Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101169
Name   oriT_pSM149B_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM149B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPO01000006 (65143..65183 [-], 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_pSM149B_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1166 GenBank   WP_130692296
Name   traA_ELI15_RS29610_pSM149B_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   753 GenBank   WP_130692276
Name   t4cp2_ELI15_RS29525_pSM149B_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   754 GenBank   WP_130692298
Name   traG_ELI15_RS29625_pSM149B_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: 45730..67757

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI15_RS29485 (ELI15_29485) 41260..42282 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELI15_RS29490 (ELI15_29490) 42279..43493 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELI15_RS29495 (ELI15_29495) 44110..44364 - 255 WP_130692270 IS66 family insertion sequence element accessory protein TnpB -
ELI15_RS39225 44405..44617 - 213 WP_245458276 hypothetical protein -
ELI15_RS29505 (ELI15_29505) 45095..45733 + 639 WP_130692272 acyl-homoserine-lactone synthase -
ELI15_RS29510 (ELI15_29510) 45730..46707 + 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
ELI15_RS29515 (ELI15_29515) 46697..47080 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELI15_RS29520 (ELI15_29520) 47073..47372 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELI15_RS29525 (ELI15_29525) 47383..49839 + 2457 WP_130692276 conjugal transfer protein TrbE virb4
ELI15_RS29530 (ELI15_29530) 49811..50614 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELI15_RS29535 (ELI15_29535) 50611..50811 + 201 WP_128408800 entry exclusion protein TrbK -
ELI15_RS29540 (ELI15_29540) 50805..51986 + 1182 WP_130692278 P-type conjugative transfer protein TrbL virB6
ELI15_RS29545 (ELI15_29545) 52007..52669 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELI15_RS29550 (ELI15_29550) 52687..53499 + 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELI15_RS29555 (ELI15_29555) 53503..53943 + 441 WP_130692284 conjugal transfer protein TrbH -
ELI15_RS29560 (ELI15_29560) 53955..55253 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELI15_RS29565 (ELI15_29565) 55562..56266 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELI15_RS29570 (ELI15_29570) 56251..56592 - 342 WP_128408807 transcriptional repressor TraM -
ELI15_RS29575 (ELI15_29575) 56818..57060 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELI15_RS29580 (ELI15_29580) 57174..57806 + 633 WP_128408809 DUF433 domain-containing protein -
ELI15_RS29585 (ELI15_29585) 57803..58177 + 375 WP_130692288 DUF5615 family PIN-like protein -
ELI15_RS29590 (ELI15_29590) 58534..59249 + 716 Protein_62 Crp/Fnr family transcriptional regulator -
ELI15_RS29595 (ELI15_29595) 59394..60014 - 621 WP_130692290 TraH family protein virB1
ELI15_RS29600 (ELI15_29600) 60032..61198 - 1167 WP_130692292 conjugal transfer protein TraB -
ELI15_RS29605 (ELI15_29605) 61188..61751 - 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELI15_RS29610 (ELI15_29610) 61748..65071 - 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELI15_RS29615 (ELI15_29615) 65326..65619 + 294 WP_128409207 conjugal transfer protein TraC -
ELI15_RS29620 (ELI15_29620) 65624..65839 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELI15_RS29625 (ELI15_29625) 65826..67757 + 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELI15_RS29630 (ELI15_29630) 68195..68644 + 450 WP_130692300 thermonuclease family protein -
ELI15_RS29635 (ELI15_29635) 68886..69200 - 315 WP_130692302 hypothetical protein -
ELI15_RS29640 (ELI15_29640) 69644..69952 + 309 WP_063473655 WGR domain-containing protein -
ELI15_RS38635 70020..70193 - 174 WP_165403408 hypothetical protein -
ELI15_RS38640 70488..70649 - 162 WP_162710370 hypothetical protein -
ELI15_RS29645 (ELI15_29645) 70950..71261 - 312 WP_027691174 DUF736 domain-containing protein -

Host bacterium

ID   1613 GenBank   NZ_SIPO01000006
Plasmid name   pSM149B_Rh07 Incompatibility group   -
Plasmid size   224057 bp Coordinate of oriT [Strand]   65143..65183 [-]
Host baterium   Rhizobium ruizarguesonis strain SM149B

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodD, fixG, fixQ, fixO, fixN
Anti-CRISPR   -