Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102781
Name   oriT_pRphaR620d in_silico
Organism   Rhizobium phaseoli strain R620
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013546 (962481..962509 [-], 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_pRphaR620d
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2053 GenBank   WP_064826469
Name   traA_AMC86_RS31005_pRphaR620d insolico UniProt ID   _
Length   1536 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1536 a.a.        Molecular weight: 170773.15 Da        Isoelectric Point: 7.2193

>WP_064826469.1 Ti-type conjugative transfer relaxase TraA [Rhizobium phaseoli]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGAASELMHEELALPDQIPAWLKMAMDG
RSIAKASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGPKKVAVLGEHSKPLRVVTPDRPNGRIVYKVWAGDKETMKAWKVAWAETANR
HLALAGHEIRLDGRSYAEQGLDGVAQKHLGPEKAALARKGRELFFAPADLARRQGMADRLLAEPELLLKQ
LGNERSTFDEKDIAKALHRCVDDPVEFANIRARLMASDELVMLKPQEMDADTGKVSEPAVFTTRDMLRIE
YHMAESARRLSNRSGYAVSRKHVAAAIERIESEDPKNLFHLDAEQVDAIRHVTGDSGIAAVVGLAGAGKS
TLLAAARLAWESEGRRVIGAALAGKAAEGLEDSSGIKSRTLASWELTWANGRDTLHRGDVLVIDEAGMVS
SQQMARVLKIAEEAEIEVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQRQEWARDASRLFARGE
VEKGLDAYAQQGHLVEAGTREEAINRIVADWTEARKQAIDRSTSEGRDGHLRGDELLVLAHTNADVHKLN
EALREVMKAEQALSDSRTFQTARGAREFAVGDRIIFLENARFLEPRARHSGPQYVKNGMLGTVVATGDKR
GDPLMSVLLDNGRNVVFSEDSYRNVDHGYASTIHKSQGATVDRTFVLATGMMDRHLTYVSMTRHRDRADL
YAVKEDFQVRSERGRRLRADHAAGVTGELVEAGEAKFRPDDEDADDSPYADIRTDDGTVHRLWGVSLPKA
LEEAGISEGDTITLRKDGVERVKVQIAVVDEATGQKRYEEREVGRNVWTAKQIETAEARQERIERESHRP
DVFSRLVERLSRSGAKTTTLDFESEAGYRAHADDFARRRGLDHLSLAAAEMEEGVSRRLAWIAEKRGQIA
KLWERASVALGLAIERERRVAYNEERSETMIGAISSEERYLIPPATDFRRSLDEDARLAQLSSPAWKERE
AILRPLLETIYRDPDAALVRLNALASDTGTEPRKLADDLAVAPDLLGRLYGSDLIVDGRAARDERNVAMA
TVKELLPLARAHATEFRRNATRFERREQTRRNYMVLSIPALSERAVARLTEIEAVRSRGGDDAYKTASAL
AAQDRTVVQEIKAVSEAITARFGSSAFTAKADAIAQRNMAERMLEELTSVRGEKLIRLFEAVRRFAEEQH
LAERQDRSKIVAGASADPQNQNVPMLAAVTEFKTPIDEEARSRVLAGPLYRQQRAALAAVASTIWRDPAG
AVDKIEELLVKGFAADRIAAAVTNDPAAYGALRGSDRLMDRMLASGRERKDAVQAVPEAAARLRSLGSAY
VNVLDAERQAIAEERRRMAVAIPGLSKSAEEVLMRLTTEAKNNGRTRNAAAASLDPSIHREFEAVSRALD
ERFGHRAIIRGEKDLFNRMPLAQRRAFEVMWERFKVLQQTVRWESSEKIVSELRNRTINRGRGIDL

  Protein domains


Predicted by InterproScan.

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

(1045-1125)

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

(1303-1397)

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(391-577)


  Protein structure



No available structure.




T4CP

ID   1709 GenBank   WP_037146751
Name   traG_AMC86_RS31020_pRphaR620d 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: 70465.33 Da        Isoelectric Point: 9.2555

>WP_037146751.1 Ti-type conjugative transfer system protein TraG [Rhizobium phaseoli]
MIARGKPHPSLLFVFAPVVVTAIAVYIAGWRWPGLAAGMPGRMEYWFLRAAPVPALLFGPLAGLLTVWAL
PLHRRRPVAMTSLLCYLGVFASYAMREFARLGPSVQTGVITWDRALSYLDMVAVLGAVAGFLAVAVSARI
SVVVPDEINRARRGTFGDADWLSMAAAAKLFPPDGEIVVGERYRVDKEIVHQLPFDANDRGTWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTHALGREVMVLDPT
NPIMGFNVLDGIETSRQKEEDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLREIVSEPEPSVLAMLRDIQENSQSDFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKPSDIVSGRKDVFLNIPASILRSYPGIGRVIIGSLINAMMQADGAFRRRALFMLDEVDLLGYMRVL
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: 973784..983339

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC86_RS31050 969355..969537 + 183 WP_037146733 hypothetical protein -
AMC86_RS31055 (AMC86_PD00894) 969670..970710 - 1041 WP_037146729 toprim domain-containing protein -
AMC86_RS31060 (AMC86_PD00895) 971073..972263 + 1191 WP_037146725 DUF1173 domain-containing protein -
AMC86_RS31065 (AMC86_PD00896) 972706..973299 + 594 WP_037146723 DUF433 domain-containing protein -
AMC86_RS31070 (AMC86_PD00897) 973415..973765 + 351 WP_237353383 type II toxin-antitoxin system VapC family toxin -
AMC86_RS31075 (AMC86_PD00898) 973784..974779 - 996 WP_037146721 P-type DNA transfer ATPase VirB11 virB11
AMC86_RS31080 (AMC86_PD00899) 974788..975963 - 1176 WP_016735275 type IV secretion system protein VirB10 virB10
AMC86_RS31085 (AMC86_PD00900) 975972..976826 - 855 WP_037146719 P-type conjugative transfer protein VirB9 virB9
AMC86_RS31090 (AMC86_PD00901) 976823..977494 - 672 WP_037146717 virB8 family protein virB8
AMC86_RS34075 (AMC86_PD00902) 977488..977775 - 288 WP_080712055 hypothetical protein -
AMC86_RS31095 (AMC86_PD00903) 977815..978747 - 933 WP_037146716 type IV secretion system protein virB6
AMC86_RS31100 (AMC86_PD00904) 978750..978983 - 234 WP_016735278 EexN family lipoprotein -
AMC86_RS31105 (AMC86_PD00905) 978980..979681 - 702 WP_016735279 P-type DNA transfer protein VirB5 virB5
AMC86_RS31110 (AMC86_PD00906) 979678..982044 - 2367 WP_064826470 VirB4 family type IV secretion system protein virb4
AMC86_RS31115 (AMC86_PD00907) 982037..982375 - 339 WP_016735282 type IV secretion system protein VirB3 virB3
AMC86_RS31120 (AMC86_PD00908) 982381..982680 - 300 WP_016735283 TrbC/VirB2 family protein virB2
AMC86_RS31125 (AMC86_PD00909) 982677..983339 - 663 WP_037147233 transglycosylase SLT domain-containing protein virB1
AMC86_RS31130 (AMC86_PD00910) 983343..983879 - 537 WP_016735285 hypothetical protein -
AMC86_RS31135 (AMC86_PD00911) 983978..984349 + 372 WP_016735286 hypothetical protein -
AMC86_RS31140 (AMC86_PD00912) 984702..985892 - 1191 WP_037147230 hypothetical protein -
AMC86_RS31145 (AMC86_PD00913) 985968..986624 - 657 WP_037147226 hypothetical protein -

Host bacterium

ID   3224 GenBank   NZ_CP013546
Plasmid name   pRphaR620d Incompatibility group   -
Plasmid size   1080727 bp Coordinate of oriT [Strand]   962481..962509 [-]
Host baterium   Rhizobium phaseoli strain R620

Cargo genes

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