Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102764
Name   oriT_pRspN113b in_silico
Organism   Rhizobium sp. N113
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013519 (215910..215938 [+], 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_pRspN113b
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2039 GenBank   WP_064811989
Name   traA_AMJ96_RS23935_pRspN113b insolico UniProt ID   A0A192M522
Length   1565 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1565 a.a.        Molecular weight: 172913.26 Da        Isoelectric Point: 7.2379

>WP_064811989.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAIMFVRAQVISRGSGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAGELMYEELALPDEIPDWLRSAISG
QSVSKASEVFWNAVDAFETRADAQLARELIIALPEELTRAENITLVRDFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGAKKVPVLGEGGKPLRVVTPDRPNGKIVYKVWAGDKETLNAWKIAWAETANR
HLALADHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLAEPELLLKQ
LGNERSTFDERDIARALHRYVDDPTDFANIRARLMASDQLVILKPQEIEAETGKVSEPAMFTTREMLRIE
YDMAQSARVLSERRGFGVSERIVTVAIERVESIESGDPKTPFRLDAEQVDAVRHVTGDGDIAAIVGLAGA
GKSTLLAAARLAWEGEGHRVIGAALAGKAAEGLQHSSGIKSRTLASWELAWANGRDTLHRGDVLVIDEAG
MVASQQMARVLKIAEEAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREAWARNASRLFA
RGEVEKGLDAYARHGHLVEAGSREETIDRIVSDWAAARREAIERSTSEGGDGRLRGDELLVLAHTNDDVR
KLNEALRSVMTQEGALGESRSFRSERGAREFAAGDRIIFLENARFLEPRAKHSGPQYVKNGMLGTVVSTG
DKRGDPLLSILLDNGRKLVFSEDSYRHVDHGYAATIHKSQGATVDRTFVLATGMMDQHLTYVSMTRHRDR
VDLYAAKEDFAAKPEWGRKPRVDHAAGVTGELVETGEAKFRPDDEDADDSPYADVRADGGTVHRLWGVSL
PKALEEAGIQEGDTVMLRKDGVERVKVQITVVDEKTGHKHYEEREVDRNVWTASQVETASARQERIERES
HRSELFNPLVERLSRSGAKTTTLDFESEASYRAHANDFARRRGLDHLSLAAAEMEESLTRRWAWIAEKRE
QVAKLWERASVALGFAIERERRVAYNEERSQTMVEATSSDARTASHSVSGASAAETRYLIPPATSFVSSV
EEDARLAQLASPAWTEREVILRPLLQKIYRDPDAALVSLNALASDIGVAPRRLADDLAVAPGRLGRMRGS
ELIVDGRAAREERNVAVAGVKELLPIARAHATEFRRNAERFELREQTRRAHMSLSIPALSERAMARLMEI
EAVRRQGGDDAYKTAFALTAKDRSVVQEIKAVSEALTARFGWSAFSAKADAIAERNIVERMPEDLTDERR
GKLTRLFEAVRRFAEEQHLAERRDRSKIVAGASVDLRTGTEKGVGKENVPIPPMLAAVTEFKVPVDDEAR
SRALASPLYRQQRAALANAATTIWRDPAEVVGKIEELLQKGFAAERIGAAVTNNPAAYGALRGSDRLMDR
MLASGRERKEATRTVPEAAARLRALGAAYANALNSERQAITDERRRMAVAIPALSKAAEEALAHLTVEVS
KDSRKLNVSAASLDPGIGREFAAVSRALDERFGRNALVRGDKDIANVVPPAQRGAFAAMQERLKVLQQTV
RLQSSEQIIVERRQQTANRSRGINL

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(394-579)

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

(1334-1425)

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

(1072-1143)


  Protein structure



No available structure.




