Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101174
Name   oriT_pSM141A_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM141A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOX01000006 (16900..16940 [-], 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_pSM141A_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1171 GenBank   WP_130692296
Name   traA_ELH98_RS28695_pSM141A_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   762 GenBank   WP_130692298
Name   traG_ELH98_RS28710_pSM141A_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   763 GenBank   WP_130692276
Name   t4cp2_ELH98_RS29070_pSM141A_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: 1568..19514

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH98_RS28610 (ELH98_28605) 1..1596 + 1596 Protein_0 conjugal transfer protein TrbE -
ELH98_RS28615 (ELH98_28610) 1568..2371 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELH98_RS28620 (ELH98_28615) 2368..2568 + 201 WP_130680525 entry exclusion protein TrbK -
ELH98_RS28625 (ELH98_28620) 2562..3743 + 1182 WP_130762999 P-type conjugative transfer protein TrbL virB6
ELH98_RS28630 (ELH98_28625) 3764..4426 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELH98_RS28635 (ELH98_28630) 4444..5256 + 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELH98_RS28640 (ELH98_28635) 5260..5700 + 441 WP_130692284 conjugal transfer protein TrbH -
ELH98_RS28645 (ELH98_28640) 5712..7010 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELH98_RS28650 (ELH98_28645) 7319..8023 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELH98_RS28655 (ELH98_28650) 8008..8349 - 342 WP_128408807 transcriptional repressor TraM -
ELH98_RS28660 (ELH98_28655) 8575..8817 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELH98_RS28665 (ELH98_28660) 8931..9563 + 633 WP_128408809 DUF433 domain-containing protein -
ELH98_RS28670 (ELH98_28665) 9560..9934 + 375 WP_130692288 DUF5615 family PIN-like protein -
ELH98_RS28675 (ELH98_28670) 10291..11006 + 716 Protein_13 Crp/Fnr family transcriptional regulator -
ELH98_RS28680 (ELH98_28675) 11151..11771 - 621 WP_130692290 TraH family protein virB1
ELH98_RS28685 (ELH98_28680) 11789..12955 - 1167 WP_130692292 conjugal transfer protein TraB -
ELH98_RS28690 (ELH98_28685) 12945..13508 - 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELH98_RS28695 (ELH98_28690) 13505..16828 - 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELH98_RS28700 (ELH98_28695) 17083..17376 + 294 WP_128409207 conjugal transfer protein TraC -
ELH98_RS28705 (ELH98_28700) 17381..17596 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELH98_RS28710 (ELH98_28705) 17583..19514 + 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELH98_RS28715 (ELH98_28710) 19952..20401 + 450 WP_130692300 thermonuclease family protein -
ELH98_RS28720 (ELH98_28715) 20643..20957 - 315 WP_130692302 hypothetical protein -
ELH98_RS28725 (ELH98_28720) 21401..21709 + 309 WP_063473655 WGR domain-containing protein -
ELH98_RS40400 21777..21950 - 174 WP_165403408 hypothetical protein -
ELH98_RS40405 22245..22406 - 162 WP_162710370 hypothetical protein -
ELH98_RS28730 (ELH98_28725) 22707..23018 - 312 WP_027691174 DUF736 domain-containing protein -

Host bacterium

ID   1618 GenBank   NZ_SIOX01000006
Plasmid name   pSM141A_Rh07 Incompatibility group   -
Plasmid size   92622 bp Coordinate of oriT [Strand]   16900..16940 [-]
Host baterium   Rhizobium ruizarguesonis strain SM141A

Cargo genes

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