Gene detail

Detailed information of HOLI00001.G51186 in Hydra oligactis

Genomic Location: HOLI00001:2780562...2784153
NR annotation: WP_110972666.1, transcription-repair coupling factor [Pseudomonas huaxiensis]
Species Hydra oligactis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

HOLI00001.g51186.t1

ATGACGCCGAGCATCGCATCGGGCAATGAGCGCCTGTCATGCGTGCAAGACGGACCTTTTTCCATGCCTCGACCTCCCGTGCCTGTTCTGCGTCTACCGCACCTTCCGGCCACCGCCGGCAAACAATCCTGGGGCAACCTGCCCGGCGCCGCCCTGAGCCTGGCCATCGCCGAAGCCGCCAGCGCCGCCAAACGCTTCACCCTGCTGCTGACCGCCGACAGCCAGAGCGCCGACCGGCTGGAGCAGGAGTTGCGCTTCTTCGCGCCGGAACTGGCGGTGCTGCCGTTCCCCGACTGGGAAACTCTGCCCTACGATCTGTTCTCGCCGCACCAGGACATCATCTCGCAGCGCATCTCCAGCCTGTACCGGCTGCCGGAGCTCGACCACGGCATTCTCGTGGTGCCGATCACCACCGCCCTGCACCGCCTCGCGCCGACCCGCTTCCTGCTGGGCAGCAGCCTGGTGCTGGACATCGGCCAGAAACTCGACGTCGAACAGATGCGCACGCGCCTGGAAGCCAGCGGCTACCGCTGCGTCGACACCGTCTACGAGCATGGCGAATTCGCCGTCCGCGGCGCCTTGATCGACCTGTTCCCGATGGGCAGCAAGCTGCCGTACCGGATCGACCTGTTCGACGACGAAATCGAGACCCTGCGCACCTTCGACCCGGAAACCCAGCGTTCGATCGACAAGGTCGACTCGGTGCGCCTGCTGCCCGCGCGCCGAGACCTGACCAGCGGGATCATCCCGGCCGGCATCGAGTACTACCTGCCGCTGTTCTTCGACGAAACCTCGACCCTGTTCGACTACCTGCCGCAGGACACCCAGGTGTTCTCGCTGCCCGGCGTGGAGCAGGCGGCGGAACACTTCTGGAACGACGTGCGCGGGCGCTACGAGGAACGCCGGATCGACCCGAGCCGGCCATTGCTGCCGCCCGCCGAACTGTTCCTGCCGGTGGAAGACTGCTTTGCCCGCCTCAAGGGCTGGCCGCGGGTTGTGGTCAGTGCCGACGATATCGGTGCCGGCGCCGGCCGCGAGCGCTTTGACGCGCGTCAGTTGCCCAACCTGGCCATCGAAGCCAAGGCCAACCAGCCACTGGCGGCGCTCTCGGATTTTCTCGACCAGTTCCCCGGCCGGGTGCTGTTCACCGCCGAATCGGCAGGTCGCCGCGAGGTGCTGCTGGAACTGCTGGAGCGCCTGAAGCTGCGGCCGCAGACCGTGGAAAACTGGGAAGACTTCGTCACCGGCAATGCCCGCCTGGCGATCACCATCGCGCCACTGGACGACGGCCTGCTGCTGGAGACACCGGCCCTTGCGCTGGTTGCCGAAAGCCCGCTGTTCGGCCAGCGCGTGATGCAACGCCGGCGCCGGGAAAAACGCAGCGACGCCAGCAACGACGCGGTCATCAAGAACCTTACCGAGCTGCGCGAAGGCGCGCCGGTAGTGCACATCGACCACGGTGTCGGCCGCTACCTGGGCCTGGCAACCCTGGAGATCGACAATCAGGCGGCCGAATTCCTCACCCTCGAATACGCCGAGGGCGCCAAGCTCTATGTACCGGTCGCCAACCTGCACCTGATCGCCCGCTACACCGGCAGCGACGATGCCCTGGCTCCGCTGCACCGCCTGGGCTCGGAAACCTGGCAGAAAGCCAAGCGCAAGGCGGCCGAGCAGGTCCGCGACGTTGCCGCCGAACTGCTCGACATCTACGCCCGCCGTGCTGCGCGCAAGGGTTATGCCTTTGCCGACCCGAGCGTCGATTACGCCACCTTCAGCGCCGGCTTCCCGTTCGAGGAAACTCCCGACCAGCAAAGCGCCATCGAAGCGGTCCGCGAAGATATGCTCGCGGCCAAGCCGATGGATCGCCTGGTCTGTGGCGACGTCGGTTTCGGCAAGACCGAAGTGGCCATGCGCGCAGCATTCATCGCCGTGCACAGCGGCCGTCAGGTGGCGATCCTGGTACCGACCACCCTGCTCGCCCAGCAGCACTACAACAGTTTCCGCGATCGTTTCGCCGACTGGCCGGTGAGCGTCGAAGTCATGAGCCGCTTCAAATCGGCCAAGGACGTCAGCAGCGCCATGGTCGAGCTGGCCGAAGGCAAGATCGATATCGTCATCGGCACCCACAAGCTGTTGCAGGACGACGTCAAGTTCAAGGACCTGGGCCTGGTCATCATCGACGAAGAACACCGTTTCGGCGTGCGCCAGAAAGAACAGCTCAAGGCCCTGCGCAGTGAAGTCGACATTCTCACCCTGACCGCCACACCGATCCCGCGCACCCTGAACATGGCGGTGGCGGGCATGCGTGACCTGTCGATCATCGCCACCCCGCCGGCCCGCCGGCTGTCGGTGCGCACCTTCGTCATGGAGCAGAACAAGAGCACCATCAAGGAGGCGCTGCTGCGCGAGTTGCTGCGCGGCGGTCAGGTGTACTACCTGCACAACGACGTGAAGAGCATCGAAAAATGCGCCGCCGACCTCGCCGAACTGGTGCCTGAGGCACGCATCGGCATCGGCCACGGGCAGATGCGCGAGCGCGAACTCGAACAGGTGATGAGCGACTTCTACCACAAGCGTTTCAACGTGCTGATCGCCTCGACCATCATCGAGACCGGCATCGACGTGCCGAGCGCCAACACCATCGTCATCGAGCGCGCCGACAAATTCGGCCTGGCCCAGTTGCACCAGTTGCGCGGCCGGGTCGGGCGCAGCCACCACCAGGCCTACGCCTACCTGCTGACGCCGCCGCGCCAGCAGATCACCGCCGACGCGGAAAAGCGCCTGGAAGCCATCGCCAACACCCAGGACCTGGGGGCCGGCTTCGTCCTCGCCACCAACGACCTGGAGATCCGCGGCGCCGGCGAACTGCTCGGCGAAGGCCAGAGCGGGCAGATCCAGGCCGTGGGCTTCACCCTGTACATGGAAATGCTCGAGCGCGCGGTCAAGGCCATTCGCAAGGGTACCCAACCAAACCTCGACCAGCCGCTGGGCGGCGGGCCGGAAATCAACCTGCGGCTGCCGGCGCTGATCCCCGAGGATTATCTGCCCGACGTGCATGCCCGGCTGATCCTGTACAAGCGCATCGCCTCGGCGGTGGACGAAGAAGGCCTCAAGGATCTGCAGGTCGAGATGATCGACCGGTTCGGCCTGCTGCCCGAGCCGACCAAGAACCTGATCCGCCTGACCCTGCTCAAGCTGCACGCGGAAAAACTCGGTATCAAGAAAGTCGATGCCGGCCCCAATGGCGGCAAGATCGAGTTCGAGGCTGAAACGCCGGTCGATCCGCTGGTGTTGATCAAGCTGATCCAGGGCCAGCCCAAACGCTACAAGTTCGAAGGCGCGACTCAATTCAAGTTCATGGTGCCCATGGAACGCGCCGATGAACGATTCACCACACTCGAAGCGCTGTTCGAGCGCCTGACACCGAAATCCGCTTGA

