Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107594
Name   oriT_pPR4 in_silico
Organism   Rhizobium leguminosarum bv. viciae strain BIHB 1217
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP022669 (24133..24166 [-], 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_pPR4
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5104 GenBank   WP_077988203
Name   traA_CHR56_RS36630_pPR4 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: 122813.06 Da        Isoelectric Point: 9.9165

>WP_077988203.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVCSMTADR
SVAGASESFWNKVEGFEKRSDAQLAKDVTIALPLELSAEQNIALMRDFVAGHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYELWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIRRRPE
IVLELITREKSVFDERDVAKVLYRYIDDARLFQSLMVRILQSPEALRLERERINLATGVREAAKYTTREM
IRLEAEMANRAIWLSGRASRGVRETVLQATFARHSRLSDEQRTAIEHVAGAARIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNQLDNKTVFVLDEAGMVSSRQM
ALLVETITKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNIRKA
VDAYAAYGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEGGTRMFAAGDQVVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEIGDAEHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKAGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVNVARTIARDRLEWTVRQKQKLADLGARLAAIGPALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAINVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGLLASRGDKQDREKALANVPALARNLERYLRERTEAELKHETEERAVRLKV
SVDIPALSSAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTSG
KTFETVTSGMTAGQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETLRQTKSQGLSLK

  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)

(387-569)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   5324 GenBank   WP_077988216
Name   t4cp2_CHR56_RS36550_pPR4 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91849.59 Da        Isoelectric Point: 5.8777

>WP_077988216.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YVYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLTIRRMETRETLERGGERIARYDELLQFARFCTTG
ESHPIRLPDIPMYLDWIATAELEHGLTPKVENRFLGVIAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVTETEDAIAQASSQLVVYGYYTPVVVL
FDRDREGLLEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYAAKSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLQPLTLAAGGDHYEIGGDNAEEGRALAFCPLSDLKSDTDRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEHLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLETRGVHDAASLLTFE

  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   5325 GenBank   WP_077988202
Name   traG_CHR56_RS36645_pPR4 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: 69510.74 Da        Isoelectric Point: 9.1051

>WP_077988202.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVMPGTLMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVAGCSGTILIAAIRETMRLSAFMTVPADKTVWAFLDPATSIGASAALLCACFALRVALIGN
AAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGGK
SPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLDP
RKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDGGGVRGVRDDFFRASALQLLTALIADVCLSGRTDEH
DQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAA
LVSGKKFATNEIASGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGYM
RIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTV
EIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGT
NRFHMVGDTPKPA

  Protein domains


Predicted by InterproScan.

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

(162-633)

  Protein structure



No available structure.



ID   5326 GenBank   WP_077988216
Name   t4cp2_CHR56_RS38135_pPR4 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91849.59 Da        Isoelectric Point: 5.8777

>WP_077988216.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YVYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLTIRRMETRETLERGGERIARYDELLQFARFCTTG
ESHPIRLPDIPMYLDWIATAELEHGLTPKVENRFLGVIAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVTETEDAIAQASSQLVVYGYYTPVVVL
FDRDREGLLEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYAAKSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLQPLTLAAGGDHYEIGGDNAEEGRALAFCPLSDLKSDTDRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEHLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLETRGVHDAASLLTFE

  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: 5187..18994

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CHR56_RS36515 (CHR56_36515) 517..1731 - 1215 Protein_2 plasmid replication protein RepC -
CHR56_RS36520 (CHR56_36520) 1920..2956 - 1037 Protein_3 plasmid partitioning protein RepB -
CHR56_RS36525 (CHR56_36525) 2953..4176 - 1224 WP_032998569 plasmid partitioning protein RepA -
CHR56_RS36530 (CHR56_36530) 4552..5190 + 639 WP_077988220 acyl-homoserine-lactone synthase -
CHR56_RS36535 (CHR56_36535) 5187..6164 + 978 WP_077988219 P-type conjugative transfer ATPase TrbB virB11
CHR56_RS36540 (CHR56_36540) 6154..6537 + 384 WP_077988218 TrbC/VirB2 family protein virB2
CHR56_RS36545 (CHR56_36545) 6530..6829 + 300 WP_077988217 conjugal transfer protein TrbD virB3
CHR56_RS36550 (CHR56_36550) 6840..9296 + 2457 WP_077988216 conjugal transfer protein TrbE virb4
CHR56_RS36555 (CHR56_36555) 9268..10071 + 804 WP_077988215 P-type conjugative transfer protein TrbJ virB5
CHR56_RS36560 (CHR56_36560) 10068..10268 + 201 WP_077988232 entry exclusion protein TrbK -
CHR56_RS36565 (CHR56_36565) 10262..11443 + 1182 WP_077988214 P-type conjugative transfer protein TrbL virB6
CHR56_RS36570 (CHR56_36570) 11464..12126 + 663 WP_077988213 conjugal transfer protein TrbF virB8
CHR56_RS36575 (CHR56_36575) 12144..12956 + 813 WP_077988212 P-type conjugative transfer protein TrbG virB9
CHR56_RS36580 (CHR56_36580) 12960..13400 + 441 WP_077988211 conjugal transfer protein TrbH -
CHR56_RS36585 (CHR56_36585) 13412..14710 + 1299 WP_077988210 IncP-type conjugal transfer protein TrbI virB10
CHR56_RS36590 (CHR56_36590) 15021..15725 + 705 WP_077988209 autoinducer binding domain-containing protein -
CHR56_RS36595 (CHR56_36595) 15729..16019 - 291 WP_077988208 transcriptional repressor TraM -
CHR56_RS36600 (CHR56_36600) 16279..16527 + 249 WP_027668121 helix-turn-helix transcriptional regulator -
CHR56_RS36605 (CHR56_36605) 16770..17387 + 618 WP_077988207 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
CHR56_RS36610 (CHR56_36610) 17380..18246 + 867 WP_094231109 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
CHR56_RS36615 (CHR56_36615) 18377..18994 - 618 WP_077988205 TraH family protein virB1
CHR56_RS36620 (CHR56_36620) 19011..20174 - 1164 WP_077988204 conjugal transfer protein TraB -
CHR56_RS36625 (CHR56_36625) 20164..20661 - 498 WP_018482041 conjugative transfer signal peptidase TraF -

Host bacterium

ID   8029 GenBank   NZ_CP022669
Plasmid name   pPR4 Incompatibility group   -
Plasmid size   327451 bp Coordinate of oriT [Strand]   24133..24166 [-]
Host baterium   Rhizobium leguminosarum bv. viciae strain BIHB 1217

Cargo genes

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