Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103922
Name   oriT_pAtCFBP5499b in_silico
Organism   Agrobacterium tumefaciens strain CFBP5499
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039891 (72613..72654 [+], 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_pAtCFBP5499b
GGTTCCAAGGGCGCAATTATACGTCGTGATACGACGCGTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2914 GenBank   WP_080830924
Name   traA_CFBP5499_RS27980_pAtCFBP5499b 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: 123748.22 Da        Isoelectric Point: 9.9274

>WP_080830924.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Agrobacterium]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVLPANAPEWARSLIADR
SVSGAIEAFWNKVEAFEKRADAQLARDLTIALPLELSAEQNIALVRDFVEKHILAKGMVADWVYHENPGN
PHIHLMTTLRPLSDESFGSKKVAVIGEDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLKIDGRSYEKQGINLEPTVHLGVGAKAIERKAEQRGVRPELERVELNEQRRSENTRRILNNPAIVLDL
ITREKSVFDERDIAKVLHRYIDDPALFQQLMLKIILNPDVLRLQRETIDFSTGEKLPARYSTRAMIRLEA
TMARQATWLSNREGRSVSPTALDATFRRHEQLSDEQKAAIERVAGPARIAAVVGRAGAGKTTMMKAAREV
WELAGYHVVGGALAGKAAEGLEKEAGIQSRTLASWELRWKRGRDLLDDKTIFIMDEAGMVASKQMAAFVD
AAVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQRAEWMRKASLDLARGNVENALSAYG
ANVRIAGERLKAEAVERLIADWNHDYDQTKTILILAHLRRDVRMLNVMAREKLVERGIVGEGHLFRTADG
ERRFDAGDQIVFLKNERSLGVKNGMIGHVVEAAANRIVATVGEGDRRRQVIVEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGTRSFSFNGGLAKVLSRRQAKETTLDYEHGQFY
REALRFAETRGLHVVQVARTMVRDRLDWTLRQKAKLVDLSRRLAAFAAHLGITQSPKTQTMKETAPMVAG
IKIFSGSVADTVGDRLGTDPALKQQWEEVSARFAYVFADPESAFRAINFDAVLADKEVANQVLRKIEVEP
ASIGPLKGKTDILATRSEREARRVAEVNVPALKRDLEQYLRMRETVTQRLQTDEQSLRQRVSIDIPALSP
GARVVLERVRDAIDRNDLPAAMAYAISNRETKLEIDGFNRAVTERFGERTLLSNSAREPSGKLYEKLSES
MKPEQKEQLKQAWPVMRTAQQLAAHERTVQSLRQAEEQRLTQRQTPVLKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(381-566)

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)


  Protein structure



No available structure.




T4CP

ID   2760 GenBank   WP_080830930
Name   traG_CFBP5499_RS27965_pAtCFBP5499b insolico UniProt ID   _
Length   646 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 646 a.a.        Molecular weight: 69204.28 Da        Isoelectric Point: 9.3374

>WP_080830930.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Agrobacterium]
MTANRLLLTILPAAIMIAALVMMSGLEHRLAALGTSAPARLALGRAGLVLPYVGAAAIGVVALFATHGST
NIKAAGLSVLAGSAVVVIIAMTREAIRLAAIASDVPAGQSVLAYADPATMLGAAVAFIGSVFALRVAIKG
NAAFAMAAPKRIGGKRAVHGEADWMKLPEAAKVFPEAGGIVIGERYRVDRDSVATMPFRSDEPQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVIEHRRKAGRKVIVLD
PTASGVGLNALDWIGRHGNTKEEDIVAVATWIMTDNAHTASARDDFFRASAMQLLTALIADVCLSGHTDE
KEQTLRQVRANLSEPEPKLRARLTKIYEGSDSDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYRNYA
GLVSGDSFSTDDLANGETDIFIALDLKVLEAHPGFARVVIGSLLNAIYNRNGDVKGRTLFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSTGMKGSSRSRSKQLNRRPLILPHEVLRMRADEQIVFTAGNAPLRCGRAVWFRREDMKACVG
ENRFHKNSSGTDSPGR

  Protein domains


Predicted by InterproScan.

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

(163-638)

  Protein structure



No available structure.



ID   2761 GenBank   WP_080831044
Name   t4cp2_CFBP5499_RS28360_pAtCFBP5499b 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: 91808.73 Da        Isoelectric Point: 6.0652

>WP_080831044.1 MULTISPECIES: conjugal transfer protein TrbE [Agrobacterium]
MVALKSFRHSGPSFADLVPYAGLVDNGVVLLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAVRVPTGDYPTEDASHFPDPVTRVIDAERRAHFQKERGHYESRHALILTWRPPEPRRSGLTR
YVYSDAGSRSATYADKAIETFLTSIREVEQYLANVVSIRRMMTRETPERGGHRVARYDELFQFIRFCITG
ENHPVRLPQIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFVF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMMMVAETEDAIAEASSQLVAYGYYTPVIVL
FDEDQSRLQEKCEAVRRLIQAEGFGARIETINATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSIWS
GSPIAPCPFYPVGSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLSLIAAQFRRYAGAQIFA
FDKGGSMLPLTLGLDGDHYQIGGDLGPSANGQARTLSFCPLAELSTDGDRAFASEWIEMLVALQGVTITP
DYRNAISRQIGLMAESRGRSISDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFEIEEL
MNMGERNLVPVLTYLFRRIEKRLTGVPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKRDYYVVSPEGRRLFDM
GLGPVALSFVGASGKEDLKRIRALHLEHGASWPLHWLQQRGIAHADTLFPTQ

  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: 147410..157095

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CFBP5499_RS28300 (CFBP5499_28300) 142446..143300 + 855 WP_080830805 alpha/beta hydrolase -
CFBP5499_RS28305 (CFBP5499_28305) 143424..143867 + 444 WP_080830803 PaaI family thioesterase -
CFBP5499_RS28310 (CFBP5499_28310) 144155..144988 - 834 WP_080830800 SDR family oxidoreductase -
CFBP5499_RS28315 (CFBP5499_28315) 145069..146487 - 1419 WP_137066522 coniferyl aldehyde dehydrogenase -
CFBP5499_RS28320 (CFBP5499_28320) 146582..147232 + 651 WP_080831087 TetR/AcrR family transcriptional regulator -
CFBP5499_RS28325 (CFBP5499_28325) 147410..148714 - 1305 WP_080831059 IncP-type conjugal transfer protein TrbI virB10
CFBP5499_RS28330 (CFBP5499_28330) 148726..149205 - 480 WP_080831056 conjugal transfer protein TrbH -
CFBP5499_RS28335 (CFBP5499_28335) 149205..150059 - 855 WP_137066524 P-type conjugative transfer protein TrbG virB9
CFBP5499_RS28340 (CFBP5499_28340) 150077..150739 - 663 WP_080831085 conjugal transfer protein TrbF virB8
CFBP5499_RS28345 (CFBP5499_28345) 150757..151947 - 1191 WP_080831051 P-type conjugative transfer protein TrbL virB6
CFBP5499_RS28350 (CFBP5499_28350) 151941..152174 - 234 WP_080831049 entry exclusion protein TrbK -
CFBP5499_RS28355 (CFBP5499_28355) 152171..152980 - 810 WP_080831047 P-type conjugative transfer protein TrbJ virB5
CFBP5499_RS28360 (CFBP5499_28360) 152952..155420 - 2469 WP_080831044 conjugal transfer protein TrbE virb4
CFBP5499_RS28365 (CFBP5499_28365) 155432..155731 - 300 WP_080831041 conjugal transfer protein TrbD virB3
CFBP5499_RS28370 (CFBP5499_28370) 155724..156134 - 411 WP_080831038 conjugal transfer pilin TrbC virB2
CFBP5499_RS28375 (CFBP5499_28375) 156124..157095 - 972 WP_080831036 P-type conjugative transfer ATPase TrbB virB11
CFBP5499_RS28380 (CFBP5499_28380) 157092..157727 - 636 WP_080831034 acyl-homoserine-lactone synthase -

Host bacterium

ID   4362 GenBank   NZ_CP039891
Plasmid name   pAtCFBP5499b Incompatibility group   -
Plasmid size   158104 bp Coordinate of oriT [Strand]   72613..72654 [+]
Host baterium   Agrobacterium tumefaciens strain CFBP5499

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA11a.5