Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101141
Name   oriT_pSM134B_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM134B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SION01000007 (15901..15941 [+], 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_pSM134B_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1140 GenBank   WP_130692296
Name   traA_ELH88_RS29435_pSM134B_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   701 GenBank   WP_130692298
Name   traG_ELH88_RS29420_pSM134B_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   702 GenBank   WP_130692276
Name   t4cp2_ELH88_RS29520_pSM134B_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: 13327..35354

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH88_RS39720 9190..9366 - 177 WP_018482051 hypothetical protein -
ELH88_RS29400 (ELH88_29405) 9823..10134 + 312 WP_027691174 DUF736 domain-containing protein -
ELH88_RS39725 10435..10596 + 162 WP_162710370 hypothetical protein -
ELH88_RS39730 10891..11064 + 174 WP_165403408 hypothetical protein -
ELH88_RS29405 (ELH88_29410) 11132..11440 - 309 WP_063473655 WGR domain-containing protein -
ELH88_RS29410 (ELH88_29415) 11884..12198 + 315 WP_130692302 hypothetical protein -
ELH88_RS29415 (ELH88_29420) 12440..12889 - 450 WP_130692300 thermonuclease family protein -
ELH88_RS29420 (ELH88_29425) 13327..15258 - 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELH88_RS29425 (ELH88_29430) 15245..15460 - 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELH88_RS29430 (ELH88_29435) 15465..15758 - 294 WP_128409207 conjugal transfer protein TraC -
ELH88_RS29435 (ELH88_29440) 16013..19336 + 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELH88_RS29440 (ELH88_29445) 19333..19896 + 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELH88_RS29445 (ELH88_29450) 19886..21052 + 1167 WP_130692292 conjugal transfer protein TraB -
ELH88_RS29450 (ELH88_29455) 21070..21690 + 621 WP_130692290 TraH family protein virB1
ELH88_RS29455 (ELH88_29460) 21835..22550 - 716 Protein_24 Crp/Fnr family transcriptional regulator -
ELH88_RS29460 (ELH88_29465) 22907..23281 - 375 WP_130692288 DUF5615 family PIN-like protein -
ELH88_RS29465 (ELH88_29470) 23278..23910 - 633 WP_128408809 DUF433 domain-containing protein -
ELH88_RS29470 (ELH88_29475) 24024..24266 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELH88_RS29475 (ELH88_29480) 24492..24833 + 342 WP_128408807 transcriptional repressor TraM -
ELH88_RS29480 (ELH88_29485) 24818..25522 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELH88_RS29485 (ELH88_29490) 25831..27129 - 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELH88_RS29490 (ELH88_29495) 27141..27581 - 441 WP_130692284 conjugal transfer protein TrbH -
ELH88_RS29495 (ELH88_29500) 27585..28397 - 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELH88_RS29500 (ELH88_29505) 28415..29077 - 663 WP_130692280 conjugal transfer protein TrbF virB8
ELH88_RS29505 (ELH88_29510) 29098..30279 - 1182 WP_130692278 P-type conjugative transfer protein TrbL virB6
ELH88_RS29510 (ELH88_29515) 30273..30473 - 201 WP_128408800 entry exclusion protein TrbK -
ELH88_RS29515 (ELH88_29520) 30470..31273 - 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELH88_RS29520 (ELH88_29525) 31245..33701 - 2457 WP_130692276 conjugal transfer protein TrbE virb4
ELH88_RS29525 (ELH88_29530) 33712..34011 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELH88_RS29530 (ELH88_29535) 34004..34387 - 384 WP_063473648 TrbC/VirB2 family protein virB2
ELH88_RS29535 (ELH88_29540) 34377..35354 - 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
ELH88_RS29540 (ELH88_29545) 35351..35989 - 639 WP_130692272 acyl-homoserine-lactone synthase -
ELH88_RS40430 36467..36679 + 213 WP_245458276 hypothetical protein -
ELH88_RS29550 (ELH88_29555) 36720..36974 + 255 WP_130692270 IS66 family insertion sequence element accessory protein TnpB -
ELH88_RS29555 (ELH88_29560) 37591..38805 + 1215 WP_027691186 plasmid partitioning protein RepA -
ELH88_RS29560 (ELH88_29565) 38802..39824 + 1023 WP_128408794 plasmid partitioning protein RepB -

Host bacterium

ID   1585 GenBank   NZ_SION01000007
Plasmid name   pSM134B_Rh07 Incompatibility group   -
Plasmid size   45540 bp Coordinate of oriT [Strand]   15901..15941 [+]
Host baterium   Rhizobium ruizarguesonis strain SM134B

Cargo genes

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