Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101177
Name   oriT_pSM122A_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM122A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SINW01000006 (3608..3648 [+], 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_pSM122A_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1174 GenBank   WP_130692296
Name   traA_ELH71_RS33430_pSM122A_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   767 GenBank   WP_130692298
Name   traG_ELH71_RS33415_pSM122A_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   768 GenBank   WP_130692276
Name   t4cp2_ELH71_RS33515_pSM122A_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: 1034..23061

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH71_RS33410 (ELH71_33405) 147..596 - 450 WP_130692300 thermonuclease family protein -
ELH71_RS33415 (ELH71_33410) 1034..2965 - 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELH71_RS33420 (ELH71_33415) 2952..3167 - 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELH71_RS33425 (ELH71_33420) 3172..3465 - 294 WP_128409207 conjugal transfer protein TraC -
ELH71_RS33430 (ELH71_33425) 3720..7043 + 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELH71_RS33435 (ELH71_33430) 7040..7603 + 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELH71_RS33440 (ELH71_33435) 7593..8759 + 1167 WP_130692292 conjugal transfer protein TraB -
ELH71_RS33445 (ELH71_33440) 8777..9397 + 621 WP_130692290 TraH family protein virB1
ELH71_RS33450 (ELH71_33445) 9542..10257 - 716 Protein_8 Crp/Fnr family transcriptional regulator -
ELH71_RS33455 (ELH71_33450) 10614..10988 - 375 WP_130692288 DUF5615 family PIN-like protein -
ELH71_RS33460 (ELH71_33455) 10985..11617 - 633 WP_128408809 DUF433 domain-containing protein -
ELH71_RS33465 (ELH71_33460) 11731..11973 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELH71_RS33470 (ELH71_33465) 12199..12540 + 342 WP_128408807 transcriptional repressor TraM -
ELH71_RS33475 (ELH71_33470) 12525..13229 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELH71_RS33480 (ELH71_33475) 13538..14836 - 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELH71_RS33485 (ELH71_33480) 14848..15288 - 441 WP_130692284 conjugal transfer protein TrbH -
ELH71_RS33490 (ELH71_33485) 15292..16104 - 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELH71_RS33495 (ELH71_33490) 16122..16784 - 663 WP_130692280 conjugal transfer protein TrbF virB8
ELH71_RS33500 (ELH71_33495) 16805..17986 - 1182 WP_130692278 P-type conjugative transfer protein TrbL virB6
ELH71_RS33505 (ELH71_33500) 17980..18180 - 201 WP_128408800 entry exclusion protein TrbK -
ELH71_RS33510 (ELH71_33505) 18177..18980 - 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELH71_RS33515 (ELH71_33510) 18952..21408 - 2457 WP_130692276 conjugal transfer protein TrbE virb4
ELH71_RS33520 (ELH71_33515) 21419..21718 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELH71_RS33525 (ELH71_33520) 21711..22094 - 384 WP_063473648 TrbC/VirB2 family protein virB2
ELH71_RS33530 (ELH71_33525) 22084..23061 - 978 WP_130764766 P-type conjugative transfer ATPase TrbB virB11
ELH71_RS33535 (ELH71_33530) 23058..23696 - 639 WP_130692272 acyl-homoserine-lactone synthase -
ELH71_RS39575 24174..24386 + 213 WP_245458276 hypothetical protein -
ELH71_RS33545 (ELH71_33540) 24427..24681 + 255 WP_130692270 IS66 family insertion sequence element accessory protein TnpB -
ELH71_RS33550 (ELH71_33545) 25298..26512 + 1215 WP_027691186 plasmid partitioning protein RepA -
ELH71_RS33555 (ELH71_33550) 26509..27531 + 1023 WP_128408794 plasmid partitioning protein RepB -

Host bacterium

ID   1621 GenBank   NZ_SINW01000006
Plasmid name   pSM122A_Rh07 Incompatibility group   -
Plasmid size   56920 bp Coordinate of oriT [Strand]   3608..3648 [+]
Host baterium   Rhizobium ruizarguesonis strain SM122A

Cargo genes

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