Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   TBD_RS04855 Genome accession   NC_007404
Coordinates   1027097..1028449 (+) Length   450 a.a.
NCBI ID   WP_011311477.1    Uniprot ID   Q3SK72
Organism   Thiobacillus denitrificans ATCC 25259     
Function   homologous recombination (predicted from homology)   
Homologous recombination

Genomic Context

Location: 1022097..1033449
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  TBD_RS04830 (Tbd_0960) pyrF 1022197..1022934 (+) 738 WP_011311472.1 orotidine-5'-phosphate decarboxylase -
  TBD_RS04835 (Tbd_0961) - 1022931..1024253 (+) 1323 WP_011311473.1 UDP-glucose dehydrogenase family protein -
  TBD_RS04840 (Tbd_0962) rfaE1 1024250..1025203 (+) 954 WP_049750215.1 D-glycero-beta-D-manno-heptose-7-phosphate kinase -
  TBD_RS04845 (Tbd_0963) rfaD 1025200..1026198 (+) 999 WP_011311475.1 ADP-glyceromanno-heptose 6-epimerase -
  TBD_RS04850 (Tbd_0964) cysM 1026195..1027088 (+) 894 WP_011311476.1 cysteine synthase CysM -
  TBD_RS04855 (Tbd_0965) radA 1027097..1028449 (+) 1353 WP_011311477.1 DNA repair protein RadA Machinery gene
  TBD_RS04860 (Tbd_0966) - 1028531..1029034 (+) 504 WP_011311478.1 hypothetical protein -
  TBD_RS04865 (Tbd_0967) - 1029122..1030024 (-) 903 WP_011311479.1 YihY/virulence factor BrkB family protein -
  TBD_RS04870 (Tbd_0968) - 1030200..1031831 (-) 1632 WP_011311480.1 peptide chain release factor 3 -

Sequence

Protein


Download         Length: 450 a.a.        Molecular weight: 47449.71 Da        Isoelectric Point: 7.6838

>NTDB_id=24667 TBD_RS04855 WP_011311477.1 1027097..1028449(+) (radA) [Thiobacillus denitrificans ATCC 25259]
MAKAKTVYTCTECGGSSPKWQGQCPACNAWNTLVETIAETAKPRFAALAATSQVQLLHEVEASEESRIATGIGELDRVLG
GGLVPGGVTLIGGDPGIGKSTLLLQALAGLAERMGTLYVSGEESARQVALRARRLALPETRLPVLPEIRLEAILAQLAAT
SPEVAVVDSIQTVYSEALTSAPGSVAQVRECAAQLTRHAKQSGTAVILVGHVTKEGAIAGPRVLEHIVDTVLYFEGDTGS
SYRLVRAFKNRFGAVNEIGVFAMTEKGLKGVSNPSAIFLSRHGEPVPGSCVLVTQEGTRPLLVEIQALVDTSHAPNPRRL
SVGLEQNRLAMLLAVLHRHAGIACFDQDVFVNAVGGVKISEPAADLAVLAAIVSSLRSQPLPDKLVMFGEVGLAGEIRPV
QRGQERLKEAAKLGFTQAIVPAANQPKQKIAGMTVHAVQRLDDAISLFRG

Nucleotide


Download         Length: 1353 bp        

>NTDB_id=24667 TBD_RS04855 WP_011311477.1 1027097..1028449(+) (radA) [Thiobacillus denitrificans ATCC 25259]
ATGGCGAAGGCCAAAACGGTTTACACCTGCACCGAGTGCGGCGGCAGCTCGCCCAAATGGCAGGGCCAGTGCCCGGCGTG
CAACGCCTGGAACACGCTGGTCGAGACGATCGCCGAGACGGCAAAGCCCCGCTTCGCCGCGCTCGCGGCGACGAGTCAGG
TACAGCTGCTGCACGAGGTCGAGGCCTCGGAGGAAAGCCGCATCGCGACAGGGATCGGCGAACTCGACCGCGTCCTGGGC
GGCGGCCTCGTCCCGGGCGGCGTCACGCTGATCGGCGGCGACCCGGGCATCGGAAAATCGACGCTGCTGCTGCAGGCGCT
CGCCGGGCTGGCGGAGCGCATGGGGACGCTCTACGTCAGCGGCGAGGAATCGGCACGTCAGGTCGCCTTGCGCGCCCGGC
GTCTTGCCCTGCCCGAAACGCGGCTGCCGGTTTTGCCCGAGATTCGGCTCGAGGCGATCCTCGCGCAGCTCGCGGCGACC
TCGCCCGAGGTCGCCGTCGTCGACTCGATCCAGACCGTTTATTCGGAGGCCCTGACCTCGGCGCCGGGATCGGTCGCGCA
GGTGCGCGAGTGCGCGGCGCAGCTCACCCGCCACGCCAAGCAGAGCGGCACCGCGGTCATCCTGGTCGGGCACGTCACCA
AGGAAGGCGCGATCGCCGGGCCGCGCGTGCTCGAGCACATTGTCGACACCGTGTTGTACTTCGAGGGGGACACGGGCTCG
AGCTACCGCCTCGTGCGCGCGTTCAAGAACCGCTTCGGGGCGGTCAACGAGATCGGCGTGTTCGCGATGACCGAAAAGGG
CCTGAAGGGCGTTTCGAACCCCTCGGCAATCTTTCTCTCGCGTCACGGCGAGCCCGTGCCGGGTTCGTGCGTGCTCGTGA
CGCAGGAAGGAACGCGCCCGCTCCTCGTCGAGATCCAGGCGCTCGTCGACACGAGTCACGCGCCCAATCCACGCCGTCTG
AGTGTCGGCCTCGAGCAGAACCGTCTCGCGATGCTACTCGCCGTCTTGCATCGCCACGCCGGCATCGCCTGTTTCGATCA
GGACGTCTTCGTCAACGCGGTCGGCGGGGTGAAGATCAGCGAGCCGGCGGCCGACCTCGCCGTCCTGGCCGCGATCGTGT
CGTCGCTTAGGAGCCAGCCGCTGCCCGACAAGCTCGTGATGTTCGGCGAAGTGGGGCTCGCCGGCGAGATCCGTCCGGTG
CAGCGCGGACAGGAGCGCCTGAAGGAAGCGGCCAAGCTCGGCTTCACCCAGGCCATCGTGCCGGCCGCGAACCAGCCCAA
GCAGAAAATCGCCGGCATGACGGTGCACGCGGTGCAGCGTCTCGACGACGCGATCAGCCTGTTCCGCGGCTAG

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(340-424)

AAA domain (AAA_25)

(63-216)

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
  AlphaFold DB Q3SK72

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

51.395

95.556

0.491
  radA Streptococcus mitis SK321

45.872

96.889

0.444
  radA Streptococcus pneumoniae D39

45.767

97.111

0.444
  radA Streptococcus pneumoniae TIGR4

45.767

97.111

0.444
  radA Streptococcus pneumoniae R6

45.767

97.111

0.444
  radA Streptococcus pneumoniae Rx1

45.767

97.111

0.444
  radA Streptococcus mitis NCTC 12261

45.642

96.889

0.442

Multiple sequence alignment