Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106729
Name   oriT_pAtAG67 in_silico
Organism   Agrobacterium fabrum strain LBA645
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP079858 (57510..57550 [+], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 41 nt

>oriT_pAtAG67
TCCAAGGGCGCAATTATACGTCGCTGACGCGACGTGCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4444 GenBank   WP_243823448
Name   traA_KXJ62_RS25900_pAtAG67 insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123609.01 Da        Isoelectric Point: 9.7191

>WP_243823448.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium fabrum]
MAIAHFSASIVSRGGGRSAVLSAAYRHCAKMEYEREARAIDYTRKQGLLHEEFVVPADAPKWVRALISDR
SVSGAVEAFWNKVEAFEKRSDAQLARDLTIALPLELTPEQNITLVRDFAEKHILAKGMVADWVYHGNPGN
PHIHLMTTLRPLTEDGFGSKKVAVIGEDGQPVRTKSGKILYQLWAGSTDDFNVLRDGWFDRLNHHLALGG
IDLKIDGRSYEKQGIELEPTIHLGVGAKAIERKAQQQGVRPELERIELNEQRRSENTRRILNNPAIVLDL
ITREKSVFDERDVAKVLHRYVDDPTVFQQLMLRIIQNPEVFRLQRDTIEFATGEKVPARYSTRAMIRLEA
TMVRQALWLSNRDGHPVSEAALAATFRRHERLSDEQKTAIERIAGPARIGAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIESRTLASWELRWNRGRDVLDDKTVFVMDEAGMVASKQMAGFVD
AVVRAGARIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
ANARITGTGLKAEAVERLIGDWNHDYDQTKTTLILAHLRRDVRMLNIMAREKLVERGIVGEGHVFKTADG
IRQFDVGDQIVFLKNEGSLGVKNGMIAHVVEVAPNRIVAVIGEGDQRRQVFVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGRRSFAFNGGLAEVLSRKNAKETTLDYERGNLY
REALRFAESRGLNIVQVARTLVRDRLDWTLRQKTRLVDLGQRLAVFAERLGLHHPPKTQTMKEAAPMIAG
IKTFSGSVADTVENKLDTDPALRQQWEEVSTRFSYVFADPETAFRAMNFDAVLADKETAKLALQTLTTAP
ASIGPLKGKTGILASKTEREDRRIAERNVPALKRDLEQYLRMRETAVQRLQADEQALRQRVSIDIPALSP
AAHVVLERVRDAIDRNDLPAAMAYALSNRETKLEIDGFNQAVTERFGERTMLTNAAREPSGKLFDKLSEG
MQPEQKERLKEAWPIMRTSQQLAAHERTVQTLRQAEDLRLAQRQTPVMKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

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

(855-951)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   4476 GenBank   WP_243823447
Name   traG_KXJ62_RS25885_pAtAG67 insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 70998.41 Da        Isoelectric Point: 9.2530

>WP_243823447.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens complex]
MTMNRLLLLILPAMIMLAAMFATSGMEQRLAAFGTSPQAKLMLGRAGLALPYIAAVAIGIIGLFAANGSA
NIKAAGLSVLAGSGVVITIATLSEVIRLNSIASSVPAEQSVLACADPVTMIGASIAFISGMFALRVAIKG
NAAFATTAPKRIGGKRAVHGEADWMKIQEAAKLFPERGGIIIGERYRVDRDSVAAMPFRAVDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVCEHRRQAGRKVIVLD
PTAGGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTET
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNVKGRTLFLLDEVARLGY
LRILETARDAGRKYGIMLTMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSTGMKGSSRSRSKQLSRRPLILPHEVLRMRSDEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
ENRFHRTGTGTDTHTEHAPPWQKEGTRP

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   4477 GenBank   WP_060716498
Name   t4cp2_KXJ62_RS26220_pAtAG67 insolico UniProt ID   _
Length   822 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 822 a.a.        Molecular weight: 92090.79 Da        Isoelectric Point: 5.4919

