Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   AVA_RS09475 Genome accession   NC_007413
Coordinates   2328872..2330395 (-) Length   507 a.a.
NCBI ID   WP_011318677.1    Uniprot ID   -
Organism   Trichormus variabilis ATCC 29413     
Function   homologous recombination (predicted from homology)   
Homologous recombination

Genomic Context

Location: 2323872..2335395
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AVA_RS09455 (Ava_1872) - 2324131..2325549 (-) 1419 WP_011318672.1 hypothetical protein -
  AVA_RS09460 (Ava_1873) - 2325804..2326589 (+) 786 WP_011318673.1 peptidoglycan-binding protein -
  AVA_RS09465 (Ava_1874) - 2326737..2327630 (-) 894 WP_011318674.1 SDH family Clp fold serine proteinase -
  AVA_RS09470 (Ava_1875) - 2327724..2328524 (-) 801 WP_011318675.1 Uma2 family endonuclease -
  AVA_RS30335 (Ava_1876) - 2328535..2328711 (-) 177 Protein_1911 Uma2 family endonuclease -
  AVA_RS09475 (Ava_1877) radA 2328872..2330395 (-) 1524 WP_011318677.1 DNA repair protein RadA Machinery gene
  AVA_RS09480 (Ava_1878) rpaB 2330572..2331300 (+) 729 WP_011318678.1 response regulator transcription factor RpaB -
  AVA_RS09485 (Ava_1879) - 2331361..2332008 (+) 648 WP_011318679.1 cofactor assembly of complex C subunit B -
  AVA_RS09490 (Ava_1880) - 2332165..2332818 (+) 654 WP_011318680.1 Uma2 family endonuclease -
  AVA_RS09495 (Ava_1881) - 2332863..2333381 (+) 519 WP_011318681.1 DUF456 domain-containing protein -

Sequence

Protein


Download         Length: 507 a.a.        Molecular weight: 54609.54 Da        Isoelectric Point: 4.9309

>NTDB_id=24701 AVA_RS09475 WP_011318677.1 2328872..2330395(-) (radA) [Trichormus variabilis ATCC 29413]
MAKPKTFYICNECGAESPQWFGKCPACGTYNSLEEQITIQSSVDVLKGGVSGWHASQNNGKAPVKPAKPRASLTFDQITD
RQIARWESGYGELDRVLGGGVVPGSMVLIGGDPGIGKSTLLLQVSNQLAQRYRILYVTGEESGQQVKLRASRLGVAKTLS
VVGDDQREESEQTPLVSIADGVGADLYVLPETDLEEILREVDSLKPNVAVIDSIQTVFFPALTSAPGSVAQVRECTAALM
KVAKHEDITMLIVGHVTKEGAIAGPKVLEHLVDTVLYFEGDRFASHRLLRTVKNRFGATHEIGIFEMVQNGLREVPNPSE
LFLGNRDDPAPGTAIVVACEGTRPIVVELQALVSPTSYPSPRRAGTGIDYNRLVQILAVLEKRVGIPMSKLDSYVASAGG
LNVEEPAVDLGIAIAIVASFRDRIVDPGTVLIGEVGLGGQVRSVSQMELRLKEAAKLGFKKAIVPKGQKFPDFDIEIIPV
AKVIDAIIAAIPHQELTEEDFNLDEDQ

Nucleotide


Download         Length: 1524 bp        

>NTDB_id=24701 AVA_RS09475 WP_011318677.1 2328872..2330395(-) (radA) [Trichormus variabilis ATCC 29413]
ATGGCAAAGCCCAAAACCTTTTACATTTGTAACGAATGTGGAGCAGAATCTCCCCAATGGTTTGGTAAGTGTCCAGCTTG
TGGTACTTACAATTCCTTAGAAGAACAGATTACCATTCAATCTTCCGTAGATGTACTTAAGGGAGGAGTTAGTGGTTGGC
ACGCATCCCAGAATAATGGTAAAGCACCTGTTAAGCCGGCAAAACCACGAGCTTCTTTAACATTTGACCAAATTACCGAT
CGCCAAATCGCTCGTTGGGAGTCTGGCTATGGAGAACTGGATCGGGTGCTTGGTGGTGGTGTGGTTCCAGGTTCGATGGT
TTTGATTGGTGGTGATCCCGGTATTGGTAAATCTACCCTATTACTACAAGTCTCAAATCAATTGGCGCAGAGATATCGTA
TTCTCTATGTCACGGGTGAAGAATCTGGGCAACAAGTAAAATTAAGAGCTTCTCGCTTAGGTGTGGCAAAAACCCTGAGT
GTTGTCGGAGATGATCAAAGGGAGGAATCAGAACAGACACCTCTAGTATCTATAGCTGATGGTGTGGGCGCAGATTTATA
TGTTTTGCCAGAAACAGATTTAGAAGAGATATTACGAGAGGTGGATTCTCTCAAGCCCAATGTGGCGGTAATTGACAGTA
TTCAAACCGTGTTTTTTCCAGCCCTGACCTCTGCGCCTGGTTCTGTCGCCCAAGTCAGGGAATGTACAGCAGCCCTAATG
AAAGTGGCAAAACATGAAGACATTACCATGTTAATTGTCGGACACGTCACCAAAGAAGGGGCGATCGCCGGGCCGAAAGT
TTTAGAACACTTAGTAGATACAGTACTCTATTTTGAAGGCGATCGCTTTGCTTCCCATCGGTTATTACGCACAGTGAAAA
ACCGCTTTGGTGCAACGCACGAAATCGGCATCTTTGAAATGGTGCAAAACGGACTACGTGAAGTCCCTAACCCTAGTGAG
TTATTTTTAGGTAACCGTGATGACCCCGCACCAGGTACAGCCATTGTCGTAGCTTGTGAAGGTACACGACCTATAGTTGT
TGAGTTACAAGCTTTAGTTAGCCCCACCAGCTACCCCTCTCCCCGCCGAGCCGGAACTGGTATAGATTATAACCGATTAG
TCCAAATTCTTGCCGTGTTAGAAAAACGGGTAGGAATTCCTATGTCCAAATTAGATTCTTACGTCGCCTCAGCTGGAGGA
TTGAATGTAGAAGAACCAGCCGTAGATTTAGGAATCGCCATTGCCATCGTTGCCAGTTTCCGCGATCGCATCGTTGATCC
TGGTACAGTCTTGATTGGCGAAGTCGGCTTAGGTGGACAAGTGCGATCGGTTTCCCAGATGGAACTCCGGTTAAAAGAAG
CAGCTAAACTGGGATTCAAGAAAGCGATCGTTCCTAAAGGGCAAAAATTTCCCGACTTTGACATTGAAATCATCCCAGTT
GCCAAAGTCATAGATGCAATTATCGCCGCCATCCCTCACCAAGAACTAACAGAAGAGGACTTCAACCTAGACGAAGATCA
ATAG

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(401-466)

KaiC (ATPase)

(89-295)

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)


Secondary structure

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



3D structure

Source ID Structure

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

50.407

97.041

0.489
  radA Streptococcus pneumoniae Rx1

45.825

96.844

0.444
  radA Streptococcus pneumoniae R6

45.825

96.844

0.444
  radA Streptococcus pneumoniae TIGR4

45.825

96.844

0.444
  radA Streptococcus pneumoniae D39

45.825

96.844

0.444
  radA Streptococcus mitis NCTC 12261

45.714

96.647

0.442
  radA Streptococcus mitis SK321

45.714

96.647

0.442

Multiple sequence alignment