Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102761
Name   oriT_pRphaN261d in_silico
Organism   Rhizobium phaseoli strain N261
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013584 (955965..955993 [-], 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_pRphaN261d
AGGGCGCAATATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2036 GenBank   WP_064820496
Name   traA_AMC79_RS31390_pRphaN261d insolico UniProt ID   A0A7X6J0B9
Length   1543 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1543 a.a.        Molecular weight: 171090.63 Da        Isoelectric Point: 7.0921

>WP_064820496.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGISFSYRGGASELMHEELALPDQIPAWLKMAMDG
RSIAKASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVSGNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGPKKVAVLGEHGKPLRVVTPDRPNGRIVYKVWAGDKETMKAWKVAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELFFAPADLARRQEMADRLLAEPELLLKQ
LGNESSTFDEKDIAKALHRYVDDPVEFANIRARLMASDELVMLKPQEMDADTGKVSEPALFTTRDMLRIE
YYMADSARRLSNRSGYAVSRKHVAAAIERIESDDPKNLFRLDAEQGDAIRHVTGDSGIAAVVGLAGAGKS
TLLAAARLAWESEGRRVIGAALAGKAAEGLEDSSGIKSRTLASWELTWANGRDTLHRGDVLVIDEAGMVS
SQQMARVLKIAEEAEIKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQRQEWARDASRLFARGE
VERGLDAYAQQGHLVEAGTREEAINRIVVDWTEARKQAIDRSTSEGRDGHLRGDELLVLAHTNADVKRLN
EALREVMKAEQALSDSRTFQTARGAREFAVGDRIIFLENARFLEPRARHSGPQYVKNGMLGTVVATGDKR
GDPLMSVLLDNGRNVVFSEDSYRNVDHGYASTIHKSQGATVDRTFVLATGMMDRHLTYVSMTRHRDRADL
YAVKEDFQVRSEWGRRLRADHAAGVTGELVETGEAKFRPDDEDADDSHYADIRTGDGTVHRLWGVSLPKA
LEEAGISEGDTITLRKDGVERVKVQIAVVDEATGQKRYDEREVDRNVWRAKQIETADARQERIERERHRP
DVFGRLVERLARSGAKTTTLDFESEAGYRAHADDFARRRGLDHLSLAAAEMEEGVSRRLAWIAEKRGQIA
KLWERASVALGLAIERERRVAYNEERSETMIGAISSEERYLIPPATDFRRSLDEDARLAQLSSPAWKERE
AILRPLLETIYRDPDAALVRLNALASYTGTEPRGLADNLAVAPDRLGRLRGSELIVEGRAARDERDVAMA
ALEELLPLVRGHATEFRRNAERFELREQARRASMSLSVPALSEQAMARLMEIEAVRTQGGDDAYKTAFAL
AAEDRSVVQEVKAVSEALTARFGWSAFTAKADAMAERNMVERMPEDLSAGRREELIRLFEAVKRFAEEQH
LAERRDRSKIVAAASAVPGAAPGKQTVTVLPMLAAVTEFKTSVDDEARSRAIAAPLYRQQRAALAEAARM
IWRDPAATVDNIESLLEKGFAADRIAAAVTNDPAAYGALRGSDRLMDRMLASGRERKDAVQAVPEAAARL
RSLGSAYVNVLDAERQAIAEERRRMAVAIPGLSKAAEGVLMRLTTEVKNNGRTRNAAAGSLDPSIHREFD
AVSRALDERFGRSAIVRGEKDLLNRMPPAQRAAFAAMQEKLKVLQQTVRWESSEKIVSELRNRTVNRGRG
IEL

  Protein domains


Predicted by InterproScan.

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

(1313-1404)

AAA domain (AAA_30)

(391-577)

MobA/MobL family (MobA_MobL)

(17-249)


  Protein structure



No available structure.




T4CP

ID   1689 GenBank   WP_064820498
Name   traG_AMC79_RS31405_pRphaN261d 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: 70447.36 Da        Isoelectric Point: 9.3885

>WP_064820498.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MIARGKPHPSLLFVFAPVVVTAIAVYIAGWRWPGLAAGMPGRMEYWFLRAAPVPALLFGPLAGLLTVWAL
PLHRRRPVAMTSLLCYLGVSASFAMREFARLGPSVQTGVITWDRALSYLDMVAVLGAVAGFLAVALSARI
SVVVPDEINRARRGTFGDADWLSMAAAAKLFPPDGEIVVGERYRVDKEIVHQLPFDANDRGTWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTHTLGREVMVLDPT
NPIMGFNVLDGIETSRQKEEDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLREIVSEPEPSVLAMLRDIQENSQSDFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GKAFKPSDIVSGRKDVFLNIPASILRSYPGIGRVIIGSLINAMMQADGAFRRRALFMLDEVDLLGYMRVL
EEARDRGRKYGVSMMLMYQSVGQLERHFGKDGATSWIEGCAFASYAAVKALDTARTVSAQCGEMTVEVKG
SSRNLGWNSRNGGTRKSESVSFQRRPLIMPHEITQSMRKDEQVIIVQGHSPIRCGRAIYFRRKEMDGVAK
ANRFVKPVP

  Protein domains


Predicted by InterproScan.

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

(165-632)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 967872..977428

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC79_RS31450 (AMC79_PD00902) 963447..963629 + 183 WP_012490320 hypothetical protein -
AMC79_RS31455 (AMC79_PD00903) 963762..964799 - 1038 WP_064820506 toprim domain-containing protein -
AMC79_RS31460 (AMC79_PD00904) 965162..966352 + 1191 WP_064820507 DUF1173 domain-containing protein -
AMC79_RS31465 (AMC79_PD00905) 966795..967388 + 594 WP_037146723 DUF433 domain-containing protein -
AMC79_RS31470 (AMC79_PD00906) 967403..967828 + 426 WP_237357452 PIN domain-containing protein -
AMC79_RS31475 (AMC79_PD00907) 967872..968867 - 996 WP_064820508 P-type DNA transfer ATPase VirB11 virB11
AMC79_RS31480 (AMC79_PD00908) 968876..970051 - 1176 WP_064820509 type IV secretion system protein VirB10 virB10
AMC79_RS31485 (AMC79_PD00909) 970060..970914 - 855 WP_037146719 P-type conjugative transfer protein VirB9 virB9
AMC79_RS31490 (AMC79_PD00910) 970911..971582 - 672 WP_037146717 virB8 family protein virB8
AMC79_RS31495 (AMC79_PD00911) 971576..971863 - 288 WP_016737562 hypothetical protein -
AMC79_RS31500 (AMC79_PD00912) 971904..972836 - 933 WP_046977230 type IV secretion system protein virB6
AMC79_RS31505 (AMC79_PD00913) 972839..973072 - 234 WP_016735278 EexN family lipoprotein -
AMC79_RS31510 (AMC79_PD00914) 973069..973770 - 702 WP_016735279 P-type DNA transfer protein VirB5 virB5
AMC79_RS31515 (AMC79_PD00915) 973767..976133 - 2367 WP_046977231 VirB4 family type IV secretion system protein virb4
AMC79_RS31520 (AMC79_PD00916) 976126..976464 - 339 WP_064820510 type IV secretion system protein VirB3 virB3
AMC79_RS31525 (AMC79_PD00917) 976470..976769 - 300 WP_064820511 TrbC/VirB2 family protein virB2
AMC79_RS31530 (AMC79_PD00918) 976766..977428 - 663 WP_064820512 transglycosylase SLT domain-containing protein virB1
AMC79_RS31535 (AMC79_PD00919) 977432..977968 - 537 WP_064820513 hypothetical protein -
AMC79_RS31540 (AMC79_PD00920) 978067..978438 + 372 WP_041684118 hypothetical protein -
AMC79_RS31545 (AMC79_PD00921) 978791..979981 - 1191 WP_064820514 hypothetical protein -
AMC79_RS31550 (AMC79_PD00922) 980056..980712 - 657 WP_064820515 hypothetical protein -

Host bacterium

ID   3204 GenBank   NZ_CP013584
Plasmid name   pRphaN261d Incompatibility group   -
Plasmid size   1074794 bp Coordinate of oriT [Strand]   955965..955993 [-]
Host baterium   Rhizobium phaseoli strain N261

Cargo genes

Drug resistance gene   -
Virulence gene   gmd
Metal resistance gene   hupE2
Degradation gene   dxnH, LinG
Symbiosis gene   noeL, fixB, fixA
Anti-CRISPR   AcrIIA8