Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106714
Name   oriT_pAtCFBP4996a in_silico
Organism   Agrobacterium leguminum strain CFBP4996
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP120213 (41445..41483 [+], 39 nt)
oriT length   39 nt
IRs (inverted repeats)      19..25, 27..33  (CGTCGCA..TGCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 39 nt

>oriT_pAtCFBP4996a
TCCAAGGGCGCAATTATACGTCGCAATGCGACGCGTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4437 GenBank   WP_080855500
Name   traA_CFBP4996_RS25765_pAtCFBP4996a 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: 123746.32 Da        Isoelectric Point: 9.9382

>WP_080855500.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Agrobacterium]
MAIAHFSASIVSRGSGRSVVLSAAYRHCARMEYEREARTIDYTRKQGLLHEEFVLPADAPQWARSLIADR
SVSSAVEAFWNRVEAFEKRTDAQLARDLTIALPLELSPEQNIALVRDFVEKHILAKGMVADWVFHDNPGN
PHIHLMTTLRPLTEDGFGSKKVAIIGDDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIELEPTIHLGVGAKAIERKAEQQGVRPELERIELNEQRRSENTRRILRNPGIVLEL
ITREKSVFDERDIAKVLHRYVDDPTVFQQLMLKIILNPDVLRLQRDTIDFATGEKVPARYSTRAMIRLEA
TMARHAMWLSNRAGHGVSEAALDATFRRHQRLSDEQKVAIERIAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIVSRTLASWELRWDRGRDVLDSKTVFVMDEAGMVASKQMAGFID
AVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALNAYG
ANAKITGERLKDEAVTSLIRDWNHSYDPTKTTLILAHLRRDVRMLNVMARKKLVERGIVGEGHLFKTADG
IRQFDVGDQIVFLKNEGSLGVKNGMIGHVVEAVPNRIVAVVGEGEHRRQIVVEQRFFSNLDHGYATTIHK
SQGTTVDRVKVLASLSLDRHLTYVAMTRHREDLHLYYGTRSFAFNGGLSKVLSRRNAKETTLDYDRGKLY
REALRFAENRGLHIVQVARTLLRDRLDWTLRQKAKLTDLGQRLAVFTERFGLAQSPKTQTMKEAEPMVAG
IKTFSDSAADTVGDQLGADPALRRQWEEVSTRFRYVFADPETAFRSMNFDVVLADKQAANQVLQKLEAEP
ASIGPLNGKTGILASKADREARRIAEVNAPALKRDLEQYLRMRETVEQRLQTDEQALRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAAMAYALSNRETKVEIDGFNQAVTERFGERTLLPNAAREPSGKLYEKLSEG
MKHEQKEQLKRAWPVMRTAQQLAAHERTVQSLKLAEEQRLTQRQTPVLKQ

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

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

(856-951)

AAA domain (AAA_30)

(382-566)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   4467 GenBank   WP_080855497
Name   traG_CFBP4996_RS25750_pAtCFBP4996a insolico UniProt ID   _
Length   647 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 647 a.a.        Molecular weight: 69270.24 Da        Isoelectric Point: 8.3233

>WP_080855497.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Agrobacterium]
MTANRLLLLTLPAAIMLAAMVMTSGMEHRLAAFGTSVQAKLLLERAGLALPYVTAAAIGVIALFAANGSG
NIKAAGLSVLAGSGVTIIIAIVREAIRLTGIAANVPAGQSVLAYVDPATAIGAGIAFMGGVFALRVAISG
NAAFATTAPKRIGGKRAVHGEADWMKMQEARKLFPDAGGIVIGELYRVDKESVAAMPFRADEKQSWGVGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVSEHRRQAGRKVIVLD
PTASGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNPRTASAREDFFRASAMQLLTALIADVCLSGHTEE
EDQTLRQVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTEALADGGVDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGDVKDRTLFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSLGQMREAYGGRDATSKWFESASWISFSAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSKQLSRRPLILPHEVLRMRSDEQIVFTSGNPPLRCGRAIWFRRDDMKSCVG
ENRFHPAASSATAAAEQ

  Protein domains


Predicted by InterproScan.

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

(163-638)

  Protein structure



No available structure.



ID   4468 GenBank   WP_080855459
Name   t4cp2_CFBP4996_RS26130_pAtCFBP4996a 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: 91978.06 Da        Isoelectric Point: 5.9943

>WP_080855459.1 MULTISPECIES: conjugal transfer protein TrbE [Agrobacterium]
MVALKSFRHSWPSFADLVPYAGLVDDGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAVRVPTADYPQASDGHFPDLVTRAIDAERRAHFQKERGHFESRHALILTWRPPEPRRSGLTR
YIYSDTASRSATYADKALESFLSSIREVEQYLANVMSIRRMMTRETSERGGFRVARYDELFQFIRFCVTG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLIENRFLGVVAIDGLPAESWPGILNALDLMPLTYRWSSRFVF
LDAEEARAKLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMMMVAETEDAIAKASSQLVAYGYYTPVIVL
FDEDQARLQEKCEAIRRLIQAEGFAARIETLNATDAFLGSLPGLSYANIREPLINTRNLADLIPLNSVWS
GSPVAPCPFYPTGSPPLMQVVSGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLSLIAAQFRRYAGAQIFA
FDKGGSMLPLTLGIDGDHYQIGGDATGEREGRVLSFCPLAELYTEGDRAFAAEWIEMLVALQGVTITPDY
RNAISRQVGLMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGTFQCFEIEELMN
MGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDA
ERSGIIDVLKESCPTKICLPNGSAREPGTREFYERIGFNERQIEIVATAIPKRDYYVVSPEGRRLFDMAL
GPVALSFVGASGKEDLKRIRSLHSEHGANWPLHWLQQRGIAHADKLFPVE

  Protein domains


Predicted by InterproScan.

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

(186-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 121555..131208

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CFBP4996_RS26085 (CFBP4996_26085) 117530..119269 - 1740 WP_080855543 hydantoinase B/oxoprolinase family protein -
CFBP4996_RS26090 (CFBP4996_26090) 119281..121317 - 2037 WP_080855451 hydantoinase/oxoprolinase family protein -
CFBP4996_RS26095 (CFBP4996_26095) 121555..122853 - 1299 WP_080855452 IncP-type conjugal transfer protein TrbI virB10
CFBP4996_RS26100 (CFBP4996_26100) 122865..123341 - 477 WP_080855453 conjugal transfer protein TrbH -
CFBP4996_RS26105 (CFBP4996_26105) 123338..124195 - 858 WP_080855454 P-type conjugative transfer protein TrbG virB9
CFBP4996_RS26110 (CFBP4996_26110) 124212..124874 - 663 WP_080855455 conjugal transfer protein TrbF virB8
CFBP4996_RS26115 (CFBP4996_26115) 124889..126079 - 1191 WP_080855456 P-type conjugative transfer protein TrbL virB6
CFBP4996_RS26120 (CFBP4996_26120) 126073..126300 - 228 WP_080855457 entry exclusion protein TrbK -
CFBP4996_RS26125 (CFBP4996_26125) 126297..127106 - 810 WP_080855458 P-type conjugative transfer protein TrbJ virB5
CFBP4996_RS26130 (CFBP4996_26130) 127078..129540 - 2463 WP_080855459 conjugal transfer protein TrbE virb4
CFBP4996_RS26135 (CFBP4996_26135) 129551..129850 - 300 WP_080855460 conjugal transfer protein TrbD virB3
CFBP4996_RS26140 (CFBP4996_26140) 129843..130247 - 405 WP_080855461 conjugal transfer pilin TrbC virB2
CFBP4996_RS26145 (CFBP4996_26145) 130237..131208 - 972 WP_080855462 P-type conjugative transfer ATPase TrbB virB11
CFBP4996_RS26150 (CFBP4996_26150) 131205..131843 - 639 WP_080855463 acyl-homoserine-lactone synthase -

Host bacterium

ID   7151 GenBank   NZ_CP120213
Plasmid name   pAtCFBP4996a Incompatibility group   -
Plasmid size   132201 bp Coordinate of oriT [Strand]   41445..41483 [+]
Host baterium   Agrobacterium leguminum strain CFBP4996

Cargo genes

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