Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107609
Name   oriT_Vaf-108|unnamed7 in_silico
Organism   Rhizobium leguminosarum strain Vaf-108
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP018235 (85963..85996 [-], 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_Vaf-108|unnamed7
TCCAAGGGCGCAATTATACGTCGCCGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5116 GenBank   WP_072642658
Name   traA_BMW22_RS40510_Vaf-108|unnamed7 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: 123211.53 Da        Isoelectric Point: 9.9330

>WP_072642658.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVGRGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADSPEWLRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLARDVTIALPIELTATQNIALVRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPVRNDAGKIVYELWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVLLFQSLMVRILRSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLEATFARHSHLSYEQRTAIEHVAGASRIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNQLDHKTVFVLDEAGMVSSRQM
AVLVETVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDTYTAHGRMIGLRLKDEAVESLIAAWDRDYEPSKTSLILAHLRRDVRMLNDMARAKLIERGVVADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVVEVGDGEHRRQVMIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYFGSRSFAKSGGLVPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLMNVARTIARDRLEWTVRQKQKLADLGARLAAIGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLERAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAINVDTMLKDQSVAQS
TLARIAEEPESFGALKGKTGLLASRGDKQDREKALANVPALARNLERYLRERAEAELKHQTEERAVRLKV
SVDIPALSSAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTSG
KTFETVTSGMTAGQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETLRQTKNQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-741)

AAA domain (AAA_30)

(387-570)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   5343 GenBank   WP_072642652
Name   t4cp2_BMW22_RS40430_Vaf-108|unnamed7 insolico UniProt ID   _
Length   784 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 784 a.a.        Molecular weight: 88066.56 Da        Isoelectric Point: 6.0192

>WP_072642652.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQVNAVLSRLG
SSWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYADKESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETLEREGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDRDREGLLEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPFAPCPFYPPKSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVAVQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLQIEIVATAMPKREYYVATPEGRRLFNMSLGPVALSFVGASGKEDLKRIRALKFEHGRDWPIHW
LETRGVHDAASLLK

  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   5344 GenBank   WP_065284311
Name   traG_BMW22_RS40525_Vaf-108|unnamed7 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: 66978..80824

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BMW22_RS40395 (BMW22_40285) 62304..63518 - 1215 WP_065284288 plasmid replication protein RepC -
BMW22_RS40400 (BMW22_40290) 63709..64746 - 1038 WP_065284289 plasmid partitioning protein RepB -
BMW22_RS40405 (BMW22_40295) 64743..65966 - 1224 WP_065284460 plasmid partitioning protein RepA -
BMW22_RS40410 (BMW22_40300) 66343..66981 + 639 WP_072642651 acyl-homoserine-lactone synthase -
BMW22_RS40415 (BMW22_40305) 66978..67955 + 978 WP_065284291 P-type conjugative transfer ATPase TrbB virB11
BMW22_RS40420 (BMW22_40310) 67945..68328 + 384 WP_065284292 TrbC/VirB2 family protein virB2
BMW22_RS40425 (BMW22_40315) 68321..68620 + 300 WP_065284293 conjugal transfer protein TrbD virB3
BMW22_RS40430 (BMW22_40320) 68631..70985 + 2355 WP_072642652 conjugal transfer protein TrbE virb4
BMW22_RS40435 (BMW22_40325) 70963..71442 + 480 Protein_81 P-type conjugative transfer protein TrbJ -
BMW22_RS40440 (BMW22_40330) 71535..72221 + 687 WP_072642645 IS6 family transposase -
BMW22_RS40445 (BMW22_40335) 72277..73170 + 894 Protein_83 P-type conjugative transfer protein TrbL -
BMW22_RS40450 (BMW22_40340) 73193..73855 + 663 WP_065284298 conjugal transfer protein TrbF virB8
BMW22_RS40455 (BMW22_40345) 73873..74685 + 813 WP_065284299 P-type conjugative transfer protein TrbG virB9
BMW22_RS40460 (BMW22_40350) 74689..75129 + 441 WP_065284300 conjugal transfer protein TrbH -
BMW22_RS40465 (BMW22_40355) 75141..76439 + 1299 WP_072642653 IncP-type conjugal transfer protein TrbI virB10
BMW22_RS40470 (BMW22_40360) 76751..77455 + 705 WP_065284302 autoinducer binding domain-containing protein -
BMW22_RS40475 (BMW22_40365) 77459..77749 - 291 WP_065284303 transcriptional repressor TraM -
BMW22_RS40480 (BMW22_40370) 78007..78255 + 249 WP_065284304 helix-turn-helix transcriptional regulator -
BMW22_RS40485 (BMW22_40375) 78494..79111 + 618 WP_072642654 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
BMW22_RS40490 (BMW22_40380) 79104..79972 + 869 Protein_92 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
BMW22_RS40495 (BMW22_40385) 80207..80824 - 618 WP_065284307 TraH family protein virB1
BMW22_RS40500 (BMW22_40390) 80841..82004 - 1164 WP_072642656 conjugal transfer protein TraB -
BMW22_RS40505 (BMW22_40395) 81994..82530 - 537 WP_065284309 conjugative transfer signal peptidase TraF -

Host bacterium

ID   8044 GenBank   NZ_CP018235
Plasmid name   Vaf-108|unnamed7 Incompatibility group   -
Plasmid size   227762 bp Coordinate of oriT [Strand]   85963..85996 [-]
Host baterium   Rhizobium leguminosarum strain Vaf-108

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   hupE
Degradation gene   -
Symbiosis gene   nodM, nodE, nodF, nodD, nodA, nodC, nodI, nodJ
Anti-CRISPR   -