Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107035
Name   oriT_pNDM_20ES in_silico
Organism   Enterobacter cloacae strain 20ES
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MF042356 (94474..94576 [-], 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_20ES
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4644 GenBank   WP_172689981
Name   traI_HTN51_RS00350_pNDM_20ES 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: 189384.55 Da        Isoelectric Point: 6.0701

>WP_172689981.1 conjugative transfer relaxase/helicase TraI [Enterobacter cloacae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGRGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
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   4742 GenBank   WP_016479979
Name   traD_HTN51_RS00355_pNDM_20ES insolico UniProt ID   _
Length   748 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 748 a.a.        Molecular weight: 83951.64 Da        Isoelectric Point: 5.1609

>WP_016479979.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISES
GEVVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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   4743 GenBank   WP_008324134
Name   traC_HTN51_RS00430_pNDM_20ES 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: 69953..95124

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTN51_RS00355 69953..72199 - 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4
HTN51_RS00630 72333..72662 - 330 WP_223856629 hypothetical protein -
HTN51_RS00635 72670..72990 - 321 WP_227543090 tetratricopeptide repeat protein -
HTN51_RS00365 73083..73514 - 432 WP_008324118 entry exclusion protein -
HTN51_RS00370 73536..76358 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
HTN51_RS00375 76358..77728 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
HTN51_RS00380 77715..78143 - 429 WP_008324122 hypothetical protein -
HTN51_RS00385 78136..78690 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTN51_RS00390 78680..78928 - 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
HTN51_RS00395 78945..79694 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
HTN51_RS00400 79725..79913 - 189 WP_008324128 conjugal transfer protein TrbE -
HTN51_RS00405 79945..81798 - 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTN51_RS00410 81795..82424 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTN51_RS00415 82441..83427 - 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
HTN51_RS00420 83430..84077 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
HTN51_RS00425 84077..84424 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
HTN51_RS00430 84421..87051 - 2631 WP_008324134 type IV secretion system protein TraC virb4
HTN51_RS00435 87044..87610 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
HTN51_RS00440 87600..88001 - 402 WP_016479985 hypothetical protein -
HTN51_RS00445 87985..88170 - 186 WP_008324139 hypothetical protein -
HTN51_RS00450 88174..88398 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
HTN51_RS00455 88518..89057 - 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
HTN51_RS00460 89079..90473 - 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
HTN51_RS00465 90460..91203 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
HTN51_RS00470 91190..91756 - 567 WP_016247535 type IV conjugative transfer system protein TraE traE
HTN51_RS00475 91771..92076 - 306 WP_172689982 type IV conjugative transfer system protein TraL traL
HTN51_RS00480 92227..92577 - 351 WP_016247536 type IV conjugative transfer system pilin TraA -
HTN51_RS00485 92635..92859 - 225 WP_008324165 TraY domain-containing protein -
HTN51_RS00490 92946..93635 - 690 WP_008324166 hypothetical protein -
HTN51_RS00495 93824..94216 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
HTN51_RS00500 94648..95124 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
HTN51_RS00505 95171..95701 - 531 WP_008324170 antirestriction protein -
HTN51_RS00510 96328..97158 - 831 WP_008324171 N-6 DNA methylase -
HTN51_RS00515 97201..97464 - 264 WP_008324174 hypothetical protein -
HTN51_RS00520 97550..97894 - 345 WP_008324177 hypothetical protein -
HTN51_RS00525 97941..98228 - 288 WP_008324178 hypothetical protein -
HTN51_RS00530 98282..98656 - 375 WP_008324180 hypothetical protein -
HTN51_RS00535 99283..99642 - 360 WP_015493069 hypothetical protein -
HTN51_RS00540 99704..100027 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   7471 GenBank   NZ_MF042356
Plasmid name   pNDM_20ES Incompatibility group   IncFIB
Plasmid size   110766 bp Coordinate of oriT [Strand]   94474..94576 [-]
Host baterium   Enterobacter cloacae strain 20ES

Cargo genes

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