Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   OHM81_RS01735 Genome accession   NZ_CP109857
Coordinates   378422..379807 (+) Length   461 a.a.
NCBI ID   WP_016448587.1    Uniprot ID   A0AAX3SMY1
Organism   Delftia tsuruhatensis strain GSK TC1     
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 333969..378200 378422..379807 flank 222


Gene organization within MGE regions


Location: 333969..379807
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  OHM81_RS01505 - 333983..334570 (-) 588 WP_338499420.1 hypothetical protein -
  OHM81_RS01510 - 335592..336530 (-) 939 WP_338499421.1 hypothetical protein -
  OHM81_RS01515 - 336542..337033 (-) 492 WP_338499422.1 helix-turn-helix transcriptional regulator -
  OHM81_RS01520 - 337030..337668 (-) 639 WP_338499423.1 hypothetical protein -
  OHM81_RS01525 - 337665..337877 (-) 213 WP_338499424.1 transcriptional regulator -
  OHM81_RS01530 - 338028..338555 (+) 528 WP_338499425.1 multiubiquitin domain-containing protein -
  OHM81_RS01535 - 338558..338935 (+) 378 WP_338499426.1 E2/UBC family protein -
  OHM81_RS01540 - 338932..340341 (+) 1410 WP_338499427.1 ThiF family adenylyltransferase -
  OHM81_RS01545 - 341438..341704 (-) 267 WP_338499428.1 hypothetical protein -
  OHM81_RS01550 - 341768..341872 (+) 105 Protein_309 transposase -
  OHM81_RS01555 - 341921..343155 (+) 1235 WP_086004667.1 IS3 family transposase -
  OHM81_RS01560 - 343189..344237 (+) 1049 Protein_311 IS3 family transposase -
  OHM81_RS01565 - 344234..344542 (-) 309 WP_338499429.1 recombinase family protein -
  OHM81_RS01570 - 345020..346039 (-) 1020 WP_338499430.1 LysR family transcriptional regulator -
  OHM81_RS01575 - 346245..347540 (+) 1296 WP_034368750.1 MFS transporter -
  OHM81_RS01580 rhmD 347570..348757 (+) 1188 WP_338499431.1 L-rhamnonate dehydratase -
  OHM81_RS01585 - 348769..349578 (+) 810 WP_338499432.1 HpcH/HpaI aldolase/citrate lyase family protein -
  OHM81_RS01590 aldA 349595..351028 (+) 1434 WP_338499433.1 aldehyde dehydrogenase -
  OHM81_RS01595 - 351042..352025 (-) 984 WP_034397791.1 alpha/beta fold hydrolase -
  OHM81_RS01600 - 352084..352599 (-) 516 WP_016448606.1 MarR family transcriptional regulator -
  OHM81_RS01605 - 352702..353679 (+) 978 WP_016448605.1 tripartite tricarboxylate transporter substrate binding protein -
  OHM81_RS01610 - 353765..355093 (+) 1329 WP_034368742.1 sulfatase-like hydrolase/transferase -
  OHM81_RS01615 - 355162..356025 (-) 864 WP_099752945.1 DUF4034 domain-containing protein -
  OHM81_RS01620 - 356465..356701 (-) 237 WP_143044705.1 hypothetical protein -
  OHM81_RS01625 - 356874..357200 (-) 327 WP_074924007.1 Imm58 family immunity protein -
  OHM81_RS01630 - 357205..359742 (-) 2538 WP_338500818.1 RHS repeat-associated core domain-containing protein -
  OHM81_RS01635 - 359749..359940 (-) 192 Protein_326 RHS repeat domain-containing protein -
  OHM81_RS01640 - 360011..360895 (-) 885 Protein_327 RHS repeat protein -
  OHM81_RS01645 - 361060..361800 (-) 741 WP_338499434.1 DUF6531 domain-containing protein -
  OHM81_RS01650 tssI 361888..364242 (-) 2355 WP_338499435.1 type VI secretion system tip protein TssI/VgrG -
  OHM81_RS01655 - 364706..365437 (+) 732 WP_016448601.1 TorF family putative porin -
  OHM81_RS01660 - 365461..365799 (+) 339 WP_012202241.1 P-II family nitrogen regulator -
  OHM81_RS01665 amt 365831..367204 (+) 1374 WP_338499436.1 ammonium transporter -
  OHM81_RS01670 - 367402..367773 (+) 372 WP_043792857.1 type II toxin-antitoxin system RelE/ParE family toxin -
  OHM81_RS01675 - 367766..368077 (+) 312 WP_016448598.1 helix-turn-helix transcriptional regulator -
  OHM81_RS01680 glcE 368214..369353 (+) 1140 WP_338499437.1 glycolate oxidase subunit GlcE -
  OHM81_RS01685 - 369379..370161 (+) 783 WP_012202244.1 YoaK family protein -
  OHM81_RS01690 glcF 370223..371473 (+) 1251 WP_154833181.1 glycolate oxidase subunit GlcF -
  OHM81_RS01695 - 371558..372424 (+) 867 WP_154833183.1 ProQ/FinO family protein -
  OHM81_RS01700 - 372733..373251 (+) 519 WP_016448593.1 AmiS/UreI family transporter -
  OHM81_RS01705 - 373279..374178 (-) 900 WP_338499438.1 DMT family transporter -
  OHM81_RS01710 lplT 374242..375543 (-) 1302 WP_016448591.1 lysophospholipid transporter LplT -
  OHM81_RS01715 alr 375678..376781 (+) 1104 WP_047218852.1 alanine racemase -
  OHM81_RS01720 - 376782..377222 (-) 441 WP_016448589.1 MarR family transcriptional regulator -
  OHM81_RS01725 - 377319..378134 (+) 816 WP_017407487.1 siderophore-interacting protein -
  OHM81_RS01735 radA 378422..379807 (+) 1386 WP_016448587.1 DNA repair protein RadA Machinery gene

