oriTDB

The information of the oriT region

oriTDB accession number	100015
Name	oriT_R100
Sequence Completeness	intact
oriT length	550 nt
oriT sequence	TTACTCTGGCCATAAGATAAAACCTTTCATTATTAAGCAACGAACTTTTCACTATAAATA TGCATATAGTGTTTACAAGTAAGAAAGACACTCCTAGCAGCGCCTCTAGGATCATCCTAT AAAAAAATGCGATCCGGCGCTAGGGGCGTCCCTAATATATATCAATGTTTTTCGTGAAAA TTGTCAGTACTGATCCTAATAAGAGTCGCTATAGGGTCGTAACAGGATCGCCAACGACTC TCTATTTAATAATTCAGAATTATTAAATATAAATAGCGTTTGTTAATTACATGATTTAAA ACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCA CCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAG GTGGAAAAATGAAAAAATGGATGTTAGCAATCTGCCTGATGTTTATAAATGGGATCTGCG AAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTAA GAATGATATC
IR (inverted repeat)	[243-255] [257-269] nt (TATTTAATAATTC..GAATTATTAAATA) [311-318] [321-328] nt (GCAAAAAC..GTTTTTGC)
Location of nic site	[337-338] nt
Conserved sequence flanking the nic site	GTAGTGTGT\|GG
Note	_
	L:243-255;R:257-269;L:311-318;R:321-328;D:337-338

Visualization of oriT structure (The oriT was characterized experimentally)

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

1

TTACTCTGGCCATAAGATAAAACCTTTCATTATTAAGCAACGAACTTTTCACTATAAATA

61

TGCATATAGTGTTTACAAGTAAGAAAGACACTCCTAGCAGCGCCTCTAGGATCATCCTAT

121

AAAAAAATGCGATCCGGCGCTAGGGGCGTCCCTAATATATATCAATGTTTTTCGTGAAAA

181

TTGTCAGTACTGATCCTAATAAGAGTCGCTATAGGGTCGTAACAGGATCGCCAACGACTC

241

TCTATTTAATAATTCAGAATTATTAAATATAAATAGCGTTTGTTAATTACATGATTTAAA

301

ACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCA

361

CCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAG

421

GTGGAAAAATGAAAAAATGGATGTTAGCAATCTGCCTGATGTTTATAAATGGGATCTGCG

481

AAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTAA

541

GAATGATATC

Reference

[1] Guja KE et al (2015) Completing the specificity swap: Single-stranded DNA recognition by F and R100 TraI relaxase domains. Plasmid. 80:1-7. [PMID:25841886]

I. Information of Relaxase

ID	14
Name	TraI_R100
GenBank accession number	BAA78885
Family	MOB_F
Length	1756 aa
UniProt ID	Q9WTB0
PDB ID	_
Pfam	TrwC [PF08751.10], Evalue: 1.20E-76, Aligned region: 10..284 TraI [PF07057.10], Evalue: 1.70E-56, Aligned region: 1434..1556 AAA_30 [PF13604.5], Evalue: 1.90E-34, Aligned region: 968..1160 AAA_19 [PF13245.5], Evalue: 1.80E-08, Aligned region: 973..1108
Note	relaxase
Protein sequence [Download]	MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRL PDGADLSRMQDGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEAL ASTRVMTDGQSETVLTGNLVMALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKV GKTGFSENVLANRIAFGKIYQSELRQRVEALGYETEVVGKHGMWEMPGVPVEAFSSRSQA IREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQTLKETGFDIRAYRDAADQRAE IRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPENGVIERARAG IDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDE RLSGELITGRRQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQR TGTGSALMAMKDAGVNTYRWQGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQ VSGVREQAILTQAIRSELKTQGVLGHPEVTMTALSPVWLDSRSRYLRDMYRPGMVMEQWN PETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRV TGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKLENGWVETPGH SVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTG FTELGGEINAQIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMER VPGELMETLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRV VGLGPTHRAVGEMRSAGVDAQTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNTDM ARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAADVVIMKEIVRQTPELREAV YSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEAQQKAMLKGET FPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLIS PREAVAEGVTLYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQT RVIRPGQERAEQHIDLAYAITAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMK QHVQVYTDNRQGWTDAINNAVQKGTAHDVLEPKPDREVMNAQRLFSTARELRDVAAGRAV LRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAGIWLNPLTTDDGNGLRGFSGE GRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGEGRPWNPGAIT GGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIE RDMVRDLQKEKTLGGD

Reference

[1] Guja KE et al (2015) Completing the specificity swap: Single-stranded DNA recognition by F and R100 TraI relaxase domains. Plasmid. 80:1-7. [PMID:25841886]

[2] Wong JJ et al (2012) Relaxosome function and conjugation regulation in F-like plasmids - a structural biology perspective. Mol Microbiol. 85(4):602-17. [PMID:22788760]

II. Auxiliary DNA-binding protein(s) of the relaxosome

#	ID	Name	GenBank	Length	Note
1	21	TraM_R100	NP_052944	127 aa	TraM of plasmid R100, responsible for initiation of conjugal transfer and conjugal-DNA metabolism
2	22	TraY_R100	NP_052946	75 aa	_

Information of T4CP

ID	14
Name	TraD_R100
SecReT4 accesion number	_
GenBank accession number	BAA78884
Family	TrwB/TraD
Length	738
UniProt ID	Q7AK62
PDB ID	_
Pfam	TrwB_AAD_bind [PF10412.8], Evalue: 3.50E-121, Aligned region: 171..561 TraD_N [PF12615.7], Evalue: 7.80E-29, Aligned region: 31..128 TraG-D_C [PF12696.6], Evalue: 2.70E-19, Aligned region: 419..542 T4SS-DNA_transf [PF02534.13], Evalue: 2.90E-07, Aligned region: 198..511
Note	Type IV Secretion System Coupling Protein
Protein sequence [Download]	MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIY WWCTSLEGMRDLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVAL VICLITFFVVSWILGRQGKQQSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPII RDSEIQNFCLHGTVGAGKSEVIRRLANYARQRGDMVVIYDRSGEFVKSYYDPSIDKILNP LDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQGSGRTIFAEAAYLMRNDPNRS YSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKAIRYLQGIEHN GDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRA FFRSPSHKIAEFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSL PDLTCYVTLPGPYPAVKLSLKYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMA SLFEPEVASGEDVTQAEQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGV SVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEV NINVHRERGEDVEPGDDF

Reference

[1] Wong JJ et al (2012) Completing the specificity swap: Single-stranded DNA recognition by F and R100 TraI relaxase domains. Mol Microbiol. 85(4):602-17. [PMID:22788760]

Information of plasmid

ID	14
Plasmid name	R100
GenBank accession number	AP000342.1
Incompatibility group	IncF (IncFII)
Genome size	94281 bp
Coordinate of oriT [Strand]	50353..50902 [-]
Drug resistance	resistance to sulfonamide and streptomycin
Heavy-metal resistance	mercury resistance
Virulence factor	_
Xenobiotic degradation	_
Host bacterium [NCBI Taxonomy ID]	Shigella flexneri 2b [1288825]

Reference

[1] Brown NL et al (1986) The nucleotide sequence of the mercuric resistance operons of plasmid R100 and transposon Tn501: further evidence for mer genes which enhance the activity of the mercuric ion detoxification system. Mol Gen Genet. 202(1):143-51. [PMID:3007931]