Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104607
Name   oriT_STEFF_15|unnamed1 in_silico
Organism   Raoultella ornithinolytica strain STEFF_15
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055217 (58545..58593 [-], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_STEFF_15|unnamed1
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3312 GenBank   WP_239614671
Name   traI_HUZ43_RS27505_STEFF_15|unnamed1 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 189768.35 Da        Isoelectric Point: 5.8658

>WP_239614671.1 conjugative transfer relaxase/helicase TraI [Raoultella ornithinolytica]
MLSFSQVKSAGSAGNYYTEKDNYYVTGSMEERWQGKGAETLELEGKVDKQVFTALLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALEQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKETIDPAEKMVEWMNT
LKETGFDIRGYREAADARAKELASAPAAPVKTDGPDIGDVVTNAIAGLSDRKVQFTYADLLARTVGQLEA
KPGVFERARGGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVTVTPDATVVRLAPF
SDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQNGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGRQTTADIISEPDKGARYNRLAQEFAVSVREGQESVAQISGTREQGVLNGIIRDTLKNEGALGTKEM
AITALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVANGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQALSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDATRTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIATQKAGLHTPAEQVIHLSIPLLESEALTFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGQGNDLLISRQTWDAEKSILTKVLEGKDAVPPLMDSVPGSLMADLTSGQRAATRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQAPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPAQEKAIQK
ALSEGEILPAGQPATLYEALVKDYADRTPEAQLQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKAVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAITA
HGAQGASEPYAIALEGVTGGRKQMASFESAYVGLSRMKLHVQVYTDSREGWVNAIQASPSKATAHDILAP
RNERAVKTADLLFGRAQPLNETAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKNDGIW
LSPLTDKDGRLEAIGGDGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPLNDTGTDIPLPPEVLAQRAAEEAQRREMGRQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




Auxiliary protein

ID   1483 GenBank   WP_020805752
Name   WP_020805752_STEFF_15|unnamed1 insolico UniProt ID   A0A377TIM3
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14772.81 Da        Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   3255 GenBank   WP_064343540
Name   traD_HUZ43_RS27500_STEFF_15|unnamed1 insolico UniProt ID   _
Length   764 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 764 a.a.        Molecular weight: 85378.44 Da        Isoelectric Point: 4.9296

>WP_064343540.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTISYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTVCVVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIQRRLDARVDGRLSALLEAREAEGSLARALFTPDEPVSESAEEKAGVQPEQTKPAEDS
VLPVPVKTSSKAAEGAGKTPDVPLSGAPVTRVKTVPLIRPEPAASVTGTAAAASTAAVSATAGGTEQELA
QQPVEADQDMLPAGMNEDGVIEDMQAYDAWLAGEQTQRDMQRREEVNINHSRSEQDDIEIGGNF

  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: 60972..85960

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ43_RS27325 (HUZ43_27205) 56939..57418 - 480 WP_142255947 hypothetical protein -
HUZ43_RS27330 (HUZ43_27210) 57413..57955 + 543 WP_142524116 antirestriction protein -
HUZ43_RS27335 (HUZ43_27215) 57978..58472 - 495 WP_228267449 transglycosylase SLT domain-containing protein -
HUZ43_RS27340 (HUZ43_27220) 58904..59296 + 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ43_RS27345 59534..60235 + 702 WP_223174962 hypothetical protein -
HUZ43_RS27350 (HUZ43_27230) 60321..60521 + 201 WP_048289787 TraY domain-containing protein -
HUZ43_RS27355 (HUZ43_27235) 60590..60958 + 369 WP_064343525 type IV conjugative transfer system pilin TraA -
HUZ43_RS27360 (HUZ43_27240) 60972..61277 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
HUZ43_RS27365 (HUZ43_27245) 61293..61859 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
HUZ43_RS27370 (HUZ43_27250) 61846..62580 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
HUZ43_RS27375 (HUZ43_27255) 62580..64001 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
HUZ43_RS27380 (HUZ43_27260) 63994..64428 + 435 WP_020322358 conjugal transfer protein TraP -
HUZ43_RS27385 (HUZ43_27265) 64462..65046 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
HUZ43_RS27390 (HUZ43_27270) 65659..65847 + 189 WP_053390286 hypothetical protein -
HUZ43_RS27395 65931..66332 + 402 WP_064343532 hypothetical protein -
HUZ43_RS27400 (HUZ43_27280) 66329..66628 + 300 WP_053390308 hypothetical protein -
HUZ43_RS27405 (HUZ43_27285) 66716..67099 + 384 WP_042946290 hypothetical protein -
HUZ43_RS27410 (HUZ43_27290) 67192..69831 + 2640 WP_064343533 type IV secretion system protein TraC virb4
HUZ43_RS27415 (HUZ43_27295) 69831..70223 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
HUZ43_RS27420 (HUZ43_27300) 70220..70846 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
HUZ43_RS27425 (HUZ43_27305) 70890..71849 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
HUZ43_RS27430 (HUZ43_27310) 71862..72509 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ43_RS27435 (HUZ43_27315) 72506..72889 + 384 WP_053390297 hypothetical protein -
HUZ43_RS27440 (HUZ43_27320) 72886..74841 + 1956 WP_064343537 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ43_RS27445 (HUZ43_27325) 74873..75133 + 261 WP_053390216 hypothetical protein -
HUZ43_RS27450 (HUZ43_27330) 75126..75737 + 612 WP_053390217 hypothetical protein -
HUZ43_RS27455 (HUZ43_27335) 75727..75969 + 243 WP_053390218 conjugal transfer protein TrbE -
HUZ43_RS27460 (HUZ43_27340) 76015..76341 + 327 WP_053390219 hypothetical protein -
HUZ43_RS27465 (HUZ43_27345) 76362..77114 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ43_RS27470 (HUZ43_27350) 77125..77361 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
HUZ43_RS27475 (HUZ43_27355) 77336..77896 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ43_RS27480 (HUZ43_27360) 77883..79253 + 1371 WP_239614669 conjugal transfer pilus assembly protein TraH traH
HUZ43_RS27485 (HUZ43_27365) 79253..82096 + 2844 WP_064343539 conjugal transfer mating-pair stabilization protein TraG traG
HUZ43_RS27490 (HUZ43_27370) 82102..82617 + 516 WP_049078360 conjugal transfer protein TraS -
HUZ43_RS27495 (HUZ43_27375) 82680..83426 + 747 WP_049078359 hypothetical protein -
HUZ43_RS27500 (HUZ43_27380) 83666..85960 + 2295 WP_064343540 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5046 GenBank   NZ_CP055217
Plasmid name   STEFF_15|unnamed1 Incompatibility group   IncFII
Plasmid size   97587 bp Coordinate of oriT [Strand]   58545..58593 [-]
Host baterium   Raoultella ornithinolytica strain STEFF_15

Cargo genes

Drug resistance gene   msr(E), mph(E), aph(3')-Ia, aadA2, qacE, sul1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -