Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102874
Name   oriT_pRsp8C3b in_silico
Organism   Rhizobium etli 8C-3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP017243 (195436..195464 [+], 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_pRsp8C3b
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2153 GenBank   WP_018247162
Name   traA_AM571_RS23495_pRsp8C3b insolico UniProt ID   A0A1L5PBL4
Length   1552 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1552 a.a.        Molecular weight: 171782.96 Da        Isoelectric Point: 7.3778

>WP_018247162.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAIMFVRAQVISRGSGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAGELMYEELALPDEIPDWLRSAISG
QSVSKASEVFWNAVDAFETRADAQLARELIIALPEELTRAENITLVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPATEEGFGAKKVPVLGEGGKPLRVVTPDRPNGKIVYKVWAGDKETMKAWKIAWAETANR
HLALAGHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLSEPELLLKQ
LGNERSTFDERDIARALHRYVDDPTDFANIRARLMASDQLVILKPKEIEAETGKVSEPAVFTTREMLRIE
YDMAQSARVLSERRGFGVSERNVTVAIERVESIESGDPKTPFRLDAEQVDAVRHVTGDGGIAAIVGLAGA
GKSTLLAAARLAWEGEGHRVIGAALAGKAAEGLQDSSGIKSRTLASWELAWANGRDTLHRGDVLVIDEAG
MVASQQMARVLKIAEEAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREAWARNASRLFA
RGEVEKGLDAYTQQGHLVEAGTREETIDRIVVDWTEARKHAIGRSISEGRDGRLRGDELLVLAHTNDDVR
KLNEALREVMAGDNALGESRSFRTERGARKFAAGDRIIFLENARFLEPRAKHSGPQYVKNGMLGTVTATG
DKRGDPLLSVLLDNGNKVVFGEDSYDNVDHGYAATIHKSQGSTVDRTFVLATGMMDRHLTYVSMTRHRDR
VDLYAAKEDFEPRPEWGRKPRVDHAAGVTGELVETGEAKFRPEDEDADDSPYADVRTDDGTAHRLWGVSL
PKALDDAGISDGDTITLRKDGVERVKVQIAIVDEETGQKRYEEREVDRNVWTARQIETAEARQERIERES
HRPDVFSRLVERLSRSGAKTTTLDFESEAGYRAQAQDFARRRGLDHLSLAAAEMEESLSRRWTWITAKRE
QVEKLWERASVALGFAIERERRFAYNEARTESHTIASASAGEPQYLIPPSTSFVRSVEADARLAQRSSPA
WTERETMLRPLLTKIYRDPDAALVALNALASDTGTEPRRLTADLAAAPDRLGRLRGSELIVDGGAALSER
KVAKAALEELLPLARAHATGFRRNAERFEMREQTRRSYMSLSIPALSERAMARLMEIEAVRNRDGDDAYK
SAFALAAEDRSVVQEIKAVSEALTARFGWSAFTAKADAVAERNMTERLPEDLTAGRREELARLFEAVKRF
AEAQHLAERQDRSKIVMAASVVRGQETENGPGKENVAVPPMLAAVIVFKTSVDDEARLRALSNPFYRQQR
GALANAATMIWRDPSGAVGKIEELLRKGFAADRIAAAVTNDPAAYGALRGSNRLLDRMLASGQERKEAMR
AVPEAAARLRALGAAHLNALDAERQAITDERRRMAVAIPALSKAAEEALAHLTVEVRKDSRKLSVSAASL
EQGIAREFAAVSRALDERFGRNALVRGDKDLVNRVPPAQRRAFEAMQERLKVLQQTVRLQSSEQIIAERR
QRAASRARGINL

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(394-580)

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

(1322-1412)

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

(1053-1130)


  Protein structure



No available structure.




T4CP

ID   1821 GenBank   WP_004676100
Name   traG_AM571_RS23480_pRsp8C3b 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: 70645.82 Da        Isoelectric Point: 9.3989

>WP_004676100.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MGLRGKPHPSLLLVLVPIAVTTITIYIVGWRWPGLAAGMSGKIEHWFLRAAPVPPLLFGPLAGLLTVWVL
PLHRRRPVAMASLLCFLSVAAFYALREFGRLAPTVQARVVPWDRALSYLDMAAVIAAVAGFMAVAVSARI
SVVVPDEIKRARRGIFGDADWLPMAAAGKLFPPDGEIVVGERYRVDKEIIHALPFDVNDRSTWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPMICLDPSTEVAPMVVEHRTNALGREVMVLDPT
NPIMGFNVLDGIEASKQKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYEGRRS
LRSLRQIVSEPEPSVLAMLRDIQEHSGSAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNISASILRSYPGIARVIIGSLINAMVQADGAFQRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNLSAQCGEMTVEVKG
SSRNIGWDTKNNASRRSENVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDQAAK
VNRFVKPVL

  Protein domains


Predicted by InterproScan.

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

(171-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 174716..184303

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AM571_RS37605 (AM571_PB00170) 171204..171429 - 226 Protein_156 chaperonin GroEL -
AM571_RS23340 (AM571_PB00172) 171724..172644 + 921 WP_004673402 zincin-like metallopeptidase domain-containing protein -
AM571_RS23345 172755..172937 - 183 WP_016737443 hypothetical protein -
AM571_RS23350 (AM571_PB00174) 173706..174077 - 372 WP_004673403 hypothetical protein -
AM571_RS23355 (AM571_PB00175) 174176..174712 + 537 WP_018446357 hypothetical protein -
AM571_RS23360 (AM571_PB00176) 174716..175357 + 642 WP_004673406 transglycosylase SLT domain-containing protein virB1
AM571_RS23365 (AM571_PB00177) 175372..175671 + 300 WP_004673407 TrbC/VirB2 family protein virB2
AM571_RS23370 (AM571_PB00178) 175677..176015 + 339 WP_018247156 type IV secretion system protein VirB3 virB3
AM571_RS23375 (AM571_PB00179) 176008..178374 + 2367 WP_004673411 VirB4 family type IV secretion system protein virb4
AM571_RS23380 (AM571_PB00180) 178371..179072 + 702 WP_004673414 P-type DNA transfer protein VirB5 virB5
AM571_RS23385 (AM571_PB00181) 179069..179302 + 234 WP_004673415 EexN family lipoprotein -
AM571_RS23390 (AM571_PB00182) 179305..180237 + 933 WP_004673418 type IV secretion system protein virB6
AM571_RS23395 (AM571_PB00183) 180277..180558 + 282 WP_004673420 hypothetical protein -
AM571_RS23400 (AM571_PB00184) 180560..181231 + 672 WP_004673422 virB8 family protein virB8
AM571_RS23405 (AM571_PB00185) 181228..182085 + 858 WP_004673424 P-type conjugative transfer protein VirB9 virB9
AM571_RS23410 (AM571_PB00186) 182094..183266 + 1173 WP_004673426 type IV secretion system protein VirB10 virB10
AM571_RS23415 (AM571_PB00187) 183275..184303 + 1029 WP_004673428 P-type DNA transfer ATPase VirB11 virB11
AM571_RS37610 184630..184923 - 294 WP_004673430 hypothetical protein -
AM571_RS23425 (AM571_PB00189) 184913..185359 - 447 WP_004673432 hypothetical protein -
AM571_RS23430 (AM571_PB00191) 185872..187062 - 1191 WP_026188839 DUF1173 domain-containing protein -
AM571_RS37070 (AM571_PB00192) 187662..187856 - 195 WP_010011691 hypothetical protein -
AM571_RS23435 (AM571_PB00193) 187958..188898 + 941 Protein_177 DUF2493 domain-containing protein -
AM571_RS23440 (AM571_PB00195) 188983..189249 + 267 WP_004676093 hypothetical protein -

Host bacterium

ID   3317 GenBank   NZ_CP017243
Plasmid name   pRsp8C3b Incompatibility group   -
Plasmid size   438379 bp Coordinate of oriT [Strand]   195436..195464 [+]
Host baterium   Rhizobium etli 8C-3

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, a9174_31165, nodD, nodJ, nodI, nodS, nodC, fixO, fixN, mLTONO_5203, nodA
Anti-CRISPR   -