Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103129
Name   oriT_pIMI-6 in_silico
Organism   Enterobacter cloacae strain N14-0444
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX786187 (132204..132260 [-], 57 nt)
oriT length   57 nt
IRs (inverted repeats)      13..20, 23..30  (GCAAAATT..AATTTTGC)
Location of nic site      39..40
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 57 nt

>oriT_pIMI-6
TAAAGTTAATCAGCAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2346 GenBank   WP_172689111
Name   traI_HTK44_RS00865_pIMI-6 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: 189268.71 Da        Isoelectric Point: 6.2261

>WP_172689111.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacter cloacae complex]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRIQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVDTAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTRHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVTA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPVTAPEVIDINSSVGQSIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDLGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEARSRERFVIDRVTGRNNSLTLRNVQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLKGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVGQ
GWVESPGRSVSDSAKVFASLSQRELDNTTLNKLALSGRAVQLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQVIEKEADRQI
RSGALLSVPVSPGNGLQLLVSRQSYNAEKSILRHVLEGKEAVTPLMDKVPDAQLAGLTDGQQNATRMILG
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
HQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLINRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDMMSGGQPATLLEAIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHEARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAVRLTATAKAQGEVPAGRAALRQAGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLEGEVRPWN
PGAITGGRVWADGLPDGTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1151)

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

(573-625)

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

(631-710)

DNA helicase TraI (TraI_C)

(1430-1551)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4CP

ID   2075 GenBank   WP_172689102
Name   traC_HTK44_RS00790_pIMI-6 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: 98774.39 Da        Isoelectric Point: 5.5375

>WP_172689102.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacter cloacae complex]
MSNPLDTVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGCNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVVQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLNDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKTIS

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(470-765)

  Protein structure



No available structure.



ID   2076 GenBank   WP_172689110
Name   traD_HTK44_RS00860_pIMI-6 insolico UniProt ID   _
Length   731 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 731 a.a.        Molecular weight: 81909.33 Da        Isoelectric Point: 5.1615

>WP_172689110.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacter cloacae complex]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGVIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQIMQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKH
QSEDEITGGRQLTDDPRAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTTDGKAEERLNAALAAREHESRSIAMLFEPDADVIAPEGGAENAGQPQQPQQPQQ
PQQPQQPAPAPRAADTTSASASVAGAAGTGGVEPELKTKAEEAEQLPPGIDESGEVVDMAAWEAWQAEQD
ELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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: 131656..156521

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTK44_RS00910 (PIMI6_00550) 126993..127142 + 150 Protein_141 DUF5431 family protein -
HTK44_RS00685 (PIMI6_00550) 127084..127209 + 126 WP_223540704 type I toxin-antitoxin system Hok family toxin -
HTK44_RS00690 (PIMI6_00555) 128086..128481 + 396 WP_172689094 ammonia monooxygenase -
HTK44_RS00695 (PIMI6_00560) 128543..128836 + 294 WP_172686993 hypothetical protein -
HTK44_RS00700 (PIMI6_00565) 128883..129227 + 345 WP_172686994 hypothetical protein -
HTK44_RS00705 (PIMI6_00570) 129313..129579 + 267 WP_172689095 hypothetical protein -
HTK44_RS00710 (PIMI6_00575) 129622..130452 + 831 WP_172689096 N-6 DNA methylase -
HTK44_RS00715 (PIMI6_00580) 131079..131609 + 531 WP_172689097 antirestriction protein -
HTK44_RS00720 (PIMI6_00585) 131656..132132 - 477 WP_172689098 transglycosylase SLT domain-containing protein virB1
HTK44_RS00725 (PIMI6_00590) 132564..132959 + 396 WP_172689099 conjugal transfer relaxosome DNA-binding protein TraM -
HTK44_RS00730 (PIMI6_00595) 133144..133848 + 705 WP_071667437 hypothetical protein -
HTK44_RS00735 (PIMI6_00600) 133957..134331 + 375 WP_040218544 TraY domain-containing protein -
HTK44_RS00740 (PIMI6_00605) 134397..134747 + 351 WP_172689118 type IV conjugative transfer system pilin TraA -
HTK44_RS00745 (PIMI6_00610) 134898..135203 + 306 WP_045911931 type IV conjugative transfer system protein TraL traL
HTK44_RS00750 (PIMI6_00615) 135218..135784 + 567 WP_025759824 type IV conjugative transfer system protein TraE traE
HTK44_RS00755 (PIMI6_00620) 135771..136514 + 744 WP_172689100 type-F conjugative transfer system secretin TraK traK
HTK44_RS00760 (PIMI6_00625) 136501..137895 + 1395 WP_172689101 F-type conjugal transfer pilus assembly protein TraB traB
HTK44_RS00765 (PIMI6_00630) 137917..138444 + 528 WP_123061130 type IV conjugative transfer system lipoprotein TraV traV
HTK44_RS00770 (PIMI6_00635) 138564..138788 + 225 WP_123061131 TraR/DksA C4-type zinc finger protein -
HTK44_RS00775 138792..138974 + 183 WP_123061132 hypothetical protein virb4
HTK44_RS00780 (PIMI6_00640) 138958..139254 + 297 WP_123061133 hypothetical protein -
HTK44_RS00785 (PIMI6_00645) 139244..139810 + 567 WP_045379430 conjugal transfer pilus-stabilizing protein TraP -
HTK44_RS00790 (pIMI6_00650) 139803..142433 + 2631 WP_172689102 type IV secretion system protein TraC virb4
HTK44_RS00795 (PIMI6_00655) 142430..142777 + 348 WP_172689103 type-F conjugative transfer system protein TrbI -
HTK44_RS00800 (PIMI6_00660) 142777..143424 + 648 WP_060446831 type-F conjugative transfer system protein TraW traW
HTK44_RS00805 (PIMI6_00665) 143427..144413 + 987 WP_172689104 conjugal transfer pilus assembly protein TraU traU
HTK44_RS00810 (PIMI6_00670) 144430..145059 + 630 WP_172689105 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTK44_RS00815 (PIMI6_00675) 145056..146936 + 1881 WP_172689106 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTK44_RS00820 (PIMI6_00680) 146968..147156 + 189 WP_025759809 conjugal transfer protein TrbE -
HTK44_RS00825 (PIMI6_00685) 147193..147936 + 744 WP_060446849 type-F conjugative transfer system pilin assembly protein TraF traF
HTK44_RS00830 147953..148201 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
HTK44_RS00835 (PIMI6_00690) 148191..148736 + 546 WP_060446834 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTK44_RS00840 (PIMI6_00700) 148775..150109 + 1335 WP_230199841 conjugal transfer pilus assembly protein TraH traH
HTK44_RS00845 (PIMI6_00705) 150109..152928 + 2820 WP_172689107 conjugal transfer mating-pair stabilization protein TraG traG
HTK44_RS00850 (PIMI6_00710) 152953..153426 + 474 WP_172689108 surface exclusion protein -
HTK44_RS00855 (PIMI6_00715) 153467..154207 + 741 WP_172689109 hypothetical protein -
HTK44_RS00860 (PIMI6_00720) 154326..156521 + 2196 WP_172689110 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3572 GenBank   NZ_KX786187
Plasmid name   pIMI-6 Incompatibility group   IncFII
Plasmid size   165469 bp Coordinate of oriT [Strand]   132204..132260 [-]
Host baterium   Enterobacter cloacae strain N14-0444

Cargo genes

Drug resistance gene   blaIMI-3
Virulence gene   hsiB1/vipA, hsiC1/vipB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -