Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100453
Name   oriT_pGUE-NDM in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019089 (38810..39271 [+], 462 nt)
oriT length   462 nt
IRs (inverted repeats)      142..151, 154..163  (ATAGGGTCGT..ACGACCCTAT)
 231..238, 241..248  (GCAAAAAC..GTTTTTGC)
Location of nic site      257..258
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 462 nt

>oriT_pGUE-NDM
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGTCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATAAAATTTGTCAGTACTGACCCTAACAAGGGTCGCCATAGGGTCGCCATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGCTAATGATTCAAAAAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAGTGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGATCTGCCAGGCCACTGATTGCTTTGATCTTGCAGGCCGGGATTACAAAATAGATCCTGATTTACTGAGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   524 GenBank   YP_006953807
Name   TraI_pGUE-NDM insolico UniProt ID   I1WZQ7
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191914.74 Da        Isoelectric Point: 6.1060

>YP_006953807.1 TraI (plasmid) [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKISGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-627)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 12818..39667

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS905_RS00060 (D616_p76066) 12818..15043 - 2226 WP_015059124 type IV conjugative transfer system coupling protein TraD virb4
HS905_RS00065 (D616_p76065) 15296..16027 - 732 WP_094658456 conjugal transfer complement resistance protein TraT -
HS905_RS00070 (D616_p76064) 16041..16550 - 510 WP_031943494 conjugal transfer entry exclusion protein TraS -
HS905_RS00075 (D616_p76063) 16547..19372 - 2826 WP_001007045 conjugal transfer mating-pair stabilization protein TraG traG
HS905_RS00080 (D616_p76062) 19369..20742 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HS905_RS00085 (D616_p76061) 20742..21104 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
HS905_RS00090 (D616_p76060) 21034..21579 - 546 WP_000059821 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS905_RS00095 (D616_p76059) 21566..21850 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HS905_RS00100 (D616_p76058) 21969..22316 - 348 WP_001287891 conjugal transfer protein TrbA -
HS905_RS00105 (D616_p76057) 22332..23075 - 744 WP_001430248 type-F conjugative transfer system pilin assembly protein TraF traF
HS905_RS00110 23068..23325 - 258 WP_000864352 conjugal transfer protein TrbE -
HS905_RS00115 (D616_p76056) 23352..25160 - 1809 WP_000821821 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS905_RS00120 (D616_p76055) 25157..25795 - 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS905_RS00125 (D616_p76054) 25804..26796 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HS905_RS00130 (D616_p76053) 26793..27425 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HS905_RS00135 (D616_p76052) 27422..27808 - 387 WP_000214092 type-F conjugative transfer system protein TrbI -
HS905_RS00140 (D616_p76051) 27805..30435 - 2631 WP_000069764 type IV secretion system protein TraC virb4
HS905_RS00145 (D616_p76050) 30561..30923 - 363 WP_000836675 hypothetical protein -
HS905_RS00150 30951..31165 - 215 Protein_30 hypothetical protein -
HS905_RS00155 (D616_p76049) 31245..31721 - 477 WP_015059129 hypothetical protein -
HS905_RS00160 (D616_p76048) 31714..31935 - 222 WP_001278695 conjugal transfer protein TraR -
HS905_RS00165 (D616_p76047) 32070..32585 - 516 WP_015059130 type IV conjugative transfer system lipoprotein TraV traV
HS905_RS00170 (D616_p76046) 32582..32833 - 252 WP_001038342 conjugal transfer protein TrbG -
HS905_RS00175 (D616_p76045) 32826..33146 - 321 WP_001057287 conjugal transfer protein TrbD virb4
HS905_RS00180 (D616_p76044) 33133..33723 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
HS905_RS00185 (D616_p76043) 33713..35140 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HS905_RS00190 (D616_p76042) 35140..35868 - 729 WP_001230813 type-F conjugative transfer system secretin TraK traK
HS905_RS00195 (D616_p76041) 35855..36421 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HS905_RS00200 (D616_p76040) 36443..36754 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HS905_RS00205 (D616_p76039) 36769..37128 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
HS905_RS00210 (D616_p76038) 37162..37389 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HS905_RS00215 (D616_p76037) 37483..38169 - 687 WP_000332484 PAS domain-containing protein -
HS905_RS00220 (D616_p76036) 38360..38743 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HS905_RS00225 39020..39667 + 648 WP_031943493 transglycosylase SLT domain-containing protein virB1
HS905_RS00230 (D616_p76035) 39963..40784 - 822 WP_001234469 DUF932 domain-containing protein -
HS905_RS00235 40902..41189 - 288 WP_000107544 hypothetical protein -
HS905_RS00520 41214..41420 - 207 WP_250695593 single-stranded DNA-binding protein -
HS905_RS00525 41490..41663 + 174 Protein_49 hypothetical protein -
HS905_RS00530 41661..41891 - 231 WP_001426396 hypothetical protein -
HS905_RS00240 42111..42236 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HS905_RS00535 42178..42327 - 150 Protein_52 plasmid maintenance protein Mok -
HS905_RS00245 (D616_p76031) 42506..43268 - 763 Protein_53 plasmid SOS inhibition protein A -
HS905_RS00250 (D616_p76030) 43265..43699 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   914 GenBank   NC_019089
Plasmid name   pGUE-NDM Incompatibility group   IncFII
Plasmid size   87021 bp Coordinate of oriT [Strand]   38810..39271 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   dfrA12, aadA2, qacE, sul1, blaNDM-1, aac(3)-IIa, blaOXA-1, aac(6')-Ib-cr
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11