Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100227
Name   oriT_Ti in_silico
Organism   Agrobacterium fabrum str. C58
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_003065 (143868..143928 [+], 61 nt)
oriT length   61 nt
IRs (inverted repeats)      19..27, 32..40  (ATACGTCGC..GCGACGCCT)
Location of nic site      11..12
Conserved sequence flanking the
  nic site    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 61 nt

>oriT_Ti
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCTTGCGTAGGGGGCCAAACAGGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   298 GenBank   NP_396650
Name   TraA_Ti insolico UniProt ID   Q44349
Length   1100 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123477.41 Da        Isoelectric Point: 9.8136

>NP_396650.2 Dtr system oriT relaxase (plasmid) [Agrobacterium fabrum str. C58]
MAIAHFSASIVSRGDGRSVVLSAAYQHCAKMEYEREARTIDYTRKQGLVHQEFILPADAPKWVRALIADC
SVAGASEAFWNKVEAFEKRSDAQLARDLTIALPRELTSEQNIALVRDFVEKHILGKGMVADWVYHDNPGN
PHIHLMTTLRPLTEDGFGAKKVAVIGEDGQLVRTKSGKILYELWAGSTDDFNVVRDGWFERLNHHLTLGG
IDLKIDGRSYEKQGIDLEPTIHLGVGAKAISRKAEQQGVRPELERIELNEERRSENTRRILKNPAIVLDL
IMREKSVFDERDVAKVLHRYVDDPAVFQQLMLRIILNPEVLRLQRDTIEFATGEKVPARYSTRAMIRLEA
TMARQAMWLSDKETHAVSTAVLAATFGRHGRLSEEQKAAIECIAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKASEGLDKEAGIESRTLSSWELRWNRGRDVLDNKTVFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALALYN
ANARIVGERLKAEAVERLIADWNRDYDQTKTTLILAHLRRDVRMLNVMAREKLVERGIVGEGHVFRTADG
ERRFHAGDQIVFLKNETLLGVKNGMIGHVVEAVPNRIVAVVGDRDHRRHVVVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGCRSFAFNGGLAKVLSRKNAKETTLDYERGKLY
REALRFAENRGLHIMQVARTMLRDRLDWTLRQKTKVSDLVHRLRALGERLGLDQSPKTQTMKEAAPMVTG
IKTFSGSVADTVGDKLGADPTLKQQWEEVSARFRYVFADPETAFRAVNFDTVLADKEAAKAVLQKLEAEP
ASIGALKGKTGILASKTEREARRVAEVNVPALKRDLEQYLRMRETATLRIVTEEQALRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAALGYALSNRETKLEIDGFNQAVTERFGERTLLSNVAREPSGKLYEKLSDG
MRPEQKEQLKQAWPIMRTAQQLAAHERTVQSLKQAEELRQTLRQAPVLKQ

  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)

(382-566)


  Protein structure


Source ID Structure
AlphaFold DB Q44349


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 41570..51237

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ATU_RS23125 (AGR_pTi_65) 36854..37579 - 726 WP_003523894 nopaline ABC transporter permease NocM -
ATU_RS23130 (AGR_pTi_66) 37581..38291 - 711 WP_010891638 nopaline ABC transporter permease NocQ -
ATU_RS23135 (AGR_pTi_67) 38365..39216 - 852 WP_010891637 nopaline ABC transporter substrate-binding protein NocT -
ATU_RS23140 (AGR_pTi_69) 39281..40054 - 774 WP_010974830 nopaline ABC transporter ATP-binding protein NocP -
ATU_RS23145 (AGR_pTi_70) 40308..41210 + 903 WP_065702830 LysR substrate-binding domain-containing protein -
ATU_RS23150 (AGR_pTi_bx125) 41214..41573 - 360 WP_010974831 hypothetical protein -
ATU_RS23155 (AGR_pTi_71) 41570..42886 - 1317 WP_010974832 IncP-type conjugal transfer protein TrbI virB10
ATU_RS23160 (AGR_pTi_72) 42899..43375 - 477 WP_010974833 conjugal transfer protein TrbH -
ATU_RS23165 (AGR_pTi_73) 43375..44229 - 855 WP_010974834 P-type conjugative transfer protein TrbG virB9
ATU_RS23170 (AGR_pTi_74) 44247..44909 - 663 WP_010891631 conjugal transfer protein TrbF virB8
ATU_RS23175 (AGR_pTi_76) 44924..46120 - 1197 WP_010974835 P-type conjugative transfer protein TrbL virB6
ATU_RS23180 (AGR_pTi_78) 46114..46332 - 219 WP_010974836 entry exclusion protein TrbK -
ATU_RS23185 (AGR_pTi_81) 46329..47087 - 759 WP_233278946 P-type conjugative transfer protein TrbJ virB5
ATU_RS23190 (AGR_pTi_83) 47104..49572 - 2469 WP_010974837 conjugal transfer protein TrbE virb4
ATU_RS23195 (AGR_pTi_85) 49583..49882 - 300 WP_010891626 conjugal transfer protein TrbD virB3
ATU_RS23200 (AGR_pTi_87) 49875..50276 - 402 WP_010974812 conjugal transfer pilin TrbC virB2
ATU_RS23205 (AGR_pTi_89) 50266..51237 - 972 WP_010891624 P-type conjugative transfer ATPase TrbB virB11
ATU_RS23210 (AGR_pTi_91) 51234..51869 - 636 WP_010974838 acyl-homoserine-lactone synthase -
ATU_RS23215 (AGR_pTi_93) 52233..53450 + 1218 WP_010891622 plasmid partitioning protein RepA -
ATU_RS23220 (AGR_pTi_94) 53680..54690 + 1011 WP_032489589 plasmid partitioning protein RepB -
ATU_RS23225 (AGR_pTi_95) 54905..56224 + 1320 WP_010974840 plasmid replication protein RepC -

Region 2: 183877..193327

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ATU_RS23780 (AGR_pTi_290) 179262..179993 - 732 WP_010974913 (dimethylallyl)adenosine tRNA methylthiotransferase -
ATU_RS23785 (AGR_pTi_2) 180831..183332 + 2502 WP_010974914 two-component system sensor kinase VirA -
ATU_RS23790 (AGR_pTi_3) 183877..184614 + 738 WP_010974915 type IV secretion system lytic transglycosylase VirB1 virB1
ATU_RS23795 (AGR_pTi_4) 184614..184979 + 366 WP_010891502 pilin major subunit VirB2 virB2
ATU_RS23800 (AGR_pTi_bx137) 184979..185305 + 327 WP_010891501 type IV secretion system protein VirB3 virB3
ATU_RS23805 (AGR_pTi_8) 185305..187674 + 2370 WP_010974916 type IV secretion/conjugal transfer ATPase VirB4 virb4
ATU_RS23810 (AGR_pTi_9) 187691..188353 + 663 WP_010891499 pilin minor subunit VirB5 -
ATU_RS23815 (AGR_pTi_10) 188454..189341 + 888 WP_010974917 type IV secretion system protein virB6
ATU_RS23820 (AGR_pTi_missing) 189377..189544 + 168 WP_010891497 type IV secretion system lipoprotein VirB7 -
ATU_RS23825 (AGR_pTi_11) 189531..190244 + 714 WP_010891496 type IV secretion system protein VirB8 virB8
ATU_RS23830 (AGR_pTi_12) 190241..191122 + 882 WP_010891495 P-type conjugative transfer protein VirB9 virB9
ATU_RS23835 (AGR_pTi_13) 191119..192252 + 1134 WP_010891494 type IV secretion system protein VirB10 virB10
ATU_RS23840 (AGR_pTi_14) 192293..193327 + 1035 WP_010974918 P-type DNA transfer ATPase VirB11 virB11
ATU_RS23845 (AGR_pTi_15) 193546..194307 + 762 WP_010891492 two-component system response regulator VirG -
ATU_RS23850 (AGR_pTi_16) 194449..195057 - 609 WP_010891491 conjugal transfer protein VirC2 -
ATU_RS23855 (AGR_pTi_18) 195060..195755 - 696 WP_010891490 conjugal transfer ATPase VirC1 -
ATU_RS23860 (AGR_pTi_19) 196026..196469 + 444 WP_010891489 T-DNA border endonuclease subunit VirD1 -
ATU_RS23865 (AGR_pTi_21) 196503..197846 + 1344 WP_010974919 T-DNA border endonuclease VirD2 -

Host bacterium

ID   689 GenBank   NC_003065
Plasmid name   Ti Incompatibility group   _
Plasmid size   214233 bp Coordinate of oriT [Strand]   143868..143928 [+]
Host baterium   Agrobacterium fabrum str. C58

Cargo genes

Drug resistance gene   -
Virulence gene   Most virulence determinants of A. tumefaciens have been found on the Ti plasmid.
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -