oriTDB
The information of the oriT region
oriTDB accession number 100096
Name oriT_pEC958  insolico
Sequence Completeness intact
oriT length 450 nt
oriT sequence ATATGTATACCTCTTTATTTTCTTATCGCATCAAATTTATTTCACATATAAAAAAATGAC AATTCATCGATGAATCGAATCGTGACGCAAGTTACGAAAATTACGATTCATGCAGCAAAT CACATCACGAATTGAATCTAGAGTCAATTCGCTTTAACTCGTTGTTTTATTATTACTGAT TCATCTATGAGTTGCGTTAAATTCATTGGTGAATCATATGCGATTCACCAATGAATCCTT TTTATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGTTAATGATTCAAATAG CAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCA ACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTG GAAAAATGAAAAAATGGATGTTAGCCATCT
IR (inverted repeat)IR1: [201-215] [222-236] nt  (ATTCATTGGTGAATC..GATTCACCAATGAAT)
IR2: [308-315] [318-325] nt  (GCAAAAAC..GTTTTTGC)
Location of nic site [334-335] nt
Conserved sequence flanking the
  nic site 		GTGGGGTGT|GG
Note
L:201-215;R:222-236;L:308-315;R:318-325;D:334-335
Visualization of oriT structure
Reference
[1] Forde BM et al (2014) The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One. 9(8):e104400. [PMID:25126841]
I. Information of Relaxase
ID 91
Name TraI_pEC958 insolico
GenBank accession number CDN85420
Family MOBF
Length 1756 aa
UniProt ID W8ZTK0
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 conjugal transfer nickase/helicase TraI
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] Forde BM et al (2014) The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One. 9(8):e104400. [PMID:25126841]


II. Auxiliary DNA-binding protein(s) of the relaxosome
# ID Name GenBank Length Note
1 131 TraM_pEC958 insolico CDN85382 127 aa _
2 132 TraY_pEC958 insolico CDN85384 75 aa conjugal transfer protein TraY
Information of T4CP
ID 91
Name TraD_pEC958 insolico
SecReT4 accesion number _
GenBank accession number CDN85419
Family TrwB/TraD
Length 732
UniProt ID W9A124
PDB ID _
Pfam TrwB_AAD_bind [PF10412.8], Evalue: 3.40E-121, Aligned region: 171..561
TraD_N [PF12615.7], Evalue: 7.70E-29, Aligned region: 31..128
TraG-D_C [PF12696.6], Evalue: 2.70E-19, Aligned region: 419..542
T4SS-DNA_transf [PF02534.13], Evalue: 2.80E-07, Aligned region: 198..511
Note type IV conjugative transfer system coupling protein TraD
Protein sequence [Download] MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIY
WWCTSLEGMRDLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVAL
VICLITFFVVSWILGRQGKQQSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPII
RDSEIQNFCLHGTVGAGKSEVIRRLANYARQRGDMVVIYDRSGEFVKSYYDPSIDKILNP
LDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQGSGRTIFAEAAYLMRNDPNRS
YSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKAIRYLQGIEHN
GDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRA
FFRSPSHKIAEFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSL
PDLTCYVTLPGPYPAVKLSLKYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMA
SLFEPEVASGEDVTQAEQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGG
IEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHR
ERGEDVEPGDDF

Reference
 N/A
Information of plasmid
ID 91
Plasmid name pEC958
GenBank accession number HG941719.1
Incompatibility group IncF
Genome size 135602 bp
Coordinate of oriT  [Strand] 26048..26497 [-]
Drug resistance insolico blaTEM-1; blaCTX-M-15; blaOXA-1; tet gene cluster (resistance to tetracycline)
Heavy-metal resistance _
Virulence factor _
Xenobiotic degradation _
Host bacterium [NCBI Taxonomy ID] Escherichia coli O25b:H4-ST131 [941322]
Reference
[1] Forde BM et al (2014) The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One. 9(8):e104400. [PMID:25126841]

Microbial Bioinformatics Group in MML, SJTU