Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101193
Name   oriT_pSM157A_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM157A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQG01000006 (29420..29460 [-], 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_pSM157A_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1189 GenBank   WP_130692296
Name   traA_ELI33_RS32655_pSM157A_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   794 GenBank   WP_130692276
Name   t4cp2_ELI33_RS32570_pSM157A_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.



ID   795 GenBank   WP_130692298
Name   traG_ELI33_RS32670_pSM157A_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 10007..32034

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI33_RS32530 (ELI33_32530) 5537..6559 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELI33_RS32535 (ELI33_32535) 6556..7770 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELI33_RS32540 (ELI33_32540) 8387..8641 - 255 WP_130692270 IS66 family insertion sequence element accessory protein TnpB -
ELI33_RS39660 8682..8894 - 213 WP_245458276 hypothetical protein -
ELI33_RS32550 (ELI33_32550) 9372..10010 + 639 WP_130692272 acyl-homoserine-lactone synthase -
ELI33_RS32555 (ELI33_32555) 10007..10984 + 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
ELI33_RS32560 (ELI33_32560) 10974..11357 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELI33_RS32565 (ELI33_32565) 11350..11649 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELI33_RS32570 (ELI33_32570) 11660..14116 + 2457 WP_130692276 conjugal transfer protein TrbE virb4
ELI33_RS32575 (ELI33_32575) 14088..14891 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELI33_RS32580 (ELI33_32580) 14888..15088 + 201 WP_128408800 entry exclusion protein TrbK -
ELI33_RS32585 (ELI33_32585) 15082..16263 + 1182 WP_130692278 P-type conjugative transfer protein TrbL virB6
ELI33_RS32590 (ELI33_32590) 16284..16946 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELI33_RS32595 (ELI33_32595) 16964..17776 + 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELI33_RS32600 (ELI33_32600) 17780..18220 + 441 WP_130692284 conjugal transfer protein TrbH -
ELI33_RS32605 (ELI33_32605) 18232..19530 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELI33_RS32610 (ELI33_32610) 19839..20543 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELI33_RS32615 (ELI33_32615) 20528..20869 - 342 WP_128408807 transcriptional repressor TraM -
ELI33_RS32620 (ELI33_32620) 21095..21337 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELI33_RS32625 (ELI33_32625) 21451..22083 + 633 WP_128408809 DUF433 domain-containing protein -
ELI33_RS32630 (ELI33_32630) 22080..22454 + 375 WP_130692288 DUF5615 family PIN-like protein -
ELI33_RS32635 (ELI33_32635) 22811..23526 + 716 Protein_25 Crp/Fnr family transcriptional regulator -
ELI33_RS32640 (ELI33_32640) 23671..24291 - 621 WP_130692290 TraH family protein virB1
ELI33_RS32645 (ELI33_32645) 24309..25475 - 1167 WP_130692292 conjugal transfer protein TraB -
ELI33_RS32650 (ELI33_32650) 25465..26028 - 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELI33_RS32655 (ELI33_32655) 26025..29348 - 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELI33_RS32660 (ELI33_32660) 29603..29896 + 294 WP_128409207 conjugal transfer protein TraC -
ELI33_RS32665 (ELI33_32665) 29901..30116 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELI33_RS32670 (ELI33_32670) 30103..32034 + 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELI33_RS32675 (ELI33_32675) 32472..32921 + 450 WP_130692300 thermonuclease family protein -
ELI33_RS32680 (ELI33_32680) 33163..33477 - 315 WP_130692302 hypothetical protein -
ELI33_RS32685 (ELI33_32685) 33921..34229 + 309 WP_063473655 WGR domain-containing protein -
ELI33_RS38990 34297..34470 - 174 WP_165403408 hypothetical protein -
ELI33_RS38995 34765..34926 - 162 WP_162710370 hypothetical protein -
ELI33_RS32690 (ELI33_32690) 35227..35538 - 312 WP_027691174 DUF736 domain-containing protein -
ELI33_RS39000 35995..36171 + 177 WP_018482051 hypothetical protein -

Host bacterium

ID   1637 GenBank   NZ_SIQG01000006
Plasmid name   pSM157A_Rh07 Incompatibility group   -
Plasmid size   57764 bp Coordinate of oriT [Strand]   29420..29460 [-]
Host baterium   Rhizobium ruizarguesonis strain SM157A

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -