oriTDB
The information of the oriT region
oriTDB accession number 100180
Name oriT_pTiC58  experimental
Sequence Completeness core
oriT length 61 nt
oriT sequence GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCTTGCGTAGGGGGCCAAACAGG G
IR (inverted repeat)[19-27] [32-40] nt  (ATACGTCGC..GCGACGCCT)
Location of nic site [11-12] nt
Conserved sequence flanking the
  nic site 		_
Note Ti plasmid
L:19-27;R:32-40;D:11-12
Visualization of oriT structure (The oriT was characterized experimentally)
Reference
[1] Cook DM et al (1992) The oriT region of the Agrobacterium tumefaciens Ti plasmid pTiC58 shares DNA sequence identity with the transfer origins of RSF1010 and RK2/RP4 and with T-region borders. J Bacteriol. 174(19):6238-46. [PMID:1400174]
[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 173
Name TraA_pTiC58 insolico
GenBank accession number AAC17212
Family MOBQ
Length 1101 aa
UniProt ID Q44349
PDB ID _
Pfam MobA_MobL [PF03389.14], Evalue: 4.40E-76, Aligned region: 17..243
AAA_30 [PF13604.5], Evalue: 1.10E-54, Aligned region: 382..570
Viral_helicase1 [PF01443.17], Evalue: 9.10E-05, Aligned region: 657..738
AAA_19 [PF13245.5], Evalue: 8.00E-09, Aligned region: 387..514
UvrD_C_2 [PF13538.5], Evalue: 1.90E-06, Aligned region: 693..737
Note similar to conjugal endonucleases MobA of RSF1010 and MobL of pTF1; contains domains similar to the TraI helicase of the F plasmid; 123 kDa protein
Protein sequence [Download] MAIAHFSASIVSRGDGRSVVLSAAYQHCAKMEYEREARTIDYTRKQGLVHQEFILPADAP
KWVRALIADCSVAGASEAFWNKVEAFEKRSDAQLARDLTIALPRELTSEQNIALVRDFVE
KHILGKGMVADWVYHDNPGNPHIHLMTTLRPLTEDGFGAKKVAVIGEDGQLVRTKSGKIL
YELWAGSTDDFNVVRDGWFERLNHHLTLGGIDLKIDGRSYEKQGIDLEPTIHLGVGAKAI
SRKAEQQGVRPELERIELNEERRSENTRRILKNPAIVLDLIMREKSVFDERDVAKVLHRY
VDDPAVFQQLMLRIILNPEVLRLQRDTIEFATGEKVPARYSTRAMIRLEATMARQAMWLS
DKETHAVSTAVLLAATFGRHGRLSEEQKAAIECIAGPARIAAVVGRAGAGKTTMMKAARE
AWELAGYRVVGGALAGKASEGLDKEAGIESRTLSSWELRWNRGRDVLDNKTVFVMDEAGM
VASKQMAGFVDAVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDW
MRKASLDLARGNVEKALALYNANARIVGERLKAEAVERLIADWNRDYDQTKTTLILAHLR
RDVRMLNVMAREKLVERGIVGEGHVFRTADGERRFHAGDQIVFLKNETLLGVKNGMIGHV
VEAVPNRIVAVVGDRDHRRHVVVEQRFYSNLDHGYATTIHKSQGATVDRVKVLASLSLDR
HLTYVAMTRHREDLQLYYGCRSFAFNGGLAKVLSRKNAKETTLDYERGKLYREALRFAEN
RGLHIMQVARTMLRDRLDWTLRQKTKVSDLVHRLRALGERLGLDQSPKTQTMKEAAPMVT
GIKTFSGSVADTVGDKLGADPTLKQQWEEVSARFRYVFADPETAFRAVNFDTVLADKEAA
KAVLQKLEAEPASIGALKGKTGILASKTEREARRVAEVNVPALKRDLEQYLRMRETATLR
IVTEEQALRQRVSIDIPALSPAARVVLERVRDAIDRNDLPAALGYALSNRETKLEIDGFN
QAVTERFGERTLLSNVAREPSGKLYEKLSDGMRPEQKEQLKQAWPIMRTAQQLAAHERTV
QSLKQAEELRQTLRQAPVLKQ
Reference
[1] Cook DM et al (1992) The oriT region of the Agrobacterium tumefaciens Ti plasmid pTiC58 shares DNA sequence identity with the transfer origins of RSF1010 and RK2/RP4 and with T-region borders. J Bacteriol. 174(19):6238-46. [PMID:1400174]


II. Auxiliary DNA-binding protein(s) of the relaxosome
# ID Name GenBank Length Note
1 249 _ insolico _ _ _
Information of T4CP
ID 173
Name TraG_pTiC58 experimental
SecReT4 accesion number _
GenBank accession number YP_009075421
Family VirD4/TraG
Length 658
UniProt ID _
PDB ID _
Pfam T4SS-DNA_transf [PF02534.13], Evalue: 1.10E-165, Aligned region: 163..641
TraG-D_C [PF12696.6], Evalue: 4.00E-33, Aligned region: 477..599
TrwB_AAD_bind [PF10412.8], Evalue: 5.40E-22, Aligned region: 223..613
Note Type IV Secretion System Coupling Protein
Protein sequence [Download] MTMNRLLLLILPAIIMLAAMFATSGMEQRLAAFGTSPQAKLMLGRAGLALPYIAAVAIGI
IGLFAANGSANIKAAGLSVLAGSGVVITIATLREVIRLNSIASSVPAEQSVLAYADPVTM
IGASIAFISGMFALRVAIKGNAAFATTAPKRIGGKRAVHGEADWMKIQEAAKLFPERGGI
IIGERYRVDRDSVAAMPFRADDRQSWGAGGKSPLLCFDGSFGSSHGIVFAGSGGFKTTSV
TIPTALKWGGGLVVLDPSSEVAPMVCEHRRQAGRKVIVLDPTAGGVGFNALDWIGRHGNT
KEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTETEDQTLRRVRA
NLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNVKGRTLF
LLDEVARLGYLRILETARDAGRKYGIMLTMIFQSLGQMREAYGGRDATSKWFESASWISF
AAINDPDTADYISKRCGDTTVEVDQTNRSTGMKGSSRSRSKQLSRRPLILPHEVLHMRSD
EQIVFTSGNPPLRCGRAIWFRRDDMKACVGENRFHRTGTGTDTHTEHAPPWQKEGTRP

Reference
[1] Hamilton CM et al (2000) The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups. J Bacteriol. 182(6):1541-8. [PMID:10692358]
[2] Cabezón E et al (1994) The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups. J Bacteriol. 176(14):4455-8. [PMID:8021231]
Information of plasmid
ID 173
Plasmid name pTiC58
GenBank accession number NC_004972.1
Genome size 8288 bp
Coordinate of oriT  [Strand]
Drug resistance _
Heavy-metal resistance experimental virulence-tumorigenic
Virulence factor _
Xenobiotic degradation _
Host bacterium [NCBI Taxonomy ID] Agrobacterium fabrum str. C58 [176299]
Reference
[1] 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