Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107581
Name   oriT_pRetKim5a in_silico
Organism   Rhizobium sp. Kim5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021125 (203725..203753 [+], 29 nt)
oriT length   29 nt
IRs (inverted repeats)      14..19, 24..29  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 29 nt

>oriT_pRetKim5a
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5095 GenBank   WP_085861369
Name   traA_KIM5_RS23650_pRetKim5a insolico UniProt ID   _
Length   1562 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1562 a.a.        Molecular weight: 172386.71 Da        Isoelectric Point: 8.0075

>WP_085861369.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAIMFVRAQVISRGSGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAGELMYEELALPDEIPDWLRSAISG
QSVSKASEVFWNAVDAFETRADAQLARELIIALPEELTRAENITLVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGAKKVPVLGEGGKPLRVVTPDRPNGKIVYKVWAGDKETMKAWKIAWAETANR
HLALAGHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLSEPELLLKQ
LGNERSTFDERDIARALHRYVDDPTDFANIRARLMASDQLVILKPQEIEAETGKVSEPAVFTTREMLRIE
YDMAQSARVLSERRGFGVSERNVTVAIERVESGDPKNPFRLDAEQVDAVRHVTGDGGIAAIVGLAGAGKS
TLLAAARLAWESEGHRVIGAALAGKAAEGLQDSSGIKSRTLASWELAWANGRDTLHRGDVLVIDEAGMVA
SQQMARVLKIAEEAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREAWARNASRLFARGE
VEKGLDAYARHGHLVEAGSREETIDRIVSDWAAARREAIERSTSEGGDGRLRGDELLVLAHTNDDVRKLN
EALRSVMTQEGALGESRSFRSERGAREFAAGDRIIFLENARFLEPRAKHSGPQYVKNGMLGTVVSTGDKR
GDPLLSILLDNGRKLVFSEDSYRHVDHGYAATIHKSQGATVDRTFVLATGMMDQHLTYVSMTRHRDRVDL
YAAKEDFAAKPEWGRKPRVDHAAGVTGELVETGQAKFRPDDEDADDSPYADVRADDGTVHRLWGVSLPKA
LEEAGIQEGDTVTLRKDGVERVKVQIAVVDEKTGHKHYEEREVDRNVWTASQVETASARQERIARESHRP
ELFNPLVERLSRSGAKTTTLDFESEASYRAHANDFARRRGLDHLSLAAAEMEQSLTRRWAWIAAKREQVE
KLWERASVALGFAIERERRVVYNEERSQTMVEATSSDARTASHSVSGASAAETRYLIPPATSFVSSVEED
ARLAQLASPAWTEREVILRPLLQKIYRDPDAALVSLNALASDIGVAPRRLADDLAAAPGRLGRLRGSELI
VDGGAAREERNLAVAAVKELLPMARAHATEFRRNAERFVLREQTRRAHMSLSIPALSERAMARLMEIEAV
RRQGGDDAYKTAFALTAKDRSVVQEIKAVSEALTARFGWSAFSAKADAIAERNIVERMPEDLTDERRGKL
TRLFDAVRRFADEQHLAERRDRSKVVAGASVVRGQETENGPGKENVAVPPMLAAVIAFKTSVDDEARLRA
LSNPFYRQQRGALANAATTIWRDPAEVVGKIEELLQKGFAAERIGAAVTNNPAAYGALRGSDRLMDRMLT
SGRERKEAVAAVPEAAARLRALGAAHLNALDAERQAITDERRRMAVAIPALSKAAEEALAHLTVEVSKDS
RKLSVSAASLDPGIGREFAAVSRALDERFGRNALVRGDKDLVNRVPPAQRRAFEAMQERLKVLQQTVRLQ
SSEQIIAERRQRAASRARGINL

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(391-576)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(1069-1140)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(1332-1422)


  Protein structure



No available structure.




T4CP

ID   5314 GenBank   WP_086156517
Name   traG_KIM5_RS23635_pRetKim5a insolico UniProt ID   _
Length   639 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 639 a.a.        Molecular weight: 70635.81 Da        Isoelectric Point: 9.5676

>WP_086156517.1 Ti-type conjugative transfer system protein TraG [Rhizobium sp. Kim5]
MGLRGKPHPSLLLVLVPIAVTTITIYIVGWRWPGLAAGMSGKIEHWFLRAAPVPPLLFGPLAGLLTVWAL
PLHRRRPVAMASLLYFLGVAAFYALREFGRLAPAVQAEVITWDRALSYLDMVAVIAAVAGFMAVAMSARI
SVVVPDEIKRARRGIFGDADWLPMTAAGKLFPPDGEIVVGERYRVDKEIIHALPFDVNDRSTWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYSGPLICLDPSTEVAPMVAGHRARALKREVMVLDPT
NPIMGFNVLDGIEASKQKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYEGRRS
LRSLRQIVSEPEPSVLAMLRDIQEHSGSAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNISASILRSYPGIARVIIGSLINAMVQADGAFQRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVKG
SSRNIGWDTKNNASRRSENVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDQAAK
VNRFVKPVL

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(170-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 183994..193554

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KIM5_RS34880 180488..180714 - 227 Protein_182 chaperonin GroEL -
KIM5_RS23500 (Kim5_PA00211) 181009..181929 + 921 WP_029875459 zincin-like metallopeptidase domain-containing protein -
KIM5_RS23505 (Kim5_PA00212) 182040..182222 - 183 WP_009993909 hypothetical protein -
KIM5_RS23510 (Kim5_PA00214) 182984..183355 - 372 WP_012489483 hypothetical protein -
KIM5_RS23515 (Kim5_PA00215) 183454..183990 + 537 WP_012489484 hypothetical protein -
KIM5_RS23520 (Kim5_PA00216) 183994..184635 + 642 WP_009991940 transglycosylase SLT domain-containing protein virB1
KIM5_RS23525 (Kim5_PA00217) 184650..184949 + 300 WP_009991942 TrbC/VirB2 family protein virB2
KIM5_RS23530 (Kim5_PA00218) 184955..185293 + 339 WP_010068249 type IV secretion system protein VirB3 virB3
KIM5_RS23535 (Kim5_PA00219) 185286..187652 + 2367 WP_086156514 VirB4 family type IV secretion system protein virb4
KIM5_RS23540 (Kim5_PA00220) 187649..188350 + 702 WP_009996884 P-type DNA transfer protein VirB5 virB5
KIM5_RS23545 (Kim5_PA00221) 188347..188580 + 234 WP_009996882 EexN family lipoprotein -
KIM5_RS23550 (Kim5_PA00222) 188583..189515 + 933 WP_009996881 type IV secretion system protein virB6
KIM5_RS34885 (Kim5_PA00223) 189555..189836 + 282 WP_012489488 hypothetical protein -
KIM5_RS23560 (Kim5_PA00224) 189838..190509 + 672 WP_029875461 virB8 family protein virB8
KIM5_RS23565 (Kim5_PA00225) 190506..191363 + 858 WP_009996879 P-type conjugative transfer protein VirB9 virB9
KIM5_RS23570 (Kim5_PA00226) 191372..192517 + 1146 WP_086156515 type IV secretion system protein VirB10 virB10
KIM5_RS23575 (Kim5_PA00227) 192526..193554 + 1029 WP_012489491 P-type DNA transfer ATPase VirB11 virB11
KIM5_RS23580 (Kim5_PA00228) 193598..194170 - 573 WP_010067915 PIN domain-containing protein -
KIM5_RS23585 (Kim5_PA00229) 194160..194606 - 447 WP_029875463 hypothetical protein -
KIM5_RS23590 (Kim5_PA00231) 195119..196309 - 1191 WP_012489493 DUF1173 domain-containing protein -
KIM5_RS34890 196620..196879 + 260 Protein_202 toprim domain-containing protein -
KIM5_RS23595 (Kim5_PA00233) 197267..197533 + 267 WP_004676093 hypothetical protein -
KIM5_RS23600 (Kim5_PA00234) 197530..197928 + 399 WP_008536014 type II toxin-antitoxin system VapC family toxin -

Host bacterium

ID   8016 GenBank   NZ_CP021125
Plasmid name   pRetKim5a Incompatibility group   -
Plasmid size   431886 bp Coordinate of oriT [Strand]   203725..203753 [+]
Host baterium   Rhizobium sp. Kim5

Cargo genes

Drug resistance gene   -
Virulence gene   hsiC1/vipB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nifX, nifE, nifK, nifD, nifH, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, nifT, nodD, nodJ, nodI, nodS, nodC, fixG, fixO, fixN, mLTONO_5203, nodA
Anti-CRISPR   AcrIF11