Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103890
Name   oriT_pAt15955 in_silico
Organism   Agrobacterium tumefaciens strain 15955
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032919 (562632..562673 [-], 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_pAt15955
GGCTCCAAGGGCGCAATTATACGTCGTGATACGACGCGTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2893 GenBank   WP_121556235
Name   traA_At15955_RS25995_pAt15955 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: 123729.21 Da        Isoelectric Point: 10.0285

>WP_121556235.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVLPANAPEWARSLIADR
SVSGAVEAFWNKVETFEKRADAQLARDLTIALPLELSAEQNIALVRDFVENHILAKGMVADWVYHENPGN
PHIHLMTTLRPLSDESFGSKKVAVIGEDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLKIDGRSYEKQGINLEPTIHLGVGAKAIERKAEQRGVRPELERVELNEQRRSENTRRILNNPAIVLDL
ITREKSVFDERDVAKVLHRYIDDPALFQQLMIKIILNRQVLRLQRETIDFSTGEKLPARYSTRAMIRLEA
TMARQATWLSNREGRGVSPTALDATFRRHERLSDEQKAAIEHVAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYHVVGGALAGKAAEGLEKEAGIQSRTLASWELRWKRGRDLLDDKTIFIMDEAGMVASKQMAGFVD
TAVRAGAKIVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREEWMRKASLDLARGNVENALSAYR
ANVRITGERLKAEAVERLIADWNHDYDQTKTILILAHLRRDVRMLNVMAREKLVERGMVGEGHLFRTADG
ERRFDAGDQIVFLKNEGSLGLKNGMIGHVVVAAANRIVATVGEGDQRRQVIVEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGTRSFSFNGGLAKVLSRRQAKETTLDYEHGQFY
REALRFAETRGLHVVQVARTMVRDRLDWTLRQKAKLVDLSRRLAAFAAHLGITQSPKTQTMKETAPMVAG
IKTFSGSVSDIVGDRLGTDPSLKRQWEEVSARFAYVFADPETAFRAMNFDALLADKEVAKQILQKLEAEP
GSIGPLKGKTGILASKPEREARRVAEVNVPALKRDLEQYLRMRETVTQRLQTDEQSLRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAAMAYAISNRETKLEIDGFNRAVTERFGERTLLSNSAREPSGKLYEKLSES
MKPEQKGQLKQAWSVMRTAQQLAAHERTVQSLRQAEEQRLTQRQTPVLKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-566)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

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

(855-951)


  Protein structure



No available structure.




T4CP

ID   2736 GenBank   WP_080863898
Name   t4cp2_At15955_RS25335_pAt15955 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   2737 GenBank   WP_038496882
Name   traG_At15955_RS26010_pAt15955 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: 420144..429815

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
At15955_RS25300 (At15955_49030) 415771..417003 + 1233 WP_080863892 CapA family protein -
At15955_RS25305 (At15955_49040) 417120..418415 + 1296 WP_080863893 peptidase T -
At15955_RS25310 (At15955_49050) 418420..419343 + 924 WP_121556230 citrulline utilization hydrolase CtlX -
At15955_RS25315 (At15955_49060) 419509..420147 + 639 WP_080863894 acyl-homoserine-lactone synthase TraI -
At15955_RS25320 (At15955_49070) 420144..421115 + 972 WP_080863895 P-type conjugative transfer ATPase TrbB virB11
At15955_RS25325 (At15955_49080) 421105..421509 + 405 WP_080863896 conjugal transfer pilin TrbC virB2
At15955_RS25330 (At15955_49090) 421502..421801 + 300 WP_080863897 conjugal transfer protein TrbD virB3
At15955_RS25335 (At15955_49100) 421813..424281 + 2469 WP_080863898 conjugal transfer protein TrbE virb4
At15955_RS25340 (At15955_49110) 424253..425062 + 810 WP_080863899 P-type conjugative transfer protein TrbJ virB5
At15955_RS25345 (At15955_49120) 425059..425286 + 228 WP_080863900 entry exclusion protein TrbK -
At15955_RS25350 (At15955_49130) 425280..426470 + 1191 WP_080863901 P-type conjugative transfer protein TrbL virB6
At15955_RS25355 (At15955_49140) 426486..427148 + 663 WP_080863902 conjugal transfer protein TrbF virB8
At15955_RS25360 (At15955_49150) 427166..428017 + 852 WP_080863994 P-type conjugative transfer protein TrbG virB9
At15955_RS25365 (At15955_49160) 428017..428496 + 480 WP_080863903 conjugal transfer protein TrbH -
At15955_RS25370 (At15955_49170) 428508..429815 + 1308 WP_080863904 IncP-type conjugal transfer protein TrbI virB10
At15955_RS25375 (At15955_49180) 430099..430272 + 174 Protein_403 integrase core domain-containing protein -
At15955_RS25380 (At15955_49190) 430381..430791 - 411 WP_080863906 helix-turn-helix domain-containing protein -
At15955_RS25385 (At15955_49200) 431128..432195 - 1068 WP_080863907 alkene reductase -
At15955_RS25390 (At15955_49220) 433211..433882 + 672 WP_233285235 ABC transporter permease -

Host bacterium

ID   4330 GenBank   NZ_CP032919
Plasmid name   pAt15955 Incompatibility group   -
Plasmid size   814493 bp Coordinate of oriT [Strand]   562632..562673 [-]
Host baterium   Agrobacterium tumefaciens strain 15955

Cargo genes

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