Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103889
Name   oriT_pAtA6 in_silico
Organism   Agrobacterium tumefaciens strain A6
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP033029 (562715..562756 [-], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      22..27, 31..36  (CGTCGT..ACGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 42 nt

>oriT_pAtA6
GGCTCCAAGGGCGCAATTATACGTCGTGATACGACGCGTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2892 GenBank   WP_121668140
Name   traA_AtA6_RS26345_pAtA6 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: 123849.41 Da        Isoelectric Point: 10.0236

>WP_121668140.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVLPANAPEWARSLIADR
SVSGAVEAFWNKVETFEKRADAQLARDLTIALPLELSAEQNIALVRDFVENHILAKGMVADWVYHENPGN
PHIHLMTTLRPLSDESFGSKKVAVIGEDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLKIDGRSYEKQGINLEPTIHLGVGAKAIERKAEQRGVRPELERVELNEQRRSENTRRILNNPAIVLDL
ITREKSVFDERDVAKVLHRYIDDPALFQQLMLKIILNPDVLRLQRETIDFSTGEKLPARYATRAMIRLEA
TMARQATWLSNREGRGVSPTALDATLRRHKRLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYHVVGGALAGKAAEGLEKEAGIQSRTLASWELRWKRGRDLLDDKTIFIMDEAGMVASKQMEAFVD
AAVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREEWMRKASLDLARGNVENALSAYR
ANVRITGERLKAEAVERLIADWNHDYDQTKTILILAHLRRDVRMLNVMAREKLVERGMVGEGHLFRTADG
ERRFDAGDQIVFLKNERSLGVKNGMIGHVVEAAANRIVATVGEGDRRRQVIVEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGTRSFSFNGGLAKVLSRRQAKETTLDYEHGQFY
REALRFAETRGLHVVQVARTMVRDRLDWTLRQKAKLVDLSRRLAAFAAHLGITQSPKTQTMKETAPMVAG
IKTFSGSVSDIVGDRLGTDPSLKRQWEEVSARFAYVFADPETAFRAMNFDALLADKEVAKQILQKLEAEP
GSIGPLKGKTGILASKPEREARRVAEVNVPALKRDLEQYLRMRETVTQRLQTDEQSLRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAAMAYAISNRETKLEIDGFNRAVTERFGERTLLSNSAREPSGKLYEKLSES
MKPEQKGQLKQAWSVMRTAQQLAAHERTVQSLRQAEEQRLTQRQTPVLKQ

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(855-951)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

AAA domain (AAA_30)

(382-566)


  Protein structure



No available structure.




T4CP

ID   2734 GenBank   WP_080863898
Name   t4cp2_AtA6_RS25685_pAtA6 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: 91854.74 Da        Isoelectric Point: 5.8866

>WP_080863898.1 conjugal transfer protein TrbE [Agrobacterium tumefaciens]
MVALKSFRHFGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAVRVPTGDYPTEEASHFPDPVTRAIDAERRAHFQKERGHYESRHALILTWRPPEPRRSGLTR
YVYSDVGSRSATYADKALESFLTSIREVEQYLANVVSIRRMMTRETPERGGHRVARYDELFQFIRFCITG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFVF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMLMVAETEDAIAEASSQLVAYGYYTPVVIL
FDDDQPSLKEKCEAVRRLIQAEGFGARIETINATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPVAPCPFYPAGSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLSLIAAQFRRYAGAQIFA
FDKGGSMLPLTLGLDGDHYQIGGDFGPSANGETRALSFCPLAELSTDGDRAFASEWIEMLVALQGVTITP
DYRNAISRQIGLMVESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLALGAFQCFEIEEL
MNMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIIATAIPKRDYYVVSPEGRRLFDM
ALGPVALSFIGATGRQDLKRIRSLHSEYGAAWPLHWLQQRGIAHADTLFPTE

  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.



