Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102517
Name   oriT_pSM164B_Rh04 in_silico
Organism   Rhizobium leguminosarum strain SM164B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQQ01000004 (44579..44616 [-], 38 nt)
oriT length   38 nt
IRs (inverted repeats)      23..28, 33..38  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 38 nt

>oriT_pSM164B_Rh04
GGATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1868 GenBank   WP_128401822
Name   traA_ELI43_RS28580_pSM164B_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: 123009.21 Da        Isoelectric Point: 9.7914

>WP_128401822.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVVPADAPEWLRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTVEQNIALMRDFVERHITAQGMIADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDDKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRVDGRSFEKQGIELEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVPEAVLQATFARHSRLSDEQRTAIEHIAGTTRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDRCVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMLGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEVGEGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLAYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETSLDYE
KSALYRQALRFAEARGLHLMNVARTIAHDRLQWAVRQSSRLADLGARLAAIGKALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAINVDAMLKDQSVAQS
TLARIAGKPESFGALKGNTGLLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPSAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDAGG
KTFETVTTGMTPGQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-569)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-740)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   1465 GenBank   WP_128411486
Name   t4cp2_ELI43_RS28435_pSM164B_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: 91617.41 Da        Isoelectric Point: 6.1236

>WP_128411486.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVSLRLFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDFERNEMSRQINAIMSRLG
SGWMIQVEAVRLATVDYATAGKSHFPDRVTRAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSRLSK
YLYSDEGSRRRSYADTVLFLFRNAIRELEQYLANIVSIRRMLTREIAERGGARVARYDELLQFIRFCVTG
ENHPVRLPDIAMYLDWVATAELQHGLSPRVESRFLGVVAIDGLPSESWPGILNGLDAMPLSYRWSSRFIF
LDAEEAKVRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEEAIAEASSQLVAYGYYTPVVVL
FENDPELLNEKVEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTRNLSDLIPLNTVWS
GNPQAPCPFYPPGSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSMLPLTLAAGGDYYDVGGDEDTSLSFCPLAELSSDADRAWASEWIESLVAMQGITITPDHRNAIS
RQIGLMAVAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAETDGLALGLFQAFEIEQVMSMGERN
LVPVLTYLFRRIEKRLTGAPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPNGAAREPGTREFYERIGFNQRQIQIVASAIPKREYYVASPDGRRLFDMALGPLTL
SFVGASSKDDLKRIRALHEEHGPEWPLHWLQQRGIKDAASLLNDT

  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.



ID   1466 GenBank   WP_245461678
Name   traG_ELI43_RS28595_pSM164B_Rh04 insolico UniProt ID   _
Length   667 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 667 a.a.        Molecular weight: 71799.22 Da        Isoelectric Point: 9.1969

>WP_245461678.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVGPAALMILAVIGMTGIEQWLSGIGKTEAARLAWGRARIALPYAASAAIGVLFLFACAGSI
NIKRAGWGVLAGCIGTMLIAAVRETLRLSALMKTLPAGKTVLAYLDPATSIGASAALLCAGFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDIVGSQAFRADSAENWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSDHTDE
KDQTLRRVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGKTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQLNGRALFLLDEVARLGY
MRILETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETAEYISKRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIIFTAGNAPLRCARAIWFRRADMRACVG
ENRFYSMGGGEREGSNSTPAVNPYETKPTVTSAGEEG

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 12240..21710

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI43_RS28400 (ELI43_28390) 7486..8751 - 1266 WP_128401851 plasmid replication protein RepC -
ELI43_RS28405 (ELI43_28395) 8990..10030 - 1041 WP_128411487 plasmid partitioning protein RepB -
ELI43_RS28410 (ELI43_28400) 10015..11232 - 1218 WP_128401849 plasmid partitioning protein RepA -
ELI43_RS28415 (ELI43_28405) 11596..12225 + 630 WP_128401848 acyl-homoserine-lactone synthase TraI -
ELI43_RS28420 (ELI43_28410) 12240..13205 + 966 WP_128401847 P-type conjugative transfer ATPase TrbB virB11
ELI43_RS28425 (ELI43_28415) 13195..13569 + 375 WP_128401846 TrbC/VirB2 family protein virB2
ELI43_RS28430 (ELI43_28420) 13566..13865 + 300 WP_128401845 conjugal transfer protein TrbD virB3
ELI43_RS28435 (ELI43_28425) 13875..16322 + 2448 WP_128411486 conjugal transfer protein TrbE virb4
ELI43_RS28440 (ELI43_28430) 16294..17094 + 801 WP_128401843 P-type conjugative transfer protein TrbJ virB5
ELI43_RS28445 (ELI43_28435) 17282..18457 + 1176 WP_128401842 P-type conjugative transfer protein TrbL virB6
ELI43_RS28450 (ELI43_28440) 18477..19139 + 663 WP_128401841 conjugal transfer protein TrbF virB8
ELI43_RS28455 (ELI43_28445) 19154..19978 + 825 WP_128401840 P-type conjugative transfer protein TrbG virB9
ELI43_RS28460 (ELI43_28450) 19975..20409 + 435 WP_128401839 conjugal transfer protein TrbH -
ELI43_RS28465 (ELI43_28455) 20421..21710 + 1290 WP_128401838 IncP-type conjugal transfer protein TrbI virB10
ELI43_RS28470 (ELI43_28460) 22295..23089 - 795 WP_245461681 autoinducer binding domain-containing protein -
ELI43_RS28475 (ELI43_28465) 23371..24102 - 732 WP_128401837 response regulator transcription factor -
ELI43_RS39205 25138..25434 + 297 WP_245462682 winged helix-turn-helix domain-containing protein -

Host bacterium

ID   2961 GenBank   NZ_SIQQ01000004
Plasmid name   pSM164B_Rh04 Incompatibility group   -
Plasmid size   528346 bp Coordinate of oriT [Strand]   44579..44616 [-]
Host baterium   Rhizobium leguminosarum strain SM164B

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   hupE2
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -