Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104624
Name   oriT_YL9|p2 in_silico
Organism   Klebsiella michiganensis strain YL9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084544 (63692..63794 [-], 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_YL9|p2
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3324 GenBank   WP_016479978
Name   traI_LD277_RS30080_YL9|p2 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   3264 GenBank   WP_101429066
Name   traD_LD277_RS30085_YL9|p2 insolico UniProt ID   _
Length   745 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 745 a.a.        Molecular weight: 83598.26 Da        Isoelectric Point: 5.1609

>WP_101429066.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEV
VDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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   3265 GenBank   WP_008324134
Name   traC_LD277_RS30165_YL9|p2 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: 39180..64342

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LD277_RS30085 (LD277_30125) 39180..41417 - 2238 WP_101429066 type IV conjugative transfer system coupling protein TraD virb4
LD277_RS30090 (LD277_30130) 41551..41880 - 330 WP_223856629 hypothetical protein -
LD277_RS30095 (LD277_30135) 41888..42226 - 339 WP_032072912 tetratricopeptide repeat protein -
LD277_RS30100 (LD277_30140) 42301..42732 - 432 WP_008324118 entry exclusion protein -
LD277_RS30105 (LD277_30145) 42754..45576 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
LD277_RS30110 (LD277_30150) 45576..46946 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
LD277_RS30115 (LD277_30155) 46933..47361 - 429 WP_008324122 hypothetical protein -
LD277_RS30120 (LD277_30160) 47354..47908 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LD277_RS30125 (LD277_30165) 47898..48146 - 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
LD277_RS30130 (LD277_30170) 48163..48912 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
LD277_RS30135 (LD277_30175) 48943..49131 - 189 WP_008324128 conjugal transfer protein TrbE -
LD277_RS30140 (LD277_30180) 49163..51016 - 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LD277_RS30145 (LD277_30185) 51013..51642 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
LD277_RS30150 (LD277_30190) 51659..52645 - 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
LD277_RS30155 (LD277_30195) 52648..53295 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
LD277_RS30160 (LD277_30200) 53295..53642 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
LD277_RS30165 (LD277_30205) 53639..56269 - 2631 WP_008324134 type IV secretion system protein TraC virb4
LD277_RS30170 (LD277_30210) 56262..56828 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
LD277_RS30175 (LD277_30215) 56818..57219 - 402 WP_016479985 hypothetical protein -
LD277_RS30180 (LD277_30220) 57203..57388 - 186 WP_008324139 hypothetical protein -
LD277_RS30185 (LD277_30225) 57392..57616 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
LD277_RS30190 (LD277_30230) 57736..58275 - 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
LD277_RS30195 (LD277_30235) 58297..59691 - 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
LD277_RS30200 (LD277_30240) 59678..60421 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
LD277_RS30205 (LD277_30245) 60408..60974 - 567 WP_016247535 type IV conjugative transfer system protein TraE traE
LD277_RS30210 (LD277_30250) 60989..61294 - 306 WP_016479987 type IV conjugative transfer system protein TraL traL
LD277_RS30215 (LD277_30255) 61445..61795 - 351 WP_016247536 type IV conjugative transfer system pilin TraA -
LD277_RS30220 (LD277_30260) 61853..62077 - 225 WP_008324165 TraY domain-containing protein -
LD277_RS30225 (LD277_30265) 62164..62853 - 690 WP_008324166 hypothetical protein -
LD277_RS30230 (LD277_30270) 63042..63434 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
LD277_RS30235 (LD277_30275) 63866..64342 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
LD277_RS30240 (LD277_30280) 64389..64919 - 531 WP_008324170 antirestriction protein -
LD277_RS30245 (LD277_30285) 65546..66376 - 831 WP_008324171 N-6 DNA methylase -
LD277_RS30250 (LD277_30290) 66419..66682 - 264 WP_008324174 hypothetical protein -
LD277_RS30255 (LD277_30295) 66768..67112 - 345 WP_008324177 hypothetical protein -
LD277_RS30260 (LD277_30300) 67159..67446 - 288 WP_008324178 hypothetical protein -
LD277_RS30265 (LD277_30305) 67500..67874 - 375 WP_008324180 hypothetical protein -
LD277_RS30270 (LD277_30310) 68501..68860 - 360 WP_015493069 hypothetical protein -
LD277_RS30275 (LD277_30315) 68922..69245 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   5063 GenBank   NZ_CP084544
Plasmid name   YL9|p2 Incompatibility group   IncFII
Plasmid size   103463 bp Coordinate of oriT [Strand]   63692..63794 [-]
Host baterium   Klebsiella michiganensis strain YL9

Cargo genes

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