Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100446
Name   oriT_pNDM10505 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019069 (48617..49167 [+], 551 nt)
oriT length   551 nt
IRs (inverted repeats)      IR1: 62..70, 71..79  (AACCCTTTC..GACAGGGTT)
  IR2: 143..150, 154..161  (TGGCCTGC..GGAGGCCA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 551 nt

>oriT_pNDM10505
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   517 GenBank   YP_006953139
Name   TraI_pNDM10505 insolico UniProt ID   C4NVS7
Length   990 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109356.90 Da        Isoelectric Point: 4.9395

>YP_006953139.1 TraI type IV conjugative transfer system protein (plasmid) [Escherichia coli]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB C4NVS7


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 46751..55841

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS804_RS00345 (pNDM10505_67) 42782..43015 - 234 WP_001191890 hypothetical protein -
HS804_RS00350 (pNDM10505_68) 42997..43614 - 618 WP_001249395 hypothetical protein -
HS804_RS00355 (pNDM10505_69) 43782..46754 + 2973 WP_001326173 MobH family relaxase -
HS804_RS00360 (pNDM10505_70) 46751..48616 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HS804_RS00365 (pNDM10505_71) 48627..49211 + 585 WP_000332868 hypothetical protein -
HS804_RS00370 (pNDM10505_72) 49168..49797 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HS804_RS00375 (pNDM10505_73) 49807..50253 + 447 WP_000122507 hypothetical protein -
HS804_RS00380 (pNDM10505_74) 50263..50640 + 378 WP_000869297 hypothetical protein -
HS804_RS00385 (pNDM10505_75) 50640..51302 + 663 WP_001231464 hypothetical protein -
HS804_RS00390 51483..51626 + 144 WP_001275801 hypothetical protein -
HS804_RS00395 (pNDM10505_76) 51638..52003 + 366 WP_001052530 hypothetical protein -
HS804_RS00400 (pNDM10505_77) 52148..52429 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HS804_RS00405 (pNDM10505_78) 52426..53052 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HS804_RS00410 (pNDM10505_79) 53036..53953 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HS804_RS00415 (pNDM10505_80) 53953..55266 + 1314 WP_024131605 TraB/VirB10 family protein traB
HS804_RS00420 (pNDM10505_81) 55263..55841 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HS804_RS00425 (pNDM10505_82) 55845..56237 + 393 WP_000479535 TraA family conjugative transfer protein -
HS804_RS00430 (pNDM10505_83) 56522..57784 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HS804_RS00435 (pNDM10505_84) 58108..59253 + 1146 WP_015058212 class C beta-lactamase CMY-6 -
HS804_RS00440 (pNDM10505_85) 59347..59880 + 534 WP_001221666 lipocalin family protein -
HS804_RS00445 (pNDM10505_86) 59877..60194 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -

Host bacterium

ID   907 GenBank   NC_019069
Plasmid name   pNDM10505 Incompatibility group   IncA/C2
Plasmid size   166744 bp Coordinate of oriT [Strand]   48617..49167 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   blaCMY-6, aac(6')-Ib, qacE, sul1, rmtC, aac(3)-IId, aph(3')-VI, blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -