Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120374
Name   oriT_pRlX2 in_silico
Organism   Rhizobium beringeri strain TP6
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140809 (243989..244029 [+], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 41 nt

>oriT_pRlX2
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12821 GenBank   WP_130759159
Name   traA_U8P73_RS30230_pRlX2 insolico UniProt ID   _
Length   1107 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1107 a.a.        Molecular weight: 122958.22 Da        Isoelectric Point: 9.6155

>WP_130759159.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADS
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDDKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVLLFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
VRLEAEMANRAIWLSGRASHGVREEVLQATFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRVGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAAGGIIAEIGEGEHRQVTIEQRFYNNLDHGYAT
TIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYEK
SALCRQAFRFAEARGLHLMNVARTIAHDRLQWAVRQKQKLADLGARLAAIGKALGLVRGSNKHSIPDTIK
EARPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAQPEAAFKAINVDAMVKDQSVAQST
LARIAGEPESFGALKGKTGVLASRGDKHDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKVS
VDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDGK
TFETVTAGMTAGQKAEVRNAWDAMRAVQQMAAHERTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-739)

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

(863-959)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)


  Protein structure



No available structure.




T4CP

ID   15066 GenBank   WP_130692298
Name   traG_U8P73_RS30215_pRlX2 insolico UniProt ID   _
Length   643 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 643 a.a.        Molecular weight: 69483.71 Da        Isoelectric Point: 9.1051

>WP_130692298.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVMPGTLMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVAGCSGTILIAAIRETMRLSAFMTVPADKTVWAFLDPATSIGASAALLCACFALRVALIGN
AAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGGK
SPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLDP
RKPDIGFNVLDWVGRFGGTKEEDIASIASWIMSDSGGVRGVRDDFFRASALQLLTALIADVCLSGHTDEK
DQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAA
LVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGYM
RIIETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTV
EIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGT
NRFHMVGDTPRPA

  Protein domains


Predicted by InterproScan.

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

(162-633)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 255676..263446

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8P73_RS30255 (U8P73_30250) 250997..251371 - 375 WP_130692288 DUF5615 family PIN-like protein -
U8P73_RS30260 (U8P73_30255) 251368..252000 - 633 WP_128408809 DUF433 domain-containing protein -
U8P73_RS30265 (U8P73_30260) 252114..252356 - 243 WP_128408808 helix-turn-helix domain-containing protein -
U8P73_RS30270 (U8P73_30265) 252582..252923 + 342 WP_130759157 transcriptional repressor TraM -
U8P73_RS30275 (U8P73_30270) 252908..253612 - 705 WP_128408806 autoinducer binding domain-containing protein -
U8P73_RS30280 (U8P73_30275) 253921..255220 - 1300 Protein_252 IncP-type conjugal transfer protein TrbI -
U8P73_RS30285 (U8P73_30280) 255232..255672 - 441 WP_130692284 conjugal transfer protein TrbH -
U8P73_RS30290 (U8P73_30285) 255676..256488 - 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
U8P73_RS30295 (U8P73_30290) 256506..257168 - 663 WP_326893021 conjugal transfer protein TrbF virB8
U8P73_RS30300 (U8P73_30295) 257189..258369 - 1181 Protein_256 P-type conjugative transfer protein TrbL -
U8P73_RS30305 (U8P73_30300) 258363..258563 - 201 WP_130759154 entry exclusion protein TrbK -
U8P73_RS30310 (U8P73_30305) 258560..259363 - 804 WP_130759153 P-type conjugative transfer protein TrbJ virB5
U8P73_RS30315 (U8P73_30310) 259335..261793 - 2459 Protein_259 conjugal transfer protein TrbE -
U8P73_RS30320 (U8P73_30315) 261804..262103 - 300 WP_027681723 conjugal transfer protein TrbD virB3
U8P73_RS30325 (U8P73_30320) 262096..262479 - 384 WP_063473648 TrbC/VirB2 family protein virB2
U8P73_RS30330 (U8P73_30325) 262469..263446 - 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
U8P73_RS30335 (U8P73_30330) 263443..264081 - 639 WP_326893022 acyl-homoserine-lactone synthase -
U8P73_RS30340 (U8P73_30335) 264559..264771 + 213 WP_245458276 hypothetical protein -

Host bacterium

ID   20803 GenBank   NZ_CP140809
Plasmid name   pRlX2 Incompatibility group   -
Plasmid size   265972 bp Coordinate of oriT [Strand]   243989..244029 [+]
Host baterium   Rhizobium beringeri strain TP6

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodE, nodF, nodA, nodC, nodI, nodJ, nifT, fixX, fixC, fixB, fixA, nifD, nifK, fixN, fixO, fixQ, fixP
Anti-CRISPR   -