Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121214
Name   oriT_pT136b in_silico
Organism   Rhizobium sp. T136
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP088011 (467321..467353 [+], 33 nt)
oriT length   33 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 33 nt

>oriT_pT136b
TCCAAGGGCGCAATTATACGTCGCTGGCGCGAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13397 GenBank   WP_024317491
Name   traA_LPB79_RS32570_pT136b insolico UniProt ID   W6S1J9
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 122775.11 Da        Isoelectric Point: 10.1192

>WP_024317491.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEELVVPSDAPEWLRMMVADR
SVAGASEAFWNKVEVFEKRSDAQLAKDVTIALPIELTAAQNIALVRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLAPDGKPIRNDAGKIVYELWAGSAEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFERQGIALEPTIHLGVGTKAIERKAEQTDRKQETPASKLERVKFQEARRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDASLFQSLMVRILQSPEALRLERERINFATGIRTPAKYTSRQM
IRLEAEMVNRAIWLSGRASHGVREAVLEATFARHARLSVEQRTAIEHVAGGERIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNEGRNHIDDKTVFVLDEAGMVSSRQM
ALFVDAVTKAGAKLVLVGDPEQLQPIGAGAGFRAIADRIGYAELETIYRQRQQWMRDASLDLARGKVGEA
VEAYRAHGRFNGLDLKAQAVESLIADWNHGYDPSKTTLILAHLRRDVRMLNEMARAKLVERGIIADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAPGRLVAELGGGEHRRLVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYE
KASFYRQALRFAEARGLHLVNVARTIAHDRLQWAVRQKQKLADLGARLAAMGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSFGQAVEDKLAADPGLKKQWEDVSTRFHLVYAQPEAAFNAINVDAMAKDQSVAQS
TLERIAGAPESFGALKGKTGLLASRADKQEREKAVANVPALARNLKRYLRERAEAEFKHETEERAVRLKV
SVDIPALSASAKQTLERVRDAIDSNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTSG
KTFETVTSGMTVSQKVEVQSAWNSMRTVQQLGSHERTTEALKQAETLRQTKSQGRSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

AAA domain (AAA_30)

(387-571)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure


Source ID Structure
AlphaFold DB W6S1J9


T4CP

ID   15699 GenBank   WP_024317494
Name   traG_LPB79_RS32555_pT136b insolico UniProt ID   _
Length   659 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 659 a.a.        Molecular weight: 70953.33 Da        Isoelectric Point: 9.2056

>WP_024317494.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVVPTALMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGVLLLFASAGSI
NIKQAGWGVVAGSSGTILVAAVRETMRLSAVIKAAPADKTVLAFLDPATSIGASAALLCACFALRVALIG
NAAFAGAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVASQAFRADSAEVWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPIVIAHRGGAGRDVFVLN
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHMDE
KDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFPTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRDTYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIDQVSRSFHAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRVCIG
ENRFHSMGGREKEASNATPAVNPYEPNRL

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   15700 GenBank   WP_024317476
Name   t4cp2_LPB79_RS32645_pT136b 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: 91872.73 Da        Isoelectric Point: 5.8129

>WP_024317476.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDFERNELSRRINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREKGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFDNTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMRMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAVRRLIQAEGYGARIETLNATDAYLGSLPGNWYCNIREPLINTCNLADLIPLNSVWP
GNPVAPCPFFAPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFLRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNVEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDYRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEHLMNLG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIHWLETRGVHDAASLLKCE

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(452-492)

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

(192-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 472492..485410

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LPB79_RS32575 (LPB79_32575) 470825..471322 + 498 WP_231052413 conjugative transfer signal peptidase TraF -
LPB79_RS32580 (LPB79_32580) 471312..472475 + 1164 WP_024317489 conjugal transfer protein TraB -
LPB79_RS32585 (LPB79_32585) 472492..473115 + 624 WP_024317488 TraH family protein virB1
LPB79_RS32590 (LPB79_32590) 473371..473913 - 543 WP_024317487 hypothetical protein -
LPB79_RS32595 (LPB79_32595) 474037..474276 - 240 WP_024317486 helix-turn-helix domain-containing protein -
LPB79_RS32600 (LPB79_32600) 474567..474857 + 291 WP_024317485 transcriptional repressor TraM -
LPB79_RS32605 (LPB79_32605) 474861..475565 - 705 WP_024317484 autoinducer binding domain-containing protein -
LPB79_RS32610 (LPB79_32610) 475890..477188 - 1299 WP_024317483 IncP-type conjugal transfer protein TrbI virB10
LPB79_RS32615 (LPB79_32615) 477200..477640 - 441 WP_024317482 conjugal transfer protein TrbH -
LPB79_RS32620 (LPB79_32620) 477644..478456 - 813 WP_024317481 P-type conjugative transfer protein TrbG virB9
LPB79_RS32625 (LPB79_32625) 478474..479136 - 663 WP_024317480 conjugal transfer protein TrbF virB8
LPB79_RS32630 (LPB79_32630) 479157..480338 - 1182 WP_024317479 P-type conjugative transfer protein TrbL virB6
LPB79_RS32635 (LPB79_32635) 480332..480529 - 198 WP_024317478 entry exclusion protein TrbK -
LPB79_RS32640 (LPB79_32640) 480526..481329 - 804 WP_024317477 P-type conjugative transfer protein TrbJ virB5
LPB79_RS32645 (LPB79_32645) 481301..483757 - 2457 WP_024317476 conjugal transfer protein TrbE virb4
LPB79_RS32650 (LPB79_32650) 483768..484067 - 300 WP_024317475 conjugal transfer protein TrbD virB3
LPB79_RS32655 (LPB79_32655) 484060..484443 - 384 WP_024317474 TrbC/VirB2 family protein virB2
LPB79_RS32660 (LPB79_32660) 484433..485410 - 978 WP_024317473 P-type conjugative transfer ATPase TrbB virB11
LPB79_RS32665 (LPB79_32665) 485421..486044 - 624 WP_024317472 acyl-homoserine-lactone synthase TraI -
LPB79_RS32670 (LPB79_32670) 486733..487956 + 1224 WP_024317471 plasmid partitioning protein RepA -
LPB79_RS32675 (LPB79_32675) 487953..488990 + 1038 WP_024317470 plasmid partitioning protein RepB -
LPB79_RS32680 (LPB79_32680) 489182..490396 + 1215 WP_024317469 plasmid replication protein RepC -

Host bacterium

ID   21642 GenBank   NZ_CP088011
Plasmid name   pT136b Incompatibility group   -
Plasmid size   806677 bp Coordinate of oriT [Strand]   467321..467353 [+]
Host baterium   Rhizobium sp. T136

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   LinG, dxnH
Symbiosis gene   nodD, nodH, nodF, nodE, nodJ, nodI, nodC, nodB, nodA, fixU, nifZ, nifB, fixX, fixC, fixB, fixA, nifW, nifS, nifH, nifD, nifK, nifE, nifN, nifX, mLTONO_5203, fixN, fixO, fixQ, nodM
Anti-CRISPR   -