Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117258
Name   oriT_pK518_NDM1 in_silico
Organism   Klebsiella michiganensis strain K518
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP023187 (22955..23057 [+], 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_pK518_NDM1
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11000 GenBank   WP_016479978
Name   traI_CKQ55_RS31205_pK518_NDM1 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   12851 GenBank   WP_008324134
Name   traC_CKQ55_RS31125_pK518_NDM1 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   12852 GenBank   WP_016479979
Name   traD_CKQ55_RS31200_pK518_NDM1 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 22407..47577

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CKQ55_RS32315 (CKQ55_31015) 17504..17827 + 324 WP_008324183 hypothetical protein -
CKQ55_RS31020 (CKQ55_31020) 17889..18248 + 360 WP_015493069 hypothetical protein -
CKQ55_RS31025 (CKQ55_31025) 18875..19249 + 375 WP_008324180 hypothetical protein -
CKQ55_RS31030 (CKQ55_31030) 19303..19590 + 288 WP_008324178 hypothetical protein -
CKQ55_RS31035 (CKQ55_31035) 19637..19981 + 345 WP_008324177 hypothetical protein -
CKQ55_RS31040 (CKQ55_31040) 20067..20330 + 264 WP_008324174 hypothetical protein -
CKQ55_RS31045 (CKQ55_31045) 20373..21203 + 831 WP_008324171 N-6 DNA methylase -
CKQ55_RS31050 (CKQ55_31050) 21830..22360 + 531 WP_008324170 antirestriction protein -
CKQ55_RS31055 (CKQ55_31055) 22407..22883 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
CKQ55_RS31060 (CKQ55_31060) 23315..23707 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
CKQ55_RS31065 (CKQ55_31065) 23896..24585 + 690 WP_008324166 hypothetical protein -
CKQ55_RS31070 (CKQ55_31070) 24672..24896 + 225 WP_008324165 TraY domain-containing protein -
CKQ55_RS31075 (CKQ55_31075) 24954..25304 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
CKQ55_RS31080 (CKQ55_31080) 25455..25760 + 306 WP_016479987 type IV conjugative transfer system protein TraL traL
CKQ55_RS31085 (CKQ55_31085) 25775..26341 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
CKQ55_RS31090 (CKQ55_31090) 26328..27071 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
CKQ55_RS31095 (CKQ55_31095) 27058..28452 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
CKQ55_RS31100 (CKQ55_31100) 28474..29013 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
CKQ55_RS31105 (CKQ55_31105) 29133..29357 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
CKQ55_RS31110 (CKQ55_31110) 29361..29546 + 186 WP_008324139 hypothetical protein -
CKQ55_RS32635 29764..29931 + 168 WP_223274120 Clp protease -
CKQ55_RS31120 (CKQ55_31120) 29921..30487 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
CKQ55_RS31125 (CKQ55_31125) 30480..33110 + 2631 WP_008324134 type IV secretion system protein TraC virb4
CKQ55_RS31130 (CKQ55_31130) 33107..33508 + 402 WP_095762646 type-F conjugative transfer system protein TrbI -
CKQ55_RS31135 (CKQ55_31135) 33453..34100 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
CKQ55_RS31140 (CKQ55_31140) 34103..35089 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
CKQ55_RS31145 (CKQ55_31145) 35106..35735 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
CKQ55_RS31150 (CKQ55_31150) 35732..37585 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CKQ55_RS31155 (CKQ55_31155) 37617..37805 + 189 WP_008324128 conjugal transfer protein TrbE -
CKQ55_RS31160 (CKQ55_31160) 37836..38585 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
CKQ55_RS31165 (CKQ55_31165) 38602..38850 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
CKQ55_RS31170 (CKQ55_31170) 38840..39394 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CKQ55_RS31175 (CKQ55_31175) 39387..39815 + 429 WP_008324122 hypothetical protein -
CKQ55_RS31180 (CKQ55_31180) 39802..41172 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
CKQ55_RS31185 (CKQ55_31185) 41172..43994 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
CKQ55_RS31190 (CKQ55_31190) 44016..44447 + 432 WP_008324118 entry exclusion protein -
CKQ55_RS32640 44522..44860 + 339 WP_032072912 tetratricopeptide repeat protein -
CKQ55_RS32645 44868..45197 + 330 WP_223856629 tetratricopeptide repeat protein -
CKQ55_RS31200 (CKQ55_31200) 45331..47577 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   17691 GenBank   NZ_CP023187
Plasmid name   pK518_NDM1 Incompatibility group   IncFII
Plasmid size   106579 bp Coordinate of oriT [Strand]   22955..23057 [+]
Host baterium   Klebsiella michiganensis strain K518

Cargo genes

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