Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102550
Name   oriT_pSM72_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM72
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SILY01000006 (33677..33710 [-], 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_pSM72_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1901 GenBank   WP_130657460
Name   traA_ELH21_RS35540_pSM72_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   1511 GenBank   WP_065276635
Name   t4cp2_ELH21_RS35440_pSM72_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.



ID   1512 GenBank   WP_130657461
Name   traG_ELH21_RS35555_pSM72_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: 69518.76 Da        Isoelectric Point: 8.9386

>WP_130657461.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALAVMPAALMILVVIGMTGIEQWLSGFGKTEAARLAWGRTGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTETLNADKSVLAYLDPATAIGAGVALMCACFALRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRIDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDGGGVRGVRDDFFRASALQLLTALIADVCLSGHTDG
HDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFATNDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKVRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPKPA

  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: 11712..28541

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH21_RS35405 (ELH21_35405) 7039..8253 - 1215 WP_065276629 plasmid replication protein RepC -
ELH21_RS35410 (ELH21_35410) 8443..9480 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELH21_RS35415 (ELH21_35415) 9477..10700 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELH21_RS35420 (ELH21_35420) 11077..11715 + 639 WP_130660092 acyl-homoserine-lactone synthase -
ELH21_RS35425 (ELH21_35425) 11712..12689 + 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELH21_RS35430 (ELH21_35430) 12679..13062 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELH21_RS35435 (ELH21_35435) 13055..13354 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELH21_RS35440 (ELH21_35440) 13365..15815 + 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELH21_RS35445 (ELH21_35445) 15793..16590 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELH21_RS35450 (ELH21_35450) 16587..16787 + 201 WP_065276637 entry exclusion protein TrbK -
ELH21_RS35455 (ELH21_35455) 16781..17962 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELH21_RS35460 (ELH21_35460) 17983..18645 + 663 WP_065276639 conjugal transfer protein TrbF virB8
ELH21_RS35465 (ELH21_35465) 18663..19475 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELH21_RS35470 (ELH21_35470) 19479..19913 + 435 WP_130657454 conjugal transfer protein TrbH -
ELH21_RS35475 (ELH21_35475) 19925..21223 + 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELH21_RS35480 (ELH21_35480) 21534..22238 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELH21_RS35485 (ELH21_35485) 22242..22565 - 324 WP_130657456 transcriptional repressor TraM -
ELH21_RS35490 (ELH21_35490) 22788..23030 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELH21_RS37880 (ELH21_35495) 23133..23564 + 432 Protein_23 hypothetical protein -
ELH21_RS35500 (ELH21_35500) 23655..24272 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELH21_RS35505 (ELH21_35505) 24265..25133 + 869 Protein_25 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELH21_RS35510 (ELH21_35510) 25344..25754 + 411 WP_018244910 transposase -
ELH21_RS35515 (ELH21_35515) 25751..26098 + 348 WP_018244911 IS66 family insertion sequence element accessory protein TnpB -
ELH21_RS35520 (ELH21_35520) 26144..27799 + 1656 WP_065276572 IS66 family transposase -
ELH21_RS35525 (ELH21_35525) 27924..28541 - 618 WP_130657457 TraH family protein virB1
ELH21_RS35530 (ELH21_35530) 28558..29721 - 1164 WP_130657458 conjugal transfer protein TraB -
ELH21_RS35535 (ELH21_35535) 29711..30274 - 564 WP_130657459 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2994 GenBank   NZ_SILY01000006
Plasmid name   pSM72_Rh08 Incompatibility group   -
Plasmid size   221530 bp Coordinate of oriT [Strand]   33677..33710 [-]
Host baterium   Rhizobium leguminosarum strain SM72

Cargo genes

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