>WP_060716498.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium/Agrobacterium group]
MVALNLFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINMIMSRLG
SGWMIQVEALRVPTIDYPADDACHFADPVTRAIDTERRTHFERESGHFESRHALILTWRPPEPRRSGLAR
YVYSDTASRSATYADTALESFRTSIREVEQYLANVVSIRRMVTRETEERGGFRIARYDELFQFIRFCITG
ENHPVRLPDIPMYLDWLVTAELQHGLTPTVESRFLGVVAIDGLAAESWPGILNSLDLMPLTYRWSSRFVF
LDEQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMMMVAETEDAIAEASSQLVAYGYYTPVIVL
FDEQQERLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLVNTRNLADLIPLNSVWS
GSPVAPCPFYPPGSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLSLIAAQFRRYADAQIFA
FDKGRSMLPLTLAIGGDHYEIGGDAAEGGERDSPRLAFCPLAELASDGDRAWAAEWIETLVALQGVTVTP
DYRNAISRQLALMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLALGAFQCFEVEEL
MNLGERNLVPVLLYMFRRVEKRLTGAPSLIILDEAWLMLGHPTFRNKIREWLKVVRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVASPEGRRLFDM
SLGPVALSFVGASGKEDLKRIRALHFEHGADWPKHWLQQRGIAHAETLFQAA

  Protein domains


Predicted by InterproScan.

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

(193-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 121164..130840

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KXJ62_RS26170 (KXJ62_26060) 116801..117586 + 786 WP_060716474 amino acid ABC transporter ATP-binding protein -
KXJ62_RS26175 (KXJ62_26065) 117732..119069 + 1338 WP_243823404 MmgE/PrpD family protein -
KXJ62_RS26180 (KXJ62_26070) 119245..121110 + 1866 WP_243823405 LysR family transcriptional regulator -
KXJ62_RS26185 (KXJ62_26075) 121164..122474 - 1311 WP_153517050 IncP-type conjugal transfer protein TrbI virB10
KXJ62_RS26190 (KXJ62_26080) 122487..122966 - 480 WP_243823406 conjugal transfer protein TrbH -
KXJ62_RS26195 (KXJ62_26085) 122966..123820 - 855 WP_071208371 P-type conjugative transfer protein TrbG virB9
KXJ62_RS26200 (KXJ62_26090) 123838..124500 - 663 WP_153517051 conjugal transfer protein TrbF virB8
KXJ62_RS26205 (KXJ62_26095) 124515..125711 - 1197 WP_243823407 P-type conjugative transfer protein TrbL virB6
KXJ62_RS26210 (KXJ62_26100) 125705..125923 - 219 WP_243823408 entry exclusion protein TrbK -
KXJ62_RS26215 (KXJ62_26105) 125920..126729 - 810 WP_153517054 P-type conjugative transfer protein TrbJ virB5
KXJ62_RS26220 (KXJ62_26110) 126701..129169 - 2469 WP_060716498 conjugal transfer protein TrbE virb4
KXJ62_RS26225 (KXJ62_26115) 129180..129479 - 300 WP_045023373 conjugal transfer protein TrbD virB3
KXJ62_RS26230 (KXJ62_26120) 129472..129879 - 408 WP_060716499 conjugal transfer pilin TrbC virB2
KXJ62_RS26235 (KXJ62_26125) 129869..130840 - 972 WP_060716500 P-type conjugative transfer ATPase TrbB virB11
KXJ62_RS26240 (KXJ62_26130) 130837..131472 - 636 WP_243823409 acyl-homoserine-lactone synthase -

Host bacterium

ID   7166 GenBank   NZ_CP079858
Plasmid name   pAtAG67 Incompatibility group   -
Plasmid size   131838 bp Coordinate of oriT [Strand]   57510..57550 [+]
Host baterium   Agrobacterium fabrum strain LBA645

Cargo genes

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