Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101199
Name   oriT_pSM122B_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM122B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SINX01000006 (55763..55803 [+], 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_pSM122B_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1195 GenBank   WP_130692296
Name   traA_ELH72_RS30795_pSM122B_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   806 GenBank   WP_130692298
Name   traG_ELH72_RS30780_pSM122B_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   807 GenBank   WP_130692276
Name   t4cp2_ELH72_RS30880_pSM122B_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: 53189..75216

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH72_RS39645 49052..49228 - 177 WP_018482051 hypothetical protein -
ELH72_RS30760 (ELH72_30760) 49685..49996 + 312 WP_027691174 DUF736 domain-containing protein -
ELH72_RS39650 50297..50458 + 162 WP_162710370 hypothetical protein -
ELH72_RS39655 50753..50926 + 174 WP_165403408 hypothetical protein -
ELH72_RS30765 (ELH72_30765) 50994..51302 - 309 WP_063473655 WGR domain-containing protein -
ELH72_RS30770 (ELH72_30770) 51746..52060 + 315 WP_130692302 hypothetical protein -
ELH72_RS30775 (ELH72_30775) 52302..52751 - 450 WP_130692300 thermonuclease family protein -
ELH72_RS30780 (ELH72_30780) 53189..55120 - 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELH72_RS30785 (ELH72_30785) 55107..55322 - 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELH72_RS30790 (ELH72_30790) 55327..55620 - 294 WP_128409207 conjugal transfer protein TraC -
ELH72_RS30795 (ELH72_30795) 55875..59198 + 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELH72_RS30800 (ELH72_30800) 59195..59758 + 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELH72_RS30805 (ELH72_30805) 59748..60914 + 1167 WP_130692292 conjugal transfer protein TraB -
ELH72_RS30810 (ELH72_30810) 60932..61552 + 621 WP_130692290 TraH family protein virB1
ELH72_RS30815 (ELH72_30815) 61697..62412 - 716 Protein_67 Crp/Fnr family transcriptional regulator -
ELH72_RS30820 (ELH72_30820) 62769..63143 - 375 WP_130692288 DUF5615 family PIN-like protein -
ELH72_RS30825 (ELH72_30825) 63140..63772 - 633 WP_128408809 DUF433 domain-containing protein -
ELH72_RS30830 (ELH72_30830) 63886..64128 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELH72_RS30835 (ELH72_30835) 64354..64695 + 342 WP_128408807 transcriptional repressor TraM -
ELH72_RS30840 (ELH72_30840) 64680..65384 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELH72_RS30845 (ELH72_30845) 65693..66991 - 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELH72_RS30850 (ELH72_30850) 67003..67443 - 441 WP_130692284 conjugal transfer protein TrbH -
ELH72_RS30855 (ELH72_30855) 67447..68259 - 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELH72_RS30860 (ELH72_30860) 68277..68939 - 663 WP_130692280 conjugal transfer protein TrbF virB8
ELH72_RS30865 (ELH72_30865) 68960..70141 - 1182 WP_130692278 P-type conjugative transfer protein TrbL virB6
ELH72_RS30870 (ELH72_30870) 70135..70335 - 201 WP_128408800 entry exclusion protein TrbK -
ELH72_RS30875 (ELH72_30875) 70332..71135 - 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELH72_RS30880 (ELH72_30880) 71107..73563 - 2457 WP_130692276 conjugal transfer protein TrbE virb4
ELH72_RS30885 (ELH72_30885) 73574..73873 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELH72_RS30890 (ELH72_30890) 73866..74249 - 384 WP_063473648 TrbC/VirB2 family protein virB2
ELH72_RS30895 (ELH72_30895) 74239..75216 - 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
ELH72_RS30900 (ELH72_30900) 75213..75851 - 639 WP_130692272 acyl-homoserine-lactone synthase -
ELH72_RS40475 76329..76541 + 213 WP_245458276 hypothetical protein -
ELH72_RS30910 (ELH72_30910) 76690..78759 - 2070 WP_130771903 recombinase family protein -
ELH72_RS30915 (ELH72_30915) 78756..79019 - 264 WP_130771901 hypothetical protein -
ELH72_RS30920 (ELH72_30920) 79046..79507 - 462 WP_130771899 helix-turn-helix domain-containing protein -

Host bacterium

ID   1643 GenBank   NZ_SINX01000006
Plasmid name   pSM122B_Rh07 Incompatibility group   -
Plasmid size   389696 bp Coordinate of oriT [Strand]   55763..55803 [+]
Host baterium   Rhizobium ruizarguesonis strain SM122B

Cargo genes

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