Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102553
Name   oriT_pSM16_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM16
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKC01000007 (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_pSM16_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1904 GenBank   WP_130784879
Name   traA_ELG73_RS33500_pSM16_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   1517 GenBank   WP_128409206
Name   traG_ELG73_RS33515_pSM16_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
ELG73_RS33375 (ELG73_33375) 171189..172211 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG73_RS33380 (ELG73_33380) 172208..173422 - 1215 WP_130784921 plasmid partitioning protein RepA -
ELG73_RS39215 174334..174546 - 213 WP_245458276 hypothetical protein -
ELG73_RS33395 (ELG73_33395) 175024..175662 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG73_RS33400 (ELG73_33400) 175659..176636 + 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG73_RS33405 (ELG73_33405) 176626..177009 + 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG73_RS33410 (ELG73_33410) 177002..177301 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG73_RS33415 (ELG73_33415) 177312..179768 + 2457 Protein_176 conjugal transfer protein TrbE -
ELG73_RS33420 (ELG73_33420) 179740..180543 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG73_RS33425 (ELG73_33425) 180540..180740 + 201 WP_128408800 entry exclusion protein TrbK -
ELG73_RS33430 (ELG73_33430) 180734..181915 + 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG73_RS33435 (ELG73_33435) 181936..182598 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG73_RS33440 (ELG73_33440) 182616..183428 + 813 WP_130784877 P-type conjugative transfer protein TrbG virB9
ELG73_RS33445 (ELG73_33445) 183432..183872 + 441 WP_128408804 conjugal transfer protein TrbH -
ELG73_RS33450 (ELG73_33450) 183884..185182 + 1299 WP_130784878 IncP-type conjugal transfer protein TrbI virB10
ELG73_RS33455 (ELG73_33455) 185491..186195 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG73_RS33460 (ELG73_33460) 186180..186521 - 342 WP_128408807 transcriptional repressor TraM -
ELG73_RS33465 (ELG73_33465) 186747..186989 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG73_RS33470 (ELG73_33470) 187103..187735 + 633 WP_128408809 DUF433 domain-containing protein -
ELG73_RS33475 (ELG73_33475) 187732..188106 + 375 WP_128408810 DUF5615 family PIN-like protein -
ELG73_RS33480 (ELG73_33480) 188463..189178 + 716 Protein_189 Crp/Fnr family transcriptional regulator -
ELG73_RS33485 (ELG73_33485) 189323..189943 - 621 WP_128408811 TraH family protein virB1
ELG73_RS33490 (ELG73_33490) 189961..191127 - 1167 WP_128408812 conjugal transfer protein TraB -
ELG73_RS33495 (ELG73_33495) 191117..191629 - 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG73_RS33500 (ELG73_33500) 191677..195003 - 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG73_RS33505 (ELG73_33505) 195258..195551 + 294 WP_128409207 conjugal transfer protein TraC -
ELG73_RS33510 (ELG73_33510) 195556..195771 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG73_RS33515 (ELG73_33515) 195758..197692 + 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG73_RS33525 (ELG73_33525) 198132..198434 + 303 Protein_197 thermonuclease family protein -
ELG73_RS33530 (ELG73_33530) 198504..199583 + 1080 WP_130784880 IS630 family transposase -
ELG73_RS33535 (ELG73_33535) 199580..199729 + 150 Protein_199 thermonuclease family protein -
ELG73_RS33540 (ELG73_33540) 199961..200275 - 315 WP_128408836 hypothetical protein -
ELG73_RS39575 (ELG73_33545) 200719..201027 + 309 WP_130784881 WGR domain-containing protein -
ELG73_RS39225 201196..201339 + 144 WP_245488070 hypothetical protein -
ELG73_RS38545 201561..201722 - 162 WP_018516739 hypothetical protein -
ELG73_RS33555 (ELG73_33555) 202023..202334 - 312 WP_127431460 DUF736 domain-containing protein -

Host bacterium

ID   2997 GenBank   NZ_SIKC01000007
Plasmid name   pSM16_Rh07 Incompatibility group   -
Plasmid size   273515 bp Coordinate of oriT [Strand]   195075..195115 [-]
Host baterium   Rhizobium leguminosarum strain SM16

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, fixG, fixQ, fixO, fixN
Anti-CRISPR   -