Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116295
Name   oriT_pAt2 in_silico
Organism   Agrobacterium tumefaciens strain Gle002
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP048568 (69001..69040 [+], 40 nt)
oriT length   40 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 40 nt

>oriT_pAt2
TCCAAGGGCGCAATTATACGTCGCTGACACGACGCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10419 GenBank   WP_174113225
Name   traA_FY133_RS27100_pAt2 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: 123770.52 Da        Isoelectric Point: 9.9361

>WP_174113225.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Agrobacterium]
MAIAHFSASIVSRGGGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPIDAPKWARAMIADR
SVSGAVEAFWNKVEDFEKRSDAQLARDLTIALPLELTPEQNIALVRDFVEKHIHAKGMVADWVYHNNPGN
PHIHLMTTLRPLTEDGFGAKKVAVTAKDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIDLEPAIHLGVGAKAIERKAQEQGFRPELERLELNEERRGENARRILRRPEIVLDL
IMREKSVFDERDVAKVLHRYIDDPAVFQQLMLRIILNPEVLRLQRDTIDFSTGEKVPARYSTRAMIRLEA
TMVRQATWLSGKDTHAVSAAVLDATLRRHERLSEEQKTAIERIAGPARIAAVVGRAGAGKTTMMKAVREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNRGRDVLDSKTIFVMDEAGMVASKQMAGFVD
TVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
ANVRITGTRLKAEAVERLIGDWNHDYDHTKTTLILAHLRRDVRMLNQMAREKLVERGIVGEGHVFKTADG
IRQFDAGDQIVFLKNEGSLGVKNGMIAHIIEAAPNRIVAVIGEGDQRRRVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGRRSFAFNGGLSKVLSRKNAKETTLDYERGSLY
REALRYAENRGLNIVQVARTLLRDQLDWTLRQKTRLDELGQRLAVFAERLGLHHPPKTQTMKEAAPMVAG
IKTFPGSVADTVGDRLGTDPALKRQWEEVSTRFAYVFADPETAFRAMNFDAVLADKDSALQVLQKLEAEP
ASIGPLKGKTGILASKTDREDRRIAELNVPALKRDLEQYLRMRENAAQRLQTDEQALRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAALGYVLSNRETKLEIDGFSKAVTERFGERTLLTNAARQPSGPLFDKLSNG
MRPAQKEQLKEAWPVMRTAQQIAAHERTTQTLKQAEELRLTQRQSPVMKQ

  Protein domains


Predicted by InterproScan.

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

(855-951)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

AAA domain (AAA_30)

(382-567)


  Protein structure



No available structure.




T4CP

ID   12164 GenBank   WP_153517022
Name   traG_FY133_RS27085_pAt2 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: 69244.33 Da        Isoelectric Point: 9.4596

>WP_153517022.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Agrobacterium]
MTVNRLLLLILPAIIMLAAMFATSGTEQRLAAFGTSPQAKLMLGRAGLALPYIAAVAIGLIGLFAANGSA
NIKAAGLSVLAGNGVVITIATLREVIRLNSITSRVPAEQSVLAYADPVTMIGVGIAFISGMFALRVAIKG
NAAFATTAPKRIGGKRAVHGEADWMKIQEAAKLFPEPGGIVIGERYRVDRDSVATMPFRADDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVYEHRRQAGRKVIVLD
PTAGGVGFNALDWIGRHGSTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTEA
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGDVKGRTLFLLDEVARLGY
LRILETARDAGRKYGTTLTMIFQSIGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSRQLSRRPLILPHEVLRMRADEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
TNRFHREEKAP

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   12165 GenBank   WP_080868325
Name   t4cp2_FY133_RS27435_pAt2 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: 137949..147619

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FY133_RS27375 (FY133_27150) 133469..134194 - 726 WP_080868320 nopaline ABC transporter permease NocM -
FY133_RS27380 (FY133_27155) 134196..134906 - 711 WP_080868351 nopaline ABC transporter permease NocQ -
FY133_RS27385 (FY133_27160) 134979..135830 - 852 WP_003523898 nopaline ABC transporter substrate-binding protein NocT -
FY133_RS27390 (FY133_27165) 135895..136668 - 774 WP_080868321 nopaline ABC transporter ATP-binding protein NocP -
FY133_RS27395 (FY133_27170) 136918..137820 + 903 WP_045023359 LysR family transcriptional regulator -
FY133_RS27400 (FY133_27175) 137949..139256 - 1308 WP_080868322 IncP-type conjugal transfer protein TrbI virB10
FY133_RS27405 (FY133_27180) 139271..139747 - 477 WP_045025162 conjugal transfer protein TrbH -
FY133_RS27410 (FY133_27185) 139747..140601 - 855 WP_070167554 P-type conjugative transfer protein TrbG virB9
FY133_RS27415 (FY133_27190) 140619..141281 - 663 WP_080868323 conjugal transfer protein TrbF virB8
FY133_RS27420 (FY133_27195) 141288..142490 - 1203 WP_080868324 P-type conjugative transfer protein TrbL virB6
FY133_RS27425 (FY133_27200) 142484..142702 - 219 WP_070167519 entry exclusion protein TrbK -
FY133_RS27430 (FY133_27205) 142699..143508 - 810 WP_070167518 P-type conjugative transfer protein TrbJ virB5
FY133_RS27435 (FY133_27210) 143480..145948 - 2469 WP_080868325 conjugal transfer protein TrbE virb4
FY133_RS27440 (FY133_27215) 145959..146258 - 300 WP_080868326 conjugal transfer protein TrbD virB3
FY133_RS27445 (FY133_27220) 146251..146658 - 408 WP_080868327 conjugal transfer pilin TrbC virB2
FY133_RS27450 (FY133_27225) 146648..147619 - 972 WP_080868328 P-type conjugative transfer ATPase TrbB virB11
FY133_RS27455 (FY133_27230) 147616..148251 - 636 WP_041723972 acyl-homoserine-lactone synthase -

Host bacterium

ID   16728 GenBank   NZ_CP048568
Plasmid name   pAt2 Incompatibility group   -
Plasmid size   148616 bp Coordinate of oriT [Strand]   69001..69040 [+]
Host baterium   Agrobacterium tumefaciens strain Gle002

Cargo genes

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