Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121232
Name   oriT_pAt12D1 in_silico
Organism   Agrobacterium tumefaciens strain 12D1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP033033 (93659..93698 [+], 40 nt)
oriT length   40 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGT..ACGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 40 nt

>oriT_pAt12D1
TCCAAGGGCGCAATTATACGTCGTTGACACGACGCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13410 GenBank   WP_080868287
Name   traA_At12D1_RS25890_pAt12D1 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: 123701.43 Da        Isoelectric Point: 9.9751

>WP_080868287.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLVHEEFLLPSDAPKWVRAMIADR
SVAGASEAFWNKVEVFERRSDAQLARDLTIALPLELTPEQNIALVRDFVDKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLTEDGFGAKKVAVTAKDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIDLEPAIHLGVGAKAMERKAQEQGFRPELERLELNEERRGENARRILRRPEIVLDL
IMREKSVFDERDVAKVLNRYIDDPAVFQQLMLRIILNPEVLRLQRDTIDFSTGEKVPARYSTRAMIRLEA
TMVRQATWLSGKDTHAVSAAVLDATLRRHERLSEEQKTAIERIAGPARIAAVVGRAGAGKTTMMKAVREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNRGRDVLDSKTVFVMDEAGMVASKQMAGFVN
TAVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
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)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

AAA domain (AAA_30)

(382-567)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   15712 GenBank   WP_080868284
Name   traG_At12D1_RS25875_pAt12D1 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: 69140.26 Da        Isoelectric Point: 9.4836

>WP_080868284.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MTVNRLLLLILPAIIMLAAMFATSGTEQRLAAFGTSPQAKLMLGRAGLALPYIAAVAIGIIGLFAANGSA
NIKAAGLSVLAGNGVVITIATLREVIRLNSIASGVPAEQSVLAFADPVTMIGVGIAFISGMFALRVAIKG
NAAFATTAPKRIGGKRAVHGEADWMKIQEAAKLFPEPSGIVIGERYRVDRDSVAAMPFRADDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVYEHRRQAGRKVIVLD
PTAGGVGFNALDWIGRHGSTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTEA
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNVKGRTLFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSIGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSRQLSRRPLILPHEVLRMRADEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
TNRFHREEKTP

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   15713 GenBank   WP_080868325
Name   t4cp2_At12D1_RS26185_pAt12D1 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: 149377..159047

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
At12D1_RS26125 (At12D1_50350) 144897..145622 - 726 WP_080868320 nopaline ABC transporter permease NocM -
At12D1_RS26130 (At12D1_50360) 145624..146334 - 711 WP_080868351 nopaline ABC transporter permease NocQ -
At12D1_RS26135 (At12D1_50370) 146407..147258 - 852 WP_003523898 nopaline ABC transporter substrate-binding protein NocT -
At12D1_RS26140 (At12D1_50380) 147323..148096 - 774 WP_080868321 nopaline ABC transporter ATP-binding protein NocP -
At12D1_RS26145 (At12D1_50390) 148346..149248 + 903 WP_045023359 LysR family transcriptional regulator -
At12D1_RS26150 (At12D1_50410) 149377..150684 - 1308 WP_080868322 IncP-type conjugal transfer protein TrbI virB10
At12D1_RS26155 (At12D1_50420) 150699..151175 - 477 WP_045025162 conjugal transfer protein TrbH -
At12D1_RS26160 (At12D1_50430) 151175..152029 - 855 WP_070167554 P-type conjugative transfer protein TrbG virB9
At12D1_RS26165 (At12D1_50440) 152047..152709 - 663 WP_080868323 conjugal transfer protein TrbF virB8
At12D1_RS26170 (At12D1_50450) 152716..153918 - 1203 WP_080868324 P-type conjugative transfer protein TrbL virB6
At12D1_RS26175 (At12D1_50460) 153912..154130 - 219 WP_070167519 entry exclusion protein TrbK -
At12D1_RS26180 (At12D1_50470) 154127..154936 - 810 WP_070167518 P-type conjugative transfer protein TrbJ virB5
At12D1_RS26185 (At12D1_50480) 154908..157376 - 2469 WP_080868325 conjugal transfer protein TrbE virb4
At12D1_RS26190 (At12D1_50490) 157387..157686 - 300 WP_080868326 conjugal transfer protein TrbD virB3
At12D1_RS26195 (At12D1_50500) 157679..158086 - 408 WP_080868327 conjugal transfer pilin TrbC virB2
At12D1_RS26200 (At12D1_50510) 158076..159047 - 972 WP_080868328 P-type conjugative transfer ATPase TrbB virB11
At12D1_RS26205 (At12D1_50520) 159044..159679 - 636 WP_041723972 acyl-homoserine-lactone synthase -

Host bacterium

ID   21660 GenBank   NZ_CP033033
Plasmid name   pAt12D1 Incompatibility group   -
Plasmid size   160006 bp Coordinate of oriT [Strand]   93659..93698 [+]
Host baterium   Agrobacterium tumefaciens strain 12D1

Cargo genes

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