Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107048
Name   oriT_pNDM1_EClY2403 in_silico
Organism   Enterobacter cloacae strain EClY2403
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY399975 (57465..57567 [+], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      89..94, 96..101  (AAATAA..TTATTT)
 28..33, 40..45  (GCAAAA..TTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 103 nt

>oriT_pNDM1_EClY2403
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4658 GenBank   WP_016479978
Name   traI_BS633_RS00460_pNDM1_EClY2403 insolico UniProt ID   A0A0G3B767
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189285.41 Da        Isoelectric Point: 6.0099

>WP_016479978.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWAAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKYISPGRKYPQPHVALPAFDRNGRKAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLEGEARPWN
PGAITGGRVWADGLPDATGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

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

(631-710)

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

(573-625)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   4763 GenBank   WP_008324134
Name   traC_BS633_RS00380_pNDM1_EClY2403 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 98841.51 Da        Isoelectric Point: 5.7676

>WP_008324134.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacterales]
MSNPLDSVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVLQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKTIS

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(470-765)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   4764 GenBank   WP_058660425
Name   traD_BS633_RS00455_pNDM1_EClY2403 insolico UniProt ID   _
Length   739 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 739 a.a.        Molecular weight: 82891.50 Da        Isoelectric Point: 5.1609

>WP_058660425.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAW
EAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 56917..82061

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BS633_RS00270 (pNDM1_EClY2403_00058) 52014..52337 + 324 WP_008324183 hypothetical protein -
BS633_RS00275 (pNDM1_EClY2403_00059) 52399..52758 + 360 WP_015493069 hypothetical protein -
BS633_RS00280 (pNDM1_EClY2403_00060) 53385..53759 + 375 WP_008324180 hypothetical protein -
BS633_RS00285 (pNDM1_EClY2403_00061) 53813..54100 + 288 WP_008324178 hypothetical protein -
BS633_RS00290 (pNDM1_EClY2403_00062) 54147..54491 + 345 WP_008324177 hypothetical protein -
BS633_RS00295 (pNDM1_EClY2403_00063) 54577..54840 + 264 WP_008324174 hypothetical protein -
BS633_RS00300 (pNDM1_EClY2403_00064) 54883..55713 + 831 WP_008324171 N-6 DNA methylase -
BS633_RS00305 (pNDM1_EClY2403_00066) 56340..56870 + 531 WP_008324170 antirestriction protein -
BS633_RS00310 (pNDM1_EClY2403_00067) 56917..57393 - 477 WP_008324168 transglycosylase SLT domain-containing protein -
BS633_RS00315 (pNDM1_EClY2403_00068) 57825..58217 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
BS633_RS00320 (pNDM1_EClY2403_00069) 58406..59095 + 690 WP_008324166 hypothetical protein -
BS633_RS00325 (pNDM1_EClY2403_00070) 59182..59406 + 225 WP_008324165 TraY domain-containing protein -
BS633_RS00330 (pNDM1_EClY2403_00071) 59464..59814 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
BS633_RS00335 (pNDM1_EClY2403_00072) 59965..60270 + 306 WP_016479987 type IV conjugative transfer system protein TraL traL
BS633_RS00340 (pNDM1_EClY2403_00073) 60285..60851 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
BS633_RS00345 (pNDM1_EClY2403_00074) 60838..61581 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
BS633_RS00350 (pNDM1_EClY2403_00075) 61568..62962 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
BS633_RS00355 (pNDM1_EClY2403_00076) 62984..63523 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
BS633_RS00360 (pNDM1_EClY2403_00077) 63643..63867 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
BS633_RS00365 (pNDM1_EClY2403_00078) 63871..64056 + 186 WP_008324139 hypothetical protein -
BS633_RS00370 (pNDM1_EClY2403_00079) 64040..64441 + 402 WP_016479985 hypothetical protein -
BS633_RS00375 (pNDM1_EClY2403_00080) 64431..64997 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
BS633_RS00380 (pNDM1_EClY2403_00081) 64990..67620 + 2631 WP_008324134 type IV secretion system protein TraC virb4
BS633_RS00385 (pNDM1_EClY2403_00082) 67617..67964 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
BS633_RS00390 (pNDM1_EClY2403_00083) 67964..68611 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
BS633_RS00395 (pNDM1_EClY2403_00084) 68614..69600 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
BS633_RS00400 (pNDM1_EClY2403_00085) 69617..70246 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
BS633_RS00405 (pNDM1_EClY2403_00086) 70243..72096 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
BS633_RS00410 (pNDM1_EClY2403_00087) 72128..72316 + 189 WP_008324128 conjugal transfer protein TrbE -
BS633_RS00415 (pNDM1_EClY2403_00088) 72347..73096 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
BS633_RS00420 (pNDM1_EClY2403_00089) 73113..73361 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
BS633_RS00425 (pNDM1_EClY2403_00090) 73351..73905 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
BS633_RS00430 (pNDM1_EClY2403_00091) 73898..74326 + 429 WP_008324122 hypothetical protein -
BS633_RS00435 (pNDM1_EClY2403_00092) 74313..75683 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
BS633_RS00440 (pNDM1_EClY2403_00093) 75683..78505 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
BS633_RS00445 (pNDM1_EClY2403_00094) 78527..78958 + 432 WP_008324118 entry exclusion protein -
BS633_RS00615 (pNDM1_EClY2403_00095) 79051..79371 + 321 WP_227543090 tetratricopeptide repeat protein -
BS633_RS00620 (pNDM1_EClY2403_00096) 79379..79708 + 330 WP_223856629 hypothetical protein -
BS633_RS00455 (pNDM1_EClY2403_00097) 79842..82061 + 2220 WP_058660425 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   7484 GenBank   NZ_KY399975
Plasmid name   pNDM1_EClY2403 Incompatibility group   IncFIB
Plasmid size   109325 bp Coordinate of oriT [Strand]   57465..57567 [+]
Host baterium   Enterobacter cloacae strain EClY2403

Cargo genes

Drug resistance gene   blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -