Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101168
Name   oriT_pSM153A_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM153A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPX01000007 (108459..108492 [-], 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_pSM153A_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1165 GenBank   WP_130657460
Name   traA_ELI24_RS32280_pSM153A_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   751 GenBank   WP_065276635
Name   t4cp2_ELI24_RS32190_pSM153A_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   752 GenBank   WP_130657461
Name   traG_ELI24_RS32295_pSM153A_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: 88188..103323

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI24_RS32155 (ELI24_32175) 83515..84729 - 1215 WP_065276629 plasmid replication protein RepC -
ELI24_RS32160 (ELI24_32180) 84919..85956 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELI24_RS32165 (ELI24_32185) 85953..87176 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELI24_RS32170 (ELI24_32190) 87553..88191 + 639 WP_130660092 acyl-homoserine-lactone synthase -
ELI24_RS32175 (ELI24_32195) 88188..89165 + 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELI24_RS32180 (ELI24_32200) 89155..89538 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELI24_RS32185 (ELI24_32205) 89531..89830 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELI24_RS32190 (ELI24_32210) 89841..92291 + 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELI24_RS32195 (ELI24_32215) 92269..93066 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELI24_RS32200 (ELI24_32220) 93063..93263 + 201 WP_130676499 entry exclusion protein TrbK -
ELI24_RS32205 (ELI24_32225) 93257..94438 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELI24_RS32210 (ELI24_32230) 94459..95121 + 663 WP_130676500 conjugal transfer protein TrbF virB8
ELI24_RS32215 (ELI24_32235) 95139..95951 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELI24_RS32220 (ELI24_32240) 95955..96389 + 435 WP_130657454 conjugal transfer protein TrbH -
ELI24_RS32225 (ELI24_32245) 96401..97699 + 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELI24_RS32230 (ELI24_32250) 98010..98714 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELI24_RS32235 (ELI24_32255) 98718..99041 - 324 WP_130654289 transcriptional repressor TraM -
ELI24_RS32240 (ELI24_32260) 99264..99506 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELI24_RS40560 (ELI24_32265) 99609..100040 + 432 Protein_102 hypothetical protein -
ELI24_RS32250 (ELI24_32270) 100131..100748 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI24_RS32255 (ELI24_32275) 100741..101220 + 480 Protein_104 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI24_RS32260 (ELI24_32280) 101217..102581 + 1365 Protein_105 IS66 family transposase -
ELI24_RS32265 (ELI24_32285) 102706..103323 - 618 WP_130657457 TraH family protein virB1
ELI24_RS32270 (ELI24_32290) 103340..104503 - 1164 WP_130657458 conjugal transfer protein TraB -
ELI24_RS32275 (ELI24_32295) 104493..105056 - 564 WP_130657459 conjugative transfer signal peptidase TraF -

Host bacterium

ID   1612 GenBank   NZ_SIPX01000007
Plasmid name   pSM153A_Rh08 Incompatibility group   -
Plasmid size   269002 bp Coordinate of oriT [Strand]   108459..108492 [-]
Host baterium   Rhizobium ruizarguesonis strain SM153A

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   -