Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102778
Name   oriT_pRphaN161d in_silico
Organism   Rhizobium phaseoli strain N161
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013589 (936266..936294 [-], 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_pRphaN161d
AGGGCGCAATATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2050 GenBank   WP_064837782
Name   traA_AMC78_RS31415_pRphaN161d insolico UniProt ID   _
Length   1545 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1545 a.a.        Molecular weight: 171311.65 Da        Isoelectric Point: 6.7554

>WP_064837782.1 Ti-type conjugative transfer relaxase TraA [Rhizobium phaseoli]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGISFSYRGGASELMHEELALPDQIPAWLKMAMDG
RSIAKASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVSGNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGPKKVAVLGEHGKPLRVVTPDRPNGRIVYKVWAGDKETMKAWKVAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELFFAPADLARRQEMADRLLAEPELLLKQ
LGNESSTFDEKDIAKALHRYVDDPVEFANIRARLMASDELVMLKPQEMDADTGKVSEPALFTTRDMLRIE
YYMADSARRLSNRSGYAVSRKHVAAAIERIESDDPKNLFRLDAEQGDAIRHVTGDSGIAAVVGLAGAGKS
TLLAAARLAWESEGRRVIGAALAGKAAEGLEDSSGIKSRTLASWELTWANGRDTLHRGDVMVIDEAGMVS
SQQMARVLKIAEEAEIKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQRQEWARDASRLFARGE
VERGLDAYAQQGHLVEAGTREEAINRIVVDWTEARKQAIDRSTSEGRDGHLRGDELLVLAHTNADVKRLN
EALREVMKAEQALSDSRTFQTARGAREFAVGDRIIFLENARFLEPRARHSGPQYVKNGMLGTVVATGDKR
GDPMLSVLLDNGRNVVFSEDSYGNVDHGYAATIHKSQGATVDRTFVLATGIMDRHLTYVSMTRHRDRADL
YAAKEDFQARSEWGRRLRADHAAGVTGELVETGEAKFRPDDEDADDSPYADIRTDDGTVHRLWGVSLPKA
LEEAGISEGDTITLRKDGVERVKVQIAVVDEATGQKRYEEREVDRNVWTAKQIETAEARQERIEREGHRP
DVFGRLVERLARSGAKTTTLDFESEAGYRAHADDFARRRGLDHLSLAAAEMEEGVSRRLAWIAEKRGQIA
KLWERASVALGLAIERERRVAYNEERSETMIGAISSEERYLMPPATDFRRSLDEDARLAQLSSPAWKERE
AILRPLLETIYRDPDAALVRLNALASDTGTEPRKLADDLAVAPDLLGRLHGSDLIVDGRAAREERDVAMA
ALAELLPLARGHATEFRRNAERFELREQTRRASMSLSVPALSERAMTRLLEIEAVRTQGGDDAYKTAFAL
AAEDRSVVQEVKAVSEALTARFGWSAFTAKADAMAERNMVERMPEDLSAGRREELTRLFEAVKRFDGEQH
LAERQDRWRIVAGAAAVPGTEQGKEQRKENVTIPPMLAAVTEFKTPVDEEARSRVLSAPLYRQQRVALAN
AARTIWRDPAGAVDKIEELLVKGFAADRIAPAVTNDPAAYGALRGSGRLMDRMLASGRERKEAVQAVPEA
AARLRSLGSAYVNVLDAERQAIAEERRRMAVAIPGLSKAAEGVLMRLTTEAKNNGRTRNAATGSLDPSIH
REFDAVSRALDERFGRSARGEKDLLNRMPPAQRAAFAAMQEKLKVLQQTVRWESSEKIVSELRNRTVNRG
RDIDL

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(391-577)

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

(1045-1125)

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

(1314-1408)

MobA/MobL family (MobA_MobL)

(17-249)


  Protein structure



No available structure.




T4CP

ID   1705 GenBank   WP_064837787
Name   traG_AMC78_RS31430_pRphaN161d 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: 70461.39 Da        Isoelectric Point: 9.3885

>WP_064837787.1 Ti-type conjugative transfer system protein TraG [Rhizobium phaseoli]
MIARGKPHPSLLFVFAPVVVTAIAVYIAGWRWPGLAAGMPGRMEYWFLRAAPVPALLFGPLAGLLTVWAL
PLHRRRPVAMTSLLCYLGVSASFAMREFARLGPSVQTGVITWDRALSYLDMVAVLGAVAGFLAVALSARI
SVVVPDEINRARRGTFGDADWLSMAAAAKLFPPDGEIVVGERYRVDKEIVHQLPFDANDRGTWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTHTLGREVMVLDPT
NPIMGFNVLDGIETSRQKEEDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLREIVSEPEPSVLAMLRDIQENSQSDFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GKAFKPSDIVSGRKDVFLNIPASILRSYPGIGRVIIGSLINAMMQADGAFRRRALFMLDEVDLLGYMRVL
EEARDRGRKYGVSMMLMYQSVGQLERHFGKDGATSWIEGCAFASYAAVKALDTARTVSAQCGEMTVEVKG
SSRNLGWNSRNGGTRKSESVSFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDGVAK
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: 947555..957110

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC78_RS31460 943125..943307 + 183 WP_037146733 hypothetical protein -
AMC78_RS31465 (AMC78_PD00861) 943440..944480 - 1041 WP_037146729 toprim domain-containing protein -
AMC78_RS31470 (AMC78_PD00862) 944843..946033 + 1191 WP_037146725 DUF1173 domain-containing protein -
AMC78_RS31475 (AMC78_PD00863) 946476..947069 + 594 WP_037146723 DUF433 domain-containing protein -
AMC78_RS31480 (AMC78_PD00864) 947084..947536 + 453 WP_016735273 PIN domain-containing protein -
AMC78_RS31485 (AMC78_PD00865) 947555..948550 - 996 WP_064829760 P-type DNA transfer ATPase VirB11 virB11
AMC78_RS31490 (AMC78_PD00866) 948559..949734 - 1176 WP_064837789 type IV secretion system protein VirB10 virB10
AMC78_RS31495 (AMC78_PD00867) 949743..950597 - 855 WP_064837791 P-type conjugative transfer protein VirB9 virB9
AMC78_RS31500 (AMC78_PD00868) 950594..951265 - 672 WP_064837792 virB8 family protein virB8
AMC78_RS34755 (AMC78_PD00869) 951259..951546 - 288 WP_080712055 hypothetical protein -
AMC78_RS31505 (AMC78_PD00870) 951586..952518 - 933 WP_064837794 type IV secretion system protein virB6
AMC78_RS31510 (AMC78_PD00871) 952521..952754 - 234 WP_012490331 EexN family lipoprotein -
AMC78_RS31515 (AMC78_PD00872) 952751..953452 - 702 WP_064837796 P-type DNA transfer protein VirB5 virB5
AMC78_RS31520 (AMC78_PD00873) 953449..955815 - 2367 WP_064837797 VirB4 family type IV secretion system protein virb4
AMC78_RS31525 (AMC78_PD00874) 955808..956146 - 339 WP_064837799 type IV secretion system protein VirB3 virB3
AMC78_RS31530 (AMC78_PD00875) 956152..956451 - 300 WP_016735283 TrbC/VirB2 family protein virB2
AMC78_RS31535 (AMC78_PD00876) 956448..957110 - 663 WP_064837801 transglycosylase SLT domain-containing protein virB1
AMC78_RS31540 (AMC78_PD00877) 957114..957650 - 537 WP_064820513 hypothetical protein -
AMC78_RS31545 (AMC78_PD00878) 957749..958120 + 372 WP_064824316 hypothetical protein -
AMC78_RS31550 (AMC78_PD00879) 958473..959663 - 1191 WP_064837803 hypothetical protein -
AMC78_RS31555 (AMC78_PD00880) 959737..960393 - 657 WP_064830295 hypothetical protein -

Host bacterium

ID   3221 GenBank   NZ_CP013589
Plasmid name   pRphaN161d Incompatibility group   -
Plasmid size   1048055 bp Coordinate of oriT [Strand]   936266..936294 [-]
Host baterium   Rhizobium phaseoli strain N161

Cargo genes

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