Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103052
Name   oriT_pHNEP28_cfr in_silico
Organism   Escherichia coli strain EP28
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT845955 (77025..77147 [-], 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_pHNEP28_cfr
GTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTTAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   942 GenBank   WP_001254386
Name   WP_001254386_pHNEP28_cfr 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

ID   943 GenBank   WP_236922144
Name   WP_236922144_pHNEP28_cfr insolico UniProt ID   _
Length   128 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 128 a.a.        Molecular weight: 14736.06 Da        Isoelectric Point: 7.1679

>WP_236922144.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia coli]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFQKMMMNK

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-123)


  Protein structure



No available structure.




T4CP

ID   1986 GenBank   WP_034169381
Name   traD_HTG34_RS00260_pHNEP28_cfr 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: 83846.52 Da        Isoelectric Point: 5.2346

>WP_034169381.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.



ID   1987 GenBank   WP_172687117
Name   traC_HTG34_RS00360_pHNEP28_cfr 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: 99350.07 Da        Isoelectric Point: 6.1921

>WP_172687117.1 type IV secretion system protein TraC [Escherichia coli]
MSNNPLETVTQAVNSLLTALKLPDESSQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVKASWLAKKNQARIDDVVNFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(468-772)

TraC protein (TraC_F_IV)

(39-277)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 46884..74815

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTG34_RS00260 46884..49100 - 2217 WP_034169381 type IV conjugative transfer system coupling protein TraD virb4
HTG34_RS00265 49151..49888 - 738 WP_158666146 hypothetical protein -
HTG34_RS00270 50091..50822 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HTG34_RS00275 50855..51352 - 498 WP_000605862 entry exclusion protein -
HTG34_RS00280 51371..54190 - 2820 WP_148116760 conjugal transfer mating-pair stabilization protein TraG traG
HTG34_RS00285 54187..55560 - 1374 WP_156841533 conjugal transfer pilus assembly protein TraH traH
HTG34_RS00290 55560..55922 - 363 WP_001443292 P-type conjugative transfer protein TrbJ -
HTG34_RS00295 55852..56397 - 546 WP_105078375 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTG34_RS00300 56384..56620 - 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
HTG34_RS00305 56781..57524 - 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HTG34_RS00310 57517..57774 - 258 WP_122986581 conjugal transfer protein TrbE -
HTG34_RS00315 57801..59609 - 1809 WP_104774095 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTG34_RS00320 59606..60028 - 423 WP_001229309 HNH endonuclease signature motif containing protein -
HTG34_RS00325 60053..60424 - 372 WP_000174465 hypothetical protein -
HTG34_RS00330 60421..61059 - 639 WP_000087539 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTG34_RS00335 61086..61604 - 519 WP_172687116 hypothetical protein -
HTG34_RS00340 61667..61975 - 309 WP_104774097 hypothetical protein -
HTG34_RS00345 62002..62994 - 993 WP_001523000 conjugal transfer pilus assembly protein TraU traU
HTG34_RS00350 62991..63623 - 633 WP_001203745 type-F conjugative transfer system protein TraW traW
HTG34_RS00355 63620..64006 - 387 WP_015059013 type-F conjugative transfer system protein TrbI -
HTG34_RS00360 64003..66633 - 2631 WP_172687117 type IV secretion system protein TraC virb4
HTG34_RS00365 66760..67110 - 351 WP_001712367 hypothetical protein -
HTG34_RS00370 67397..67720 - 324 WP_034169358 hypothetical protein -
HTG34_RS00695 67721..67937 - 217 Protein_74 hypothetical protein -
HTG34_RS00375 67976..68125 - 150 WP_172687118 hypothetical protein -
HTG34_RS00385 69468..69788 - 321 Protein_77 hypothetical protein -
HTG34_RS00390 69781..70002 - 222 WP_148116758 conjugal transfer protein TraR -
HTG34_RS00395 70137..70652 - 516 WP_000809907 type IV conjugative transfer system lipoprotein TraV traV
HTG34_RS00400 70649..70900 - 252 WP_001038341 conjugal transfer protein TrbG -
HTG34_RS00405 70893..71213 - 321 WP_001057291 DUF2689 domain-containing protein virb4
HTG34_RS00410 71200..71784 - 585 WP_148116757 conjugal transfer pilus-stabilizing protein TraP -
HTG34_RS00415 71774..73201 - 1428 WP_031570446 F-type conjugal transfer pilus assembly protein TraB traB
HTG34_RS00420 73201..73929 - 729 WP_021532669 type-F conjugative transfer system secretin TraK traK
HTG34_RS00425 73916..74482 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HTG34_RS00430 74504..74815 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTG34_RS00435 74820..75182 - 363 WP_000340273 type IV conjugative transfer system pilin TraA -
HTG34_RS00440 75216..75443 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTG34_RS00445 75537..76223 - 687 WP_015059009 PAS domain-containing protein -
HTG34_RS00450 76410..76796 - 387 WP_236922144 conjugal transfer relaxosome DNA-binding protein TraM -
HTG34_RS00455 77151..77720 + 570 Protein_91 transglycosylase SLT domain-containing protein -
HTG34_RS00460 78015..78836 - 822 WP_063097562 DUF932 domain-containing protein -
HTG34_RS00465 78942..79238 - 297 WP_001272240 hypothetical protein -
HTG34_RS00470 79262..79468 - 207 WP_024208114 hypothetical protein -
HTG34_RS00700 79538..79710 + 173 Protein_95 hypothetical protein -

Host bacterium

ID   3495 GenBank   NZ_KT845955
Plasmid name   pHNEP28_cfr Incompatibility group   IncR
Plasmid size   108837 bp Coordinate of oriT [Strand]   77025..77147 [-]
Host baterium   Escherichia coli strain EP28

Cargo genes

Drug resistance gene   qnrS1, tet(M), blaTEM-1B, cfr, floR
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -