Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105934
Name   oriT_pCF10-NDM in_silico
Organism   Citrobacter youngae strain CF10
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP102502 (103682..103730 [+], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..11, 18..23  (GCAAAA..TTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pCF10-NDM
AATCAGCAAAACTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4002 GenBank   WP_057064462
Name   traI_NUG39_RS25505_pCF10-NDM insolico UniProt ID   A0AA40NJB4
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 188948.08 Da        Isoelectric Point: 6.0680

>WP_057064462.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKIFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQCMAEWMQT
LKATGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLASTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTRVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGAVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVGQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQVIEKEADRQI
RSGALLSVPVSPGNGLQLLVSRQSYNAEKSILRHVLEGKEAVTPLMDKVPDAQLAGLTDGQQNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRGVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLAGEARPWN
PGAITGGRVWADSLPDSTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDGPAGGADVAV
RDVVRDMERIKETPASPLTLPDAPEERRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)

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

(573-625)

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

(631-710)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   4007 GenBank   WP_057064463
Name   traD_NUG39_RS25510_pCF10-NDM insolico UniProt ID   _
Length   722 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 722 a.a.        Molecular weight: 80873.32 Da        Isoelectric Point: 5.1609

>WP_057064463.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGVIVALTLSIKLTWQTFVNGMVWYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVIAPEASAENTGQPQQPQQLTP
APRAADAPSASASAAGAAGTGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAEQDELSPQERQR
REEVNINVHRAPEKDLEPGGYI

  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   4008 GenBank   WP_008324134
Name   traC_NUG39_RS25585_pCF10-NDM 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: 78425..104288

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NUG39_RS25510 (NUG39_25510) 78425..80593 - 2169 WP_057064463 type IV conjugative transfer system coupling protein TraD virb4
NUG39_RS25515 (NUG39_25515) 80712..81512 - 801 WP_226999298 hypothetical protein -
NUG39_RS25520 (NUG39_25520) 81549..82025 - 477 WP_071886900 hypothetical protein -
NUG39_RS25525 (NUG39_25525) 82113..83081 - 969 WP_000654812 IS5-like element IS903B family transposase -
NUG39_RS25530 (NUG39_25530) 83099..85927 - 2829 WP_257749357 conjugal transfer mating-pair stabilization protein TraG traG
NUG39_RS25535 (NUG39_25535) 85927..87303 - 1377 WP_086551404 conjugal transfer pilus assembly protein TraH traH
NUG39_RS25540 (NUG39_25540) 87300..87845 - 546 WP_045379409 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NUG39_RS25545 (NUG39_25545) 87835..88083 - 249 WP_045379412 type-F conjugative transfer system pilin chaperone TraQ -
NUG39_RS25550 (NUG39_25550) 88100..88849 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
NUG39_RS25555 (NUG39_25555) 88880..89068 - 189 WP_008324128 conjugal transfer protein TrbE -
NUG39_RS25560 (NUG39_25560) 89100..90953 - 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NUG39_RS25565 (NUG39_25565) 90950..91579 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
NUG39_RS25570 (NUG39_25570) 91596..92582 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
NUG39_RS25575 (NUG39_25575) 92585..93232 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
NUG39_RS25580 (NUG39_25580) 93232..93579 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
NUG39_RS25585 (NUG39_25585) 93576..96206 - 2631 WP_008324134 type IV secretion system protein TraC virb4
NUG39_RS25590 (NUG39_25590) 96199..96765 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
NUG39_RS25595 (NUG39_25595) 96755..97156 - 402 WP_257749361 hypothetical protein -
NUG39_RS25600 (NUG39_25600) 97140..97325 - 186 WP_008324139 hypothetical protein -
NUG39_RS25605 (NUG39_25605) 97329..97553 - 225 WP_016247532 TraR/DksA C4-type zinc finger protein -
NUG39_RS25610 (NUG39_25610) 97673..98212 - 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
NUG39_RS25615 (NUG39_25615) 98234..99628 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
NUG39_RS25620 (NUG39_25620) 99615..100358 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
NUG39_RS25625 (NUG39_25625) 100345..100911 - 567 WP_016247535 type IV conjugative transfer system protein TraE traE
NUG39_RS25630 (NUG39_25630) 100926..101231 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
NUG39_RS25635 (NUG39_25635) 101382..101732 - 351 WP_016247536 type IV conjugative transfer system pilin TraA -
NUG39_RS25640 (NUG39_25640) 101790..102014 - 225 WP_008324165 TraY domain-containing protein -
NUG39_RS25645 (NUG39_25645) 102101..102790 - 690 WP_008324166 hypothetical protein -
NUG39_RS25650 (NUG39_25650) 102979..103371 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
NUG39_RS25655 (NUG39_25655) 103803..104288 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
NUG39_RS25660 (NUG39_25660) 104321..104650 - 330 WP_011977736 DUF5983 family protein -
NUG39_RS25665 (NUG39_25665) 104683..105504 - 822 WP_032454971 DUF932 domain-containing protein -
NUG39_RS25670 (NUG39_25670) 106320..106719 - 400 Protein_115 hypothetical protein -

Host bacterium

ID   6371 GenBank   NZ_CP102502
Plasmid name   pCF10-NDM Incompatibility group   IncFIB
Plasmid size   138196 bp Coordinate of oriT [Strand]   103682..103730 [+]
Host baterium   Citrobacter youngae strain CF10

Cargo genes

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