Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120436
Name   oriT_p2-L2724hy-SFO-1 in_silico
Organism   Citrobacter portucalensis strain L2724hy
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP136603 (93345..93447 [-], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      89..94, 96..101  (AAATAA..TTATTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 103 nt

>oriT_p2-L2724hy-SFO-1
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTTCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12871 GenBank   WP_022652257
Name   traI_RY846_RS26390_p2-L2724hy-SFO-1 insolico UniProt ID   A0A3S5I3M3
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189292.49 Da        Isoelectric Point: 6.1121

>WP_022652257.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMHT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVVPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
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)

AAA domain (AAA_30)

(967-1148)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   15120 GenBank   WP_023307203
Name   traD_RY846_RS26395_p2-L2724hy-SFO-1 insolico UniProt ID   _
Length   733 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 733 a.a.        Molecular weight: 82212.80 Da        Isoelectric Point: 5.1609

>WP_023307203.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENVGQPQQPQQPQQ
PQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAE
QDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   15121 GenBank   WP_008324134
Name   traC_RY846_RS26470_p2-L2724hy-SFO-1 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: 66010..93995

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RY846_RS26395 (RY846_26395) 66010..68211 - 2202 WP_023307203 type IV conjugative transfer system coupling protein TraD virb4
RY846_RS26400 (RY846_26400) 68345..69019 - 675 WP_008324909 tetratricopeptide repeat protein -
RY846_RS26405 (RY846_26405) 69094..69525 - 432 WP_008324118 entry exclusion protein -
RY846_RS26410 (RY846_26410) 69547..72369 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
RY846_RS26415 (RY846_26415) 72369..73739 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
RY846_RS26420 (RY846_26420) 73726..74154 - 429 WP_008324122 hypothetical protein -
RY846_RS26425 (RY846_26425) 74147..74701 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
RY846_RS26430 (RY846_26430) 74691..74939 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
RY846_RS26435 (RY846_26435) 74956..75705 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
RY846_RS26440 (RY846_26440) 75736..75924 - 189 WP_008324128 conjugal transfer protein TrbE -
RY846_RS26445 (RY846_26445) 75956..77809 - 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
RY846_RS26450 (RY846_26450) 77806..78435 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
RY846_RS26455 (RY846_26455) 78452..79438 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
RY846_RS26460 (RY846_26460) 79441..80088 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
RY846_RS26465 (RY846_26465) 80088..80435 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
RY846_RS26470 (RY846_26470) 80432..83062 - 2631 WP_008324134 type IV secretion system protein TraC virb4
RY846_RS26475 (RY846_26475) 83055..83621 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
RY846_RS26480 (RY846_26480) 83611..84012 - 402 WP_008324137 hypothetical protein -
RY846_RS26485 (RY846_26485) 83996..84181 - 186 WP_022652254 hypothetical protein -
RY846_RS26490 (RY846_26490) 84185..84409 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
RY846_RS26495 (RY846_26495) 84529..85068 - 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
RY846_RS26500 (RY846_26500) 85090..86484 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
RY846_RS26505 (RY846_26505) 86471..87214 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
RY846_RS26510 (RY846_26510) 87201..87767 - 567 WP_008324158 type IV conjugative transfer system protein TraE traE
RY846_RS26515 (RY846_26515) 87782..88087 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
RY846_RS26520 (RY846_26520) 88238..88579 - 342 WP_326926118 type IV conjugative transfer system pilin TraA -
RY846_RS26525 (RY846_26525) 88688..89233 + 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -
RY846_RS26530 (RY846_26530) 89370..89942 + 573 WP_001493762 recombinase family protein -
RY846_RS26535 (RY846_26535) 89979..91370 + 1392 WP_001493761 ISKra4-like element ISKpn19 family transposase -
RY846_RS26540 (RY846_26540) 91506..91730 - 225 WP_008324165 TraY domain-containing protein -
RY846_RS26545 (RY846_26545) 91817..92506 - 690 WP_008324166 hypothetical protein -
RY846_RS26550 (RY846_26550) 92695..93087 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
RY846_RS26555 (RY846_26555) 93519..93995 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
RY846_RS26560 (RY846_26560) 94042..94572 - 531 WP_008324170 antirestriction protein -
RY846_RS26565 (RY846_26565) 95199..96029 - 831 WP_022652253 N-6 DNA methylase -
RY846_RS26570 (RY846_26570) 96072..96335 - 264 WP_008324174 hypothetical protein -
RY846_RS26575 (RY846_26575) 96421..96765 - 345 WP_022652252 hypothetical protein -
RY846_RS26580 (RY846_26580) 96812..97099 - 288 WP_008324178 hypothetical protein -
RY846_RS26585 (RY846_26585) 97153..97527 - 375 WP_008324180 hypothetical protein -
RY846_RS26590 (RY846_26590) 98248..98514 - 267 WP_022652251 hypothetical protein -
RY846_RS26595 (RY846_26595) 98576..98899 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   20865 GenBank   NZ_CP136603
Plasmid name   p2-L2724hy-SFO-1 Incompatibility group   IncFIB
Plasmid size   131226 bp Coordinate of oriT [Strand]   93345..93447 [-]
Host baterium   Citrobacter portucalensis strain L2724hy

Cargo genes

Drug resistance gene   fosA3, blaSFO-1
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -