Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103263
Name   oriT_pECB11 in_silico
Organism   Escherichia coli strain CH292B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY865321 (55258..55381 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pECB11
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2439 GenBank   WP_061093447
Name   traI_HTM69_RS00550_pECB11 insolico UniProt ID   A0A2Z4I1F4
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192119.90 Da        Isoelectric Point: 6.0788

>WP_061093447.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

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

(633-712)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   1036 GenBank   WP_000124981
Name   WP_000124981_pECB11 insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9

ID   1037 GenBank   WP_001254386
Name   WP_001254386_pECB11 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   2206 GenBank   WP_015059012
Name   traC_HTM69_RS00440_pECB11 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99393.22 Da        Isoelectric Point: 6.3465

>WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 54686..78348

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTM69_RS00335 50658..51092 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTM69_RS00340 51089..51851 + 763 Protein_65 plasmid SOS inhibition protein A -
HTM69_RS00615 52030..52179 + 150 Protein_66 plasmid maintenance protein Mok -
HTM69_RS00345 52121..52246 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTM69_RS00595 52565..52861 - 297 Protein_68 hypothetical protein -
HTM69_RS00360 53161..53457 + 297 WP_001272251 hypothetical protein -
HTM69_RS00365 53568..54389 + 822 WP_001234445 DUF932 domain-containing protein -
HTM69_RS00370 54686..55333 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
HTM69_RS00375 55610..55993 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HTM69_RS00380 56184..56870 + 687 WP_015059009 PAS domain-containing protein -
HTM69_RS00385 56964..57191 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTM69_RS00390 57225..57590 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
HTM69_RS00395 57605..57916 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTM69_RS00400 57938..58504 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
HTM69_RS00405 58491..59219 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTM69_RS00410 59219..60646 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
HTM69_RS00415 60636..61226 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HTM69_RS00420 61213..61410 + 198 WP_001324648 conjugal transfer protein TrbD -
HTM69_RS00425 61422..61673 + 252 WP_001038341 conjugal transfer protein TrbG -
HTM69_RS00430 61670..62185 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
HTM69_RS00435 62320..62541 + 222 WP_001278692 conjugal transfer protein TraR -
HTM69_RS00440 62701..65328 + 2628 WP_015059012 type IV secretion system protein TraC virb4
HTM69_RS00445 65325..65711 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
HTM69_RS00450 65708..66340 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
HTM69_RS00455 66337..67329 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTM69_RS00460 67356..67664 + 309 WP_000412447 hypothetical protein -
HTM69_RS00465 67727..68248 + 522 WP_015059014 hypothetical protein -
HTM69_RS00470 68275..68913 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTM69_RS00475 68910..69281 + 372 WP_000056336 hypothetical protein -
HTM69_RS00480 69307..69729 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
HTM69_RS00485 69726..71576 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTM69_RS00490 71603..71860 + 258 WP_053913405 conjugal transfer protein TrbE -
HTM69_RS00495 71853..72596 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
HTM69_RS00500 72757..72993 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
HTM69_RS00505 72980..73525 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTM69_RS00510 73515..73829 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
HTM69_RS00515 73783..74175 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
HTM69_RS00520 74162..75535 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
HTM69_RS00525 75532..78348 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
HTM69_RS00530 78381..78902 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
HTM69_RS00535 78927..79658 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
HTM69_RS00540 79861..80598 + 738 WP_015059020 hypothetical protein -
HTM69_RS00545 80649..82886 + 2238 Protein_106 type IV conjugative transfer system coupling protein TraD -

Host bacterium

ID   3706 GenBank   NZ_KY865321
Plasmid name   pECB11 Incompatibility group   ColE10
Plasmid size   92545 bp Coordinate of oriT [Strand]   55258..55381 [+]
Host baterium   Escherichia coli strain CH292B

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, fosA3, blaTEM-1B, blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -