Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117823
Name   oriT_unitig_2_pilon in_silico
Organism   Citrobacter koseri strain AR_0025
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026698 (20441..20543 [+], 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_unitig_2_pilon
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTTCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11324 GenBank   WP_022652257
Name   traI_AM352_RS23845_unitig_2_pilon 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   13234 GenBank   WP_008324134
Name   traC_AM352_RS23760_unitig_2_pilon 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   13235 GenBank   WP_023307203
Name   traD_AM352_RS23840_unitig_2_pilon 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 19893..46173

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AM352_RS23650 (AM352_23740) 15077..15424 - 348 WP_000609174 IS66 family insertion sequence element accessory protein TnpB -
AM352_RS23660 (AM352_23750) 16361..16735 + 375 WP_008324180 hypothetical protein -
AM352_RS23665 (AM352_23755) 16789..17076 + 288 WP_008324178 hypothetical protein -
AM352_RS23670 (AM352_23760) 17123..17467 + 345 WP_022652252 hypothetical protein -
AM352_RS23675 (AM352_23765) 17553..17816 + 264 WP_008324174 hypothetical protein -
AM352_RS23680 (AM352_23770) 17859..18689 + 831 WP_022652253 N-6 DNA methylase -
AM352_RS23685 (AM352_23775) 19316..19846 + 531 WP_008324170 antirestriction protein -
AM352_RS23690 (AM352_23780) 19893..20369 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
AM352_RS23695 (AM352_23785) 20801..21193 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
AM352_RS23700 (AM352_23790) 21382..22071 + 690 WP_008324166 hypothetical protein -
AM352_RS23705 (AM352_23795) 22158..22382 + 225 WP_008324165 TraY domain-containing protein -
AM352_RS23710 (AM352_23800) 22440..22790 + 351 WP_008324162 type IV conjugative transfer system pilin TraA -
AM352_RS23715 (AM352_23805) 22941..23246 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
AM352_RS23720 (AM352_23810) 23261..23827 + 567 WP_008324158 type IV conjugative transfer system protein TraE traE
AM352_RS23725 (AM352_23815) 23814..24557 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
AM352_RS23730 (AM352_23820) 24544..25938 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
AM352_RS23735 (AM352_23825) 25960..26499 + 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
AM352_RS23740 (AM352_23830) 26619..26843 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
AM352_RS23745 (AM352_23835) 26847..27032 + 186 WP_022652254 hypothetical protein -
AM352_RS23750 (AM352_23840) 27016..27417 + 402 WP_008324137 hypothetical protein -
AM352_RS23755 (AM352_23845) 27407..27973 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
AM352_RS23760 (AM352_23850) 27966..30596 + 2631 WP_008324134 type IV secretion system protein TraC virb4
AM352_RS23765 (AM352_23855) 30593..30940 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
AM352_RS23770 (AM352_23860) 30940..31587 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
AM352_RS23775 (AM352_23865) 31590..32576 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
AM352_RS23780 (AM352_23870) 32593..33222 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
AM352_RS23785 (AM352_23875) 33219..35072 + 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AM352_RS23790 (AM352_23880) 35104..35292 + 189 WP_008324128 conjugal transfer protein TrbE -
AM352_RS23795 (AM352_23885) 35323..36072 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
AM352_RS23800 (AM352_23890) 36089..36337 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
AM352_RS23805 (AM352_23895) 36327..36881 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AM352_RS23810 (AM352_23900) 36874..37302 + 429 WP_008324122 hypothetical protein -
AM352_RS23815 (AM352_23905) 37289..38659 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
AM352_RS23820 (AM352_23910) 38659..41481 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
AM352_RS23825 (AM352_23915) 41503..41934 + 432 WP_008324118 entry exclusion protein -
AM352_RS23830 (AM352_23920) 42009..42683 + 675 WP_008324909 tetratricopeptide repeat protein -
AM352_RS23835 (AM352_23925) 42834..43865 + 1032 WP_001395480 IS630-like element ISEc33 family transposase -
AM352_RS23840 (AM352_23930) 43972..46173 + 2202 WP_023307203 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   18256 GenBank   NZ_CP026698
Plasmid name   unitig_2_pilon Incompatibility group   IncFII
Plasmid size   82058 bp Coordinate of oriT [Strand]   20441..20543 [+]
Host baterium   Citrobacter koseri strain AR_0025

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -