Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107042
Name   oriT_pNDM_22ES in_silico
Organism   Enterobacter cloacae strain 22ES
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MF042358 (84105..84207 [-], 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_pNDM_22ES
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4651 GenBank   WP_101415845
Name   traI_HTN57_RS00320_pNDM_22ES insolico UniProt ID   _
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189299.44 Da        Isoelectric Point: 6.0099

>WP_101415845.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGAGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
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)

AAA domain (AAA_30)

(967-1150)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   4753 GenBank   WP_101429066
Name   traD_HTN57_RS00325_pNDM_22ES insolico UniProt ID   _
Length   745 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 745 a.a.        Molecular weight: 83598.26 Da        Isoelectric Point: 5.1609

>WP_101429066.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEV
VDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(172-560)

  Protein structure



No available structure.



ID   4754 GenBank   WP_008324134
Name   traC_HTN57_RS00400_pNDM_22ES 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 59593..84755

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTN57_RS00325 59593..61830 - 2238 WP_101429066 type IV conjugative transfer system coupling protein TraD virb4
HTN57_RS00600 61964..62293 - 330 WP_223856629 hypothetical protein -
HTN57_RS00605 62301..62639 - 339 WP_032072912 tetratricopeptide repeat protein -
HTN57_RS00335 62714..63145 - 432 WP_008324118 entry exclusion protein -
HTN57_RS00340 63167..65989 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
HTN57_RS00345 65989..67359 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
HTN57_RS00350 67346..67774 - 429 WP_008324122 hypothetical protein -
HTN57_RS00355 67767..68321 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTN57_RS00360 68311..68559 - 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
HTN57_RS00365 68576..69325 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
HTN57_RS00370 69356..69544 - 189 WP_008324128 conjugal transfer protein TrbE -
HTN57_RS00375 69576..71429 - 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTN57_RS00380 71426..72055 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTN57_RS00385 72072..73058 - 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
HTN57_RS00390 73061..73708 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
HTN57_RS00395 73708..74055 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
HTN57_RS00400 74052..76682 - 2631 WP_008324134 type IV secretion system protein TraC virb4
HTN57_RS00405 76675..77241 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
HTN57_RS00410 77231..77632 - 402 WP_016479985 hypothetical protein -
HTN57_RS00415 77616..77801 - 186 WP_008324139 hypothetical protein -
HTN57_RS00420 77805..78029 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
HTN57_RS00425 78149..78688 - 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
HTN57_RS00430 78710..80104 - 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
HTN57_RS00435 80091..80834 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
HTN57_RS00440 80821..81387 - 567 WP_016247535 type IV conjugative transfer system protein TraE traE
HTN57_RS00445 81402..81707 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
HTN57_RS00450 81858..82208 - 351 WP_016247536 type IV conjugative transfer system pilin TraA -
HTN57_RS00455 82266..82490 - 225 WP_008324165 TraY domain-containing protein -
HTN57_RS00460 82577..83266 - 690 WP_008324166 hypothetical protein -
HTN57_RS00465 83455..83847 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
HTN57_RS00470 84279..84755 + 477 WP_008324168 transglycosylase SLT domain-containing protein -
HTN57_RS00475 84802..85332 - 531 WP_008324170 antirestriction protein -
HTN57_RS00480 85959..86789 - 831 WP_008324171 N-6 DNA methylase -
HTN57_RS00485 86832..87044 - 213 WP_058655950 hypothetical protein -
HTN57_RS00490 87181..87525 - 345 WP_008324177 hypothetical protein -
HTN57_RS00495 87572..87859 - 288 WP_008324178 hypothetical protein -
HTN57_RS00500 87913..88287 - 375 WP_008324180 hypothetical protein -
HTN57_RS00505 88914..89273 - 360 WP_015493069 hypothetical protein -
HTN57_RS00510 89335..89658 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   7478 GenBank   NZ_MF042358
Plasmid name   pNDM_22ES Incompatibility group   IncFIB
Plasmid size   100393 bp Coordinate of oriT [Strand]   84105..84207 [-]
Host baterium   Enterobacter cloacae strain 22ES

Cargo genes

Drug resistance gene   blaNDM-1, rmtC, sul1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -