Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101191
Name   oriT_pSM164C_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM164C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQR01000006 (30826..30859 [-], 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_pSM164C_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1187 GenBank   WP_130657460
Name   traA_ELI44_RS33390_pSM164C_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   792 GenBank   WP_065276635
Name   t4cp2_ELI44_RS33290_pSM164C_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   793 GenBank   WP_130657461
Name   traG_ELI44_RS33405_pSM164C_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: 8861..25690

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI44_RS33255 (ELI44_33250) 4188..5402 - 1215 WP_130666354 plasmid replication protein RepC -
ELI44_RS33260 (ELI44_33255) 5592..6629 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELI44_RS33265 (ELI44_33260) 6626..7849 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELI44_RS33270 (ELI44_33265) 8226..8864 + 639 WP_130660092 acyl-homoserine-lactone synthase -
ELI44_RS33275 (ELI44_33270) 8861..9838 + 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELI44_RS33280 (ELI44_33275) 9828..10211 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELI44_RS33285 (ELI44_33280) 10204..10503 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELI44_RS33290 (ELI44_33285) 10514..12964 + 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELI44_RS33295 (ELI44_33290) 12942..13739 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELI44_RS33300 (ELI44_33295) 13736..13936 + 201 WP_065276637 entry exclusion protein TrbK -
ELI44_RS33305 (ELI44_33300) 13930..15111 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELI44_RS33310 (ELI44_33305) 15132..15794 + 663 WP_065276639 conjugal transfer protein TrbF virB8
ELI44_RS33315 (ELI44_33310) 15812..16624 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELI44_RS33320 (ELI44_33315) 16628..17062 + 435 WP_130657454 conjugal transfer protein TrbH -
ELI44_RS33325 (ELI44_33320) 17074..18372 + 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELI44_RS33330 (ELI44_33325) 18683..19387 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELI44_RS33335 (ELI44_33330) 19391..19714 - 324 WP_130657456 transcriptional repressor TraM -
ELI44_RS33340 (ELI44_33335) 19937..20179 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELI44_RS38430 (ELI44_33340) 20282..20713 + 432 Protein_22 hypothetical protein -
ELI44_RS33350 (ELI44_33345) 20804..21421 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI44_RS33355 (ELI44_33350) 21414..22282 + 869 Protein_24 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI44_RS33360 (ELI44_33355) 22493..22903 + 411 WP_130688390 transposase -
ELI44_RS33365 (ELI44_33360) 22900..23247 + 348 WP_018244911 IS66 family insertion sequence element accessory protein TnpB -
ELI44_RS33370 (ELI44_33365) 23293..24948 + 1656 WP_065276572 IS66 family transposase -
ELI44_RS33375 (ELI44_33370) 25073..25690 - 618 WP_130657457 TraH family protein virB1
ELI44_RS33380 (ELI44_33375) 25707..26870 - 1164 WP_130657458 conjugal transfer protein TraB -
ELI44_RS33385 (ELI44_33380) 26860..27423 - 564 WP_130657459 conjugative transfer signal peptidase TraF -

Host bacterium

ID   1635 GenBank   NZ_SIQR01000006
Plasmid name   pSM164C_Rh08 Incompatibility group   -
Plasmid size   301385 bp Coordinate of oriT [Strand]   30826..30859 [-]
Host baterium   Rhizobium ruizarguesonis strain SM164C

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   -