Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101181
Name   oriT_pSM134A_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM134A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOM01000007 (220776..220816 [+], 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_pSM134A_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1178 GenBank   WP_130692296
Name   traA_ELH87_RS31650_pSM134A_Rh07 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: 122959.16 Da        Isoelectric Point: 9.4990

>WP_130692296.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADS
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDDKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVLLFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
VRLEAEMANRAIWLSGRASHGVREEVLQATFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRVGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAAGGIIAEIGEGEHRQVTIEQRFYNNLDHGYAT
TIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYEK
SALCRQAFRFAEARGLHLMNVARTIAHDRLQWAVRQKQKLADLGARLAAIGKALGLVRGSNKHSIPDTIK
EARPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAQPEAAFKAINVDAMVEDQSVAQST
LARIAGEPESFGALKGKTGVLASRGDKHDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKVS
VDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDGK
TFETVTAGMTAGQKAEVRNAWDAMRAVQQMAAHERTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-739)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)

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

(863-959)


  Protein structure



No available structure.




T4CP

ID   775 GenBank   WP_130692298
Name   traG_ELH87_RS31635_pSM134A_Rh07 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   776 GenBank   WP_130692276
Name   t4cp2_ELH87_RS31735_pSM134A_Rh07 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: 91738.38 Da        Isoelectric Point: 5.7923

>WP_130692276.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNEQSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRSHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLIPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMSMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPISPCPFYPPNAPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATSEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLETRGVHDAASLLKYV

  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: 218202..240229

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH87_RS39795 214065..214241 - 177 WP_018482051 hypothetical protein -
ELH87_RS31615 (ELH87_31610) 214698..215009 + 312 WP_027691174 DUF736 domain-containing protein -
ELH87_RS39800 215310..215471 + 162 WP_162710370 hypothetical protein -
ELH87_RS39805 215766..215939 + 174 WP_165403408 hypothetical protein -
ELH87_RS31620 (ELH87_31615) 216007..216315 - 309 WP_063473655 WGR domain-containing protein -
ELH87_RS31625 (ELH87_31620) 216759..217073 + 315 WP_130692302 hypothetical protein -
ELH87_RS31630 (ELH87_31625) 217315..217764 - 450 WP_130692300 thermonuclease family protein -
ELH87_RS31635 (ELH87_31630) 218202..220133 - 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELH87_RS31640 (ELH87_31635) 220120..220335 - 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELH87_RS31645 (ELH87_31640) 220340..220633 - 294 WP_128409207 conjugal transfer protein TraC -
ELH87_RS31650 (ELH87_31645) 220888..224211 + 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELH87_RS31655 (ELH87_31650) 224208..224771 + 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELH87_RS31660 (ELH87_31655) 224761..225927 + 1167 WP_130692292 conjugal transfer protein TraB -
ELH87_RS31665 (ELH87_31660) 225945..226565 + 621 WP_130692290 TraH family protein virB1
ELH87_RS31670 (ELH87_31665) 226710..227425 - 716 Protein_225 Crp/Fnr family transcriptional regulator -
ELH87_RS31675 (ELH87_31670) 227782..228156 - 375 WP_130692288 DUF5615 family PIN-like protein -
ELH87_RS31680 (ELH87_31675) 228153..228785 - 633 WP_128408809 DUF433 domain-containing protein -
ELH87_RS31685 (ELH87_31680) 228899..229141 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELH87_RS31690 (ELH87_31685) 229367..229708 + 342 WP_128408807 transcriptional repressor TraM -
ELH87_RS31695 (ELH87_31690) 229693..230397 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELH87_RS31700 (ELH87_31695) 230706..232004 - 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELH87_RS31705 (ELH87_31700) 232016..232456 - 441 WP_130692284 conjugal transfer protein TrbH -
ELH87_RS31710 (ELH87_31705) 232460..233272 - 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELH87_RS31715 (ELH87_31710) 233290..233952 - 663 WP_130692280 conjugal transfer protein TrbF virB8
ELH87_RS31720 (ELH87_31715) 233973..235154 - 1182 WP_130692278 P-type conjugative transfer protein TrbL virB6
ELH87_RS31725 (ELH87_31720) 235148..235348 - 201 WP_128408800 entry exclusion protein TrbK -
ELH87_RS31730 (ELH87_31725) 235345..236148 - 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELH87_RS31735 (ELH87_31730) 236120..238576 - 2457 WP_130692276 conjugal transfer protein TrbE virb4
ELH87_RS31740 (ELH87_31735) 238587..238886 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELH87_RS31745 (ELH87_31740) 238879..239262 - 384 WP_063473648 TrbC/VirB2 family protein virB2
ELH87_RS31750 (ELH87_31745) 239252..240229 - 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
ELH87_RS31755 (ELH87_31750) 240226..240864 - 639 WP_130692272 acyl-homoserine-lactone synthase -
ELH87_RS40575 241342..241554 + 213 WP_245458276 hypothetical protein -
ELH87_RS31765 (ELH87_31760) 241595..241849 + 255 WP_130692270 IS66 family insertion sequence element accessory protein TnpB -
ELH87_RS31770 (ELH87_31765) 242466..243680 + 1215 WP_027691186 plasmid partitioning protein RepA -
ELH87_RS31775 (ELH87_31770) 243677..244699 + 1023 WP_128408794 plasmid partitioning protein RepB -

Host bacterium

ID   1625 GenBank   NZ_SIOM01000007
Plasmid name   pSM134A_Rh07 Incompatibility group   -
Plasmid size   389003 bp Coordinate of oriT [Strand]   220776..220816 [+]
Host baterium   Rhizobium ruizarguesonis strain SM134A

Cargo genes

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