Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115278
Name   oriT_pEC1382-2 in_silico
Organism   Enterobacter kobei strain EC1382
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP096851 (60998..61100 [-], 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_pEC1382-2
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9767 GenBank   WP_016479978
Name   traI_M2B19_RS26915_pEC1382-2 insolico UniProt ID   A0A0G3B767
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189285.41 Da        Isoelectric Point: 6.0099

>WP_016479978.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
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   11390 GenBank   WP_016479979
Name   traD_M2B19_RS26920_pEC1382-2 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.



ID   11391 GenBank   WP_008324134
Name   traC_M2B19_RS27000_pEC1382-2 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: 36477..61648

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
M2B19_RS26920 (M2B19_26930) 36477..38723 - 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4
M2B19_RS26925 (M2B19_26935) 38857..39186 - 330 WP_223856629 tetratricopeptide repeat protein -
M2B19_RS26930 (M2B19_26940) 39194..39532 - 339 WP_032072912 tetratricopeptide repeat protein -
M2B19_RS26935 (M2B19_26945) 39607..40038 - 432 WP_008324118 entry exclusion protein -
M2B19_RS26940 (M2B19_26950) 40060..42882 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
M2B19_RS26945 (M2B19_26955) 42882..44252 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
M2B19_RS26950 (M2B19_26960) 44239..44667 - 429 WP_008324122 hypothetical protein -
M2B19_RS26955 (M2B19_26965) 44660..45214 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
M2B19_RS26960 (M2B19_26970) 45204..45452 - 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
M2B19_RS26965 (M2B19_26975) 45469..46218 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
M2B19_RS26970 (M2B19_26980) 46249..46437 - 189 WP_008324128 conjugal transfer protein TrbE -
M2B19_RS26975 (M2B19_26985) 46469..48322 - 1854 WP_309164728 type-F conjugative transfer system mating-pair stabilization protein TraN traN
M2B19_RS26980 (M2B19_26990) 48319..48948 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
M2B19_RS26985 (M2B19_26995) 48965..49951 - 987 Protein_55 conjugal transfer pilus assembly protein TraU -
M2B19_RS26990 (M2B19_27000) 49954..50601 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
M2B19_RS26995 (M2B19_27005) 50601..50948 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
M2B19_RS27000 (M2B19_27010) 50945..53575 - 2631 WP_008324134 type IV secretion system protein TraC virb4
M2B19_RS27005 (M2B19_27015) 53568..54134 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
M2B19_RS27010 (M2B19_27020) 54124..54525 - 402 WP_016479985 hypothetical protein -
M2B19_RS27015 (M2B19_27025) 54509..54694 - 186 WP_008324139 hypothetical protein -
M2B19_RS27020 (M2B19_27030) 54698..54922 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
M2B19_RS27025 (M2B19_27035) 55042..55581 - 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
M2B19_RS27030 (M2B19_27040) 55603..56997 - 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
M2B19_RS27035 (M2B19_27045) 56984..57727 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
M2B19_RS27040 (M2B19_27050) 57714..58280 - 567 WP_016247535 type IV conjugative transfer system protein TraE traE
M2B19_RS27045 (M2B19_27055) 58295..58600 - 306 WP_016479987 type IV conjugative transfer system protein TraL traL
M2B19_RS27050 (M2B19_27060) 58751..59101 - 351 WP_016247536 type IV conjugative transfer system pilin TraA -
M2B19_RS27055 (M2B19_27065) 59159..59383 - 225 WP_008324165 TraY domain-containing protein -
M2B19_RS27060 (M2B19_27070) 59470..60159 - 690 WP_008324166 hypothetical protein -
M2B19_RS27065 (M2B19_27075) 60348..60740 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
M2B19_RS27070 (M2B19_27080) 61172..61648 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
M2B19_RS27075 (M2B19_27085) 61695..62225 - 531 WP_008324170 antirestriction protein -
M2B19_RS27080 (M2B19_27090) 62852..63682 - 831 WP_008324171 N-6 DNA methylase -
M2B19_RS27085 (M2B19_27095) 63725..63988 - 264 WP_008324174 hypothetical protein -
M2B19_RS27090 (M2B19_27100) 64074..64418 - 345 WP_008324177 hypothetical protein -
M2B19_RS27095 (M2B19_27105) 64465..64752 - 288 WP_008324178 hypothetical protein -
M2B19_RS27100 (M2B19_27110) 64806..65180 - 375 WP_008324180 hypothetical protein -
M2B19_RS27105 (M2B19_27115) 65807..66166 - 360 WP_015493069 hypothetical protein -
M2B19_RS27110 (M2B19_27120) 66228..66551 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   15714 GenBank   NZ_CP096851
Plasmid name   pEC1382-2 Incompatibility group   IncFII
Plasmid size   108996 bp Coordinate of oriT [Strand]   60998..61100 [-]
Host baterium   Enterobacter kobei strain EC1382

Cargo genes

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