Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120826
Name   oriT_pRlX4 in_silico
Organism   Rhizobium johnstonii strain TP25
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140849 (247704..247744 [+], 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_pRlX4
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13136 GenBank   WP_130759159
Name   traA_U8P77_RS34070_pRlX4 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   15416 GenBank   WP_130692298
Name   traG_U8P77_RS34055_pRlX4 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.



ID   15417 GenBank   WP_130759152
Name   t4cp2_U8P77_RS34155_pRlX4 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91786.31 Da        Isoelectric Point: 5.5010

>WP_130759152.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNEQSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRSHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLIPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPSNSPPLVQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRVLAFCPLSDLNSDVDRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEELMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLETRGVHDAASLLRFE

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(192-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 245130..267157

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8P77_RS34020 (U8P77_34015) 240993..241169 - 177 WP_018482051 hypothetical protein -
U8P77_RS34025 (U8P77_34020) 241626..241937 + 312 WP_027691174 DUF736 domain-containing protein -
U8P77_RS34030 (U8P77_34025) 242238..242399 + 162 WP_162710370 hypothetical protein -
U8P77_RS34035 (U8P77_34030) 242694..242867 + 174 WP_165403408 hypothetical protein -
U8P77_RS34040 (U8P77_34035) 242935..243243 - 309 WP_063473655 WGR domain-containing protein -
U8P77_RS34045 (U8P77_34040) 243687..244001 + 315 WP_130692302 hypothetical protein -
U8P77_RS34050 (U8P77_34045) 244243..244692 - 450 WP_130692300 thermonuclease family protein -
U8P77_RS34055 (U8P77_34050) 245130..247061 - 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
U8P77_RS34060 (U8P77_34055) 247048..247263 - 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
U8P77_RS34065 (U8P77_34060) 247268..247561 - 294 WP_128409207 conjugal transfer protein TraC -
U8P77_RS34070 (U8P77_34065) 247816..251139 + 3324 WP_130759159 Ti-type conjugative transfer relaxase TraA -
U8P77_RS34075 (U8P77_34070) 251136..251699 + 564 WP_130692294 conjugative transfer signal peptidase TraF -
U8P77_RS34080 (U8P77_34075) 251689..252855 + 1167 WP_130692292 conjugal transfer protein TraB -
U8P77_RS34085 (U8P77_34080) 252873..253493 + 621 WP_130692290 TraH family protein virB1
U8P77_RS34090 (U8P77_34085) 253638..254353 - 716 Protein_252 Crp/Fnr family transcriptional regulator -
U8P77_RS34095 (U8P77_34090) 254710..255084 - 375 WP_130692288 DUF5615 family PIN-like protein -
U8P77_RS34100 (U8P77_34095) 255081..255713 - 633 WP_128408809 DUF433 domain-containing protein -
U8P77_RS34105 (U8P77_34100) 255827..256069 - 243 WP_128408808 helix-turn-helix domain-containing protein -
U8P77_RS34110 (U8P77_34105) 256295..256636 + 342 WP_130759157 transcriptional repressor TraM -
U8P77_RS34115 (U8P77_34110) 256621..257325 - 705 WP_128408806 autoinducer binding domain-containing protein -
U8P77_RS34120 (U8P77_34115) 257634..258932 - 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
U8P77_RS34125 (U8P77_34120) 258944..259384 - 441 WP_130692284 conjugal transfer protein TrbH -
U8P77_RS34130 (U8P77_34125) 259388..260200 - 813 WP_327208369 P-type conjugative transfer protein TrbG virB9
U8P77_RS34135 (U8P77_34130) 260218..260880 - 663 WP_130692280 conjugal transfer protein TrbF virB8
U8P77_RS34140 (U8P77_34135) 260901..262082 - 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
U8P77_RS34145 (U8P77_34140) 262076..262276 - 201 WP_130759154 entry exclusion protein TrbK -
U8P77_RS34150 (U8P77_34145) 262273..263076 - 804 WP_130759153 P-type conjugative transfer protein TrbJ virB5
U8P77_RS34155 (U8P77_34150) 263048..265504 - 2457 WP_130759152 conjugal transfer protein TrbE virb4
U8P77_RS34160 (U8P77_34155) 265515..265814 - 300 WP_027681723 conjugal transfer protein TrbD virB3
U8P77_RS34165 (U8P77_34160) 265807..266190 - 384 WP_063473648 TrbC/VirB2 family protein virB2
U8P77_RS34170 (U8P77_34165) 266180..267157 - 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
U8P77_RS34175 (U8P77_34170) 267154..267792 - 639 WP_130759151 acyl-homoserine-lactone synthase -
U8P77_RS34180 (U8P77_34175) 268270..268482 + 213 WP_245458276 hypothetical protein -

Host bacterium

ID   21255 GenBank   NZ_CP140849
Plasmid name   pRlX4 Incompatibility group   -
Plasmid size   269394 bp Coordinate of oriT [Strand]   247704..247744 [+]
Host baterium   Rhizobium johnstonii strain TP25

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodE, nodF, nodD, nodA, nodC, nodI, nodJ, nifT, nifA, fixX, fixC, fixB, fixA, nifH, nifD, nifK, nifE, nifN, fixN, fixO, fixQ, fixG
Anti-CRISPR   -