Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102581
Name   oriT_pSM79_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM79
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIME01000005 (35075..35108 [-], 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_pSM79_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1929 GenBank   WP_130657460
Name   traA_ELH27_RS32845_pSM79_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   1556 GenBank   WP_065276635
Name   t4cp2_ELH27_RS32740_pSM79_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   1557 GenBank   WP_130657461
Name   traG_ELH27_RS32860_pSM79_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..29939

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH27_RS32705 (ELH27_32710) 7039..8253 - 1215 WP_130767419 plasmid replication protein RepC -
ELH27_RS32710 (ELH27_32715) 8443..9480 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELH27_RS32715 (ELH27_32720) 9477..10700 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELH27_RS32720 (ELH27_32725) 11077..11715 + 639 WP_130660092 acyl-homoserine-lactone synthase -
ELH27_RS32725 (ELH27_32730) 11712..12689 + 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELH27_RS32730 (ELH27_32735) 12679..13062 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELH27_RS32735 (ELH27_32740) 13055..13354 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELH27_RS32740 (ELH27_32745) 13365..15815 + 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELH27_RS32745 (ELH27_32750) 15793..16590 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELH27_RS32750 (ELH27_32755) 16587..16787 + 201 WP_065276637 entry exclusion protein TrbK -
ELH27_RS32755 (ELH27_32760) 16781..17962 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELH27_RS32760 (ELH27_32765) 17983..18645 + 663 WP_065276639 conjugal transfer protein TrbF virB8
ELH27_RS32765 (ELH27_32770) 18663..19475 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELH27_RS32770 (ELH27_32775) 19479..19913 + 435 WP_130657454 conjugal transfer protein TrbH -
ELH27_RS32775 (ELH27_32780) 19925..21223 + 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELH27_RS32780 (ELH27_32785) 21534..22238 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELH27_RS32785 (ELH27_32790) 22242..22565 - 324 WP_130657456 transcriptional repressor TraM -
ELH27_RS32790 (ELH27_32795) 22788..23030 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELH27_RS38425 (ELH27_32800) 23133..23564 + 432 Protein_23 hypothetical protein -
ELH27_RS32800 (ELH27_32805) 23655..24272 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELH27_RS32805 (ELH27_32810) 24265..25133 + 869 Protein_25 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELH27_RS32810 (ELH27_32815) 25344..25754 + 411 WP_018244910 transposase -
ELH27_RS32815 (ELH27_32820) 25751..26098 + 348 WP_018244911 IS66 family insertion sequence element accessory protein TnpB -
ELH27_RS32820 (ELH27_32825) 26144..27763 + 1620 Protein_28 IS66 family transposase -
ELH27_RS32825 (ELH27_32830) 27837..28871 + 1035 WP_128405660 IS110 family transposase -
ELH27_RS32830 (ELH27_32835) 29322..29939 - 618 WP_130657457 TraH family protein virB1
ELH27_RS32835 (ELH27_32840) 29956..31119 - 1164 WP_130657458 conjugal transfer protein TraB -
ELH27_RS32840 (ELH27_32845) 31109..31672 - 564 WP_130657459 conjugative transfer signal peptidase TraF -

Host bacterium

ID   3025 GenBank   NZ_SIME01000005
Plasmid name   pSM79_Rh08 Incompatibility group   -
Plasmid size   318943 bp Coordinate of oriT [Strand]   35075..35108 [-]
Host baterium   Rhizobium leguminosarum strain SM79

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   -