Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102563
Name   oriT_pSM19_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM19
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKF01000006 (195075..195115 [-], 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_pSM19_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1914 GenBank   WP_130784879
Name   traA_ELG76_RS34565_pSM19_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   1534 GenBank   WP_128409206
Name   traG_ELG76_RS34580_pSM19_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: 175659..197692

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG76_RS34440 (ELG76_34435) 171189..172211 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG76_RS34445 (ELG76_34440) 172208..173422 - 1215 WP_130784921 plasmid partitioning protein RepA -
ELG76_RS39880 174334..174546 - 213 WP_245458276 hypothetical protein -
ELG76_RS34460 (ELG76_34455) 175024..175662 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG76_RS34465 (ELG76_34460) 175659..176636 + 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG76_RS34470 (ELG76_34465) 176626..177009 + 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG76_RS34475 (ELG76_34470) 177002..177301 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG76_RS34480 (ELG76_34475) 177312..179768 + 2457 Protein_176 conjugal transfer protein TrbE -
ELG76_RS34485 (ELG76_34480) 179740..180543 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG76_RS34490 (ELG76_34485) 180540..180740 + 201 WP_128408800 entry exclusion protein TrbK -
ELG76_RS34495 (ELG76_34490) 180734..181915 + 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG76_RS34500 (ELG76_34495) 181936..182598 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG76_RS34505 (ELG76_34500) 182616..183428 + 813 WP_130784877 P-type conjugative transfer protein TrbG virB9
ELG76_RS34510 (ELG76_34505) 183432..183872 + 441 WP_128408804 conjugal transfer protein TrbH -
ELG76_RS34515 (ELG76_34510) 183884..185182 + 1299 WP_130784878 IncP-type conjugal transfer protein TrbI virB10
ELG76_RS34520 (ELG76_34515) 185491..186195 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG76_RS34525 (ELG76_34520) 186180..186521 - 342 WP_128408807 transcriptional repressor TraM -
ELG76_RS34530 (ELG76_34525) 186747..186989 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG76_RS34535 (ELG76_34530) 187103..187735 + 633 WP_128408809 DUF433 domain-containing protein -
ELG76_RS34540 (ELG76_34535) 187732..188106 + 375 WP_128408810 DUF5615 family PIN-like protein -
ELG76_RS34545 (ELG76_34540) 188463..189178 + 716 Protein_189 Crp/Fnr family transcriptional regulator -
ELG76_RS34550 (ELG76_34545) 189323..189943 - 621 WP_128408811 TraH family protein virB1
ELG76_RS34555 (ELG76_34550) 189961..191127 - 1167 WP_128408812 conjugal transfer protein TraB -
ELG76_RS34560 (ELG76_34555) 191117..191629 - 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG76_RS34565 (ELG76_34560) 191677..195003 - 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG76_RS34570 (ELG76_34565) 195258..195551 + 294 WP_128409207 conjugal transfer protein TraC -
ELG76_RS34575 (ELG76_34570) 195556..195771 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG76_RS34580 (ELG76_34575) 195758..197692 + 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG76_RS34590 (ELG76_34585) 198132..198434 + 303 Protein_197 thermonuclease family protein -
ELG76_RS34595 (ELG76_34590) 198504..199583 + 1080 WP_130784880 IS630 family transposase -
ELG76_RS34600 (ELG76_34595) 199580..199729 + 150 Protein_199 thermonuclease family protein -
ELG76_RS34605 (ELG76_34600) 199961..200275 - 315 WP_128408836 hypothetical protein -
ELG76_RS40210 (ELG76_34605) 200719..201027 + 309 WP_130784881 WGR domain-containing protein -
ELG76_RS39890 201196..201339 + 144 WP_245488070 hypothetical protein -
ELG76_RS39195 201561..201722 - 162 WP_018516739 hypothetical protein -
ELG76_RS34620 (ELG76_34615) 202023..202334 - 312 WP_127431460 DUF736 domain-containing protein -

Host bacterium

ID   3007 GenBank   NZ_SIKF01000006
Plasmid name   pSM19_Rh07 Incompatibility group   -
Plasmid size   227459 bp Coordinate of oriT [Strand]   195075..195115 [-]
Host baterium   Rhizobium leguminosarum strain SM19

Cargo genes

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