ID   2735 GenBank   WP_038496882
Name   traG_AtA6_RS26360_pAtA6 insolico UniProt ID   _
Length   645 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 645 a.a.        Molecular weight: 69298.32 Da        Isoelectric Point: 9.3471

>WP_038496882.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium/Agrobacterium group]
MTANRLLLAILPAAIMIAVMILTSGLEHRLAALGTTAPAKLVLGRAGLALPYVAATAIGVVALFAANGST
NIKAAGLSVLVGSAVVIIIAVAREAIRLAGIAGNVPAGQSVLAYADPATLIGAGIAFLGSVFALRVSIMG
SAAFATAAPKRIGGRRAVHGEADWMKMQEAAKLFPEHGGIVIGERYRVDRDSIATMQFRADEPQSWGAGG
RSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVSEHRRQAGRKVIVLD
PTASGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNARTASARDDFFRASAMQLLTALIADVCLSGHTDE
KDQTLRQVRANLSEPEPKLRARLTKIYEGSDSDFVKENVSVFVNMTPETFFGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLANGGTDIFIALDLKVLEAHPGFARVVIGSLLNAIYNRKGDVKDRTLFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSLGQMREAYGRRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSKQLNRRPLILPHEVLRMRADEQIVFTSGNAPLRCGRAVWFRREDMKACVG
ENRFHKNSSGTDNPL

  Protein domains


Predicted by InterproScan.

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

(163-638)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 420227..429898

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AtA6_RS25650 (AtA6_49750) 415854..417086 + 1233 WP_080863892 CapA family protein -
AtA6_RS25655 (AtA6_49760) 417203..418498 + 1296 WP_080863893 peptidase T -
AtA6_RS25660 (AtA6_49770) 418503..419426 + 924 WP_121556230 citrulline utilization hydrolase CtlX -
AtA6_RS25665 (AtA6_49780) 419592..420230 + 639 WP_080863894 acyl-homoserine-lactone synthase TraI -
AtA6_RS25670 (AtA6_49790) 420227..421198 + 972 WP_080863895 P-type conjugative transfer ATPase TrbB virB11
AtA6_RS25675 (AtA6_49800) 421188..421592 + 405 WP_080863896 conjugal transfer pilin TrbC virB2
AtA6_RS25680 (AtA6_49810) 421585..421884 + 300 WP_080863897 conjugal transfer protein TrbD virB3
AtA6_RS25685 (AtA6_49820) 421896..424364 + 2469 WP_080863898 conjugal transfer protein TrbE virb4
AtA6_RS25690 (AtA6_49830) 424336..425145 + 810 WP_080863899 P-type conjugative transfer protein TrbJ virB5
AtA6_RS25695 (AtA6_49840) 425142..425369 + 228 WP_080863900 entry exclusion protein TrbK -
AtA6_RS25700 (AtA6_49850) 425363..426553 + 1191 WP_080863901 P-type conjugative transfer protein TrbL virB6
AtA6_RS25705 (AtA6_49860) 426569..427231 + 663 WP_080863902 conjugal transfer protein TrbF virB8
AtA6_RS25710 (AtA6_49870) 427249..428100 + 852 WP_080863994 P-type conjugative transfer protein TrbG virB9
AtA6_RS25715 (AtA6_49880) 428100..428579 + 480 WP_080863903 conjugal transfer protein TrbH -
AtA6_RS25720 (AtA6_49890) 428591..429898 + 1308 WP_080863904 IncP-type conjugal transfer protein TrbI virB10
AtA6_RS25725 (AtA6_49900) 430182..430355 + 174 Protein_404 integrase core domain-containing protein -
AtA6_RS25730 (AtA6_49910) 430464..430874 - 411 WP_080863906 helix-turn-helix domain-containing protein -
AtA6_RS25735 (AtA6_49920) 431211..432278 - 1068 WP_080863907 alkene reductase -
AtA6_RS25740 (AtA6_49940) 433207..433965 + 759 WP_080863908 ABC transporter permease -

Host bacterium

ID   4329 GenBank   NZ_CP033029
Plasmid name   pAtA6 Incompatibility group   -
Plasmid size   815853 bp Coordinate of oriT [Strand]   562715..562756 [-]
Host baterium   Agrobacterium tumefaciens strain A6

Cargo genes

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