Transcript

HOLI00001.g51186.t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P30958	Transcription-repair-coupling factor OS=Escherichia coli (strain K12) OX=83333 GN=mfd PE=1 SV=2
P45128	Transcription-repair-coupling factor OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=mfd PE=3 SV=1
O52236	Transcription-repair-coupling factor OS=Myxococcus xanthus OX=34 GN=mfd PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0013155 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03461 all species →	TRCF	TRCF domain	Domain	Interproscan
PF00270 all species →	DEAD	DEAD/DEAH box helicase	Domain	Interproscan
PF02559 all species →	CarD_TRCF_RID	CarD-like/TRCF RID domain	Domain	Interproscan
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF17757 all species →	UvrB_inter	UvrB interaction domain	Domain	Interproscan
PF21132 all species →	MFD_D3	MFD, D3 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR036101 all species →	Homologous_superfamily	CarD-like/TRCF, RNAP-interacting domain superfamily	Interproscan
IPR004576 all species →	Family	Transcription-repair coupling factor	Interproscan
IPR005118 all species →	Domain	Transcription-repair-coupling factor, C-terminal domain	Interproscan
IPR037235 all species →	Homologous_superfamily	TRCF-like, C-terminal D7 domain	Interproscan
IPR011545 all species →	Domain	DEAD/DEAH box helicase domain	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR003711 all species →	Domain	CarD-like/TRCF, RNAP-interacting domain	Interproscan
IPR047112 all species →	Family	ATP-dependent DNA helicase RecG/Transcription-repair-coupling factor	Interproscan
IPR041471 all species →	Domain	UvrB, interaction domain	Interproscan
IPR048635 all species →	Domain	Transcription-repair-coupling factor, D3 domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47964 all species →	ATP-DEPENDENT DNA HELICASE HOMOLOG RECG, CHLOROPLASTIC	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003678 all species →	Molecular Function	DNA helicase activity	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
K03723	mfd; transcription-repair coupling factor (superfamily II helicase)	EC:5.6.2.4	DNA repair and recombination proteins	ko03400	deepkoala

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