oriTDB
The information of the oriT region
oriTDB accession number 100008
Name oriT_R388  experimental
Sequence Completeness intact
oriT length 402 nt
oriT sequence CCGCCTCGTCCTCCAAAAGTGCCTGCTTTTCCGGGCTTAGCCGTACTTGGATGGGGTCGC CTAGTGCCATGTCCTCTCCCGTAGTGTTACTGTAGTGGTTCAATCCTAGCATTTACAAGG GGTTGCGGCAATATTGTAGTGGCATAACACTACACAGGTTTTCGTCCTTGGCGTGGAAGT CATTGTAAATCAATGACTTACGCGCACCGAAAGGTGCGTATTGTCTATAGCCCAGATTTA AGGATACCAACCCGGCTTTTAAGGACGGAAACCATGCGATAACGCCAGCGTGACCCTAAA GAGGGTCAAAACTGCTCCCAATGCGCTATGCGCATTGGGTTATCGTGCAGCAATGATGCA ACTATAATGCTATGATGGTGCTACAATGATGCAGAAAATGAG
IR (inverted repeat)IR1: [135-141] [148-154] nt  (TGTAGTG..CACTACA)
IR2: [177-184] [192-199] nt  (AAGTCATT..AATGACTT)
IR3: [203-208] [213-218] nt  (CGCACC..GGTGCG)
IR4: [317-326] [330-339] nt  (CCCAATGCGC..GCGCATTGGG)
Location of nic site [226-227] nt
Conserved sequence flanking the
  nic site 		TGTCT|ATAGC
Note _
L:135-141;R:148-154;L:177-184;R:192-199;L:203-208;R:213-218;L:317-326;R:330-339;D:226-227
Visualization of oriT structure (The oriT was characterized experimentally)
Reference
[1] Llosa M et al (1991) Structural and functional analysis of the origin of conjugal transfer of the broad-host-range IncW plasmid R388 and comparison with the related IncN plasmid R46. Mol Gen Genet. 226(3):473-83. [PMID:2038309]
[2] Revilla C et al (2008) Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob Agents Chemother. 52(4):1472-80. [PMID:18268088]
[3] Llosa M et al (1995) Nicking activity of TrwC directed against the origin of transfer of the IncW plasmid R388. J Mol Biol. 246(1):54-62. [PMID:7853404]
[4] Paterson ES et al (1997) Localization of the nic site of IncN conjugative plasmid pCU1 through formation of a hybrid oriT. J Bacteriol. 179(18):5768-76. [PMID:9294433]
I. Information of Relaxase
ID 7
Name TrwC_R388 experimental
GenBank accession number FAA00039
Family MOBF
Length 966 aa
UniProt ID Q2NKF7
PDB ID _
Pfam TrwC [PF08751.10], Evalue: 2.20E-83, Aligned region: 12..288
AAA_30 [PF13604.5], Evalue: 2.60E-44, Aligned region: 472..659
Viral_helicase1 [PF01443.17], Evalue: 9.50E-07, Aligned region: 492..697
UvrD_C_2 [PF13538.5], Evalue: 1.40E-07, Aligned region: 847..894
Note relaxase and DNA helicaseactivities
Protein sequence [Download] MLSHMVLTRQDIGRAASYYEDGADDYYAKDGDASEWQGKGAEELGLSGEVDSKRFRELLA
GNIGEGHRIMRSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQ
AEARAQARQKIQGKTRIETTGNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRAL
KNDEIVKRTRYLGAVYNAELAHELQKLGYQLRYGKDGNFDLAHIDRQQIEGFSKRTEQIA
EWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAEWQATAKELGIDFSRREWSGR
EKGGSEKQAHSFMPSDEAAKRAVRYAINHLTERQSVMDERELVDTAMKHAVGAARLEDIQ
KELLRQTETGYLIREAPRYRPGGQTGPTDEPGKTRAEWVAELAAKGMKQGAARERVDNAI
KTGGLVPIEPRYTTQTALEREKRILQIERDGRGAVAPVIAAEAARERLASTNLNQGQREA
AELIVSAANRVVGVQGFAGTGKSHMLDTAKQMIEGEGYHVRALAAYGSQVKALRELNVEA
NTLASFLRAKDKNIDSRTVLVIDEAGVVPTRLMEQTLKLAEKAGARVVLMGDTAQTKAIE
AGRPFDQLQAAGMQTAHMREIQRQKNPELKIAVELAAAGKASSSLERIKDVTEIKNHHER
RAAVAEAYIALKPDERDRTLIVSGTNEARREINQIVREGLGTAGKGIEFDTLVRVDTTQA
ERRHSKNYQVGHVIQPERDYAKTGLQRGELYRVVETGPGNRLTVIGEHDGQRIQFSPMTH
TKISVYQPERAELAVGDTIRITRNDKHLDLANGDRMKVVAVEDRKVTVTDGKRNVELPTD
KPLHVDHAYATTVHSSQGLTSDRVLIDAHAESRTTRKDVYYVAISRARFEARVFTNDRGK
LPAAIARENIKSAAHDLARDRGGRSAAAERQREQQRERERNRQTQQPAHDRQKAAREAER
GMEAGR
Reference
[1] Revilla C et al (2008) Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob Agents Chemother. 52(4):1472-80. [PMID:18268088]
[2] Llosa M et al (1995) Nicking activity of TrwC directed against the origin of transfer of the IncW plasmid R388. J Mol Biol. 246(1):54-62. [PMID:7853404]
[3] Llosa M et al (1994) Genetic organization of the conjugal DNA processing region of the IncW plasmid R388. J Mol Biol. 235(2):448-64. [PMID:8289274]
[4] de la Cruz F et al (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev. 34(1):18-40. [PMID:19919603]
[5] Fernández-López R et al (2006) Dynamics of the IncW genetic backbone imply general trends in conjugative plasmid evolution. FEMS Microbiol Rev. 30(6):942-66. [PMID:17026718]


II. Auxiliary DNA-binding protein(s) of the relaxosome
# ID Name GenBank Length Note
1 13 TrwA_R388 experimental YP_009182121 121 aa TrwA, together with TrwC and plasmid R388 oriT, forms a stable nucleoprotein structure, the relaxosome
Information of T4CP
ID 7
Name TrwB_R388 experimental
SecReT4 accesion number _
GenBank accession number FAA00040
Family TrwB/TraD
Length 507
UniProt ID Q04230
PDB ID 1E9R, 1E9S, 1GKI, 1GL6, 1GL7
Pfam TrwB_AAD_bind [PF10412.8], Evalue: 5.90E-97, Aligned region: 109..491
TraG-D_C [PF12696.6], Evalue: 2.70E-21, Aligned region: 350..472
T4SS-DNA_transf [PF02534.13], Evalue: 1.50E-12, Aligned region: 297..489
Note Type IV Secretion System Coupling Protein
Protein sequence [Download] MHPDDQRKVSAGIVIVLPLIFWITAVQKTEVLGSPKLLALWELMKLTPQKPILLLSALGG
LAVGVLFVWLLNSVGQGEFGGAPFKRFLRGTRIVSGGKLKRMTREKAKQVTVAGVPMPRD
AEPRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDMLSKFGRDKDIILNPYDQ
RTKGWSFFNEIRNDYDWQRYALSVVPRGKTDEAEEWASYGRLLLRETAKKLALIGTPSMR
ELFHWTTIATFDDLRGFLEGTLAESLFAGSNEASKALTSARFVLSDKLPEHVTMPDGDFS
IRSWLEDPNGGNLFITWREDMGPALRPLISAWVDVVCTSILSLPEEPKRRLWLFIDELAS
LEKLASLADALTKGRKAGLRVVAGLQSTSQLDDVYGVKEAQTLRASFRSLVVLGGSRTDP
KTNEDMSLSLGEHEVERDRYSKNTGKHHSTGRALERVRERVVMPAEIANLPDLTAYVGFA
GNRPIAKVPLEIKQFANRQPAFVEGTI

Reference
[1] Llosa M et al (1994) Localization of the nic site of IncN conjugative plasmid pCU1 through formation of a hybrid oriT. J Mol Biol. 235(2):448-64. [PMID:8289274]
[2] de la Cruz F et al (2010) Localization of the nic site of IncN conjugative plasmid pCU1 through formation of a hybrid oriT. FEMS Microbiol Rev. 34(1):18-40. [PMID:19919603]
[3] Fernández-López R et al (2006) Localization of the nic site of IncN conjugative plasmid pCU1 through formation of a hybrid oriT. FEMS Microbiol Rev. 30(6):942-66. [PMID:17026718]
[4] Cabezón E et al (1994) Localization of the nic site of IncN conjugative plasmid pCU1 through formation of a hybrid oriT. J Bacteriol. 176(14):4455-8. [PMID:8021231]
Information of plasmid
ID 7
Plasmid name R388
GenBank accession number NC_028464.1
Incompatibility group IncW
Genome size 33913 bp
Coordinate of oriT  [Strand] 15948..16349 [-]
Drug resistance experimental resistance to trimethoprim and sulfonamide
Heavy-metal resistance _
Virulence factor _
Xenobiotic degradation _
Host bacterium [NCBI Taxonomy ID] Escherichia coli [562]
Reference
[1] Revilla C et al (2008) Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob Agents Chemother. 52(4):1472-80. [PMID:18268088]

Microbial Bioinformatics Group in MML, SJTU