Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102577
Name   oriT_pSM126A_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM126A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOA01000005 (10760..10793 [+], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 34 nt

>oriT_pSM126A_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1925 GenBank   WP_130657460
Name   traA_ELH75_RS31615_pSM126A_Rh08 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: 122987.83 Da        Isoelectric Point: 9.6219

>WP_130657460.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKFVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKVEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQGPEALRLERERINFATGSRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLEATFARHSRLSDEQRTAIEHVAGATRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWEIRWNQSRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDAALDLARGNVGKA
VDAYRGYGHVRGLDLKAQAVESLIADWNHGYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLGKVVEASRNRIVAEVGEGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYD
KASFYGQALRFAEARGFHLVNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSFPDTI
KEAKPMVSGITTFPQTLDQAVEDKLAADPGLKKQWEDVSTRFQLVYATPEAAFKAIDVDTMLKDQSVAQS
TLARIAGEPESFGAIKGKTGLLASRGDKQDREKAIANVPALARNLERYLRERAEAELKHETEERAVRLKV
SVDIPALSSAAKQTLERVRDVIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTDGQKAEVQSTWNSMRTVQQLAAYERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(686-740)

AAA domain (AAA_30)

(387-572)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   1552 GenBank   WP_130759824
Name   traG_ELH75_RS31600_pSM126A_Rh08 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: 69558.74 Da        Isoelectric Point: 8.9360

>WP_130759824.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTINRIALAVMPAALMILVVIGMTGIEQWLSGFGKTEAARLAWGRTGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTETLNADKSVLAYLDPATAIGAGVALMCACFALRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRIDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSDHTDE
KDQTLRRVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGKTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQLNGRALFLLDEVARLGY
MRILETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPKPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   1553 GenBank   WP_065276635
Name   t4cp2_ELH75_RS31715_pSM126A_Rh08 insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 91588.38 Da        Isoelectric Point: 5.9977

>WP_065276635.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKPFRVTGPSFADLVPYAGLIDDGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSKDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNALRELEQYFANSLSIRRMETRETFERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETQDAIAQASSRLVAYGYYTPVVVL
FDIDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRTLKSEHGHDWPIHWLETRGVHDAASLFK

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 8183..32757

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH75_RS37450 3565..3738 + 174 WP_165403408 hypothetical protein -
ELH75_RS31580 (ELH75_31575) 3806..4114 - 309 WP_130657465 WGR domain-containing protein -
ELH75_RS31585 (ELH75_31580) 4465..5958 - 1494 WP_130657464 group II intron reverse transcriptase/maturase -
ELH75_RS31590 (ELH75_31585) 6740..7054 + 315 WP_130657463 hypothetical protein -
ELH75_RS31595 (ELH75_31590) 7297..7800 - 504 WP_197726741 thermonuclease family protein -
ELH75_RS31600 (ELH75_31595) 8183..10117 - 1935 WP_130759824 Ti-type conjugative transfer system protein TraG virb4
ELH75_RS31605 (ELH75_31600) 10104..10319 - 216 WP_027668129 type IV conjugative transfer system coupling protein TraD -
ELH75_RS31610 (ELH75_31605) 10324..10617 - 294 WP_011654562 conjugal transfer protein TraC -
ELH75_RS31615 (ELH75_31610) 10873..14199 + 3327 WP_130657460 Ti-type conjugative transfer relaxase TraA -
ELH75_RS31620 (ELH75_31615) 14196..14759 + 564 WP_130657459 conjugative transfer signal peptidase TraF -
ELH75_RS31625 (ELH75_31620) 14749..15912 + 1164 WP_130657458 conjugal transfer protein TraB -
ELH75_RS31630 (ELH75_31625) 15929..16546 + 618 WP_130657457 TraH family protein virB1
ELH75_RS31640 (ELH75_31635) 18371..18718 - 348 WP_018244911 IS66 family insertion sequence element accessory protein TnpB -
ELH75_RS31645 (ELH75_31640) 18715..19125 - 411 WP_018244910 transposase -
ELH75_RS31650 (ELH75_31645) 19336..20204 - 869 Protein_19 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELH75_RS31655 (ELH75_31650) 20197..20814 - 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELH75_RS38010 (ELH75_31655) 20905..21336 - 432 Protein_21 hypothetical protein -
ELH75_RS31665 (ELH75_31660) 21439..21681 - 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELH75_RS31670 (ELH75_31665) 21904..22227 + 324 WP_130657456 transcriptional repressor TraM -
ELH75_RS31675 (ELH75_31670) 22231..22935 - 705 WP_130759825 autoinducer binding domain-containing protein -
ELH75_RS31680 (ELH75_31675) 23246..24544 - 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELH75_RS31685 (ELH75_31680) 24556..24990 - 435 WP_130657454 conjugal transfer protein TrbH -
ELH75_RS31690 (ELH75_31685) 24994..25806 - 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELH75_RS31695 (ELH75_31690) 25824..26486 - 663 WP_065276639 conjugal transfer protein TrbF virB8
ELH75_RS31700 (ELH75_31695) 26507..27688 - 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELH75_RS31705 (ELH75_31700) 27682..27882 - 201 WP_065276637 entry exclusion protein TrbK -
ELH75_RS31710 (ELH75_31705) 27879..28676 - 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELH75_RS31715 (ELH75_31710) 28654..31104 - 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELH75_RS31720 (ELH75_31715) 31115..31414 - 300 WP_130654279 conjugal transfer protein TrbD virB3
ELH75_RS31725 (ELH75_31720) 31407..31790 - 384 WP_065276633 TrbC/VirB2 family protein virB2
ELH75_RS31730 (ELH75_31725) 31780..32757 - 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELH75_RS31735 (ELH75_31730) 32754..33392 - 639 WP_130660092 acyl-homoserine-lactone synthase -
ELH75_RS31740 (ELH75_31735) 33769..34992 + 1224 WP_065276670 plasmid partitioning protein RepA -
ELH75_RS31745 (ELH75_31740) 34989..36026 + 1038 WP_130657451 plasmid partitioning protein RepB -
ELH75_RS31750 (ELH75_31745) 36216..37430 + 1215 WP_065276629 plasmid replication protein RepC -

Host bacterium

ID   3021 GenBank   NZ_SIOA01000005
Plasmid name   pSM126A_Rh08 Incompatibility group   -
Plasmid size   41634 bp Coordinate of oriT [Strand]   10760..10793 [+]
Host baterium   Rhizobium leguminosarum strain SM126A

Cargo genes

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