T4CP

ID   1692 GenBank   WP_064811988
Name   traG_AMJ96_RS23920_pRspN113b 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: 70745.97 Da        Isoelectric Point: 9.5675

>WP_064811988.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MGLRGKPHPSLLLVLVPIAVTTITIYIVGWRWPGLAAGMSGKIEHWFLRAAPVPPLLFGPLAGLLTVWAL
PLHRRRPVAMASLLYFLGVAAFYALREFGRLAPAVQAEVITWDRALSYLDMVAVIAAVAGFMAVAMSARI
SVVVPDEIKRARRGIFGDADWLPMRAAGKLFPPEGEIVVGERYRVDKEIVHALPFDANDRSTWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYSGPLICLDPSTEVAPMVAEHRARALKREVMVLDPT
NPIMGFNVLDGIEASKQKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYEGRRS
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNIPASILRSYPGIARVIIGSLINAMVQADGAFQRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVKG
SSRNIGWDTKNNASRRSENVTFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDQAAK
VNRFVKPVL

  Protein domains


Predicted by InterproScan.

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

(168-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 196149..205737

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMJ96_RS33645 192633..192859 - 227 Protein_187 chaperonin GroEL -
AMJ96_RS23795 (AMJ96_PB00184) 193154..194074 + 921 WP_064811974 zincin-like metallopeptidase domain-containing protein -
AMJ96_RS23800 194185..194367 - 183 WP_016737443 hypothetical protein -
AMJ96_RS23805 (AMJ96_PB00186) 195139..195510 - 372 WP_042120136 hypothetical protein -
AMJ96_RS23810 (AMJ96_PB00187) 195609..196145 + 537 WP_064811975 hypothetical protein -
AMJ96_RS23815 (AMJ96_PB00188) 196149..196808 + 660 WP_064811976 lytic transglycosylase domain-containing protein virB1
AMJ96_RS23820 (AMJ96_PB00189) 196805..197104 + 300 WP_009997887 TrbC/VirB2 family protein virB2
AMJ96_RS23825 (AMJ96_PB00190) 197110..197448 + 339 WP_009997888 type IV secretion system protein VirB3 virB3
AMJ96_RS23830 (AMJ96_PB00191) 197441..199807 + 2367 WP_064811977 VirB4 family type IV secretion system protein virb4
AMJ96_RS23835 (AMJ96_PB00192) 199804..200505 + 702 WP_064811978 P-type DNA transfer protein VirB5 virB5
AMJ96_RS23840 (AMJ96_PB00193) 200502..200735 + 234 WP_010007459 EexN family lipoprotein -
AMJ96_RS23845 (AMJ96_PB00194) 200739..201671 + 933 WP_040111793 type IV secretion system protein virB6
AMJ96_RS33650 (AMJ96_PB00195) 201711..201992 + 282 WP_080771758 hypothetical protein -
AMJ96_RS23850 (AMJ96_PB00196) 201994..202665 + 672 WP_064811979 virB8 family protein virB8
AMJ96_RS23855 (AMJ96_PB00197) 202662..203519 + 858 WP_064811980 P-type conjugative transfer protein VirB9 virB9
AMJ96_RS23860 (AMJ96_PB00198) 203528..204700 + 1173 WP_064811981 type IV secretion system protein VirB10 virB10
AMJ96_RS23865 (AMJ96_PB00199) 204709..205737 + 1029 WP_010008207 P-type DNA transfer ATPase VirB11 virB11
AMJ96_RS23870 (AMJ96_PB00200) 205781..206359 - 579 WP_064811982 PIN domain-containing protein -
AMJ96_RS23875 (AMJ96_PB00201) 206349..206795 - 447 WP_225881772 DNA-binding protein -
AMJ96_RS23880 (AMJ96_PB00203) 207307..208497 - 1191 WP_064811984 DUF1173 domain-containing protein -
AMJ96_RS33655 208808..209067 + 260 Protein_207 toprim domain-containing protein -
AMJ96_RS23890 (AMJ96_PB00204) 209453..209719 + 267 WP_004676093 hypothetical protein -
AMJ96_RS23895 (AMJ96_PB00205) 209716..210114 + 399 WP_064811986 type II toxin-antitoxin system VapC family toxin -

Host bacterium

ID   3207 GenBank   NZ_CP013519
Plasmid name   pRspN113b Incompatibility group   -
Plasmid size   435821 bp Coordinate of oriT [Strand]   215910..215938 [+]
Host baterium   Rhizobium sp. N113

Cargo genes

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