oriTDB
The information of the oriT region
oriTDB accession number 100048
Name oriT_pTi-SAKURA  insolico
Sequence Completeness incomplete
oriT length 16 nt
oriT sequence CGTCGCTGGCGCGACG
IR (inverted repeat)[1-6] [11-16] nt  (CGTCGC..GCGACG)
Location of nic site _
Conserved sequence flanking the
  nic site 		_
Note Ti plasmid
L:1-6;R:11-16
Visualization of oriT structure
Reference
[1] Suzuki K et al (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene. 242(1-2):331-6. [PMID:10721727]
[2] Wetzel ME et al (2015) The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups. Genome Biol Evol. 7(12):3337-57. [PMID:26590210]
I. Information of Relaxase
ID 46
Name TraA_pTi-SAKURA insolico
GenBank accession number NP_053349
Family MOBQ
Length 1194 aa
UniProt ID Q9R6F0
PDB ID _
Pfam MobA_MobL [PF03389.14], Evalue: 3.40E-76, Aligned region: 17..243
AAA_30 [PF13604.5], Evalue: 3.20E-55, Aligned region: 381..570
AAA_19 [PF13245.5], Evalue: 2.30E-12, Aligned region: 386..513
Viral_helicase1 [PF01443.17], Evalue: 4.10E-05, Aligned region: 656..737
Note Dtr system oriT relaxase; Provisional
Protein sequence [Download] MAIAHFSASIVSRGDGRSAVLSAAYRHCAKMDYEREARTIDYTRKVGLLHEEFLLPDHAP
KWVRMLIADRSVAGASEAFWNRVEAFEKRIDAQLAKDLTVALPLELTAEQNIALVRDFVE
KHILSRGMVADWVYHDNPGNPHIHLMTTLRPLTEDGFGAKKVAVIGEDGEPLRTKAGKIV
YELWAGGTDDFNAFRYAWFERMNHHLALNGINLRVDGRSYEKQGIDLVPTIHLGVGAKAI
ERKAEGEGRKAELERLELNEERREENARRIRENPKLVLDLITREKSVFDERDVAKILHRY
IDDAGMFRNMMARIMQSGQVLRLERERISLATGKREPSKFTTHELIRLEATMARSAMWLD
RRSSHGVGKVLLDATFARHDRLSQEQRTALAHIAGANRIAAVVGRAGAGKTTMMKAARET
WEAAGYRVVGAALAGKAAEGLEKEAGIIARTLSSWELRWQQERDRLDDRTVMVLDEAGMV
SSRQMAMLVQAATEAGAKLVLVGDPDQLQPIEAGAAFRAITDRIGYAELGTIYRQREAWM
RRASVDLAHRQVGSALAAYDRANLIHSHWSKDEAIASLIEDWNRDYDPARSSLILAHRRL
DVRALNELARERLVGRGFVGEGFAFRTEEGERRFDAGDRIVFLKNEGSLGVKNGMLAKVV
EAAPGRFVAEIGEGEDGRQVTVDQHLYANVDHGYATTIHKSQGATVDDVRVLASGTMDRH
LTYVALTRHRDAARLYVGMNEFTNRGGVLVDHGEAPYENKPENHDSYFVTLETGEGKQNT
IWGVDLRRAMAEAAPQIGDRIGLDHKGSEMVRLPDGKKVKRHTWKVVDIRELALSRMTER
MSRDAAKETTLDYENASFYRAALRFADTHGLRVMNVARTMMRDRLDWTVRQKQRLARLGS
RLLAIGGKLGLVSSTHQQQSLSSNMKEVRPMVAGITIHPKSLDQAVEDKLAADPGLKKQW
EEVSSRFHLIYAQPEAAFRAVDVDAALKDPATAKSTLAKIANEPESFGALKGKTGLFASR
VEKEDRDIAHVNAPALSRDLERYLQMRTNAMQRLEAEERAIRHRVSIDIPALSPSARTVL
ERVRDAIDRNDLPAALGYAVSDKEAKLEIDGFNKAVSERFGERSLLTNAAREPSGRLFEQ
LAKGLQPQEKEHLAEAWPVMRTAQQLAAHERTAATLKQVEDLRLSQRQTPVIKQ
Reference
[1] Suzuki K et al (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene. 242(1-2):331-6. [PMID:10721727]


II. Auxiliary DNA-binding protein(s) of the relaxosome
# ID Name GenBank Length Note
1 76 TraC_pTi-SAKURA insolico NP_053348 98 aa conjugal transfer protein TraC; Provisional
2 77 TraD_pTi-SAKURA insolico NP_053347 71 aa conjugal transfer protein TraD; Provisional
Information of T4CP
ID 46
Name TraG_pTi-SAKURA insolico
SecReT4 accesion number 10954926
GenBank accession number NP_053346
Family VirD4/TraG
Length 649
UniProt ID Q9R6F3
PDB ID _
Pfam T4SS-DNA_transf [PF02534.13], Evalue: 1.50E-157, Aligned region: 163..642
TraG-D_C [PF12696.6], Evalue: 9.50E-34, Aligned region: 477..599
TrwB_AAD_bind [PF10412.8], Evalue: 2.50E-23, Aligned region: 224..614
Note conjugal transfer coupling protein TraG
Protein sequence [Download] MTANRILLAVVPATTMIAAVILMPGIEHWLAAFGRTAQAKLMLGRFGIALPYIAAAAIGT
MFLFAANGAANIKTAGWGVVSGNVAAIIIAMIREAARLSGIAGSVPTDQSVLAYTDPATA
LGAAGPFLAGVFALRVVIKGNAAFASPAPRRVRGKRAVHGEADWMGVVEAGRLFPDAGGI
VIGERYRVDRDSVAGMSFRADQRETWGAGGKSPLLCFDGSFGSSHGIVFAGSGGFKTTSV
TIPTALKWGGGLVVLDPSSEVAPMVSEHRRKAGRKVIVLDPATPAIGFNALDWIGRFGGT
KEEDIVAVATWIMTDNARTASARDDFFRASAMQLLTALIADVCLSGHTDEQDQTLRRVRA
NLSEPEPKLRERLTRIYEQSESEFVRENVAVFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGDSFSTDDLAKGETDIFIALDLKVLEAHPGLARVVIGAFLNAIYNRNGEVEGRTLF
LLDEVARLGYLRILETARDAGRKYGITLTLIFQSLGQMREAYGGRDATSKWFESASWISF
AAINDPDTADYISKRCGDTTIEVDQTNRSTGMKGSSRSRSKQLSNRRLILPHEVMRMRTD
EQIVFTAGNAPLRCGRAIWFRRDEMTRIVGKNRFHQGDAPAKGPEPSTP

Reference
[1] Suzuki K et al (2000) The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups. Gene. 242(1-2):331-6. [PMID:10721727]
Information of plasmid
ID 46
Plasmid name pTi-SAKURA
GenBank accession number NC_002147.1
Genome size 206479 bp
Coordinate of oriT  [Strand]
Drug resistance _
Heavy-metal resistance _
Virulence factor experimental virulence-tumorigenic; virulence ( vir ) gene regions for pathogenicity
Xenobiotic degradation _
Host bacterium [NCBI Taxonomy ID] Agrobacterium tumefaciens MAFF 301001 [358]
Reference
[1] Suzuki K et al (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene. 242(1-2):331-6. [PMID:10721727]
[2] Wetzel ME et al (2015) The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups. Genome Biol Evol. 7(12):3337-57. [PMID:26590210]

Microbial Bioinformatics Group in MML, SJTU