Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101198
Name   oriT_pSM148C_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM148C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPM01000006 (121351..121391 [-], 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_pSM148C_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1194 GenBank   WP_130692296
Name   traA_ELI13_RS30685_pSM148C_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   804 GenBank   WP_130692276
Name   t4cp2_ELI13_RS30600_pSM148C_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   805 GenBank   WP_130692298
Name   traG_ELI13_RS30700_pSM148C_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: 101938..123964

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI13_RS30560 (ELI13_30560) 97468..98490 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELI13_RS30565 (ELI13_30565) 98487..99701 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELI13_RS30570 (ELI13_30570) 100318..100572 - 255 WP_130692270 IS66 family insertion sequence element accessory protein TnpB -
ELI13_RS39490 100613..100825 - 213 WP_245458276 hypothetical protein -
ELI13_RS30580 (ELI13_30580) 101303..101941 + 639 WP_130692272 acyl-homoserine-lactone synthase -
ELI13_RS30585 (ELI13_30585) 101938..102915 + 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
ELI13_RS30590 (ELI13_30590) 102905..103288 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELI13_RS30595 (ELI13_30595) 103281..103580 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELI13_RS30600 (ELI13_30600) 103591..106047 + 2457 WP_130692276 conjugal transfer protein TrbE virb4
ELI13_RS30605 (ELI13_30605) 106019..106822 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELI13_RS30610 (ELI13_30610) 106819..107019 + 201 WP_128408800 entry exclusion protein TrbK -
ELI13_RS30615 (ELI13_30615) 107013..108194 + 1182 WP_130692278 P-type conjugative transfer protein TrbL virB6
ELI13_RS30620 (ELI13_30620) 108215..108877 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELI13_RS30625 (ELI13_30625) 108895..109707 + 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELI13_RS30630 (ELI13_30630) 109711..110151 + 441 WP_130692284 conjugal transfer protein TrbH -
ELI13_RS30635 (ELI13_30635) 110163..111461 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELI13_RS30640 (ELI13_30640) 111770..112474 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELI13_RS30645 (ELI13_30645) 112459..112800 - 342 WP_128408807 transcriptional repressor TraM -
ELI13_RS30650 (ELI13_30650) 113026..113268 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELI13_RS30655 (ELI13_30655) 113382..114014 + 633 WP_128408809 DUF433 domain-containing protein -
ELI13_RS30660 (ELI13_30660) 114011..114385 + 375 WP_130692288 DUF5615 family PIN-like protein -
ELI13_RS30665 (ELI13_30665) 114742..115457 + 716 Protein_114 Crp/Fnr family transcriptional regulator -
ELI13_RS30670 (ELI13_30670) 115602..116222 - 621 WP_130692290 TraH family protein virB1
ELI13_RS30675 (ELI13_30675) 116240..117406 - 1167 WP_130692292 conjugal transfer protein TraB -
ELI13_RS30680 (ELI13_30680) 117396..117959 - 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELI13_RS30685 (ELI13_30685) 117956..121279 - 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELI13_RS30690 (ELI13_30690) 121533..121826 + 294 WP_128409207 conjugal transfer protein TraC -
ELI13_RS30695 (ELI13_30695) 121831..122046 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELI13_RS30700 (ELI13_30700) 122033..123964 + 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELI13_RS30705 (ELI13_30705) 124402..124851 + 450 WP_130692300 thermonuclease family protein -
ELI13_RS30710 (ELI13_30710) 125093..125407 - 315 WP_130692302 hypothetical protein -
ELI13_RS30715 (ELI13_30715) 125851..126159 + 309 WP_063473655 WGR domain-containing protein -
ELI13_RS38815 126227..126400 - 174 WP_165403408 hypothetical protein -
ELI13_RS38820 126695..126856 - 162 WP_162710370 hypothetical protein -
ELI13_RS30720 (ELI13_30720) 127157..127468 - 312 WP_027691174 DUF736 domain-containing protein -

Host bacterium

ID   1642 GenBank   NZ_SIPM01000006
Plasmid name   pSM148C_Rh07 Incompatibility group   -
Plasmid size   159524 bp Coordinate of oriT [Strand]   121351..121391 [-]
Host baterium   Rhizobium ruizarguesonis strain SM148C

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nifE, nifD, nifH, fixA, fixB, fixC, fixX, nifT, nodJ, nodI, nodC, nodA, nodD, nodF, nodE, nodM
Anti-CRISPR   -