Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101157
Name   oriT_pSM157B_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM157B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQH01000006 (91189..91222 [-], 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_pSM157B_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1154 GenBank   WP_130657460
Name   traA_ELI34_RS29470_pSM157B_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   729 GenBank   WP_065276635
Name   t4cp2_ELI34_RS29335_pSM157B_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   730 GenBank   WP_130657461
Name   traG_ELI34_RS29485_pSM157B_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: 62699..72210

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI34_RS29300 (ELI34_29305) 58026..59240 - 1215 WP_130666985 plasmid replication protein RepC -
ELI34_RS29305 (ELI34_29310) 59430..60467 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELI34_RS29310 (ELI34_29315) 60464..61687 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELI34_RS29315 (ELI34_29320) 62064..62702 + 639 WP_130657452 acyl-homoserine-lactone synthase -
ELI34_RS29320 (ELI34_29325) 62699..63676 + 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELI34_RS29325 (ELI34_29330) 63666..64049 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELI34_RS29330 (ELI34_29335) 64042..64341 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELI34_RS29335 (ELI34_29340) 64352..66802 + 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELI34_RS29340 (ELI34_29345) 66780..67577 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELI34_RS29345 (ELI34_29350) 67574..67774 + 201 WP_065276637 entry exclusion protein TrbK -
ELI34_RS29350 (ELI34_29355) 67768..68949 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELI34_RS29355 (ELI34_29360) 68970..69632 + 663 WP_065276639 conjugal transfer protein TrbF virB8
ELI34_RS29360 (ELI34_29365) 69650..70462 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELI34_RS29365 (ELI34_29370) 70466..70900 + 435 WP_130657454 conjugal transfer protein TrbH -
ELI34_RS29370 (ELI34_29375) 70912..72210 + 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELI34_RS29375 (ELI34_29380) 72656..72997 + 342 WP_063963361 transposase -
ELI34_RS29380 (ELI34_29385) 72994..73341 + 348 WP_057210537 IS66 family insertion sequence element accessory protein TnpB -
ELI34_RS29385 (ELI34_29390) 73420..75078 + 1659 WP_130654681 IS66 family transposase -
ELI34_RS29390 (ELI34_29395) 75078..75662 + 585 WP_130654682 plasmid pRiA4b ORF-3 family protein -
ELI34_RS29395 (ELI34_29400) 75710..76357 + 648 WP_130666986 autoinducer binding domain-containing protein -
ELI34_RS29400 (ELI34_29405) 76361..76684 - 324 WP_130657456 transcriptional repressor TraM -
ELI34_RS29405 (ELI34_29410) 76907..77149 + 243 WP_130654290 helix-turn-helix transcriptional regulator -

Host bacterium

ID   1601 GenBank   NZ_SIQH01000006
Plasmid name   pSM157B_Rh08 Incompatibility group   -
Plasmid size   280083 bp Coordinate of oriT [Strand]   91189..91222 [-]
Host baterium   Rhizobium ruizarguesonis strain SM157B

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   -