oriTDB
The information of the oriT region
oriTDB accession number 100015
Name oriT_R100  experimental
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)
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 experimental
GenBank accession number BAA78885
Family MOBF
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 experimental NP_052944 127 aa TraM of plasmid R100, responsible for initiation of conjugal transfer and conjugal-DNA metabolism
2 22 TraY_R100 experimental NP_052946 75 aa _
Information of T4CP
ID 14
Name TraD_R100 experimental
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 insolico resistance to sulfonamide and streptomycin
Heavy-metal resistance experimental 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]

Microbial Bioinformatics Group in MML, SJTU