Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102724
Name   oriT_pCFSAN004179G in_silico
Organism   Escherichia coli strain 08-00022
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP012501 (200541..200893 [+], 353 nt)
oriT length   353 nt
IRs (inverted repeats)      192..198, 206..212  (TATAAAA..TTTTATA)
 197..202, 204..209  (AAAATA..TATTTT)
 186..192, 196..202  (TATTTTT..AAAAATA)
 104..110, 118..124  (TTTAAAT..ATTTAAA)
 106..111, 113..118  (TAAATC..GATTTA)
 93..98, 106..111  (GATTTA..TAAATC)
 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_pCFSAN004179G
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCGTTTAATATCATTGAGTTGTATTTGTGGATTTATATTGTTTAAATCTGATTTATTTAAAGCAGCGTCGTTAACGCAGCTACAGCAACGCGCCGACACCGCTTTGTAGGGGTGGTACTAACTATTTTTATAAAAAATATTATTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTATTTTTTTATAGGATACCGCCAGGGGCGCTGCTAGCGGTGCGTCCCTGCTTGCATTATGAACTCTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   818 GenBank   WP_001151539
Name   WP_001151539_pCFSAN004179G insolico UniProt ID   A0A0B1KNX7
Length   125 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 125 a.a.        Molecular weight: 14339.42 Da        Isoelectric Point: 5.3221

>WP_001151539.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Escherichia]
MAKVNLYISNDAYEKINVIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQIEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKND

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure


Source ID Structure
AlphaFold DB A0A0B1KNX7


T4CP

ID   1650 GenBank   WP_047088906
Name   traC_CP48_RS01260_pCFSAN004179G 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: 99295.98 Da        Isoelectric Point: 5.9660

>WP_047088906.1 type IV secretion system protein TraC [Escherichia coli]
MNNPLEAVTQAVNSLLTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNFKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.



ID   1651 GenBank   WP_047088736
Name   traD_CP48_RS01390_pCFSAN004179G insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81410.98 Da        Isoelectric Point: 5.0486

>WP_047088736.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Escherichia]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKLSWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATIVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDLNPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGENVTQGEQPQQPASSVI
NDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQQMQRCEEVN
INVHRERGEDVEPGDDF

  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: 202872..231928

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CP48_RS01180 (CP48_p01325) 198445..198732 + 288 WP_000107542 hypothetical protein -
CP48_RS31165 (CP48_p01330) 198851..199672 + 822 Protein_240 DUF932 domain-containing protein -
CP48_RS30255 (CP48_p01340) 199970..200479 - 510 Protein_241 transglycosylase SLT domain-containing protein -
CP48_RS01205 (CP48_p01350) 200894..201271 + 378 WP_001151539 conjugal transfer relaxosome DNA-binding protein TraM -
CP48_RS01210 (CP48_p01355) 201471..202118 + 648 WP_042966703 transcriptional regulator TraJ family protein -
CP48_RS01215 (CP48_p01360) 202237..202464 + 228 WP_000589558 conjugal transfer relaxosome protein TraY -
CP48_RS01220 (CP48_p01365) 202498..202857 + 360 WP_000340268 type IV conjugative transfer system pilin TraA -
CP48_RS01225 (CP48_p01370) 202872..203183 + 312 WP_000012108 type IV conjugative transfer system protein TraL traL
CP48_RS01230 (CP48_p01375) 203205..203771 + 567 WP_000399757 type IV conjugative transfer system protein TraE traE
CP48_RS01235 (CP48_p01380) 203758..204486 + 729 WP_001355329 type-F conjugative transfer system secretin TraK traK
CP48_RS01240 (CP48_p01385) 204486..205904 + 1419 WP_047088902 F-type conjugal transfer pilus assembly protein TraB traB
CP48_RS01245 (CP48_p01390) 205894..206481 + 588 WP_047088903 conjugal transfer pilus-stabilizing protein TraP -
CP48_RS01250 (CP48_p01395) 206468..206788 + 321 WP_047088904 conjugal transfer protein TrbD -
CP48_RS01255 (CP48_p01400) 206785..207300 + 516 WP_047088905 type IV conjugative transfer system lipoprotein TraV traV
CP48_RS28155 (CP48_p01405) 207435..207656 + 222 WP_042966711 conjugal transfer protein TraR -
CP48_RS01260 (CP48_p01415) 207816..210443 + 2628 WP_047088906 type IV secretion system protein TraC virb4
CP48_RS01265 (CP48_p01420) 210440..210826 + 387 WP_047088907 type-F conjugative transfer system protein TrbI -
CP48_RS01270 (CP48_p01425) 210823..211455 + 633 WP_047088908 type-F conjugative transfer system protein TraW traW
CP48_RS01275 (CP48_p01430) 211452..212444 + 993 WP_047088909 conjugal transfer pilus assembly protein TraU traU
CP48_RS01280 (CP48_p01435) 212760..214331 - 1572 WP_000381395 IS66-like element ISCro1 family transposase -
CP48_RS01285 (CP48_p01440) 214351..214698 - 348 WP_000624622 IS66 family insertion sequence element accessory protein TnpB -
CP48_RS01290 (CP48_p01445) 214698..215375 - 678 WP_001339397 IS66-like element accessory protein TnpA -
CP48_RS01295 (CP48_p01450) 215375..216091 - 717 WP_065224995 IS66-like element accessory protein TnpA -
CP48_RS01300 (CP48_p01455) 216170..216661 + 492 WP_040091623 hypothetical protein -
CP48_RS01305 (CP48_p01460) 216688..217326 + 639 WP_040091622 type-F conjugative transfer system pilin assembly protein TrbC trbC
CP48_RS28165 (CP48_p01465) 217323..217703 + 381 WP_024213661 hypothetical protein -
CP48_RS01310 (CP48_p01470) 217938..219842 + 1905 WP_236927347 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CP48_RS01315 (CP48_p01475) 219856..220113 + 258 WP_040091333 conjugal transfer protein TrbE -
CP48_RS01320 (CP48_p01480) 220106..220849 + 744 WP_040091331 type-F conjugative transfer system pilin assembly protein TraF traF
CP48_RS32860 220863..221226 + 364 Protein_268 hypothetical protein -
CP48_RS01335 (CP48_p01500) 221605..221886 + 282 WP_000049684 type-F conjugative transfer system pilin chaperone TraQ -
CP48_RS01340 (CP48_p01505) 221873..222409 + 537 WP_040091329 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CP48_RS01345 (CP48_p01510) 222399..222713 + 315 WP_040091328 P-type conjugative transfer protein TrbJ -
CP48_RS01350 (CP48_p01515) 222667..223059 + 393 WP_040091326 F-type conjugal transfer protein TrbF -
CP48_RS01355 (CP48_p01520) 223046..224419 + 1374 WP_024212142 conjugal transfer pilus assembly protein TraH traH
CP48_RS01360 (CP48_p01525) 224416..227238 + 2823 WP_047088737 conjugal transfer mating-pair stabilization protein TraG traG
CP48_RS01365 (CP48_p01530) 227254..227751 + 498 WP_040090738 entry exclusion protein -
CP48_RS01370 (CP48_p01535) 227783..228514 + 732 WP_040090739 conjugal transfer complement resistance protein TraT -
CP48_RS01375 (CP48_p01540) 228574..228834 + 261 WP_040090733 hypothetical protein -
CP48_RS30265 (CP48_p01545) 229002..229719 + 718 Protein_278 hypothetical protein -
CP48_RS01390 (CP48_p01550) 229775..231928 + 2154 WP_047088736 type IV conjugative transfer system coupling protein TraD virb4
CP48_RS01395 (CP48_p01560) 231937..232335 - 399 WP_040090742 type II toxin-antitoxin system VapC family toxin -
CP48_RS01400 (CP48_p01565) 232335..232562 - 228 WP_000450526 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   3167 GenBank   NZ_CP012501
Plasmid name   pCFSAN004179G Incompatibility group   IncFIB
Plasmid size   242187 bp Coordinate of oriT [Strand]   200541..200893 [+]
Host baterium   Escherichia coli strain 08-00022

Cargo genes

Drug resistance gene   -
Virulence gene   estIa, faeC, faeD, faeE, faeF, faeH, faeI, faeJ, stcE, exeE, exeG, hlyD, hlyB, hlyA, hlyC
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7, AcrIF11