Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102919
Name   oriT_pCombat2C1-1 in_silico
Organism   Escherichia coli strain Combat2C1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP019244 (32377..32499 [+], 123 nt)
oriT length   123 nt
IRs (inverted repeats)      100..105, 118..123  (TTTAAT..ATTAAA)
 38..45, 48..55  (GCAAAAAC..GTTTTTGC)
 2..9, 14..21  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 123 nt

>oriT_pCombat2C1-1
GTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTTAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   893 GenBank   WP_000124981
Name   WP_000124981_pCombat2C1-1 insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9

ID   894 GenBank   WP_001254386
Name   WP_001254386_pCombat2C1-1 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   1864 GenBank   WP_105078449
Name   traC_BWI82_RS27205_pCombat2C1-1 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99352.00 Da        Isoelectric Point: 5.8465

>WP_105078449.1 type IV secretion system protein TraC [Escherichia coli]
MSNNPLETVTQAVNSLLTALKLPDESSQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

  Protein structure



No available structure.



ID   1865 GenBank   WP_024245293
Name   traD_BWI82_RS27305_pCombat2C1-1 insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 82786.39 Da        Isoelectric Point: 5.2346

>WP_024245293.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
IQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 31804..62614

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BWI82_RS27610 27414..27602 - 189 WP_001299721 hypothetical protein -
BWI82_RS28335 27624..27773 + 150 Protein_41 plasmid maintenance protein Mok -
BWI82_RS27065 (BWI82_27085) 27715..27840 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
BWI82_RS27830 28141..28437 - 297 Protein_43 hypothetical protein -
BWI82_RS27835 (BWI82_27095) 28507..28779 + 273 WP_236920881 single-stranded DNA-binding protein -
BWI82_RS27080 (BWI82_27100) 28733..29056 + 324 WP_000533253 hypothetical protein -
BWI82_RS27085 (BWI82_27105) 29115..29357 + 243 WP_000540591 hypothetical protein -
BWI82_RS28340 (BWI82_27110) 29557..29980 - 424 Protein_47 hypothetical protein -
BWI82_RS28345 (BWI82_27120) 30050..30256 + 207 WP_000547968 hypothetical protein -
BWI82_RS27105 (BWI82_27125) 30280..30576 + 297 WP_001272251 hypothetical protein -
BWI82_RS27110 (BWI82_27130) 30687..31508 + 822 WP_021553189 DUF932 domain-containing protein -
BWI82_RS27115 (BWI82_27135) 31804..32373 - 570 Protein_51 transglycosylase SLT domain-containing protein -
BWI82_RS27120 (BWI82_27140) 32728..33111 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
BWI82_RS27125 (BWI82_27145) 33302..33988 + 687 WP_015059009 PAS domain-containing protein -
BWI82_RS27130 (BWI82_27150) 34082..34309 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
BWI82_RS27135 (BWI82_27155) 34343..34705 + 363 WP_000340273 type IV conjugative transfer system pilin TraA -
BWI82_RS27140 (BWI82_27160) 34710..35021 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
BWI82_RS27145 (BWI82_27165) 35043..35609 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
BWI82_RS27150 (BWI82_27170) 35596..36324 + 729 WP_021532669 type-F conjugative transfer system secretin TraK traK
BWI82_RS27155 (BWI82_27175) 36324..37751 + 1428 WP_031570446 F-type conjugal transfer pilus assembly protein TraB traB
BWI82_RS27160 (BWI82_27180) 37741..38325 + 585 WP_148116757 conjugal transfer pilus-stabilizing protein TraP -
BWI82_RS27165 (BWI82_27185) 38312..38632 + 321 WP_001057291 DUF2689 domain-containing protein virb4
BWI82_RS27170 (BWI82_27190) 38625..38876 + 252 WP_001038341 conjugal transfer protein TrbG -
BWI82_RS27175 (BWI82_27195) 38873..39388 + 516 WP_000809907 type IV conjugative transfer system lipoprotein TraV traV
BWI82_RS27180 (BWI82_27200) 39523..39744 + 222 WP_148116758 conjugal transfer protein TraR -
BWI82_RS27185 (BWI82_27205) 39737..40057 + 321 Protein_65 hypothetical protein -
BWI82_RS27190 (BWI82_27210) 40147..41375 + 1229 WP_088895425 IS3-like element IS2 family transposase -
BWI82_RS28350 41588..41804 + 217 Protein_67 hypothetical protein -
BWI82_RS27195 (BWI82_27215) 41805..42128 + 324 WP_034169358 hypothetical protein -
BWI82_RS27620 42415..42765 + 351 WP_001712367 hypothetical protein -
BWI82_RS27205 (BWI82_27225) 42892..45522 + 2631 WP_105078449 type IV secretion system protein TraC virb4
BWI82_RS27210 (BWI82_27230) 45519..45905 + 387 WP_000099690 type-F conjugative transfer system protein TrbI -
BWI82_RS27215 (BWI82_27235) 45902..46534 + 633 WP_001203745 type-F conjugative transfer system protein TraW traW
BWI82_RS27220 (BWI82_27240) 46531..47523 + 993 WP_001523000 conjugal transfer pilus assembly protein TraU traU
BWI82_RS27225 (BWI82_27245) 47550..47858 + 309 WP_104774097 hypothetical protein -
BWI82_RS27230 (BWI82_27250) 47921..48439 + 519 WP_000009088 hypothetical protein -
BWI82_RS27235 (BWI82_27255) 48466..49104 + 639 WP_000087539 type-F conjugative transfer system pilin assembly protein TrbC trbC
BWI82_RS27240 (BWI82_27260) 49101..49472 + 372 WP_000174465 hypothetical protein -
BWI82_RS27245 (BWI82_27265) 49497..49919 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
BWI82_RS27250 (BWI82_27270) 49916..51724 + 1809 WP_104774095 type-F conjugative transfer system mating-pair stabilization protein TraN traN
BWI82_RS27255 (BWI82_27275) 51751..52008 + 258 WP_122986581 conjugal transfer protein TrbE -
BWI82_RS27260 (BWI82_27280) 52001..52744 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
BWI82_RS27265 (BWI82_27285) 52905..53141 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
BWI82_RS27270 (BWI82_27290) 53128..53673 + 546 WP_105078375 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
BWI82_RS27275 (BWI82_27295) 53603..53965 + 363 WP_001443292 P-type conjugative transfer protein TrbJ -
BWI82_RS27280 (BWI82_27300) 53965..55338 + 1374 WP_156841533 conjugal transfer pilus assembly protein TraH traH
BWI82_RS27285 (BWI82_27305) 55335..58154 + 2820 WP_148116760 conjugal transfer mating-pair stabilization protein TraG traG
BWI82_RS27290 (BWI82_27310) 58173..58670 + 498 WP_000605862 entry exclusion protein -
BWI82_RS27295 (BWI82_27315) 58703..59434 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
BWI82_RS27300 (BWI82_27320) 59637..60374 + 738 WP_158666146 hypothetical protein -
BWI82_RS27305 (BWI82_27325) 60425..62614 + 2190 WP_024245293 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3362 GenBank   NZ_CP019244
Plasmid name   pCombat2C1-1 Incompatibility group   IncFII
Plasmid size   71430 bp Coordinate of oriT [Strand]   32377..32499 [+]
Host baterium   Escherichia coli strain Combat2C1

Cargo genes

Drug resistance gene   oqxB, oqxA
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -