Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102582
Name   oriT_pSM135B_Rh04 in_silico
Organism   Rhizobium leguminosarum strain SM135B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOP01000004 (349132..349167 [+], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      15..21, 26..32  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_pSM135B_Rh04
AAGGGCGCAATTATACGTCGCTGACGCGACGTCTTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1930 GenBank   WP_130719407
Name   traA_ELH90_RS35020_pSM135B_Rh04 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: 123062.99 Da        Isoelectric Point: 9.7536

>WP_130719407.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARKIDYTRKRGLLHEEFVIPVDAPQWLRTMIADR
SVSGASEAFWNRVEAFEKRSDAQLAKDVTIALPIELSAGQNIALVRDFVGRHITANGMVADWVYHDAAGN
PHVHLMTTLRPLTEDGFGAKKVAVLGPDGNLLRNDSGKILYEAWAGSVDDFHVFRDGWFACQNEHLALAG
LDIRIDGRSFEAQGVELTPTIHLGVGTKAIERKAEQAKAKVSVWALKLERIELQEDRRVENARRIQRRPE
IVLDLITREKSVFDERDVAKILHRYIDDTGLFQSLMVRILQSPETLPLERERIEFGTGIRTPAKYTTRDL
IRLEADMTNRAIWLAARNSHGVKKSVLEATFAHHSRLSQEQRSAIAHLAATEQVAAVVGRAGAGKTTMMT
AAREAWESSGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELDWNEGRNQLDGRTVFVLDEAGMVSSRQM
AVFVEAASKAGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREHWMRDASLDLARGNIATA
VDAYRANDRLLGSELKAHAVENLIADWNRDYDPTKTTLILAHLRRDVRMLNELARENLVERGIVATGFAF
RTEEGNRNFAAGDQIVFLRNEGSLGVKNGMIGKVVEAAPCRILVEVGQDEHRRQVTVDQRFYNNVDHGYA
ITIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHRDDLAVYYGSRSFAKAGGLIPILSRKNAKEMTLDYE
KNSLYRQALRFSEARGLHLMNVARTIARDRLDWTVRQKQKLADLGARLLAIGSMLGVADRIAKSSLPNAI
KESKPMVSGISTFPKSIEQVVEDKLAADAGLRTQWEDVSTRFHLVYAQPEAAFRAVDVDAMLKDQSTAKA
TLAKIAAEPASFGALRGKTGIFANRSDKHDRDRAIANGPALARNLERYLRQRTEAERKYDAEERGVRLKI
SIDIPALSPAARQTLERVRDAIDRNDLAAGFEYALADKLVNAELEGLAKAVSERFGERTFLGVASKDASG
GTYKSITSGMNPTQKAEMRIAWDWIRTIQQLSAHRNTTEALKQAQTVRQTKGPGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)


  Protein structure



No available structure.




T4CP

ID   1558 GenBank   WP_130719405
Name   traG_ELH90_RS35005_pSM135B_Rh04 insolico UniProt ID   _
Length   682 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 682 a.a.        Molecular weight: 74201.75 Da        Isoelectric Point: 9.3084

>WP_130719405.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTANKIALVGLPITLMILVTIGMTGSEQWLSAFGKTEAGRRMLGRAGIALPYIASATVGMIVLFASAGST
NIKLAGWSVVGGSSVTILIAALRETVRLVALLDQLPTARSALFYADPATMIGAAAALISAAFALRVSLVG
NAAFATAEPKRILGRRALHGEADWMKMTQAGKLFPDAGGIVIGERYRVDKDSTAAQAFRTDSPETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVVLDPSKEVAPMIIKHRSQAGRDVHILD
PRNRDTGFNALDWIGRHGGTKEEDIAAVASWIMSDNGGARGVRDDFFRASALQLLTALIADVCLSGHTLK
EHQTLRQVRKNLAEPEPKLRERLQRIHGNSKSEFVKENVASFVNMTPETFSGVYANAVKETHWLSYLNYA
ALVSGSSFSTDELARGDLDVFINIDLKTLEAHSGLARVIIGSFLNAIYNHDGDLKGRALFLLDEVARLGY
MRILETARDAGRKYGISLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIDQVSRSFQSKGTSRTRSKQLAARPLIQPHEVLRMRPDEQIVFTAGNPPLRCGRAIWFRRDDMRMRVV
ENRFHALAGGAKERLNSSHPAKIDEITTGVRSVGEEWNEIGQEPHDPFQEES

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(163-635)

  Protein structure



No available structure.



ID   1559 GenBank   WP_130719428
Name   t4cp2_ELH90_RS35150_pSM135B_Rh04 insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 91370.94 Da        Isoelectric Point: 5.2674

>WP_130719428.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVSLRVFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDLERNEISRQINAILSRLG
SGWMIQVEAVRLATVDYAAAGKSDFPDRVTRAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSTLSK
YIYSDEGSRKQSYADTVLFIFRNAIREVEQYLANVISIRRMMTRETTERGGARVARYDELLQFIRFCVTG
DNYPIRLPDVPMYLDWIATAELQHGLAPKVENRFLGVVAVDGLPSESWPGILNNLDLMPLSYRWSSRFIF
LDAEEAKVRLERTRKKWQQKVRPFFDQLFQTQSRSIDQDAMSMVAETEHAIAEASSQLVAYGYYTPVVVL
FENDPERLKEQMEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNVREPLINTRNLSDLIPLNSVWS
GNPQAPCPFYPPDSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYEDAQIFA
FDKGGSMMPLTLAVGGDHYEVGGDEGTGLSFCPLSDLSSEGDRAWACEWIESLVAMQGITITPDHRNAIS
RQIGLMAGAPGRSISDFVSGVQIREIKDALNHYTIDGPMGHLLDAETDGLALGVFQTFEIEQVMNTGERN
LVPVLTYLFRRIEKRLTGAPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPNGAAREPGTRDFYERIGFNDRQIEIVATAIPKREYYVASPEGRRLFDMALGPLTL
SFVGASGKEDLKRVRALSEEYGPEWPIQWLQTRGIKDAASLLEDA

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 369288..378765

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH90_RS35095 (ELH90_35095) 364745..366139 - 1395 WP_130719417 amidohydrolase family protein -
ELH90_RS40105 (ELH90_35100) 366129..366680 - 552 WP_342635959 response regulator transcription factor -
ELH90_RS35105 (ELH90_35105) 367454..368191 + 738 WP_130719419 response regulator transcription factor -
ELH90_RS35110 (ELH90_35110) 368579..369262 + 684 WP_245499002 autoinducer binding domain-containing protein -
ELH90_RS35115 (ELH90_35115) 369288..370583 - 1296 WP_130719421 IncP-type conjugal transfer protein TrbI virB10
ELH90_RS35120 (ELH90_35120) 370596..371024 - 429 WP_130719422 conjugal transfer protein TrbH -
ELH90_RS35125 (ELH90_35125) 371027..371848 - 822 WP_130719423 P-type conjugative transfer protein TrbG virB9
ELH90_RS35130 (ELH90_35130) 371865..372527 - 663 WP_130719424 conjugal transfer protein TrbF virB8
ELH90_RS35135 (ELH90_35135) 372551..373729 - 1179 WP_130719425 P-type conjugative transfer protein TrbL virB6
ELH90_RS35145 (ELH90_35145) 373911..374711 - 801 WP_130719427 P-type conjugative transfer protein TrbJ virB5
ELH90_RS35150 (ELH90_35150) 374683..377130 - 2448 WP_130719428 conjugal transfer protein TrbE virb4
ELH90_RS35155 (ELH90_35155) 377141..377437 - 297 WP_130719441 conjugal transfer protein TrbD virB3
ELH90_RS35160 (ELH90_35160) 377430..377810 - 381 WP_130719429 TrbC/VirB2 family protein virB2
ELH90_RS35165 (ELH90_35165) 377800..378765 - 966 WP_130719430 P-type conjugative transfer ATPase TrbB virB11
ELH90_RS35170 (ELH90_35170) 378779..379408 - 630 WP_130719431 acyl-homoserine-lactone synthase TraI -
ELH90_RS35175 (ELH90_35175) 379772..380989 + 1218 WP_018247073 plasmid partitioning protein RepA -
ELH90_RS35180 (ELH90_35180) 380974..382014 + 1041 WP_018448901 plasmid partitioning protein RepB -
ELH90_RS35185 (ELH90_35185) 382254..383519 + 1266 WP_130719432 plasmid replication protein RepC -

Host bacterium

ID   3026 GenBank   NZ_SIOP01000004
Plasmid name   pSM135B_Rh04 Incompatibility group   -
Plasmid size   388771 bp Coordinate of oriT [Strand]   349132..349167 [+]
Host baterium   Rhizobium leguminosarum strain SM135B

Cargo genes

Drug resistance gene   -
Virulence gene   gmd
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   noeL
Anti-CRISPR   AcrIIA7