Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102547
Name   oriT_pSM5_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIJS01000005 (66758..66798 [+], 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_pSM5_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1898 GenBank   WP_130784879
Name   traA_ELG63_RS33350_pSM5_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   1507 GenBank   WP_128409206
Name   traG_ELG63_RS33335_pSM5_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: 64181..86214

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG63_RS33295 (ELG63_33295) 59539..59850 + 312 WP_127431460 DUF736 domain-containing protein -
ELG63_RS37855 60151..60312 + 162 WP_018516739 hypothetical protein -
ELG63_RS38350 60534..60677 - 144 WP_245488070 hypothetical protein -
ELG63_RS38710 (ELG63_33305) 60846..61154 - 309 WP_130784881 WGR domain-containing protein -
ELG63_RS33310 (ELG63_33310) 61598..61912 + 315 WP_130872651 hypothetical protein -
ELG63_RS33315 (ELG63_33315) 62144..62293 - 150 Protein_65 thermonuclease family protein -
ELG63_RS33320 (ELG63_33320) 62290..63369 - 1080 WP_130784880 IS630 family transposase -
ELG63_RS33325 (ELG63_33325) 63439..63741 - 303 Protein_67 thermonuclease family protein -
ELG63_RS33335 (ELG63_33335) 64181..66115 - 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG63_RS33340 (ELG63_33340) 66102..66317 - 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG63_RS33345 (ELG63_33345) 66322..66615 - 294 WP_128409207 conjugal transfer protein TraC -
ELG63_RS33350 (ELG63_33350) 66870..70196 + 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG63_RS33355 (ELG63_33355) 70244..70756 + 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG63_RS33360 (ELG63_33360) 70746..71912 + 1167 WP_128408812 conjugal transfer protein TraB -
ELG63_RS33365 (ELG63_33365) 71930..72550 + 621 WP_128408811 TraH family protein virB1
ELG63_RS33370 (ELG63_33370) 72695..73410 - 716 Protein_75 Crp/Fnr family transcriptional regulator -
ELG63_RS33375 (ELG63_33375) 73767..74141 - 375 WP_128408810 DUF5615 family PIN-like protein -
ELG63_RS33380 (ELG63_33380) 74138..74770 - 633 WP_128408809 DUF433 domain-containing protein -
ELG63_RS33385 (ELG63_33385) 74884..75126 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG63_RS33390 (ELG63_33390) 75352..75693 + 342 WP_128408807 transcriptional repressor TraM -
ELG63_RS33395 (ELG63_33395) 75678..76382 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELG63_RS33400 (ELG63_33400) 76691..77989 - 1299 WP_130872652 IncP-type conjugal transfer protein TrbI virB10
ELG63_RS33405 (ELG63_33405) 78001..78441 - 441 WP_128408804 conjugal transfer protein TrbH -
ELG63_RS33410 (ELG63_33410) 78445..79257 - 813 WP_130784877 P-type conjugative transfer protein TrbG virB9
ELG63_RS33415 (ELG63_33415) 79275..79937 - 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG63_RS33420 (ELG63_33420) 79958..81139 - 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG63_RS33425 (ELG63_33425) 81133..81333 - 201 WP_128408800 entry exclusion protein TrbK -
ELG63_RS33430 (ELG63_33430) 81330..82133 - 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG63_RS33435 (ELG63_33435) 82105..84561 - 2457 Protein_88 conjugal transfer protein TrbE -
ELG63_RS33440 (ELG63_33440) 84572..84871 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG63_RS33445 (ELG63_33445) 84864..85247 - 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG63_RS33450 (ELG63_33450) 85237..86214 - 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG63_RS33455 (ELG63_33455) 86211..86849 - 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG63_RS38360 87327..87539 + 213 WP_245458276 hypothetical protein -
ELG63_RS33470 (ELG63_33470) 88451..89665 + 1215 WP_130784921 plasmid partitioning protein RepA -
ELG63_RS33475 (ELG63_33475) 89662..90684 + 1023 WP_128408794 plasmid partitioning protein RepB -

Host bacterium

ID   2991 GenBank   NZ_SIJS01000005
Plasmid name   pSM5_Rh07 Incompatibility group   -
Plasmid size   261648 bp Coordinate of oriT [Strand]   66758..66798 [+]
Host baterium   Rhizobium leguminosarum strain SM5

Cargo genes

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