Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103927
Name   oriT_pAtCFBP7129c in_silico
Organism   Agrobacterium tumefaciens strain CFBP7129
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039926 (88179..88222 [+], 44 nt)
oriT length   44 nt
IRs (inverted repeats)      21..27, 32..38  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 44 nt

>oriT_pAtCFBP7129c
GGTTCCAAGGGCGCAATTATACGTCGCTGATGCGACGTGCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2919 GenBank   WP_137006627
Name   traA_CFBP7129_RS30120_pAtCFBP7129c 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: 123772.49 Da        Isoelectric Point: 10.0583

>WP_137006627.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAIAHFSASIVSRGGGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLVHEEFMLPADAPKWVRAMIADR
SVAGASEAFWNKVEAFEKRADAQLARDLTIALPLELPAEQNIALVRDFVEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLTGDGFGTKKVAVIGEDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIDLEPTIHLGVGAKAIERKAKEQGIRPELERIELNEDRRSENARRILRRPEIVLDL
ITREKSVFDERDVAKVLHRYVDDPALFQQLMLRIILNPEVLRLQRDTIDFSTGQKVPARYSTRAMIRLEA
TMVRQTTWLSGKETHAVSASVLDTTFQRHARLSEEQKTAIERIAGPTRIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIHSRTLASWELRWNRGRDVLDRKTVFVMDEAGMVASKQMARFVD
TAVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASRDLARGDVEKALTAYD
ANVRITGTRLKAEAVERLIGDWNHDYDQTKTTLILAHLRRDVRMLNVMAREKLVERGIVGEGHVFKTPDG
IRQFEAGDQIVFLKNETSLGVKNGMIAHVIEAAPSRIVAVVGEGDQRRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGRRSFAFNGGLAKVLSRKNAKETTLDYERGKLY
REALRFAESRGLNIVQVARTLVRDRLNWTLRQKTKLVDLGQRLAVFAERLGLHYPPKTHKLKEAAPMVAG
IKTFSGSVADTVGDKLGADLALKQQWEEVSARFAYVFADPETAFRAMNFDNVLADKDSARQALQKLEAEP
TSIGALKGKTGILASKTEREARRIAELNVPALKRDLEQYLRMRETASQRLQADEQALRQRVSIDIPALST
AARVVLERVRDAIDRNDLPAAMGYALSNRETKQEIDGFNQAITERFGERTLLTNPARQPSGTLFDKLSEG
MQPEQKERLKEAWPVMRTAQQIAAHERTTQTLNQAEELRLTQRQSTVMKQ

  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)

(382-567)


  Protein structure



No available structure.




T4CP

ID   2768 GenBank   WP_137006625
Name   traG_CFBP7129_RS30105_pAtCFBP7129c insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 71042.40 Da        Isoelectric Point: 9.0768

>WP_137006625.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens complex]
MTMNRLLLLILPAIIMLAAMFATSGMEQRLAAFGTSPQAKLMLGRAGLALPYIAAVAIGIIGLFAANGSA
NIKAAGLSVLAGSGVVITIATLCEVIRLNSIASSVPAEQSVLAYADPVTMIGASIAFISGMFALRVAIKG
NAAFATTAPKRIGGKRAVHGEADWMKIQEAAKLFPERGGIIIGERYRVDRDSVAAMPFRADDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVCEHRRQAGRKVIVLD
PTAGGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTEA
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNVKGRTLFLLDEVARLGY
LRILETARDAGRKYGIMLTMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSTGMKGSSRSRSKQLSRRPLILPHEVLRMRSDEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
ENRFHRTGTGTDTHTEHAPPWQKEGTRP

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   2769 GenBank   WP_080868325
Name   t4cp2_CFBP7129_RS30410_pAtCFBP7129c 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: 92115.82 Da        Isoelectric Point: 5.6807

>WP_080868325.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium/Agrobacterium group]
MVALKLFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDSERNEVSRQINMIMSRLG
SGWMVQVEALRVPTIDYPVGDTCHFPDPVTRAIDTERRSHFERESGHFESRHALILTWRPPEPRRSGLAR
YVYSDTASRSATYADTALDSFRTSIREFEQYLANVVSIRRMVTRETEERGGFRVARYDELFQFIRFCITG
ENHPVRLPDIPMYLDWLVTAELQHGLTPTVENRFLGVVAIDGLAAESWPGILNSLDLMPLTYRWSSRFVF
LDEQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMMMVAETEDAIAEASSQLVAYGYYTPVILL
FDEQQERLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLVNTRNLADLIPLNSVWS
GSPVAPCPFYPPGSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLSLIAAQFRRYADAQIFA
FDKGRSMLPLTRAIGGDHYEIGGDTAEGGEGASPQLAFCPLAELASDSDRAWAAEWIETLVALQGVTVTP
DYRNAISRQLGLMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLALGAFQCFEVEEL
MNMGERNLVPVLLYMFRRVEKRLTGAPSLIILDEAWLMLGHPTFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVASPEGRRLFDM
SLGPVALSFVGASGKEDLKRIRALHFQHGADWPKHWLQQRGIAHAETLFQAA

  Protein domains


Predicted by InterproScan.

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

(188-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 144997..154665

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CFBP7129_RS30350 (CFBP7129_30350) 140517..141242 - 726 WP_080868320 nopaline ABC transporter permease NocM -
CFBP7129_RS30355 (CFBP7129_30355) 141244..141954 - 711 WP_045025159 nopaline ABC transporter permease NocQ -
CFBP7129_RS30360 (CFBP7129_30360) 142027..142878 - 852 WP_003523898 nopaline ABC transporter substrate-binding protein NocT -
CFBP7129_RS30365 (CFBP7129_30365) 142943..143716 - 774 WP_080868321 nopaline ABC transporter ATP-binding protein NocP -
CFBP7129_RS30370 (CFBP7129_30370) 143966..144868 + 903 WP_137006652 LysR family transcriptional regulator -
CFBP7129_RS30375 (CFBP7129_30375) 144997..146304 - 1308 WP_137006653 IncP-type conjugal transfer protein TrbI virB10
CFBP7129_RS30380 (CFBP7129_30380) 146317..146793 - 477 WP_137006654 conjugal transfer protein TrbH -
CFBP7129_RS30385 (CFBP7129_30385) 146793..147647 - 855 WP_070167554 P-type conjugative transfer protein TrbG virB9
CFBP7129_RS30390 (CFBP7129_30390) 147665..148327 - 663 WP_080868323 conjugal transfer protein TrbF virB8
CFBP7129_RS30395 (CFBP7129_30395) 148334..149536 - 1203 WP_080868324 P-type conjugative transfer protein TrbL virB6
CFBP7129_RS30400 (CFBP7129_30400) 149530..149748 - 219 WP_070167519 entry exclusion protein TrbK -
CFBP7129_RS30405 (CFBP7129_30405) 149745..150554 - 810 WP_070167518 P-type conjugative transfer protein TrbJ virB5
CFBP7129_RS30410 (CFBP7129_30410) 150526..152994 - 2469 WP_080868325 conjugal transfer protein TrbE virb4
CFBP7129_RS30415 (CFBP7129_30415) 153005..153304 - 300 WP_080868326 conjugal transfer protein TrbD virB3
CFBP7129_RS30420 (CFBP7129_30420) 153297..153704 - 408 WP_137006655 conjugal transfer pilin TrbC virB2
CFBP7129_RS30425 (CFBP7129_30425) 153694..154665 - 972 WP_080868328 P-type conjugative transfer ATPase TrbB virB11
CFBP7129_RS30430 (CFBP7129_30430) 154662..155297 - 636 WP_137006656 acyl-homoserine-lactone synthase -

Host bacterium

ID   4367 GenBank   NZ_CP039926
Plasmid name   pAtCFBP7129c Incompatibility group   -
Plasmid size   155663 bp Coordinate of oriT [Strand]   88179..88222 [+]
Host baterium   Agrobacterium tumefaciens strain CFBP7129

Cargo genes

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