Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103851
Name   oriT_pAt1D1609b in_silico
Organism   Agrobacterium tumefaciens strain 1D1609
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026928 (167638..167675 [+], 38 nt)
oriT length   38 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: 38 nt

>oriT_pAt1D1609b
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGCCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2861 GenBank   WP_104680633
Name   traA_At1D1609_RS29215_pAt1D1609b 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: 122711.90 Da        Isoelectric Point: 9.7386

>WP_104680633.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWLHSMIDDR
SVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAKCMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLAPDGKPIRNDAGKIVYDLWAGSTEDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGTKAIERKAEQSDRTSETSAPKLERIELQEARRSENARRIQRGPE
IVLELITREKSVFDERDVAKVLYRYIDDIRLFQSLMVRILQSPEALRLERERMNLATGVREPAKYTTREM
IRLETEMANRAIWLSGRVSHGVREAVLQATFARHVRLSDEQRTAVEHVAGGERIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNQGRNQLDNKTVIVLDEAGMVSSRQM
ARLVEAVTTAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRLQWMRDASLDFARGNIRKA
VDAYTAHGRMIGLRLKDEAVESLITAWDRDYDPSKTSLILAHLRRDVRMLNDKARAKLVERGVVADGFAF
KTEDGTRMLAAGDQIVFLKNEGSLGVKNGMLAKVVEAAPGRIVAEVGEGEHRRQVMIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGGRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVKVARTIAYDRLQWAVRQQQRLADLGARLAAVGAALGLVRGSNKQSPANST
KEAKPMVSGITTFPKSFEQAVEDKLAADPGLKKQWEGVSTRFHLVYAQPEAAFKAINVDAMIKDQSVAQS
TLAKVAGDPESFGALKGRTGVLASRADKQDREKAIANVPALARNLERYLRERAEAELKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMAPGQKAEVQSAWNSMRTVQQLAAHERTTEALKQAETLRQTKSHGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)

AAA domain (AAA_30)

(387-570)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure



No available structure.




T4CP

ID   2694 GenBank   WP_104680630
Name   traG_At1D1609_RS29200_pAt1D1609b insolico UniProt ID   _
Length   635 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 635 a.a.        Molecular weight: 68904.81 Da        Isoelectric Point: 9.0646

>WP_104680630.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MTINRIALAVGPTALMILVVIGMTGIEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGIVFLFASAGAI
NIKQAGWGVLAGCSGTILIAVTRETMRLAAFTQALPADKTIFAYLDPATSIGASAALMCACFALRVAFIG
NAAFARAEPKRIQGKRALHGEADWMRVTEAAKLFPDTGGIVIGEHYRVDKDSVAALAFRADNAKTWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPEIGFNVLDWVGRFGETKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
KEQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFTTNDIAAGNTDVFINIDLKTLETHSGLARVVIGSFLNAIYNRDGQLEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGTTT
VEIDQVSRSFQSRGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRKLVQ
TNRFQ

  Protein domains


Predicted by InterproScan.

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

(163-629)

  Protein structure



No available structure.



ID   2695 GenBank   WP_104680648
Name   t4cp2_At1D1609_RS29290_pAt1D1609b 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: 91731.39 Da        Isoelectric Point: 5.6006

>WP_104680648.1 conjugal transfer protein TrbE [Agrobacterium tumefaciens]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQAEAIRIPTVDYPSEDRCHFSDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFLFKSTVRELEQYFANTLSIRRMETRETAERGGERIARYDELLQFARFCITG
ESHPIRLPDVPMYIDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAQEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDGDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYAPNSPPLMQVATGSTAFRFNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAADGDHYEIGGDSAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALLHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIERRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSSAIPKREYYVVTPEGRRLFDMSLGP
VALSFVGASGKEDLKHIQALKSKHGRDWPIHWLETRGVHDAASLLRFE

  Protein domains


Predicted by InterproScan.

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: 172786..186618

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
At1D1609_RS29220 (At1D1609_56330) 171074..171616 + 543 WP_104680634 conjugative transfer signal peptidase TraF -
At1D1609_RS29225 (At1D1609_56340) 171606..172769 + 1164 WP_104680635 conjugal transfer protein TraB -
At1D1609_RS29230 (At1D1609_56350) 172786..173403 + 618 WP_104680636 TraH family protein virB1
At1D1609_RS29235 (At1D1609_56360) 173635..175200 + 1566 WP_104680637 Fic family protein -
At1D1609_RS29240 (At1D1609_56370) 175314..175535 - 222 WP_104680638 helix-turn-helix transcriptional regulator -
At1D1609_RS29245 (At1D1609_56380) 175749..176069 + 321 WP_104680639 transcriptional repressor TraM -
At1D1609_RS29250 (At1D1609_56390) 176073..176777 - 705 WP_104680640 autoinducer binding domain-containing protein -
At1D1609_RS29255 (At1D1609_56400) 177099..178394 - 1296 WP_104680641 IncP-type conjugal transfer protein TrbI virB10
At1D1609_RS29260 (At1D1609_56410) 178406..178846 - 441 WP_104680642 conjugal transfer protein TrbH -
At1D1609_RS29265 (At1D1609_56420) 178850..179662 - 813 WP_104680643 P-type conjugative transfer protein TrbG virB9
At1D1609_RS29270 (At1D1609_56430) 179680..180342 - 663 WP_104680644 conjugal transfer protein TrbF virB8
At1D1609_RS29275 (At1D1609_56440) 180362..181543 - 1182 WP_104680645 P-type conjugative transfer protein TrbL virB6
At1D1609_RS29280 (At1D1609_56450) 181537..181737 - 201 WP_104680646 entry exclusion protein TrbK -
At1D1609_RS29285 (At1D1609_56460) 181734..182537 - 804 WP_104680647 P-type conjugative transfer protein TrbJ virB5
At1D1609_RS29290 (At1D1609_56470) 182509..184965 - 2457 WP_104680648 conjugal transfer protein TrbE virb4
At1D1609_RS29295 (At1D1609_56480) 184976..185275 - 300 WP_104680649 conjugal transfer protein TrbD virB3
At1D1609_RS29300 (At1D1609_56490) 185268..185651 - 384 WP_104680650 TrbC/VirB2 family protein virB2
At1D1609_RS29305 (At1D1609_56500) 185641..186618 - 978 WP_104680651 P-type conjugative transfer ATPase TrbB virB11
At1D1609_RS29310 (At1D1609_56510) 186629..187252 - 624 WP_104680652 acyl-homoserine-lactone synthase -

Host bacterium

ID   4291 GenBank   NZ_CP026928
Plasmid name   pAt1D1609b Incompatibility group   -
Plasmid size   187640 bp Coordinate of oriT [Strand]   167638..167675 [+]
Host baterium   Agrobacterium tumefaciens strain 1D1609

Cargo genes

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