Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115745
Name   oriT_pNDM_22ES in_silico
Organism   Enterobacter hormaechei strain 22ES
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM008904 (22276..22378 [+], 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   10084 GenBank   WP_101415845
Name   traI_CS900_RS07575_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   11776 GenBank   WP_008324134
Name   traC_CS900_RS07495_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.



ID   11777 GenBank   WP_101429066
Name   traD_CS900_RS07570_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 21728..46890

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CS900_RS07385 (CS900_07360) 16825..17148 + 324 WP_008324183 hypothetical protein -
CS900_RS07390 (CS900_07365) 17210..17569 + 360 WP_015493069 hypothetical protein -
CS900_RS07395 (CS900_07370) 18196..18570 + 375 WP_008324180 hypothetical protein -
CS900_RS07400 (CS900_07375) 18624..18911 + 288 WP_008324178 hypothetical protein -
CS900_RS07405 (CS900_07380) 18958..19302 + 345 WP_008324177 hypothetical protein -
CS900_RS07410 (CS900_07385) 19388..19651 + 264 WP_008324174 hypothetical protein -
CS900_RS07415 (CS900_07390) 19694..20524 + 831 WP_008324171 N-6 DNA methylase -
CS900_RS07420 (CS900_07395) 21151..21681 + 531 WP_008324170 antirestriction protein -
CS900_RS07425 (CS900_07400) 21728..22204 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
CS900_RS07430 (CS900_07405) 22636..23028 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
CS900_RS07435 (CS900_07410) 23217..23906 + 690 WP_008324166 hypothetical protein -
CS900_RS07440 (CS900_07415) 23993..24217 + 225 WP_008324165 TraY domain-containing protein -
CS900_RS07445 (CS900_07420) 24275..24625 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
CS900_RS07450 (CS900_07425) 24776..25081 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
CS900_RS07455 (CS900_07430) 25096..25662 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
CS900_RS07460 (CS900_07435) 25649..26392 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
CS900_RS07465 (CS900_07440) 26379..27773 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
CS900_RS07470 (CS900_07445) 27795..28334 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
CS900_RS07475 (CS900_07450) 28454..28678 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
CS900_RS07480 (CS900_07455) 28682..28867 + 186 WP_008324139 hypothetical protein -
CS900_RS07485 (CS900_07460) 28851..29252 + 402 WP_016479985 hypothetical protein -
CS900_RS07490 (CS900_07465) 29242..29808 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
CS900_RS07495 (CS900_07470) 29801..32431 + 2631 WP_008324134 type IV secretion system protein TraC virb4
CS900_RS07500 (CS900_07475) 32428..32775 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
CS900_RS07505 (CS900_07480) 32775..33422 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
CS900_RS07510 (CS900_07485) 33425..34411 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
CS900_RS07515 (CS900_07490) 34428..35057 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
CS900_RS07520 (CS900_07495) 35054..36907 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CS900_RS07525 (CS900_07500) 36939..37127 + 189 WP_008324128 conjugal transfer protein TrbE -
CS900_RS07530 (CS900_07505) 37158..37907 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
CS900_RS07535 (CS900_07510) 37924..38172 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
CS900_RS07540 (CS900_07515) 38162..38716 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CS900_RS07545 (CS900_07520) 38709..39137 + 429 WP_008324122 hypothetical protein -
CS900_RS07550 (CS900_07525) 39124..40494 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
CS900_RS07555 (CS900_07530) 40494..43316 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
CS900_RS07560 (CS900_07535) 43338..43769 + 432 WP_008324118 entry exclusion protein -
CS900_RS27055 43844..44182 + 339 WP_032072912 tetratricopeptide repeat protein -
CS900_RS27060 44190..44519 + 330 WP_223856629 tetratricopeptide repeat protein -
CS900_RS07570 (CS900_07545) 44653..46890 + 2238 WP_101429066 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   16178 GenBank   NZ_CM008904
Plasmid name   pNDM_22ES Incompatibility group   IncFII
Plasmid size   106482 bp Coordinate of oriT [Strand]   22276..22378 [+]
Host baterium   Enterobacter hormaechei strain 22ES

Cargo genes

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