Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102566
Name   oriT_pSM25_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM25
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKK01000006 (29714..29754 [-], 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_pSM25_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1916 GenBank   WP_130784879
Name   traA_ELG81_RS33295_pSM25_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   1537 GenBank   WP_128409206
Name   traG_ELG81_RS33310_pSM25_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: 10298..32331

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG81_RS33170 (ELG81_33175) 5828..6850 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG81_RS33175 (ELG81_33180) 6847..8061 - 1215 WP_130784921 plasmid partitioning protein RepA -
ELG81_RS39395 8973..9185 - 213 WP_245458276 hypothetical protein -
ELG81_RS33190 (ELG81_33195) 9663..10301 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG81_RS33195 (ELG81_33200) 10298..11275 + 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG81_RS33200 (ELG81_33205) 11265..11648 + 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG81_RS33205 (ELG81_33210) 11641..11940 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG81_RS33210 (ELG81_33215) 11951..14407 + 2457 Protein_12 conjugal transfer protein TrbE -
ELG81_RS33215 (ELG81_33220) 14379..15182 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG81_RS33220 (ELG81_33225) 15179..15379 + 201 WP_128408800 entry exclusion protein TrbK -
ELG81_RS33225 (ELG81_33230) 15373..16554 + 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG81_RS33230 (ELG81_33235) 16575..17237 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG81_RS33235 (ELG81_33240) 17255..18067 + 813 WP_130784877 P-type conjugative transfer protein TrbG virB9
ELG81_RS33240 (ELG81_33245) 18071..18511 + 441 WP_128408804 conjugal transfer protein TrbH -
ELG81_RS33245 (ELG81_33250) 18523..19821 + 1299 WP_130784878 IncP-type conjugal transfer protein TrbI virB10
ELG81_RS33250 (ELG81_33255) 20130..20834 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG81_RS33255 (ELG81_33260) 20819..21160 - 342 WP_128408807 transcriptional repressor TraM -
ELG81_RS33260 (ELG81_33265) 21386..21628 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG81_RS33265 (ELG81_33270) 21742..22374 + 633 WP_128408809 DUF433 domain-containing protein -
ELG81_RS33270 (ELG81_33275) 22371..22745 + 375 WP_128408810 DUF5615 family PIN-like protein -
ELG81_RS33275 (ELG81_33280) 23102..23817 + 716 Protein_25 Crp/Fnr family transcriptional regulator -
ELG81_RS33280 (ELG81_33285) 23962..24582 - 621 WP_128408811 TraH family protein virB1
ELG81_RS33285 (ELG81_33290) 24600..25766 - 1167 WP_128408812 conjugal transfer protein TraB -
ELG81_RS33290 (ELG81_33295) 25756..26268 - 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG81_RS33295 (ELG81_33300) 26316..29642 - 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG81_RS33300 (ELG81_33305) 29897..30190 + 294 WP_128409207 conjugal transfer protein TraC -
ELG81_RS33305 (ELG81_33310) 30195..30410 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG81_RS33310 (ELG81_33315) 30397..32331 + 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG81_RS33320 (ELG81_33325) 32771..33073 + 303 Protein_33 thermonuclease family protein -
ELG81_RS33325 (ELG81_33330) 33143..34222 + 1080 WP_130784880 IS630 family transposase -
ELG81_RS33330 (ELG81_33335) 34219..34368 + 150 Protein_35 thermonuclease family protein -
ELG81_RS33335 (ELG81_33340) 34600..34914 - 315 WP_128408836 hypothetical protein -
ELG81_RS39840 (ELG81_33345) 35358..35666 + 309 WP_130784881 WGR domain-containing protein -
ELG81_RS39405 35835..35978 + 144 WP_245488070 hypothetical protein -
ELG81_RS38805 36200..36361 - 162 WP_018516739 hypothetical protein -
ELG81_RS33350 (ELG81_33355) 36662..36973 - 312 WP_127431460 DUF736 domain-containing protein -

Host bacterium

ID   3010 GenBank   NZ_SIKK01000006
Plasmid name   pSM25_Rh07 Incompatibility group   -
Plasmid size   61505 bp Coordinate of oriT [Strand]   29714..29754 [-]
Host baterium   Rhizobium leguminosarum strain SM25

Cargo genes

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