Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102554
Name   oriT_pSM4_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIJR01000006 (130176..130216 [-], 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_pSM4_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1905 GenBank   WP_130784879
Name   traA_ELG62_RS36425_pSM4_Rh07 insolico UniProt ID   _
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 122892.96 Da        Isoelectric Point: 9.7033

>WP_130784879.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVCSMIADR
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKIALLGPDGKPVRNDAGKLVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKTQASAPKLERIELQGERRSENARRIERRPE
IVLDLITREKSVFDERDVAKVLYRYIDDAALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTRDM
VRLEAEMANRAIWLSGRASHGVREEVLQTTFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLAKVLESAPGRIVAEVGDGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVNVARTIAHDRIHWAVRQKQNLADLGARLAAISTALGLARGSNKHSIPNTI
KGAKPMVSGITTFPKSLDHAVEDKLAADPGLKKQWEDVSTRFQLVYAQPEAVFKAINVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGVLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTADQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure



No available structure.




T4CP

ID   1518 GenBank   WP_130788633
Name   t4cp2_ELG62_RS36340_pSM4_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: 91673.41 Da        Isoelectric Point: 5.7027

>WP_130788633.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTLAIDAERRAHFAREQGHFESKHALVLTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMSMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPISPCPFYPPNAPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATSEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIHWLETRGVHDAASLLKYV

  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   1519 GenBank   WP_128409206
Name   traG_ELG62_RS36440_pSM4_Rh07 insolico UniProt ID   _
Length   644 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 644 a.a.        Molecular weight: 69653.97 Da        Isoelectric Point: 9.3813

>WP_128409206.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVMPGTLMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVAGCSGTILIAAIRETMRLSSFMKTVPADKTVLAFLDPATSIGASAALLCACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDVGGIVIGERYRVDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSGHRGRAGRDVFLLD
PRKPDIGFNVLDWVGRFGGTKEEDIASIASWIMSDSGGVRGVRDDFFRASALQLLTALIADVCLSGHTDE
KDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPRPA

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(163-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 110760..132793

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG62_RS36300 (ELG62_36305) 106290..107312 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG62_RS36305 (ELG62_36310) 107309..108523 - 1215 WP_130784921 plasmid partitioning protein RepA -
ELG62_RS38380 109435..109647 - 213 WP_245458276 hypothetical protein -
ELG62_RS36320 (ELG62_36325) 110125..110763 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG62_RS36325 (ELG62_36330) 110760..111737 + 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG62_RS36330 (ELG62_36335) 111727..112110 + 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG62_RS36335 (ELG62_36340) 112103..112402 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG62_RS36340 (ELG62_36345) 112413..114869 + 2457 WP_130788633 conjugal transfer protein TrbE virb4
ELG62_RS36345 (ELG62_36350) 114841..115644 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG62_RS36350 (ELG62_36355) 115641..115841 + 201 WP_128408800 entry exclusion protein TrbK -
ELG62_RS36355 (ELG62_36360) 115835..117016 + 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG62_RS36360 (ELG62_36365) 117037..117699 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG62_RS36365 (ELG62_36370) 117717..118529 + 813 WP_130784877 P-type conjugative transfer protein TrbG virB9
ELG62_RS36370 (ELG62_36375) 118533..118973 + 441 WP_128408804 conjugal transfer protein TrbH -
ELG62_RS36375 (ELG62_36380) 118985..120283 + 1299 WP_130784878 IncP-type conjugal transfer protein TrbI virB10
ELG62_RS36380 (ELG62_36385) 120592..121296 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG62_RS36385 (ELG62_36390) 121281..121622 - 342 WP_128408807 transcriptional repressor TraM -
ELG62_RS36390 (ELG62_36395) 121848..122090 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG62_RS36395 (ELG62_36400) 122204..122836 + 633 WP_128408809 DUF433 domain-containing protein -
ELG62_RS36400 (ELG62_36405) 122833..123207 + 375 WP_128408810 DUF5615 family PIN-like protein -
ELG62_RS36405 (ELG62_36410) 123564..124279 + 716 Protein_116 Crp/Fnr family transcriptional regulator -
ELG62_RS36410 (ELG62_36415) 124424..125044 - 621 WP_130854265 TraH family protein virB1
ELG62_RS36415 (ELG62_36420) 125062..126228 - 1167 WP_128408812 conjugal transfer protein TraB -
ELG62_RS36420 (ELG62_36425) 126218..126781 - 564 WP_128408813 conjugative transfer signal peptidase TraF -
ELG62_RS36425 (ELG62_36430) 126778..130104 - 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG62_RS36430 (ELG62_36435) 130359..130652 + 294 WP_128409207 conjugal transfer protein TraC -
ELG62_RS36435 (ELG62_36440) 130657..130872 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG62_RS36440 (ELG62_36445) 130859..132793 + 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG62_RS36450 (ELG62_36455) 133233..133535 + 303 Protein_124 thermonuclease family protein -
ELG62_RS36455 (ELG62_36460) 133605..134684 + 1080 WP_130784880 IS630 family transposase -
ELG62_RS36460 (ELG62_36465) 134681..134830 + 150 Protein_126 thermonuclease family protein -
ELG62_RS36465 (ELG62_36470) 135062..135376 - 315 WP_128408836 hypothetical protein -
ELG62_RS38615 (ELG62_36475) 135820..136128 + 309 WP_130784881 WGR domain-containing protein -
ELG62_RS38390 136297..136440 + 144 WP_245488070 hypothetical protein -
ELG62_RS37885 136662..136823 - 162 WP_018516739 hypothetical protein -
ELG62_RS36480 (ELG62_36485) 137124..137435 - 312 WP_127431460 DUF736 domain-containing protein -

Host bacterium

ID   2998 GenBank   NZ_SIJR01000006
Plasmid name   pSM4_Rh07 Incompatibility group   -
Plasmid size   196965 bp Coordinate of oriT [Strand]   130176..130216 [-]
Host baterium   Rhizobium leguminosarum strain SM4

Cargo genes

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