Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106399
Name   oriT_pNDM_20ES in_silico
Organism   Enterobacter cloacae strain 20ES
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM008911 (16191..16293 [+], 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   4283 GenBank   WP_172689981
Name   traI_CS906_RS03440_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   4303 GenBank   WP_008324134
Name   traC_CS906_RS03360_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.



ID   4304 GenBank   WP_016479979
Name   traD_CS906_RS03435_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15643..40814

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CS906_RS03250 (CS906_05695) 10740..11063 + 324 WP_008324183 hypothetical protein -
CS906_RS03255 (CS906_05700) 11125..11484 + 360 WP_015493069 hypothetical protein -
CS906_RS03260 (CS906_05705) 12111..12485 + 375 WP_008324180 hypothetical protein -
CS906_RS03265 (CS906_05710) 12539..12826 + 288 WP_008324178 hypothetical protein -
CS906_RS03270 (CS906_05715) 12873..13217 + 345 WP_008324177 hypothetical protein -
CS906_RS03275 (CS906_05720) 13303..13566 + 264 WP_008324174 hypothetical protein -
CS906_RS03280 (CS906_05725) 13609..14439 + 831 WP_008324171 N-6 DNA methylase -
CS906_RS03285 (CS906_05730) 15066..15596 + 531 WP_008324170 antirestriction protein -
CS906_RS03290 (CS906_05735) 15643..16119 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
CS906_RS03295 (CS906_05740) 16551..16943 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
CS906_RS03300 (CS906_05745) 17132..17821 + 690 WP_008324166 hypothetical protein -
CS906_RS03305 (CS906_05750) 17908..18132 + 225 WP_008324165 TraY domain-containing protein -
CS906_RS03310 (CS906_05755) 18190..18540 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
CS906_RS03315 (CS906_05760) 18691..18996 + 306 WP_172689982 type IV conjugative transfer system protein TraL traL
CS906_RS03320 (CS906_05765) 19011..19577 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
CS906_RS03325 (CS906_05770) 19564..20307 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
CS906_RS03330 (CS906_05775) 20294..21688 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
CS906_RS03335 (CS906_05780) 21710..22249 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
CS906_RS03340 (CS906_05785) 22369..22593 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
CS906_RS03345 (CS906_05790) 22597..22782 + 186 WP_008324139 hypothetical protein -
CS906_RS03350 (CS906_05795) 22766..23167 + 402 WP_016479985 hypothetical protein -
CS906_RS03355 (CS906_05800) 23157..23723 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
CS906_RS03360 (CS906_05805) 23716..26346 + 2631 WP_008324134 type IV secretion system protein TraC virb4
CS906_RS03365 (CS906_05810) 26343..26690 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
CS906_RS03370 (CS906_05815) 26690..27337 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
CS906_RS03375 (CS906_05820) 27340..28326 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
CS906_RS03380 (CS906_05825) 28343..28972 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
CS906_RS03385 (CS906_05830) 28969..30822 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CS906_RS03390 (CS906_05835) 30854..31042 + 189 WP_008324128 conjugal transfer protein TrbE -
CS906_RS03395 (CS906_05840) 31073..31822 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
CS906_RS03400 (CS906_05845) 31839..32087 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
CS906_RS03405 (CS906_05850) 32077..32631 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CS906_RS03410 (CS906_05855) 32624..33052 + 429 WP_008324122 hypothetical protein -
CS906_RS03415 (CS906_05860) 33039..34409 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
CS906_RS03420 (CS906_05865) 34409..37231 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
CS906_RS03425 (CS906_05870) 37253..37684 + 432 WP_008324118 entry exclusion protein -
CS906_RS28215 37759..38097 + 339 WP_032072912 tetratricopeptide repeat protein -
CS906_RS28220 38105..38434 + 330 WP_223856629 hypothetical protein -
CS906_RS03435 (CS906_05880) 38568..40814 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   6836 GenBank   NZ_CM008911
Plasmid name   pNDM_20ES Incompatibility group   IncFII
Plasmid size   110766 bp Coordinate of oriT [Strand]   16191..16293 [+]
Host baterium   Enterobacter cloacae strain 20ES

Cargo genes

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