Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118334
Name   oriT_pAvF25d in_silico
Organism   Agrobacterium vitis strain F2/5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055273 (54700..54742 [+], 43 nt)
oriT length   43 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: 43 nt

>oriT_pAvF25d
GGATCCAAGGGCGCAATTATACGTCGCGATGCGACGCCTTGCG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11644 GenBank   WP_174113338
Name   traA_AVF2S5_RS25900_pAvF25d 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: 123251.84 Da        Isoelectric Point: 9.8308

>WP_174113338.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium vitis]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEYEREARTIDYTRKHGLLHEEFVLPTDAPKWVRSLIADR
SVSGAVEAFWNRVEAFEKRSDAQLARDLTIALPLELSPEQNIALVRDFVEKHILAKGMIADWVYHDNPGN
PHIHLLTTLRPLTEDGFGSKKVVIIGEDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIELEPTIHLGVGAKAIERKAEQQGVRPELERIELNEERRSENTRRILRNPAIVLDL
ITREKSVFDERDVAKVLHRYVDDPAVFQQLMLRIILNPEVLRLQRDTIDFATGEKVPARYSTRAMIRLET
TMARQAMWLSNRAGHGVSEAALDATFRRHQRLSDEQKTAIERIAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNCGRDVLDNRCVFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYG
ANAKITGERLKDEVVKSLITDWNHSYDPKKTTLILAHLRRDVGMLNVMAREKLVERGIVGEGHSFITADG
IRQFDAGDQIVFLKNEGSLGVKNGMIGHVVEAAPNRIVAATGEGEHRRHVVVEQHFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGSRSFSFNGGLAKVLSRKNAKETTLDYERGQFY
REALRFAEARGLHIARVARTLVRDRLDWTLRQKSRLVDLGQRLTAFAARLGFTQSPETQTMKEAAPMVAG
IKTFAGSVADTVGDKLGSDPALKRQWEEVSARFAYVFADPEAAFRSMHFDTVLADKEMAKQVLRKLEVEP
ASIGPLKGKTGILASNADREARRVAEVNVPALKRDLEQYLRMRETIAQKLQTAEQAQRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAAMAYALSNRETKLEIDGFNQAVTERFGERTLLSNAARVPSGRLYEKLAEG
MKPEQKEQLKQAWPVMRTAQQLAAHERTVQSLKLAEEHRLTQRQTPVLKQ

  Protein domains


Predicted by InterproScan.

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

(855-951)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(678-736)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-566)


  Protein structure



No available structure.




T4CP

ID   13628 GenBank   WP_222192627
Name   traG_AVF2S5_RS25885_pAvF25d 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: 69088.18 Da        Isoelectric Point: 9.7050

>WP_222192627.1 Ti-type conjugative transfer system protein TraG [Agrobacterium vitis]
MTANRLLLAILPAAIMVAAMILMSGMEHRLTALGTTAQAKLMLGRAGLALPYVAATAIGVVALFAANGSA
NIKAAGLSVLAGNGVVITIATLREVIRLNSIASSVPAEQSVLAYTDPVTMIGVGIAFISGMFALRVAIRG
NAAFATTAPKRIGGKRAVHGEAHWMKVQEAAKLFPEPGGIVIGERYRVDRDSVAAMPFRADDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVSEHRRQAGRKVIVLD
PTAGGVGFNALHWIGRHGNTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTEA
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGVSFSTDDLADGGTDIFIALDLKVLEAHPGFARVVIGSLLNAIYNRNGNVKGRTLFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSLGQMREAYGGRDATSKWFESASWISFSAINDPDTADYISKRCGDTT
VEVDQTNRSTGMKGSSRSRSKQLSRRPLILPHEVLRMRTDEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
ENRFHSNEKST

  Protein domains


Predicted by InterproScan.

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

(164-638)

  Protein structure



No available structure.



ID   13629 GenBank   WP_174059006
Name   t4cp2_AVF2S5_RS26280_pAvF25d 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: 91330.06 Da        Isoelectric Point: 5.4719

>WP_174059006.1 MULTISPECIES: conjugal transfer protein TrbE [Agrobacterium]
MVALKSFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNDVSRQINAILARLG
SGWMIQVEAVRVPTADYPQESDCHFPDLVTRAIDAERRAHFQKERGHFESRHALILTWRPPEPHRSGLTR
YIYSDTASRSATHADRALDSFLSSIREVEQYLANVVSIRRMMTRETSERGGFRVARYDELFQFIRFCVTG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLIENRFLGVVAIDGLAAESWPGILSALDLMPLTYRWSSRFIF
LDAEEARAKLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMMMVAETEDAIAEASSQLVAYGYYTPVIVL
FEEDQTQLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSAVAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLSLIAAQFRRYAGAQIFA
FDKGGSMLPLTLGLDGDHYQIGGDATGGGEGKALSFCPLADLTTDGDRAFAAEWIEMLVALQGVTITPDY
RNAISRQVGLMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGSFQCFEIEELMN
MGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDA
ERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKRDYYVVSPEGRRLFDMAL
GPIALSFVGASGKEDLKSIRALHSEHGASWPLQWLQQRGIAHAETLFQTE

  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: 139433..149099

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AVF2S5_RS26230 (AVF2S5_26175) 135115..137145 - 2031 WP_174059001 hydantoinase/oxoprolinase family protein -
AVF2S5_RS26235 (AVF2S5_26180) 137240..138355 - 1116 WP_235695114 FAD-dependent oxidoreductase -
AVF2S5_RS26240 (AVF2S5_26185) 138488..139378 + 891 WP_174059002 LysR substrate-binding domain-containing protein -
AVF2S5_RS26245 (AVF2S5_26190) 139433..140746 - 1314 WP_174113349 IncP-type conjugal transfer protein TrbI virB10
AVF2S5_RS26250 (AVF2S5_26195) 140759..141235 - 477 WP_174059030 conjugal transfer protein TrbH -
AVF2S5_RS26255 (AVF2S5_26200) 141235..142089 - 855 WP_174059004 P-type conjugative transfer protein TrbG virB9
AVF2S5_RS26260 (AVF2S5_26205) 142106..142768 - 663 WP_010892441 conjugal transfer protein TrbF virB8
AVF2S5_RS26265 (AVF2S5_26210) 142783..143970 - 1188 WP_174059005 P-type conjugative transfer protein TrbL virB6
AVF2S5_RS26270 (AVF2S5_26215) 143964..144191 - 228 WP_174113350 entry exclusion protein TrbK -
AVF2S5_RS26275 (AVF2S5_26220) 144188..144997 - 810 WP_174113351 P-type conjugative transfer protein TrbJ virB5
AVF2S5_RS26280 (AVF2S5_26225) 144969..147431 - 2463 WP_174059006 conjugal transfer protein TrbE virb4
AVF2S5_RS26285 (AVF2S5_26230) 147442..147741 - 300 WP_003523575 conjugal transfer protein TrbD virB3
AVF2S5_RS26290 (AVF2S5_26235) 147734..148138 - 405 WP_003523573 conjugal transfer pilin TrbC virB2
AVF2S5_RS26295 (AVF2S5_26240) 148128..149099 - 972 WP_174059007 P-type conjugative transfer ATPase TrbB virB11
AVF2S5_RS26300 (AVF2S5_26245) 149096..149734 - 639 WP_174059008 acyl-homoserine-lactone synthase -

Host bacterium

ID   18767 GenBank   NZ_CP055273
Plasmid name   pAvF25d Incompatibility group   -
Plasmid size   150182 bp Coordinate of oriT [Strand]   54700..54742 [+]
Host baterium   Agrobacterium vitis strain F2/5

Cargo genes

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