oriTDB

The information of the oriT region

oriTDB accession number	100180
Name	oriT_pTiC58
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)

1...5....10....15....20....25....30....35....40....45....50....55....60

1

GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCTTGCGTAGGGGGCCAAACAGG

61

G

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
GenBank accession number	AAC17212
Family	MOB_Q
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	_	_	_	_

Information of T4CP

ID	173
Name	TraG_pTiC58
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	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]