Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   KJS28_RS04090 Genome accession   NZ_AP023418
Coordinates   829325..830695 (+) Length   456 a.a.
NCBI ID   WP_213541844.1    Uniprot ID   A0A810PY29
Organism   Vescimonas coprocola strain MM50     
Function   homologous recombination (predicted from homology)   
Homologous recombination

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
ICE 812672..837455 829325..830695 within 0


Gene organization within MGE regions


Location: 812672..837455
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  KJS28_RS03990 (MM50RIKEN_07820) - 813594..814061 (-) 468 WP_021859111.1 GNAT family N-acetyltransferase -
  KJS28_RS03995 (MM50RIKEN_07830) - 814085..814255 (-) 171 WP_021859110.1 DUF6472 family protein -
  KJS28_RS04000 (MM50RIKEN_07840) - 814252..815652 (-) 1401 WP_213541831.1 MATE family efflux transporter -
  KJS28_RS04005 (MM50RIKEN_07850) - 815744..816358 (-) 615 WP_213541832.1 single-stranded DNA-binding protein -
  KJS28_RS04010 (MM50RIKEN_07860) - 816479..817345 (+) 867 WP_021859107.1 radical SAM protein -
  KJS28_RS04015 (MM50RIKEN_07870) ruvC 817533..818045 (+) 513 WP_213541833.1 crossover junction endodeoxyribonuclease RuvC -
  KJS28_RS04020 (MM50RIKEN_07880) ruvA 818048..818650 (+) 603 WP_213541834.1 Holliday junction branch migration protein RuvA -
  KJS28_RS04025 (MM50RIKEN_07890) ruvB 818680..819720 (+) 1041 WP_213541835.1 Holliday junction branch migration DNA helicase RuvB -
  KJS28_RS04030 (MM50RIKEN_07900) glmM 819740..821107 (+) 1368 WP_213541836.1 phosphoglucosamine mutase -
  KJS28_RS04035 (MM50RIKEN_07910) - 821161..821784 (+) 624 WP_213541837.1 sigma-70 family RNA polymerase sigma factor -
  KJS28_RS04040 (MM50RIKEN_07920) - 821820..822098 (+) 279 WP_021859101.1 zinc-ribbon domain containing protein -
  KJS28_RS04045 (MM50RIKEN_07930) - 822282..822491 (+) 210 WP_021859100.1 DUF1858 domain-containing protein -
  KJS28_RS04050 (MM50RIKEN_07940) - 822555..823253 (+) 699 WP_213541838.1 class I SAM-dependent methyltransferase -
  KJS28_RS04055 (MM50RIKEN_07950) - 823237..824019 (+) 783 WP_213541839.1 Nif3-like dinuclear metal center hexameric protein -
  KJS28_RS04060 (MM50RIKEN_07960) - 824035..824769 (+) 735 WP_021859097.1 YebC/PmpR family DNA-binding transcriptional regulator -
  KJS28_RS04065 (MM50RIKEN_07970) - 825007..825456 (+) 450 WP_213541840.1 8-oxo-dGTP diphosphatase -
  KJS28_RS04070 (MM50RIKEN_07980) - 825574..826500 (-) 927 WP_213541841.1 transketolase family protein -
  KJS28_RS04075 (MM50RIKEN_07990) - 826505..827314 (-) 810 WP_213541842.1 transketolase -
  KJS28_RS04080 (MM50RIKEN_08000) - 827400..828416 (-) 1017 WP_021859092.1 tyrosine recombinase XerC -
  KJS28_RS04085 (MM50RIKEN_08010) - 828585..829304 (+) 720 WP_213541843.1 N-acetylmuramoyl-L-alanine amidase -
  KJS28_RS04090 (MM50RIKEN_08020) radA 829325..830695 (+) 1371 WP_213541844.1 DNA repair protein RadA Machinery gene
  KJS28_RS04095 (MM50RIKEN_08030) - 830983..831846 (-) 864 WP_213541845.1 TIGR03915 family putative DNA repair protein -
  KJS28_RS04100 (MM50RIKEN_08040) - 831851..833119 (-) 1269 WP_213541846.1 putative DNA modification/repair radical SAM protein -
  KJS28_RS04105 (MM50RIKEN_08050) - 833403..835835 (+) 2433 WP_213541847.1 ATP-dependent helicase -
  KJS28_RS04110 (MM50RIKEN_08060) - 835993..836685 (+) 693 WP_213541848.1 iron-sulfur cluster assembly scaffold protein -

Sequence

Protein


Download         Length: 456 a.a.        Molecular weight: 49660.61 Da        Isoelectric Point: 6.4946

>NTDB_id=83144 KJS28_RS04090 WP_213541844.1 829325..830695(+) (radA) [Vescimonas coprocola strain MM50]
MKAKTVFFCTECGNETPKWSGRCPACGAWNTIVEQTDKPVKSGRKSVFSTTVKAERITELGTSDEIRFLTGMGELDRVLG
GGAVKGSLVLVGGAPGIGKSTLMLQICKKLGEFSKVLYVSGEESTHQLKLRAQRLRVESENLYVLSETCLGNVMECVREE
KPDVLIVDSIQTLYNEEMDSPAGGVGQVKDCTMALMQLAKGQGITVFVIGHVNKEGSIAGPKVLEHMVDCVLYFEGDQHM
TYRILRAAKNRFGATNEIGVFEMMDWGLKEVENPSEMLLSGRPKDAPGTCVTCAMEGARPVLAEVQALIAPASAANPRRM
SNGFDYNRFAMLLAVLEKRGNLKVSQCDAYLNIIGGLTLEEPAADLSAVVAIASSYLDKPVPSHMAAIGEVGLSGEIRSI
NHMEQRLSEVQRLGFTQCIVPEHRVKEMKELPHLELLPVQNVAQALQLLVQGKLMK

Nucleotide


Download         Length: 1371 bp        

>NTDB_id=83144 KJS28_RS04090 WP_213541844.1 829325..830695(+) (radA) [Vescimonas coprocola strain MM50]
ATGAAAGCGAAGACTGTTTTTTTCTGCACGGAGTGCGGCAATGAGACGCCCAAGTGGTCGGGACGCTGTCCCGCCTGTGG
TGCATGGAATACCATTGTGGAGCAGACGGATAAGCCGGTAAAAAGCGGAAGAAAGTCTGTTTTTTCCACAACTGTAAAGG
CAGAACGCATCACAGAACTGGGTACCTCTGACGAGATCCGCTTCCTGACGGGTATGGGGGAGCTGGACCGGGTTTTGGGG
GGCGGCGCCGTCAAGGGATCACTGGTCTTGGTGGGCGGTGCGCCGGGTATTGGCAAATCTACACTGATGCTCCAGATCTG
TAAAAAATTGGGAGAGTTCTCCAAGGTGCTGTACGTTTCCGGCGAGGAATCCACCCACCAGCTGAAGCTGCGGGCGCAGC
GGCTCCGGGTGGAGAGCGAAAATCTGTATGTTTTGTCGGAGACGTGTTTAGGGAATGTCATGGAATGTGTCCGGGAGGAA
AAACCGGATGTGCTCATCGTGGACTCCATCCAGACACTGTATAATGAAGAGATGGATTCTCCCGCCGGCGGCGTGGGGCA
GGTGAAGGACTGTACCATGGCCCTGATGCAACTGGCAAAGGGACAGGGCATTACGGTATTTGTCATCGGCCACGTCAACA
AGGAGGGCTCTATCGCAGGTCCCAAGGTGTTGGAGCACATGGTGGACTGCGTGCTGTATTTCGAGGGCGATCAGCACATG
ACCTACCGCATCCTGCGGGCAGCCAAGAACCGTTTCGGCGCCACCAACGAGATCGGCGTCTTTGAAATGATGGACTGGGG
CCTGAAGGAGGTGGAGAATCCCTCCGAAATGCTGCTGTCGGGCCGTCCCAAGGATGCACCGGGGACCTGCGTCACCTGCG
CTATGGAGGGAGCCCGCCCGGTTTTGGCGGAGGTGCAGGCTCTCATCGCTCCGGCCAGCGCCGCCAATCCCCGGCGCATG
AGCAACGGCTTTGACTACAACCGCTTTGCGATGCTGCTGGCGGTGCTGGAGAAGCGGGGGAATCTGAAGGTCTCCCAGTG
TGATGCATACCTGAATATCATCGGTGGTCTAACGCTGGAGGAACCGGCGGCAGATCTGTCCGCTGTGGTGGCCATCGCCT
CCAGCTATCTGGACAAGCCCGTTCCCAGCCATATGGCCGCCATCGGAGAGGTGGGACTGTCTGGGGAAATACGGTCTATC
AATCACATGGAGCAGCGTCTATCTGAGGTGCAGCGACTGGGTTTCACGCAGTGCATCGTCCCGGAGCACCGGGTCAAAGA
GATGAAAGAACTGCCGCATCTGGAGCTTCTGCCGGTACAGAACGTGGCGCAGGCTCTCCAGCTGCTGGTACAGGGAAAGC
TGATGAAGTGA

Domains

Predicted by InterproScan.

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-34)

Lon protease (S16) C-terminal proteolytic domain (Lon_C)

(360-448)

AAA domain (AAA_25)

(74-216)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A810PY29

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  radA Bacillus subtilis subsp. subtilis str. 168

51.754

100

0.518
  radA Streptococcus mitis NCTC 12261

48.322

98.026

0.474
  radA Streptococcus pneumoniae Rx1

48.322

98.026

0.474
  radA Streptococcus pneumoniae D39

48.322

98.026

0.474
  radA Streptococcus pneumoniae R6

48.322

98.026

0.474
  radA Streptococcus pneumoniae TIGR4

48.322

98.026

0.474
  radA Streptococcus mitis SK321

48.322

98.026

0.474

Multiple sequence alignment