Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102708
Name   oriT_W25K|unnamed2 in_silico
Organism   Escherichia coli strain W25K
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP091041 (8589..8941 [-], 353 nt)
oriT length   353 nt
IRs (inverted repeats)      192..198, 206..212  (TATAAAA..TTTTATA)
 197..202, 204..209  (AAAACA..TGTTTT)
 129..134, 148..153  (CGGTGC..GCACCG)
 104..110, 118..124  (TTTAAAT..ATTTAAA)
 106..111, 113..118  (TAAATC..GATTTA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 353 nt

>oriT_W25K|unnamed2
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCTACGCAAAAACAAGTTTTTGCTGATTTGATTTTAATATCATGTGCTTATATTCATGAATTTATATTATTTAAATCAGATTTATTTAAAACAGCGGTGCAGGCGCGGCTATGGCACCGTGTCTGCACCGCTTTGTAGGGGTGGTGCTGACTATTTTTATAAAAAACATTGTTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCCAGGGGCGCTGCTAGCGGTGCGTTCCTGTTTTCATTGTGAATTTTAGTGTTTCGAAATTAACTTTGTTTTATGTTTAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   807 GenBank   WP_071782156
Name   WP_071782156_W25K|unnamed2 insolico UniProt ID   A0A2I6FMV0
Length   71 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 71 a.a.        Molecular weight: 8103.17 Da        Isoelectric Point: 9.9216

>WP_071782156.1 conjugal transfer relaxosome protein TraY [Escherichia coli]
MSRGRTRAAPGNKVLLILDETTNQKLLAARDRSGRTKTNEVFIRLKDHLNRFPDFYNSSLVKEEAEGIDD
I

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A2I6FMV0

ID   808 GenBank   WP_001151534
Name   WP_001151534_W25K|unnamed2 insolico UniProt ID   A0A2I6FMW7
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14555.57 Da        Isoelectric Point: 4.8662

>WP_001151534.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia coli]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQAEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYSNMVEDIREKVSVEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A2I6FMW7


T4CP

ID   1636 GenBank   WP_001064261
Name   traC_L1O49_RS25415_W25K|unnamed2 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: 99278.94 Da        Isoelectric Point: 6.1932

>WP_001064261.1 type IV secretion system protein TraC [Escherichia coli]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGINLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
AGGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(467-763)

  Protein structure



No available structure.



ID   1637 GenBank   WP_001385161
Name   traD_L1O49_RS25945_W25K|unnamed2 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: 83550.19 Da        Isoelectric Point: 5.0485

>WP_001385161.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINLEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRHEEVNINVHRERGEDVEPGDDF

  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: 1997..9512

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L1O49_RS25420 (L1O49_25420) 1641..1862 - 222 WP_001278685 conjugal transfer protein TraR -
L1O49_RS25425 (L1O49_25425) 1997..2512 - 516 WP_000809905 type IV conjugative transfer system lipoprotein TraV traV
L1O49_RS25430 (L1O49_25430) 2509..2760 - 252 WP_001038341 conjugal transfer protein TrbG -
L1O49_RS25435 (L1O49_25435) 2772..2969 - 198 WP_001423674 conjugal transfer protein TrbD -
L1O49_RS25440 (L1O49_25440) 2956..3540 - 585 WP_001423675 conjugal transfer pilus-stabilizing protein TraP -
L1O49_RS25445 (L1O49_25445) 3530..4978 - 1449 WP_000146643 F-type conjugal transfer pilus assembly protein TraB traB
L1O49_RS25450 (L1O49_25450) 4978..5706 - 729 WP_001230776 type-F conjugative transfer system secretin TraK traK
L1O49_RS25455 (L1O49_25455) 5693..6259 - 567 WP_064986971 type IV conjugative transfer system protein TraE traE
L1O49_RS25460 (L1O49_25460) 6281..6592 - 312 WP_000012125 type IV conjugative transfer system protein TraL traL
L1O49_RS25465 (L1O49_25465) 6607..6972 - 366 WP_000338819 type IV conjugative transfer system pilin TraA -
L1O49_RS25470 (L1O49_25470) 7016..7231 - 216 WP_071782156 conjugal transfer relaxosome protein TraY -
L1O49_RS25475 (L1O49_25475) 7367..8014 - 648 WP_000332521 conjugal transfer transcriptional regulator TraJ -
L1O49_RS25480 (L1O49_25480) 8205..8588 - 384 WP_001151534 conjugal transfer relaxosome DNA-binding protein TraM -
L1O49_RS25485 (L1O49_25485) 8910..9512 + 603 WP_077632063 transglycosylase SLT domain-containing protein virB1
L1O49_RS25490 (L1O49_25490) 9808..10629 - 822 WP_001424949 DUF932 domain-containing protein -
L1O49_RS25495 (L1O49_25495) 10747..11034 - 288 WP_000107541 hypothetical protein -
L1O49_RS25500 (L1O49_25500) 11094..11280 + 187 Protein_17 pilus protein -
L1O49_RS25505 (L1O49_25505) 11581..11706 - 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
L1O49_RS25510 (L1O49_25510) 11648..11797 - 150 Protein_19 DUF5431 family protein -
L1O49_RS25515 (L1O49_25515) 11971..12733 - 763 Protein_20 plasmid SOS inhibition protein A -
L1O49_RS25520 (L1O49_25520) 12730..13164 - 435 WP_000845912 conjugation system SOS inhibitor PsiB -

Region 2: 82825..99079

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L1O49_RS25945 (L1O49_25945) 82825..85032 - 2208 WP_001385161 type IV conjugative transfer system coupling protein TraD virb4
L1O49_RS25950 (L1O49_25950) 85258..86046 - 789 WP_225882984 hypothetical protein -
L1O49_RS25955 (L1O49_25955) 86261..86572 + 312 WP_000522221 heavy metal-binding domain-containing protein -
L1O49_RS25960 (L1O49_25960) 86575..89394 - 2820 WP_001007033 conjugal transfer mating-pair stabilization protein TraG traG
L1O49_RS25965 (L1O49_25965) 89391..90764 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
L1O49_RS25970 (L1O49_25970) 90751..91143 - 393 WP_000126336 F-type conjugal transfer protein TrbF -
L1O49_RS25975 (L1O49_25975) 91097..91411 - 315 WP_001385158 P-type conjugative transfer protein TrbJ -
L1O49_RS25980 (L1O49_25980) 91401..91955 - 555 WP_000052621 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
L1O49_RS25985 (L1O49_25985) 91942..92226 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
L1O49_RS25990 (L1O49_25990) 92345..92692 - 348 WP_001287903 conjugal transfer protein TrbA -
L1O49_RS25995 (L1O49_25995) 92708..93451 - 744 WP_001030375 type-F conjugative transfer system pilin assembly protein TraF traF
L1O49_RS26000 (L1O49_26000) 93444..93701 - 258 WP_000864325 conjugal transfer protein TrbE -
L1O49_RS26005 (L1O49_26005) 93728..95536 - 1809 WP_000821839 type-F conjugative transfer system mating-pair stabilization protein TraN traN
L1O49_RS26010 (L1O49_26010) 95533..96171 - 639 WP_001104087 type-F conjugative transfer system pilin assembly protein TrbC trbC
L1O49_RS26015 (L1O49_26015) 96199..96651 - 453 WP_001385157 hypothetical protein -
L1O49_RS26020 (L1O49_26020) 96644..96958 - 315 WP_001423717 hypothetical protein -
L1O49_RS26025 (L1O49_26025) 96969..97432 - 464 Protein_123 ATP-binding protein -
L1O49_RS26030 (L1O49_26030) 97458..98450 - 993 WP_000830834 conjugal transfer pilus assembly protein TraU traU
L1O49_RS26035 (L1O49_26035) 98447..99079 - 633 WP_001203748 type-F conjugative transfer system protein TraW traW
L1O49_RS26040 (L1O49_26040) 99076..99462 - 387 WP_000214057 type-F conjugative transfer system protein TrbI -

Host bacterium

ID   3151 GenBank   NZ_CP091041
Plasmid name   W25K|unnamed2 Incompatibility group   IncFIB
Plasmid size   100605 bp Coordinate of oriT [Strand]   8589..8941 [-]
Host baterium   Escherichia coli strain W25K

Cargo genes

Drug resistance gene   -
Virulence gene   eltA, eltB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -