Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116313
Name   oriT_pAt2 in_silico
Organism   Agrobacterium fabrum strain Kin001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP048562 (194865..194900 [+], 36 nt)
oriT length   36 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: 36 nt

>oriT_pAt2
GGTTCCAAGGGCGCAATTATACGTCGCGATGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10424 GenBank   WP_262519129
Name   traA_FY134_RS27030_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: 123746.27 Da        Isoelectric Point: 9.8726

>WP_262519129.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium fabrum]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPADAPKWVRSLIADR
SVAGASEVFWNKVEAFEKRSDAQLARDLTIALPLELSAEQNIALVRDFVEKNVLAKGMVADWVFHDNPGN
PHIHLMTTLRPLTENGFGSKKTAVIAEDGQPVRTKTGKILYELWAGSTEDFNVLRDGWFERLNHHLALDG
IDLRIDGRSYEKQGIDLEPTIHLGVGAKAIERKAEEQGIRPELERIELNEQRRAENTRRILKNPTIVLDL
ITREKSVFDERDVAKILHRYIDDPAVFQQLLIRIILNPDVLRLQRETIDFATGEKLPARYSTRAMIRLEA
TMARHSVWLSSQEGRGVSDTVLDATFRRHERLSEEQKAAIERIAGPTRIAAVVGRAGAGKTTMMKAAREA
WERAGYRVVGGALAGKAAEGLDKQAGIQSRTLASWELRWGSGRDVLDDKTVFVMDEAGMVASKQLAGFVD
AVVRTGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMREASLDLARGNVEKALAAYD
ANVRITGTRLKAEAVETLIADWNHDYDQTKTTLILAHLRRDVRMLNIMAREKLVERGIVGDGHVFKTADG
VRQFDAGDQIVFLKNEGSLGVKNGMIAHVVEAAPNRIVAMIGEGDQRRQVTVEQRFYSNLDHGYATTIHK
SQGTTVDKVKVLASLSLDRHLTYVALTRHREDLQLYFGQRSFAYRGGLSKVLSRKNAKETTLDYERGTLY
RQALQFAENRGLHIMQVARTLVRDRLDWKLRQKNRLADLIRRLRALGERLGLQQSRNTQTMKEAAPMVAG
IKTFPGSVADTVGDRLGADPALKQQWEEVSARFRYVFADPETAFRAMNFDDVLANKEIARHALQKVETDP
ASIGPLKGKTGILASKADREARRVAGVNVPALKRDLEQYLRMRETAAQKLQMEEQVMRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAAMGYALSNRETKQEIDGFNQAITERFGERTLLANTAREPSGKLYEKLSEG
MKPEQKEQLKEAWPVMRTAQQLAAHERTTQTLKQVEELRLTQRQSSVMKQ

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

AAA domain (AAA_30)

(382-567)

MobA/MobL family (MobA_MobL)

(17-243)

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

(855-951)


  Protein structure



No available structure.




T4CP

ID   12171 GenBank   WP_262519127
Name   traG_FY134_RS27015_pAt2 insolico UniProt ID   _
Length   638 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 638 a.a.        Molecular weight: 68546.72 Da        Isoelectric Point: 9.6974

>WP_262519127.1 Ti-type conjugative transfer system protein TraG [Agrobacterium fabrum]
MTANKLLLLILPAAIMVAAMAMTSGMEHRLAALGANPQARLIFGRAGLALPYVAAAAIGVMALFATNGSA
NIKAAAASVLAGSGAVIVVAILREAIRLKGIARDVPAGQSVLAYADPATMIGAGIAFVSGVFALRVAIKG
NAAFAAGGPRRIGGKRAVHGEADWMKMAEAAKLFPEPGGIVIGERYRVDRDSVAAMPFRANEPPSWGAGG
KSSLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVVEHRRRAGRKVIVLD
PAVQGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNARSASARDDFFRASAMQLLTALIADVCLSGHTDE
EDQTLRRVRKNLSEPEPQLRARLTKIYEQSESDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGDRFSTDDLAKGGTDIFIALDLKVLEAHPGLARVMIGSLLNAIYNRNGDVNGRTLFLLDEVARLGY
LRILETARDAGRKYGITLALIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSKQLSRRPLILPHEVLRMRADEQIVFTSGNAPLRCGRAIWFRRDEMKACVG
ENRFHLKE

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   12172 GenBank   WP_262519161
Name   t4cp2_FY134_RS27260_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: 91666.49 Da        Isoelectric Point: 5.8090

>WP_262519161.1 conjugal transfer protein TrbE [Agrobacterium fabrum]
MVALNSFRHSGPSFADLMPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAIRVPTGDYPTAADSHFPDPVTRAIDAERRAHFQTERGHFESRHALILTWRPPEPRRSGLIR
YIYADAASRSAGYADTTLRSFLSSIREAEQYLANVVSIRRMMTRETSDRGGFRIARYDELFQFIRFCVTG
ENHPVRLPDIPMYLDWLVAAELQHGLTPMVENRFLGVVAIDGLPAESWPGILNTLDRMPLTYRWSSRFVF
LDAEEARSRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVL
FEQDQASLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPNAPCPYYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYADARVFA
FDKGGSMLPLTLGLNGDHYQIGGEIGSSVSGEMTALAFCPLAELSTDGDRAWATGWIEMLVTLQGVTITP
DYRNAISRQLALMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFEVEEL
MSMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNDRQIEIVATSIPKREYYVVSPEGRRLFNM
ALGPVALSFVGATGKEDLKQIRSLHSEHGAMWPLNWLQQRGIANAETLFPTY

  Protein domains


Predicted by InterproScan.

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

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 237747..247433

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FY134_RS27205 (FY134_27035) 233637..235085 - 1449 WP_262519153 APC family permease -
FY134_RS27210 (FY134_27040) 235211..236239 + 1029 WP_262519154 AraC family transcriptional regulator -
FY134_RS27930 236342..236575 - 234 WP_316963341 helix-turn-helix domain-containing protein -
FY134_RS27935 236627..237085 - 459 WP_316963336 DJ-1/PfpI family protein -
FY134_RS27220 (FY134_27050) 237298..237495 + 198 WP_316963337 hypothetical protein -
FY134_RS27225 (FY134_27055) 237747..239069 - 1323 WP_262519155 IncP-type conjugal transfer protein TrbI virB10
FY134_RS27230 (FY134_27060) 239081..239557 - 477 WP_262519156 conjugal transfer protein TrbH -
FY134_RS27235 (FY134_27065) 239557..240411 - 855 WP_262519279 P-type conjugative transfer protein TrbG virB9
FY134_RS27240 (FY134_27070) 240429..241091 - 663 WP_262519157 conjugal transfer protein TrbF virB8
FY134_RS27245 (FY134_27075) 241109..242299 - 1191 WP_262519158 P-type conjugative transfer protein TrbL virB6
FY134_RS27250 (FY134_27080) 242293..242520 - 228 WP_262519159 entry exclusion protein TrbK -
FY134_RS27255 (FY134_27085) 242517..243326 - 810 WP_262519160 P-type conjugative transfer protein TrbJ virB5
FY134_RS27260 (FY134_27090) 243298..245766 - 2469 WP_262519161 conjugal transfer protein TrbE virb4
FY134_RS27265 (FY134_27095) 245776..246075 - 300 WP_262519162 conjugal transfer protein TrbD virB3
FY134_RS27270 (FY134_27100) 246068..246472 - 405 WP_262519163 conjugal transfer pilin TrbC virB2
FY134_RS27275 (FY134_27105) 246462..247433 - 972 WP_262519164 P-type conjugative transfer ATPase TrbB virB11
FY134_RS27280 (FY134_27110) 247430..248068 - 639 WP_262519165 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   16746 GenBank   NZ_CP048562
Plasmid name   pAt2 Incompatibility group   -
Plasmid size   248434 bp Coordinate of oriT [Strand]   194865..194900 [+]
Host baterium   Agrobacterium fabrum strain Kin001

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11