Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107659
Name   oriT_NZLR1|p3 in_silico
Organism   Rhizobium sp. NZLR1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP071635 (258698..258731 [+], 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_NZLR1|p3
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5148 GenBank   WP_207585654
Name   traA_J3O30_RS30275_NZLR1|p3 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: 122884.06 Da        Isoelectric Point: 9.9302

>WP_207585654.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [unclassified Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVCSMTADR
SVAGASESFWNKVEGFEKRSDAQLAKDVTIALPLELTAVQNIALMHDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIRRRPE
IVLELITREKSVFDERDVAKVLYRYIDDARLFQSLMVRILQRPEALRLERERINLATGVREAAKYTTREM
IRLEAEMANRAIWLSGRASRGVRETVLQATFARHSRLSDEQRTAIEHVAGAARIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTVSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALLVETATKAGAKLVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQRQQWMRDASLDLARGKVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRKLNDMARAKLVERGVVAHGFAF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLAKVLEAVAGRIVAEIGDGEHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVNVARTIAHDRLQWAVRQSSRLADLGARLAAIGAALGLVRDSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAINVDTMLKDQSVAQS
TLAKIAGEPESFGALKGKTGLLASRVDKQDREKAVANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPSAKRTLERVRDAIDRNDLPSGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTSGMTAGQKAEVRSAWNSMRTVQQLGSHERTTEAAKQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)

AAA domain (AAA_30)

(387-570)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   5384 GenBank   WP_207585653
Name   traG_J3O30_RS30260_NZLR1|p3 insolico UniProt ID   _
Length   643 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 643 a.a.        Molecular weight: 69364.55 Da        Isoelectric Point: 9.2523

>WP_207585653.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVMPGTLMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVAGCSGTILIAAIRETMRLSAFMTVPADKTVWAFLDPATSIGASAALLCACFALRVALIGN
AAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGGK
SPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLDP
RKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDGGGVRGVRDDFFRASALQLLTALIADVCLSGRTDEH
DQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAA
LVSGKKFATNDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGALKGRALFLLDEVARLGYM
RILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTV
ESDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRNDMKACVGT
NRFHMVGDTPKPA

  Protein domains


Predicted by InterproScan.

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

(162-633)

  Protein structure



No available structure.



ID   5385 GenBank   WP_131645514
Name   t4cp2_J3O30_RS30355_NZLR1|p3 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: 91579.23 Da        Isoelectric Point: 5.8086

>WP_131645514.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YVYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLTIRRMETRETLERGGERIARYDELLQFARFCTTG
ESHPIRLPDIPMYLDWIATAELEHGLTPKVENRFLGVIAIDGLPAESWPGILNSLDMMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSNREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYAANSPPLMQVASGSTSFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLQPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLIGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQFLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIVDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRTLKSEHGHDWPIHWLETRGVQDAASLLK

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 263870..278132

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J3O30_RS30280 (J3O30_30280) 262203..262700 + 498 WP_246762898 conjugative transfer signal peptidase TraF -
J3O30_RS30285 (J3O30_30285) 262690..263853 + 1164 WP_207585656 conjugal transfer protein TraB -
J3O30_RS30290 (J3O30_30290) 263870..264487 + 618 WP_131704616 TraH family protein virB1
J3O30_RS30295 (J3O30_30295) 264722..265591 - 870 WP_131704615 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
J3O30_RS30300 (J3O30_30300) 265584..266201 - 618 WP_131598842 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
J3O30_RS33540 266291..266720 - 430 Protein_280 hypothetical protein -
J3O30_RS30305 (J3O30_30305) 266817..267059 - 243 WP_130654290 helix-turn-helix transcriptional regulator -
J3O30_RS30310 (J3O30_30310) 267283..267606 + 324 WP_131614000 transcriptional repressor TraM -
J3O30_RS30315 (J3O30_30315) 267610..268314 - 705 WP_131614001 autoinducer binding domain-containing protein -
J3O30_RS30320 (J3O30_30320) 268625..269923 - 1299 WP_207585657 IncP-type conjugal transfer protein TrbI virB10
J3O30_RS30325 (J3O30_30325) 269935..270375 - 441 WP_207585658 conjugal transfer protein TrbH -
J3O30_RS30330 (J3O30_30330) 270379..271191 - 813 WP_207585659 P-type conjugative transfer protein TrbG virB9
J3O30_RS30335 (J3O30_30335) 271209..271871 - 663 WP_131614005 conjugal transfer protein TrbF virB8
J3O30_RS30340 (J3O30_30340) 271892..273070 - 1179 WP_207585660 P-type conjugative transfer protein TrbL virB6
J3O30_RS30345 (J3O30_30345) 273084..273260 - 177 WP_018516718 entry exclusion protein TrbK -
J3O30_RS30350 (J3O30_30350) 273254..274051 - 798 WP_131645513 P-type conjugative transfer protein TrbJ virB5
J3O30_RS30355 (J3O30_30355) 274029..276479 - 2451 WP_131645514 conjugal transfer protein TrbE virb4
J3O30_RS30360 (J3O30_30360) 276490..276789 - 300 WP_131645515 conjugal transfer protein TrbD virB3
J3O30_RS30365 (J3O30_30365) 276782..277165 - 384 WP_207585661 TrbC/VirB2 family protein virB2
J3O30_RS30370 (J3O30_30370) 277155..278132 - 978 WP_207585662 P-type conjugative transfer ATPase TrbB virB11
J3O30_RS30375 (J3O30_30375) 278129..278767 - 639 WP_131645517 acyl-homoserine-lactone synthase -
J3O30_RS30380 (J3O30_30380) 279144..280367 + 1224 WP_032982647 plasmid partitioning protein RepA -
J3O30_RS30385 (J3O30_30385) 280364..281401 + 1038 WP_207585663 plasmid partitioning protein RepB -
J3O30_RS30390 (J3O30_30390) 281592..282806 + 1215 WP_207585703 plasmid replication protein RepC -

Host bacterium

ID   8094 GenBank   NZ_CP071635
Plasmid name   NZLR1|p3 Incompatibility group   -
Plasmid size   328074 bp Coordinate of oriT [Strand]   258698..258731 [+]
Host baterium   Rhizobium sp. NZLR1

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixG, fixQ, fixO, fixN, nifN, nifE, nifK, nifD, nifH, fixA, fixB, fixC, fixX, nifB, nodJ, nodI, nodC, nodA, nodD, nodF, nodE, nodM
Anti-CRISPR   -