Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102796
Name   oriT_Vaf10|unnamed3 in_silico
Organism   Rhizobium leguminosarum strain Vaf10
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP016290 (256508..256541 [-], 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_Vaf10|unnamed3
TCCAAGGGCGCAATTATACGTCGCCGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2070 GenBank   WP_065284310
Name   traA_BA011_RS35695_Vaf10|unnamed3 insolico UniProt ID   A0A1B1CMV8
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 123224.57 Da        Isoelectric Point: 9.9668

>WP_065284310.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVGRGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADSPEWLRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLARDVTIALPIELTATQNIALVRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVLLFQSLMVRILRSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLEATFARHSHLSYEQRTAIEHVAGASRIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNQLDHKTVFVLDEAGMVSSRQM
AVLVETVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDTYTAHGRMIGLRLKDEAVESLIAAWDRDYEPSKTSLILAHLRRDVRMLNDMARAKLIERGVVADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVVEVGDGEHRRQVMIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYFGSRSFAKSGGLVPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLMNVARTIARDRLEWTVRQKQKLADLGARLAAIGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLERAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAINVDTMLKDQSVAQS
TLARIAEEPESFGALKGKTGLLASRGDKQDREKALANVPALARNLERYLRERAEAELKHQTEERAVRLKV
SVDIPALSSAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTSG
KTFETVTSGMTAGQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETLRQTKNQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-741)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)

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

(864-960)


  Protein structure


Source ID Structure
AlphaFold DB A0A1B1CMV8


T4CP

ID   1729 GenBank   WP_065284294
Name   t4cp2_BA011_RS35615_Vaf10|unnamed3 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: 91708.64 Da        Isoelectric Point: 6.1282

>WP_065284294.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQVNAVLSRLG
SSWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYADKESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETLEREGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDRDREGLLEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPFAPCPFYPPKSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVAVQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKFEHGRDWPIHWLETRGVHDAASLLK

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(187-400)

  Protein structure



No available structure.



ID   1730 GenBank   WP_065284311
Name   traG_BA011_RS35710_Vaf10|unnamed3 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: 69411.41 Da        Isoelectric Point: 9.1846

>WP_065284311.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTINRIALAVMPAALMILVVIGMTGIEQWLSGFDKTEAARLAWGRTGIALPYVASAAIGVLLLFSSAGSI
NIKQAGWGVVAGSSGTILVAAVRETVRLSGFMKTVPADKTVLAYLDPATSIGASTALLGACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEIAPMVSAHRSGAGRDVFVLD
PRKPGIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
HDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFATNDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNREGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTHSKQLAARPLIQPHEVLRIRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMIGDTPKSA

  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: 237478..251369

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BA011_RS35580 (BA011_34430) 232804..234018 - 1215 WP_065284288 plasmid replication protein RepC -
BA011_RS35585 (BA011_34435) 234209..235246 - 1038 WP_065284289 plasmid partitioning protein RepB -
BA011_RS35590 (BA011_34440) 235243..236466 - 1224 WP_065284460 plasmid partitioning protein RepA -
BA011_RS35595 (BA011_34445) 236843..237481 + 639 WP_065284290 acyl-homoserine-lactone synthase -
BA011_RS35600 (BA011_34450) 237478..238455 + 978 WP_065284291 P-type conjugative transfer ATPase TrbB virB11
BA011_RS35605 (BA011_34455) 238445..238828 + 384 WP_065284292 TrbC/VirB2 family protein virB2
BA011_RS35610 (BA011_34460) 238821..239120 + 300 WP_065284293 conjugal transfer protein TrbD virB3
BA011_RS35615 (BA011_34465) 239131..241581 + 2451 WP_065284294 conjugal transfer protein TrbE virb4
BA011_RS35620 (BA011_34470) 241559..242356 + 798 WP_065284295 P-type conjugative transfer protein TrbJ virB5
BA011_RS35625 (BA011_34475) 242350..242523 + 174 WP_065284296 entry exclusion protein TrbK -
BA011_RS35630 (BA011_34480) 242528..243715 + 1188 WP_065284297 P-type conjugative transfer protein TrbL virB6
BA011_RS35635 (BA011_34485) 243738..244400 + 663 WP_065284298 conjugal transfer protein TrbF virB8
BA011_RS35640 (BA011_34490) 244418..245230 + 813 WP_065284299 P-type conjugative transfer protein TrbG virB9
BA011_RS35645 (BA011_34495) 245234..245674 + 441 WP_065284300 conjugal transfer protein TrbH -
BA011_RS35650 (BA011_34500) 245686..246984 + 1299 WP_065284301 IncP-type conjugal transfer protein TrbI virB10
BA011_RS35655 (BA011_34505) 247296..248000 + 705 WP_065284302 autoinducer binding domain-containing protein -
BA011_RS35660 (BA011_34510) 248004..248294 - 291 WP_065284303 transcriptional repressor TraM -
BA011_RS35665 (BA011_34515) 248552..248800 + 249 WP_065284304 helix-turn-helix transcriptional regulator -
BA011_RS35670 (BA011_34520) 249039..249656 + 618 WP_072642654 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
BA011_RS35675 (BA011_34525) 249649..250517 + 869 Protein_257 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
BA011_RS35680 (BA011_34530) 250752..251369 - 618 WP_065284307 TraH family protein virB1
BA011_RS35685 (BA011_34535) 251386..252549 - 1164 WP_065284308 conjugal transfer protein TraB -
BA011_RS35690 (BA011_34540) 252539..253075 - 537 WP_065284309 conjugative transfer signal peptidase TraF -

Host bacterium

ID   3239 GenBank   NZ_CP016290
Plasmid name   Vaf10|unnamed3 Incompatibility group   -
Plasmid size   557598 bp Coordinate of oriT [Strand]   256508..256541 [-]
Host baterium   Rhizobium leguminosarum strain Vaf10

Cargo genes

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