Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101550
Name   oriT_L1M3-CIP07|unnamed1 in_silico
Organism   Escherichia coli strain L1M3-CIP07
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAPUCH010000076 (1..189 [+], 189 nt)
oriT length   189 nt
IRs (inverted repeats)      29..35, 43..49  (TATAAAA..TTTTATA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 189 nt

>oriT_L1M3-CIP07|unnamed1
GCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1373 GenBank   WP_332374687
Name   traI_O2E79_RS23910_L1M3-CIP07|unnamed1 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192031.54 Da        Isoelectric Point: 5.9284

>WP_332374687.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEKRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVAGGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPATLPVSDSPFTALKL
ESGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTSFVDLGREINA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQEAIQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGSGDRVRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDDRQGWTDAINNAVQKGTAHDVL
EPKADREVMNAERLFSSARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAGQERDRAAITEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

AAA domain (AAA_30)

(969-1156)

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

(575-627)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   490 GenBank   WP_001151524
Name   WP_001151524_L1M3-CIP07|unnamed1 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22

ID   491 GenBank   WP_024182454
Name   WP_024182454_L1M3-CIP07|unnamed1 insolico UniProt ID   A0A376HJP2
Length   131 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 131 a.a.        Molecular weight: 15181.46 Da        Isoelectric Point: 10.3458

>WP_024182454.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Enterobacteriaceae]
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEKNITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(70-117)

TraY domain (TraY)

(16-59)


  Protein structure


Source ID Structure
AlphaFold DB A0A376HJP2


T4CP

ID   1005 GenBank   WP_021519755
Name   traC_O2E79_RS23805_L1M3-CIP07|unnamed1 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99327.25 Da        Isoelectric Point: 6.5173

>WP_021519755.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVKASWLAKKNQARIDDVVNFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLFPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-763)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   1006 GenBank   WP_156841535
Name   traD_O2E79_RS23905_L1M3-CIP07|unnamed1 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83567.22 Da        Isoelectric Point: 5.0504

>WP_156841535.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEIIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2356..26989

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
O2E79_RS23745 (O2E79_23645) 190..573 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
O2E79_RS23750 (O2E79_23650) 760..1449 + 690 WP_115264864 conjugal transfer transcriptional regulator TraJ -
O2E79_RS23755 (O2E79_23655) 1548..1943 + 396 WP_024182454 conjugal transfer relaxosome DNA-bindin protein TraY -
O2E79_RS23760 (O2E79_23660) 1976..2341 + 366 WP_115264865 type IV conjugative transfer system pilin TraA -
O2E79_RS23765 (O2E79_23665) 2356..2667 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
O2E79_RS23770 (O2E79_23670) 2689..3255 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
O2E79_RS23775 (O2E79_23675) 3242..3970 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
O2E79_RS23780 (O2E79_23680) 3970..5397 + 1428 WP_000146635 F-type conjugal transfer pilus assembly protein TraB traB
O2E79_RS23785 (O2E79_23685) 5387..5974 + 588 WP_000002771 conjugal transfer pilus-stabilizing protein TraP -
O2E79_RS23790 (O2E79_23690) 5961..6278 + 318 WP_024228802 conjugal transfer protein TrbD -
O2E79_RS23795 (O2E79_23695) 6278..6793 + 516 WP_021559014 type IV conjugative transfer system lipoprotein TraV traV
O2E79_RS23800 (O2E79_23700) 6928..7149 + 222 WP_001278689 conjugal transfer protein TraR -
O2E79_RS23805 (O2E79_23705) 7309..9936 + 2628 WP_021519755 type IV secretion system protein TraC virb4
O2E79_RS23810 (O2E79_23710) 9933..10319 + 387 WP_000214100 type-F conjugative transfer system protein TrbI -
O2E79_RS23815 (O2E79_23715) 10316..10948 + 633 WP_332374674 type-F conjugative transfer system protein TraW traW
O2E79_RS23820 (O2E79_23720) 10945..11937 + 993 WP_021559016 conjugal transfer pilus assembly protein TraU traU
O2E79_RS23825 (O2E79_23725) 11946..12584 + 639 WP_089527312 type-F conjugative transfer system pilin assembly protein TrbC trbC
O2E79_RS23830 (O2E79_23730) 12581..12961 + 381 WP_000174466 hypothetical protein -
O2E79_RS23835 (O2E79_23735) 13197..15059 + 1863 WP_248872284 type-F conjugative transfer system mating-pair stabilization protein TraN traN
O2E79_RS23840 (O2E79_23740) 15086..15346 + 261 WP_000864323 conjugal transfer protein TrbE -
O2E79_RS23845 (O2E79_23745) 15339..16082 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
O2E79_RS23850 (O2E79_23750) 16098..16445 + 348 WP_001287913 conjugal transfer protein TrbA -
O2E79_RS23855 (O2E79_23755) 16447..16761 - 315 WP_000415566 protein ArtA -
O2E79_RS23860 (O2E79_23760) 16842..17126 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
O2E79_RS23865 (O2E79_23765) 17113..17658 + 546 WP_021553231 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
O2E79_RS23870 (O2E79_23770) 17648..17962 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
O2E79_RS23875 (O2E79_23775) 17916..18308 + 393 WP_332374682 F-type conjugal transfer protein TrbF -
O2E79_RS23880 (O2E79_23780) 18295..19668 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
O2E79_RS23885 (O2E79_23785) 19665..22481 + 2817 WP_072649640 conjugal transfer mating-pair stabilization protein TraG traG
O2E79_RS23890 (O2E79_23790) 22514..23035 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
O2E79_RS23895 (O2E79_23795) 23060..23791 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
O2E79_RS23900 (O2E79_23800) 23994..24731 + 738 WP_000199911 hypothetical protein -
O2E79_RS23905 (O2E79_23805) 24782..26989 + 2208 WP_156841535 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1994 GenBank   NZ_JAPUCH010000076
Plasmid name   L1M3-CIP07|unnamed1 Incompatibility group   -
Plasmid size   52214 bp Coordinate of oriT [Strand]   1..189 [+]
Host baterium   Escherichia coli strain L1M3-CIP07

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -