Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102545
Name   oriT_pSM24_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKJ01000007 (29586..29626 [-], 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_pSM24_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1896 GenBank   WP_130808408
Name   traA_ELG80_RS34870_pSM24_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: 122864.90 Da        Isoelectric Point: 9.7033

>WP_130808408.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVCSMIADR
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKIALLGPDGKPVRNDAGKLVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKTQASAPKLERIELQGERRSENARRIERRPE
IVLDLITREKSVFDERDVAKVLYRYIDDAALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTRDM
VRLEAEMANRAIWLSGRASHGVREEVLQTTFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTAFVLDEAGMVSSRQM
ALFVEAVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLAKVLESAPGRIVAEVGDGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVNVARTIAHDRIHWAVRQKQNLADLGARLAAISTALGLARGSNKHSIPNTI
KGAKPMVSGITTFPKSLDHAVEDKLAADPGLKKQWEDVSTRFQLVYAQPEAVFKAINVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGVLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTADQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)

AAA domain (AAA_30)

(387-570)


  Protein structure



No available structure.




T4CP

ID   1504 GenBank   WP_128409206
Name   traG_ELG80_RS34885_pSM24_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: 10280..32203

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG80_RS34745 (ELG80_34745) 5810..6832 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG80_RS34750 (ELG80_34750) 6829..8043 - 1215 WP_130784921 plasmid partitioning protein RepA -
ELG80_RS39355 8955..9167 - 213 WP_245458276 hypothetical protein -
ELG80_RS34765 (ELG80_34765) 9645..10283 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG80_RS34770 (ELG80_34770) 10280..11257 + 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG80_RS34775 (ELG80_34775) 11247..11630 + 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG80_RS34780 (ELG80_34780) 11623..11922 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG80_RS34785 (ELG80_34785) 11933..14279 + 2347 Protein_12 conjugal transfer protein TrbE -
ELG80_RS34790 (ELG80_34790) 14251..15054 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG80_RS34795 (ELG80_34795) 15051..15251 + 201 WP_128408800 entry exclusion protein TrbK -
ELG80_RS34800 (ELG80_34800) 15245..16426 + 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG80_RS34805 (ELG80_34805) 16447..17109 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG80_RS34810 (ELG80_34810) 17127..17939 + 813 WP_130784877 P-type conjugative transfer protein TrbG virB9
ELG80_RS34815 (ELG80_34815) 17943..18383 + 441 WP_128408804 conjugal transfer protein TrbH -
ELG80_RS34820 (ELG80_34820) 18395..19693 + 1299 WP_130784878 IncP-type conjugal transfer protein TrbI virB10
ELG80_RS34825 (ELG80_34825) 20002..20706 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG80_RS34830 (ELG80_34830) 20691..21032 - 342 WP_128408807 transcriptional repressor TraM -
ELG80_RS34835 (ELG80_34835) 21258..21500 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG80_RS34840 (ELG80_34840) 21614..22246 + 633 WP_128408809 DUF433 domain-containing protein -
ELG80_RS34845 (ELG80_34845) 22243..22617 + 375 WP_128408810 DUF5615 family PIN-like protein -
ELG80_RS34850 (ELG80_34850) 22974..23689 + 716 Protein_25 Crp/Fnr family transcriptional regulator -
ELG80_RS34855 (ELG80_34855) 23834..24454 - 621 WP_128408811 TraH family protein virB1
ELG80_RS34860 (ELG80_34860) 24472..25638 - 1167 WP_128408812 conjugal transfer protein TraB -
ELG80_RS34865 (ELG80_34865) 25628..26140 - 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG80_RS34870 (ELG80_34870) 26188..29514 - 3327 WP_130808408 Ti-type conjugative transfer relaxase TraA -
ELG80_RS34875 (ELG80_34875) 29769..30062 + 294 WP_128409207 conjugal transfer protein TraC -
ELG80_RS34880 (ELG80_34880) 30067..30282 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG80_RS34885 (ELG80_34885) 30269..32203 + 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG80_RS34895 (ELG80_34895) 32643..32945 + 303 Protein_33 thermonuclease family protein -
ELG80_RS34900 (ELG80_34900) 33015..34094 + 1080 WP_130784880 IS630 family transposase -
ELG80_RS34905 (ELG80_34905) 34091..34240 + 150 Protein_35 thermonuclease family protein -
ELG80_RS34910 (ELG80_34910) 34472..34786 - 315 WP_128408836 hypothetical protein -
ELG80_RS39740 (ELG80_34915) 35230..35538 + 309 WP_130784881 WGR domain-containing protein -
ELG80_RS39365 35707..35850 + 144 WP_245488070 hypothetical protein -
ELG80_RS38655 36072..36233 - 162 WP_018516739 hypothetical protein -
ELG80_RS34925 (ELG80_34925) 36534..36845 - 312 WP_127431460 DUF736 domain-containing protein -

Host bacterium

ID   2989 GenBank   NZ_SIKJ01000007
Plasmid name   pSM24_Rh07 Incompatibility group   -
Plasmid size   98110 bp Coordinate of oriT [Strand]   29586..29626 [-]
Host baterium   Rhizobium leguminosarum strain SM24

Cargo genes

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