Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119755
Name   oriT_pHNNC189-3 in_silico
Organism   Raoultella ornithinolytica strain NC189
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MN548434 (59081..59183 [+], 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_pHNNC189-3
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12484 GenBank   WP_016479978
Name   traI_KM116_RS00455_pHNNC189-3 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   14667 GenBank   WP_008324134
Name   traC_KM116_RS00375_pHNNC189-3 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   14668 GenBank   WP_016479979
Name   traD_KM116_RS00450_pHNNC189-3 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: 58533..83704

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KM116_RS00265 53630..53953 + 324 WP_008324183 hypothetical protein -
KM116_RS00270 54015..54374 + 360 WP_015493069 hypothetical protein -
KM116_RS00275 55001..55375 + 375 WP_008324180 hypothetical protein -
KM116_RS00280 55429..55716 + 288 WP_008324178 hypothetical protein -
KM116_RS00285 55763..56107 + 345 WP_008324177 hypothetical protein -
KM116_RS00290 56193..56456 + 264 WP_008324174 hypothetical protein -
KM116_RS00295 56499..57329 + 831 WP_008324171 N-6 DNA methylase -
KM116_RS00300 57956..58486 + 531 WP_008324170 antirestriction protein -
KM116_RS00305 58533..59009 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
KM116_RS00310 59441..59833 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
KM116_RS00315 60022..60711 + 690 WP_008324166 hypothetical protein -
KM116_RS00320 60798..61022 + 225 WP_008324165 TraY domain-containing protein -
KM116_RS00325 61080..61430 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
KM116_RS00330 61581..61886 + 306 WP_016479987 type IV conjugative transfer system protein TraL traL
KM116_RS00335 61901..62467 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
KM116_RS00340 62454..63197 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
KM116_RS00345 63184..64578 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
KM116_RS00350 64600..65139 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
KM116_RS00355 65259..65483 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
KM116_RS00360 65487..65672 + 186 WP_008324139 hypothetical protein -
KM116_RS00365 65656..66057 + 402 WP_016479985 hypothetical protein -
KM116_RS00370 66047..66613 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
KM116_RS00375 66606..69236 + 2631 WP_008324134 type IV secretion system protein TraC virb4
KM116_RS00380 69233..69580 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
KM116_RS00385 69580..70227 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
KM116_RS00390 70230..71216 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
KM116_RS00395 71233..71862 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
KM116_RS00400 71859..73712 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KM116_RS00405 73744..73932 + 189 WP_008324128 conjugal transfer protein TrbE -
KM116_RS00410 73963..74712 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
KM116_RS00415 74729..74977 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
KM116_RS00420 74967..75521 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KM116_RS00425 75514..75942 + 429 WP_008324122 hypothetical protein -
KM116_RS00430 75929..77299 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
KM116_RS00435 77299..80121 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
KM116_RS00440 80167..80574 + 408 WP_233406080 entry exclusion protein -
KM116_RS00685 80649..80987 + 339 WP_032072912 tetratricopeptide repeat protein -
KM116_RS00690 80995..81324 + 330 WP_223856629 tetratricopeptide repeat protein -
KM116_RS00450 81458..83704 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   20185 GenBank   NZ_MN548434
Plasmid name   pHNNC189-3 Incompatibility group   IncFIB
Plasmid size   124023 bp Coordinate of oriT [Strand]   59081..59183 [+]
Host baterium   Raoultella ornithinolytica strain NC189

Cargo genes

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