Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101492
Name   oriT_p2560-1 in_silico
Organism   Escherichia coli strain GN02560
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JALJQO010000003 (23073..23196 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      92..99, 113..120  (ATAATGTA..TACATTAT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_p2560-1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTACTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   467 GenBank   WP_001254388
Name   WP_001254388_p2560-1 insolico UniProt ID   W9A0Z2
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9072.20 Da        Isoelectric Point: 10.2071

>WP_001254388.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacterales]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB W9A0Z2

ID   468 GenBank   WP_001151566
Name   WP_001151566_p2560-1 insolico UniProt ID   A0A142CMX1
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14476.46 Da        Isoelectric Point: 4.8498

>WP_001151566.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYETQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPENDEG

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A142CMX1


T4CP

ID   952 GenBank   WP_001064258
Name   traC_MWG49_RS00285_p2560-1 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: 99195.72 Da        Isoelectric Point: 5.8689

>WP_001064258.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLKSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNYKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFQPLQRDMIGKFGAARDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-763)

  Protein structure



No available structure.



ID   953 GenBank   WP_023356304
Name   traD_MWG49_RS00980_p2560-1 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83847.55 Da        Isoelectric Point: 5.1657

>WP_023356304.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 2215..23768

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MWG49_RS00200 (MWG49_00200) 1..2218 - 2218 Protein_0 conjugal transfer mating-pair stabilization protein TraG -
MWG49_RS00205 (MWG49_00205) 2215..3588 - 1374 WP_000944328 conjugal transfer pilus assembly protein TraH traH
MWG49_RS00210 (MWG49_00210) 3575..3967 - 393 WP_000659962 F-type conjugal transfer protein TrbF -
MWG49_RS00215 (MWG49_00215) 3948..4295 - 348 WP_071571857 P-type conjugative transfer protein TrbJ -
MWG49_RS00220 (MWG49_00220) 4225..4770 - 546 WP_000059829 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
MWG49_RS00225 (MWG49_00225) 4757..5041 - 285 WP_001617873 type-F conjugative transfer system pilin chaperone TraQ -
MWG49_RS00230 (MWG49_00230) 5168..5488 - 321 WP_001348757 conjugal transfer protein TrbA -
MWG49_RS00240 (MWG49_00240) 6388..7368 - 981 Protein_8 IS5-like element ISKpn26 family transposase -
MWG49_RS00245 (MWG49_00245) 7498..8241 - 744 WP_001030401 type-F conjugative transfer system pilin assembly protein TraF traF
MWG49_RS00250 (MWG49_00250) 8234..8491 - 258 WP_000864347 conjugal transfer protein TrbE -
MWG49_RS00255 (MWG49_00255) 8518..10368 - 1851 WP_000821866 type-F conjugative transfer system mating-pair stabilization protein TraN traN
MWG49_RS00260 (MWG49_00260) 10365..11003 - 639 WP_001080259 type-F conjugative transfer system pilin assembly protein TrbC trbC
MWG49_RS00265 (MWG49_00265) 11012..11317 - 306 WP_000224413 hypothetical protein -
MWG49_RS00270 (MWG49_00270) 11347..12339 - 993 WP_000830190 conjugal transfer pilus assembly protein TraU traU
MWG49_RS00275 (MWG49_00275) 12336..12968 - 633 WP_001203727 type-F conjugative transfer system protein TraW traW
MWG49_RS00280 (MWG49_00280) 12965..13351 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
MWG49_RS00285 (MWG49_00285) 13348..15975 - 2628 WP_001064258 type IV secretion system protein TraC virb4
MWG49_RS00290 (MWG49_00290) 16135..16356 - 222 WP_001278694 conjugal transfer protein TraR -
MWG49_RS00295 (MWG49_00295) 16491..17006 - 516 WP_000809886 type IV conjugative transfer system lipoprotein TraV traV
MWG49_RS00300 (MWG49_00300) 17006..17317 - 312 WP_001057272 conjugal transfer protein TrbD -
MWG49_RS00305 (MWG49_00305) 17304..17870 - 567 WP_001617877 conjugal transfer pilus-stabilizing protein TraP -
MWG49_RS00310 (MWG49_00310) 17860..19311 - 1452 WP_000146687 F-type conjugal transfer pilus assembly protein TraB traB
MWG49_RS00315 (MWG49_00315) 19311..20039 - 729 WP_001230808 type-F conjugative transfer system secretin TraK traK
MWG49_RS00320 (MWG49_00320) 20026..20592 - 567 WP_000399791 type IV conjugative transfer system protein TraE traE
MWG49_RS00325 (MWG49_00325) 20614..20925 - 312 WP_000012107 type IV conjugative transfer system protein TraL traL
MWG49_RS00330 (MWG49_00330) 20930..21292 - 363 WP_000338606 type IV conjugative transfer system pilin TraA -
MWG49_RS00335 (MWG49_00335) 21326..21553 - 228 WP_001254388 conjugal transfer relaxosome protein TraY -
MWG49_RS00340 (MWG49_00340) 21641..22318 - 678 WP_001348626 PAS domain-containing protein -
MWG49_RS00345 (MWG49_00345) 22452..22835 - 384 WP_001151566 conjugal transfer relaxosome DNA-binding protein TraM -
MWG49_RS00350 (MWG49_00350) 23178..23768 + 591 WP_001376243 transglycosylase SLT domain-containing protein virB1
MWG49_RS00355 (MWG49_00355) 24065..24886 - 822 WP_001234469 DUF932 domain-containing protein -
MWG49_RS00360 (MWG49_00360) 25005..25292 - 288 WP_000107535 hypothetical protein -
MWG49_RS00365 (MWG49_00365) 25317..25523 - 207 WP_000275859 hypothetical protein -
MWG49_RS00370 (MWG49_00370) 25593..25766 + 174 Protein_34 hypothetical protein -
MWG49_RS00375 (MWG49_00375) 25764..25994 - 231 WP_001426396 hypothetical protein -
MWG49_RS00380 (MWG49_00380) 26214..26339 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
MWG49_RS00385 (MWG49_00385) 26281..26430 - 150 Protein_37 plasmid maintenance protein Mok -

Host bacterium

ID   1936 GenBank   NZ_JALJQO010000003
Plasmid name   p2560-1 Incompatibility group   IncFIA
Plasmid size   136332 bp Coordinate of oriT [Strand]   23073..23196 [-]
Host baterium   Escherichia coli strain GN02560

Cargo genes

Drug resistance gene   blaTEM-1B
Virulence gene   senB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -