Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102489
Name   oriT_pLPU83b in_silico
Organism   Rhizobium favelukesii strain LPU83
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CBYB010000034 (37241..37273 [-], 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_pLPU83b
TCCAAGGGCGCAATTATACGTCGCTGGCGCGAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1853 GenBank   WP_024317491
Name   traA_LPU83_RS34595_pLPU83b 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   1445 GenBank   WP_024317476
Name   t4cp2_LPU83_RS34375_pLPU83b 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.



ID   1446 GenBank   WP_024317494
Name   traG_LPU83_RS34610_pLPU83b 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 19184..32102

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LPU83_RS33475 (LPU83_pLPU83b_0322) 14198..15412 - 1215 WP_024317469 plasmid replication protein RepC -
LPU83_RS33575 (LPU83_pLPU83b_0323) 15604..16641 - 1038 WP_024317470 plasmid partitioning protein RepB -
LPU83_RS33580 (LPU83_pLPU83b_0324) 16638..17861 - 1224 WP_024317471 plasmid partitioning protein RepA -
LPU83_RS33595 (LPU83_pLPU83b_0325) 18550..19173 + 624 WP_024317472 acyl-homoserine-lactone synthase TraI -
LPU83_RS33600 (LPU83_pLPU83b_0326) 19184..20161 + 978 WP_024317473 P-type conjugative transfer ATPase TrbB virB11
LPU83_RS34040 (LPU83_pLPU83b_0327) 20151..20534 + 384 WP_024317474 TrbC/VirB2 family protein virB2
LPU83_RS34125 (LPU83_pLPU83b_0328) 20527..20826 + 300 WP_024317475 conjugal transfer protein TrbD virB3
LPU83_RS34375 (LPU83_pLPU83b_0329) 20837..23293 + 2457 WP_024317476 conjugal transfer protein TrbE virb4
LPU83_RS34395 (LPU83_pLPU83b_0330) 23265..24068 + 804 WP_024317477 P-type conjugative transfer protein TrbJ virB5
LPU83_RS34420 (LPU83_pLPU83b_0331) 24065..24262 + 198 WP_024317478 entry exclusion protein TrbK -
LPU83_RS34440 (LPU83_pLPU83b_0332) 24256..25437 + 1182 WP_024317479 P-type conjugative transfer protein TrbL virB6
LPU83_RS34445 (LPU83_pLPU83b_0333) 25458..26120 + 663 WP_024317480 conjugal transfer protein TrbF virB8
LPU83_RS34450 (LPU83_pLPU83b_0334) 26138..26950 + 813 WP_024317481 P-type conjugative transfer protein TrbG virB9
LPU83_RS34460 (LPU83_pLPU83b_0335) 26954..27394 + 441 WP_024317482 conjugal transfer protein TrbH -
LPU83_RS34465 (LPU83_pLPU83b_0336) 27406..28704 + 1299 WP_024317483 IncP-type conjugal transfer protein TrbI virB10
LPU83_RS34510 (LPU83_pLPU83b_0337) 29029..29733 + 705 WP_024317484 autoinducer binding domain-containing protein -
LPU83_RS34515 (LPU83_pLPU83b_0338) 29737..30027 - 291 WP_024317485 transcriptional repressor TraM -
LPU83_RS34540 (LPU83_pLPU83b_0339) 30318..30557 + 240 WP_024317486 helix-turn-helix transcriptional regulator -
LPU83_RS73815 (LPU83_pLPU83b_0340) 30681..31223 + 543 WP_024317487 hypothetical protein -
LPU83_RS34575 (LPU83_pLPU83b_0341) 31479..32102 - 624 WP_024317488 TraH family protein virB1
LPU83_RS34580 (LPU83_pLPU83b_0342) 32119..33282 - 1164 WP_024317489 conjugal transfer protein TraB -
LPU83_RS34585 (LPU83_pLPU83b_0343) 33272..33769 - 498 WP_231052413 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2933 GenBank   NZ_CBYB010000034
Plasmid name   pLPU83b Incompatibility group   -
Plasmid size   42790 bp Coordinate of oriT [Strand]   37241..37273 [-]
Host baterium   Rhizobium favelukesii strain LPU83

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -