCGTAGAGCAACTTTCCAAACATGTCGTAGCCCTCAATAATTCGGCACTTCATAGAAACGGTGAATCGCCCCGAGTTTCGAGGATCTATTTCACTCCCCTTCCGGGGTTCTTTTCGCCTTTCCCTCACGGTACTGGTTCACTATCGGTCGATCACGAGTATTTAGCCTTGGAGGATGGTCCCCCCATCTTCAAACAGGATTTCACGTGTCCCGCCCTACTTCTCGTACGCTTAGTTCCACATCCAGAATTTCGTCTACAGGGCTATCACCTGCTATGGCCGAACTTTCCAGTCCGTTTGACTATTCCACATGCTACAACGTACAGGCTCTTCCAATTTCGCTCGCCACTACTTTCGGAATCTCGGTTGATTTCTTTTCCTCGAGCTACTGAGATGTTTCAGTTCGCCCAGTTCGCCTCCACTGGTCTATGGATTCAACCAGGGATACCGCTTGCGCGGTGGGTTTCCCCATTCGGAGGTCTGCGGATCAATGCTCGTTTGCCAGCTCCCCGCAGCTTTTCGCAGGCTACCACGTCCTTCTTCGCCTGTGATCGCCTAGGCATCCACCGTATGCACTTACTCGCTTGA

Transcript

BRAKERKRET00000023397

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P77243	2-methylcitrate dehydratase OS=Escherichia coli (strain K12) OX=83333 GN=prpD PE=1 SV=3
Q8Z903	2-methylcitrate dehydratase OS=Salmonella typhi OX=90370 GN=prpD PE=1 SV=1
P74840	2-methylcitrate dehydratase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) OX=99287 GN=prpD PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0058493 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF19305 all species →	MmgE_PrpD_C	MmgE/PrpD C-terminal domain	Domain	Interproscan
PF03972 all species →	MmgE_PrpD_N	MmgE/PrpD N-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045337 all species →	Domain	MmgE/PrpD, C-terminal	Interproscan
IPR042188 all species →	Homologous_superfamily	MmgE/PrpD superfamily, domain 2	Interproscan
IPR036148 all species →	Homologous_superfamily	MmgE/PrpD superfamily	Interproscan
IPR036679 all species →	Homologous_superfamily	FlgN-like superfamily	Interproscan
IPR042183 all species →	Homologous_superfamily	MmgE/PrpD superfamily, domain 1	Interproscan
IPR012705 all species →	Family	2-methylcitrate dehydratase PrpD	Interproscan
IPR045336 all species →	Domain	MmgE/PrpD, N-terminal	Interproscan
IPR005656 all species →	Family	MmgE/PrpD	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16943 all species →	2-METHYLCITRATE DEHYDRATASE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016829 all species →	Molecular Function	lyase activity	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0044780 all species →	Biological Process	bacterial-type flagellum assembly	Interproscan
GO:0019679 all species →	Biological Process	propionate metabolic process, methylcitrate cycle	Interproscan
GO:0047547 all species →	Molecular Function	2-methylcitrate dehydratase activity	Interproscan
GO:0051537 all species →	Molecular Function	2 iron, 2 sulfur cluster 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

No KEGG orthology assignment for BRAKERKREP00000023397.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000023397.1 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

21TPM > 0

7Conditions

288.0Max TPM

71.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	11	69.66	288.03
Whole	6	6	96.32	107.31
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	74.03	74.03
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	71.84	71.84
symbioic hydra M9 strain · symbioic hydra rep1	1	1	61.92	61.92
symbioic hydra M9 strain · symbioic hydra rep2	1	1	43.58	43.58
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
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977	288.03
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	181.61
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	169.20
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	152.34
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	142.13
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	79.23
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	77.94
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	74.23
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	60.38
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	27.68
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	1.02
SRR21134055	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
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	107.31
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	101.65
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	93.96
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	93.69
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	92.90
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	88.42
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	74.03
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	71.84
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	61.92
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	43.58
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.