Sequence

Protein


Download         Length: 461 a.a.        Molecular weight: 48096.64 Da        Isoelectric Point: 7.6673

>NTDB_id=750221 OHM81_RS01735 WP_016448587.1 378422..379807(+) (radA) [Delftia tsuruhatensis strain GSK TC1]
MAKDKTTFICNACGGSSPRWLGKCPACGAWNSLIEAVAEPAGAGKNRLSQPQGYAGLANAQAVMPLSAIEAQDVARTPSG
IEELDRVLGGGIVEGGVVLIGGDPGIGKSTLLLQAMDALHRVGLPTLYVTGEESGAQVALRSRRLGLEASQVNVLAEIQL
EKILATMEATQPAVVVIDSIQTVYSDQLSSAPGSVAQVRECAAHLTRAAKTTGITVILVGHVTKEGALAGPRVLEHMVDT
VLYFEGDTHSNFRLVRAIKNRFGAVNEIGVFAMTEKGLKGVTNPSAIFLSQHSEPVPGSCVLVTLEGTRPMLVEIQALVD
QGGPAPRRLSVGLDRDRLAMLLAVLSRHAGVACADQDVFVNAVGGVRISEPAADLAVMLSITSSLRGRALPKGFLAFGEV
GLAGEVRPAPRGQERLKEAAKLGFTMAVVPKANAPKKAIPGLTVHAVERVDEAMNIVRGMG

Nucleotide


Download         Length: 1386 bp        

>NTDB_id=750221 OHM81_RS01735 WP_016448587.1 378422..379807(+) (radA) [Delftia tsuruhatensis strain GSK TC1]
ATGGCCAAAGACAAAACCACGTTCATCTGCAATGCCTGCGGCGGCTCCAGCCCGCGCTGGCTGGGCAAGTGCCCGGCCTG
CGGGGCCTGGAATTCGCTGATCGAGGCCGTTGCCGAGCCTGCGGGCGCGGGCAAGAACCGGCTCAGCCAGCCGCAGGGCT
ATGCGGGCCTGGCCAATGCCCAGGCCGTGATGCCGCTGTCGGCCATCGAGGCCCAGGACGTGGCGCGCACGCCCAGCGGC
ATCGAGGAGCTGGACCGCGTGCTGGGCGGCGGCATTGTCGAAGGCGGCGTGGTGCTGATTGGTGGCGACCCCGGCATCGG
CAAGTCCACCCTGCTGCTGCAGGCCATGGATGCGCTGCACCGCGTGGGCCTGCCCACGCTGTATGTGACCGGCGAGGAAA
GCGGTGCCCAGGTCGCGCTGCGTTCGCGCCGCCTGGGGCTGGAGGCCAGCCAGGTCAATGTGCTGGCCGAGATCCAGCTG
GAGAAGATCCTCGCCACCATGGAGGCCACGCAGCCGGCCGTGGTCGTCATCGACTCCATTCAGACCGTGTACTCGGACCA
GCTGTCCTCGGCGCCGGGCTCGGTGGCCCAGGTGCGCGAATGCGCGGCCCACCTCACGCGCGCGGCCAAGACCACGGGCA
TCACCGTGATCCTGGTCGGCCATGTGACCAAGGAAGGCGCCCTGGCCGGCCCGCGCGTGCTGGAGCACATGGTGGACACC
GTGCTCTACTTCGAGGGCGACACGCACAGCAACTTCCGCCTGGTGCGCGCCATCAAGAACCGCTTTGGCGCCGTCAACGA
GATCGGCGTCTTCGCCATGACGGAGAAGGGCCTCAAGGGCGTCACCAACCCCAGCGCCATCTTCCTGTCCCAGCACAGCG
AGCCGGTGCCGGGCTCCTGCGTGCTGGTCACGCTGGAGGGCACGCGGCCCATGCTGGTGGAAATACAGGCCCTGGTCGAC
CAGGGCGGCCCCGCGCCCCGGCGCCTGTCCGTGGGCCTGGACCGGGACCGGCTGGCCATGCTGCTGGCCGTGCTCAGCCG
CCATGCGGGCGTGGCCTGCGCGGACCAGGATGTGTTCGTCAACGCCGTGGGCGGCGTGCGCATCAGCGAGCCTGCGGCCG
ACCTGGCCGTCATGCTGTCCATCACCTCCAGCCTGCGCGGCCGCGCCCTGCCCAAGGGATTCCTGGCCTTTGGCGAAGTG
GGCCTGGCCGGCGAAGTGCGCCCCGCGCCGCGCGGCCAGGAGCGCCTGAAGGAAGCCGCCAAGCTCGGCTTCACCATGGC
CGTGGTGCCCAAGGCCAATGCGCCCAAGAAGGCCATCCCCGGCCTGACCGTGCATGCCGTGGAGCGCGTGGACGAAGCCA
TGAACATCGTCCGAGGGATGGGCTGA

Domains

Predicted by InterproScan.

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

AAA domain (AAA_25)

(68-226)


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

48.684

98.915

0.482
  radA Streptococcus mitis NCTC 12261

47.368

98.915

0.469
  radA Streptococcus pneumoniae Rx1

48.19

95.879

0.462
  radA Streptococcus pneumoniae D39

48.19

95.879

0.462
  radA Streptococcus pneumoniae R6

48.19

95.879

0.462
  radA Streptococcus pneumoniae TIGR4

48.19

95.879

0.462
  radA Streptococcus mitis SK321

48.961

93.926

0.46