Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103921
Name   oriT_pAtCFBP5499a in_silico
Organism   Agrobacterium tumefaciens strain CFBP5499
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039890 (287303..287344 [-], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      22..27, 31..36  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 42 nt

>oriT_pAtCFBP5499a
GGTTCCAAGGGCGCAATTATACGTCGCGATGCGACGCGTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2913 GenBank   WP_080830268
Name   traA_CFBP5499_RS26875_pAtCFBP5499a 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: 123908.74 Da        Isoelectric Point: 10.1327

>WP_080830268.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Agrobacterium]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFLLSDDAPKWVRSLVSDR
SVSGAVEAFWNKVEAFEKRADAQLARDLTIALPLELSAEQNITLVRDFVEKHILSKGMVADWVYHDNPGN
PHVHLMTTLRPLTEDGFGSKKVAVIGEDGQPVRTKSGKILYELWAGSTDDFNLLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIDLQATLHLGVGAKAIERKAESHGVRPELERIELNEQRRSENTRRIMRNPAIVLDL
IMREKSVFDERDIAKVLHRYVYDPAVFQQLMLKIILNPHVLRLQRDTIDFTTGDKLPARYSTRAMIRLEA
TMARQAMWLLNREGRGVFQSALDAAFRRHERLSDEQKVAIERVAGPARIAAVVGRAGAGKTTMMKVAREA
WELTGYRVVGGALAGKAAEGLEKEAGIVSRTLASWELRWNRGRDVLDDRTIFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELDTIYRQREDWMRKASLDLARGNVERALVAYQ
GQGRVLGSRLKSDAIANLIGDWNRDYDQTKAALILAHLRRDVRMLNVMAREKLVERGIVGVGHVFKTADG
ERRFDTGDQIVFLKNEGSLWLKNGMIGHVVEAQPNRIVAVVGEGDQQRQVIVEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGTRSFSFNGGLAKVLSRKNAKETTLDYERGQLY
REALRFSEARGLHIVQVARTLVRDRVDWTLRQKAKLVDLGRRLDAFAARLGFTRIPDTQTMKEAAPMVAG
IRTFSGSVADTVGDKLGADPALKRQWEEVSARFAYVFADPETAFRAMNLDAVLADKEMAKQVLRKLEIEP
ASIGPLNGKTGILATRSEREARRVAEVNVPALKRDLAHYLRMRETVNQRLQTDEQALRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAAMAYALRNRETKLEIDGFNQAVTQRFGERTLSSNAAREPSGKLYEQLSEG
MKSEQKEQLKQAWPVMRTAQQLAAHERTVRSLKVAEEQRLTQRQTPVLKQ

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(691-736)

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

(855-951)

AAA domain (AAA_30)

(382-565)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   2758 GenBank   WP_080830549
Name   t4cp2_CFBP5499_RS26540_pAtCFBP5499a insolico UniProt ID   _
Length   820 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 820 a.a.        Molecular weight: 91748.54 Da        Isoelectric Point: 5.4861

>WP_080830549.1 MULTISPECIES: conjugal transfer protein TrbE [Agrobacterium]
MVALKSFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAIRVPTGDYPTEEASHFPDPVTRAIDAERRAHFQKERGHYESRHALILTWRPPEPRRSGLTR
YVYSDVGSRSATYADKALETFLTSIREVEQYLGNVVSIRRMMTRETPERGGHRVARYDELFQFVRFCITG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARTRLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVL
FDEDQSRLQEKCEAVRRLIQAEGFGARIETINATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPVAPCPFYPAGSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLSLIAAQFRRYAGAQIFA
FDNGGSMLPLTLGIEGDHYQIGGDMPEEGEGRALSFCPLADLSSDADRAWASEWIEMLVALQGVTITPDY
RNAISRQIALMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFEIEELMN
MGERNLVPVLTYLFRRIEKRLTGSPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDA
ERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKRDYYVVSPEGRRLFDMAL
GPVALSFVGASGKEDLKRIRALHLEHGAAWPLYWLQQRGIAHADTLFPTQ

  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   2759 GenBank   WP_080830270
Name   traG_CFBP5499_RS26890_pAtCFBP5499a insolico UniProt ID   _
Length   641 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 641 a.a.        Molecular weight: 68603.44 Da        Isoelectric Point: 8.9952

>WP_080830270.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Agrobacterium]
MTANRTLLAVLPAIIMLVTMVLTSGLEHRLAALGTSPQAKLMLGRAGLALPYIAAAAIGVIALFAVNGSA
NIKTAGGSVLAGNAVTGAVAVVREIVRLAGIAGNVPAGQSVLAYSDPATMVGAAAALFSGIFALRIALKG
NAAFVASGPRRIGGKRAVHGEADWMKLPEAAKLFPEAGGIVIGERYRVDRDSVAAMPFRADDKKSWGGGG
KASLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGVVVLDPSSEVAPMVIEHRRTAGRKVIVLD
PTASDVGFNALDWIGRHGNTKEEDIVAVATWIMTDSARTASARDDFFTASAMQLLTALIADVCLSGHTDE
KEQTLRRVRANLSEPEPQLRARLTKIYEGSGSDFVKENVAVFVNMTPETFSGVYANAVKDTHWLSYPNYA
SLVSGDSFSTDDLADGETDIFIALDLKVLEAHPGLARLVIGSLLNAIYNRNGDVKGRTLFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSTGMKGSSRSRSKQLSRRPLILPHEVLRMRSDEQIVFSSGNPPLRCGRAIWFRRDDMKACVG
ENRFHRDEQSI

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 209147..218815

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CFBP5499_RS26505 (CFBP5499_26505) 204775..206007 + 1233 WP_080830543 CapA family protein -
CFBP5499_RS26510 (CFBP5499_26510) 206124..207419 + 1296 WP_080830544 peptidase T -
CFBP5499_RS26515 (CFBP5499_26515) 207424..208347 + 924 WP_130932601 citrulline utilization hydrolase CtlX -
CFBP5499_RS26520 (CFBP5499_26520) 208512..209150 + 639 WP_080830545 acyl-homoserine-lactone synthase TraI -
CFBP5499_RS26525 (CFBP5499_26525) 209147..210118 + 972 WP_080830546 P-type conjugative transfer ATPase TrbB virB11
CFBP5499_RS26530 (CFBP5499_26530) 210108..210518 + 411 WP_080830547 conjugal transfer pilin TrbC virB2
CFBP5499_RS26535 (CFBP5499_26535) 210511..210810 + 300 WP_080830548 conjugal transfer protein TrbD virB3
CFBP5499_RS26540 (CFBP5499_26540) 210822..213284 + 2463 WP_080830549 conjugal transfer protein TrbE virb4
CFBP5499_RS26545 (CFBP5499_26545) 213256..214065 + 810 WP_080830550 P-type conjugative transfer protein TrbJ virB5
CFBP5499_RS26550 (CFBP5499_26550) 214062..214289 + 228 WP_080830551 entry exclusion protein TrbK -
CFBP5499_RS26555 (CFBP5499_26555) 214283..215473 + 1191 WP_080830552 P-type conjugative transfer protein TrbL virB6
CFBP5499_RS26560 (CFBP5499_26560) 215489..216151 + 663 WP_080830553 conjugal transfer protein TrbF virB8
CFBP5499_RS26565 (CFBP5499_26565) 216169..217020 + 852 WP_080830634 P-type conjugative transfer protein TrbG virB9
CFBP5499_RS26570 (CFBP5499_26570) 217020..217499 + 480 WP_080830554 conjugal transfer protein TrbH -
CFBP5499_RS26575 (CFBP5499_26575) 217511..218815 + 1305 WP_080830555 IncP-type conjugal transfer protein TrbI virB10
CFBP5499_RS26580 (CFBP5499_26580) 219083..219769 + 687 WP_080830556 HAD family phosphatase -
CFBP5499_RS26585 (CFBP5499_26585) 220135..220680 + 546 WP_080830557 GXWXG domain-containing protein -
CFBP5499_RS26590 (CFBP5499_26590) 220731..221684 + 954 WP_080830558 sensor domain-containing diguanylate cyclase -
CFBP5499_RS26595 (CFBP5499_26595) 221876..222580 + 705 WP_080830635 transcriptional regulator TraR -

Host bacterium

ID   4361 GenBank   NZ_CP039890
Plasmid name   pAtCFBP5499a Incompatibility group   -
Plasmid size   438854 bp Coordinate of oriT [Strand]   287303..287344 [-]
Host baterium   Agrobacterium tumefaciens strain CFBP5499

Cargo genes

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