Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121157
Name   oriT_pYUSHP29-2 in_silico
Organism   Leclercia adecarboxylata strain SH19PE29
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP087282 (20843..20898 [-], 56 nt)
oriT length   56 nt
IRs (inverted repeats)      22..28, 32..38  (GCAAGAC..GTCTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 56 nt

>oriT_pYUSHP29-2
ATGAATTTAAAGATAAAATCTGCAAGACAACGTCTTGCGTGGGGTGTGATGTTTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13357 GenBank   WP_230431584
Name   traI_LO739_RS23690_pYUSHP29-2 insolico UniProt ID   _
Length   1810 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1810 a.a.        Molecular weight: 197574.90 Da        Isoelectric Point: 6.5095

>WP_230431584.1 conjugative transfer relaxase/helicase TraI [Leclercia adecarboxylata]
MMSVAPVASAGSAAGYYSNSDNYYFLGNLQSLWLGEGAKELGLEGNVRGEDLTAVLEGRLPDGSRLGREI
NGNHVHRPGHDLTFSAPKSVSILALIGNDKAMLEAHNHAVRVAAGYVEKLISARVTKDGVTSIAHTGKMV
AAAFTHDTSRNLDPLIHTHLLIANMTEHEGKWKALATDYIHNAGFIETVMKHQVTLGKIYRGALRQRVET
LGHEVEEVGKHGMWEIKAIPEEVREEYSSRGREIRGAVGADATLRSRDVAAKDTRQAKVDPSRLRLMERW
LGQMKEKGFDLKAYQESVVPRESGLRDVPLPTERVSPVPADRTEPGAVARSAPEDKTGKNPELPALPAER
DDTARQPGSHLADTLRQPSLTEPEKTPERSVSLPARDLHADTPQPDLAEAVRLAISQLSDARTRFTFGEL
MLTTAELSEQLPEIRDIRVAIDAALKDGMIVPLDSEKGVFTSRIHLLDELSIQALSQEHLKSTKVVSFTR
PAQYAPPALAVAETDALVLMNAPSGVAGIRDLTVQLTGISTANGRDVQVLASSAERAISLAKSDTLRDRL
VSRQHILSGDFHLKPQSTLIIEGAERLGLKETLVLLGEARAQDAQLVFLDSAGRQANGNAMSVLESAGVA
RSRRTEPAPGLEAEVISIANKRDRYEALANRFAELSGGSENVTAVVVGKREQAQLTGLVRDALQNAGQLG
RDGAEIEARQPVWLDSKTRRMPGSYRPGMVLEDRRDAKARKSYVIDRVHDDTRVLSLVDGDGVLTRMKIG
EVSADWRLFSSETLHVATGEKLLAVAGDREHSLKAKDRLEVTAITGKGIEVKRGDETLTLPKDQPLYVTH
AYVSAPGGRDNDTGVVLAALNTRDISTQTMNSLAQSGHRAEVFTAEVQDRAEARLQRMKTNASPVQLVRT
LSGKDDVSEAVSTLRDNVQSDAELAVWRAVNDQRHVTFSELKLADEAVKFHPDFDAIDGQIRAMVKKGDL
LEVSVGGEPKLVARSTWEMEKAILRVVEEGKNTQQPLLDQVPADVLSGLTRGQKAATSLVLGSTDQFTGV
QGYAGVGKTTQMKAVMAALDTLPTDARPVLTGLAPTHQAVKEMSDVGVQARTIKSFIVEHDQATAAGEKP
DYKGQMFLIDESSMAGNQDTAALFQAIAAGGGRAVSMGDVDQFEAVDSGAPFRLMQERSPMDVAIMKEIV
RQKDVQLRGAVHDIIDNRIGAALRRIEAQPADRISREAGAKAPGSAFQETGSPVQDIVRDWTERTADARD
RTLIITQLNADRRAVNVGIHRQLAERGELGDKAITIPVLDKISHTRHEFNQMKPWASGMVVKRGDRYQDV
LAVDRNGNTITVRDEEGKIGLYSPKELITGDVQLFKRKTIEVRSGDQLRFTATDREQGMTANQRFTVDAV
SDTGDIRLRGTDGVVTINPKDIRAQQHVDYAWAVTGYGAQGTSTDYVISLEGTSGGREMMATRRAFYITA
SRAKEHVQIYTDGKKDWTKAVTKPEGDIKTAHEALAPETQRQQAKAIWAMGQPLTKTAIGRAWVRHQDMG
EASLTAKVIPATRRFPEPALALPVYDNNGKSAGLALVSLVSSPEGRLTQGDTRMVMTERARGAVLQRSQS
GNTVVVNDLAAALDAVRTHPKDGVVWQTGQEPLSAHLLKVTGGVRGDEEIRLNFGNLPGQDELQRQSELK
LAEQAREQEAVRQQPDDARAIVLPAEESVKLRPEELNPEKTVPLTPDSWVLASVREREQPDARELQLADS
VRKDIAVPDKSAGEESRASRIIADLARAEQDRVRQTSDSGRGRMPEIEEQTLTRTIQKER

  Protein domains


Predicted by InterproScan.

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

(708-786)

AAA domain (AAA_30)

(1029-1219)

DNA helicase TraI (TraI_C)

(1470-1581)

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

(651-701)

TrwC relaxase (TrwC)

(11-285)


  Protein structure



No available structure.




T4CP

ID   15646 GenBank   WP_230431583
Name   traD_LO739_RS23685_pYUSHP29-2 insolico UniProt ID   _
Length   871 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 871 a.a.        Molecular weight: 97078.12 Da        Isoelectric Point: 5.2053

>WP_230431583.1 type IV conjugative transfer system coupling protein TraD [Leclercia adecarboxylata]
MSFAGKNLTQGGQMTAYRWRMFLQVNNWIGFWMFIFFAVLTSAIFLWHIPGETLNNGSLWWFAWMNSSFI
DLMPTTGTPKIYDVHYWYAPTATAMVLNMTLPQIYTDPYMQAMGDQVLSELQWAAGASGIFSMVVFAAVT
WFIADIGRKESEDEYISGMQLTDRPAEVNSLLRKSGELSDLRVGDLHMVRMAEVLNFLMHGTIGVGKSTL
IRWLLDHIRKRGDRAIIYDSGCTFTETHYNPSTDFILNAHDERCANWQMWGECIDAVDYDNLAASLIPVE
GESDPFWVSSSRTIFADLAIRMSADPQRSIEKFLKTLLSLSMKSLRDYLANTPSANLVEEKIEKTAISIR
SVVTNYAKALRYLQGLDDGTKPPFTIREWMTQERYDSSWLFISTQARHRKSVRPLISLWVSLATLMLQSM
GENSERRVWFIIDEAPSLQRIPELAETLAEARKFGGCFVLGMQNMAQLVHVYGRELAKSIFDLMNTRMYG
RSPSAEMAKVVEEELGNQRRRKIREQNSYGLDQVRDGVSLGKDEVNEPVVDYEQIMRLPNLSFYVRLPGE
YPVVRLKLKYRALKKRHAGLMERNIRDALSPELEKVIQENERAATAAGLTFPTGDEVLEKGTETTPAAGS
TAPVSSAGAPATLPPCEEKPVTEPATGKKPARVMPVIRNLQPVAVPVMSGAHATIAEAAPDNHNTVTAPV
TSSEKSNVISLHQGRHSPADSSPEASMTDESAPSTPSEPDIAETPAEQVALPAALQRLRNMTTAAEQPAT
SVLSILQKARQRPATSENNTGTGDNNGGESMNLEMKVTALPDGGLSVTTAGKPVTPANPEEAHRTNRQLA
QEEENILLHRDAGDPGYDENDQYYYDREPEL

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(182-569)

F sex factor protein N terminal (TraD_N)

(32-136)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 22884..49025

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LO739_RS23525 (LO739_23520) 18960..19253 + 294 WP_172693768 hypothetical protein -
LO739_RS23530 (LO739_23525) 19268..20086 + 819 WP_230431590 DUF932 domain-containing protein -
LO739_RS23535 (LO739_23530) 20114..20653 - 540 WP_172693819 lytic transglycosylase domain-containing protein -
LO739_RS23540 (LO739_23535) 21264..21650 + 387 WP_172693770 relaxosome protein TraM -
LO739_RS23545 (LO739_23540) 21689..22330 - 642 WP_172693771 Arc family DNA-binding protein -
LO739_RS23550 (LO739_23545) 22527..22880 + 354 WP_172693772 type IV conjugative transfer system pilin TraA -
LO739_RS23555 (LO739_23550) 22884..23186 + 303 WP_172693773 type IV conjugative transfer system protein TraL traL
LO739_RS23560 (LO739_23555) 23192..23776 + 585 WP_172693774 TraE/TraK family type IV conjugative transfer system protein traE
LO739_RS23565 (LO739_23560) 23788..24528 + 741 WP_172693775 type-F conjugative transfer system secretin TraK traK
LO739_RS23570 (LO739_23565) 24525..25928 + 1404 WP_172693776 F-type conjugal transfer pilus assembly protein TraB traB
LO739_RS23575 (LO739_23570) 25939..26379 + 441 WP_172693777 hypothetical protein -
LO739_RS23580 (LO739_23575) 26373..26834 + 462 WP_172693778 hypothetical protein -
LO739_RS23585 (LO739_23580) 26865..27260 + 396 WP_172693779 hypothetical protein -
LO739_RS23590 (LO739_23585) 27318..27881 + 564 WP_172693780 type IV conjugative transfer system lipoprotein TraV traV
LO739_RS23595 (LO739_23590) 27878..30478 + 2601 WP_172693781 type IV secretion system protein TraC virb4
LO739_RS23600 (LO739_23595) 30475..30879 + 405 WP_172693782 type-F conjugative transfer system protein TrbI -
LO739_RS23605 (LO739_23600) 30876..31511 + 636 WP_172693783 type-F conjugative transfer system protein TraW traW
LO739_RS23610 (LO739_23605) 31508..31804 + 297 WP_172693784 hypothetical protein -
LO739_RS23615 (LO739_23610) 31795..32319 + 525 WP_172693785 hypothetical protein -
LO739_RS23620 (LO739_23615) 32391..32600 + 210 WP_172693786 hypothetical protein -
LO739_RS23625 (LO739_23620) 32732..33676 + 945 WP_230431591 conjugal transfer pilus assembly protein TraU traU
LO739_RS23630 (LO739_23625) 33686..34303 + 618 WP_172693788 type-F conjugative transfer system pilin assembly protein TrbC trbC
LO739_RS23635 (LO739_23630) 34300..36159 + 1860 WP_172693789 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LO739_RS23640 (LO739_23635) 36156..36938 + 783 WP_172693790 type-F conjugative transfer system pilin assembly protein TraF traF
LO739_RS23645 (LO739_23640) 36948..37424 + 477 WP_230431582 hypothetical protein -
LO739_RS23650 (LO739_23645) 37411..37632 + 222 WP_172693792 hypothetical protein -
LO739_RS23655 (LO739_23650) 37622..38221 + 600 WP_172693793 F-type conjugal transfer protein TrbB traF
LO739_RS23660 (LO739_23655) 38239..38508 + 270 WP_172693794 hypothetical protein -
LO739_RS23665 (LO739_23660) 38501..39865 + 1365 WP_172693795 conjugal transfer pilus assembly protein TraH traH
LO739_RS23670 (LO739_23665) 39865..43002 + 3138 Protein_54 conjugal transfer mating-pair stabilization protein TraG -
LO739_RS23675 (LO739_23670) 44257..44814 + 558 WP_172693796 hypothetical protein -
LO739_RS23680 (LO739_23675) 44971..45702 + 732 WP_172693797 complement resistance protein TraT -
LO739_RS23685 (LO739_23680) 46410..49025 + 2616 WP_230431583 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21585 GenBank   NZ_CP087282
Plasmid name   pYUSHP29-2 Incompatibility group   IncFII
Plasmid size   132089 bp Coordinate of oriT [Strand]   20843..20898 [-]
Host baterium   Leclercia adecarboxylata strain SH19PE29

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   pcoE, pcoS, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -