Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121170
Name   oriT_pS13D in_silico
Organism   Salmonella sp. S13 strain DS13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MT657397 (24278..24401 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 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_pS13D
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   7389 GenBank   WP_001254386
Name   WP_001254386_pS13D 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   7390 GenBank   WP_000124981
Name   WP_000124981_pS13D 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   7391 GenBank   WP_033548869
Name   WP_033548869_pS13D insolico UniProt ID   A0A1M1NID7
Length   138 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15270.40 Da        Isoelectric Point: 5.0270

>WP_033548869.1 MULTISPECIES: hypothetical protein [Enterobacterales]
MPTITAKVSDELLAYIDQVSGGNRSEYLRRCLEAGPGDLESGLKIVTNQLSDVNRKLDYLFDRASDADFG
SLRDELKAITETLSGVTFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A1M1NID7


T4CP

ID   15660 GenBank   WP_015059012
Name   traC_I5Z93_RS00100_pS13D 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: 99393.22 Da        Isoelectric Point: 6.3465

>WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   15661 GenBank   WP_000009363
Name   traD_I5Z93_RS00915_pS13D insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84259.95 Da        Isoelectric Point: 5.0504

>WP_000009363.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1311..24973

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
I5Z93_RS00005 1..732 - 732 WP_021559024 conjugal transfer complement resistance protein TraT -
I5Z93_RS00010 757..1248 - 492 WP_121097654 conjugal transfer entry exclusion protein TraS -
I5Z93_RS00015 1311..4127 - 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
I5Z93_RS00020 4124..5497 - 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
I5Z93_RS00025 5484..5876 - 393 WP_000126338 F-type conjugal transfer protein TrbF -
I5Z93_RS00030 5830..6144 - 315 WP_001384255 P-type conjugative transfer protein TrbJ -
I5Z93_RS00035 6134..6679 - 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
I5Z93_RS00040 6666..6947 - 282 WP_000549793 type-F conjugative transfer system pilin chaperone TraQ -
I5Z93_RS00045 7063..7806 - 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
I5Z93_RS00050 7799..8056 - 258 WP_053913405 conjugal transfer protein TrbE -
I5Z93_RS00055 8083..9933 - 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
I5Z93_RS00060 9930..10352 - 423 WP_001229309 HNH endonuclease -
I5Z93_RS00065 10378..10749 - 372 WP_000056336 hypothetical protein -
I5Z93_RS00070 10746..11384 - 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
I5Z93_RS00075 11411..11932 - 522 WP_015059014 hypothetical protein -
I5Z93_RS00080 11995..12303 - 309 WP_000412447 hypothetical protein -
I5Z93_RS00085 12330..13322 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
I5Z93_RS00090 13319..13951 - 633 WP_001203735 type-F conjugative transfer system protein TraW traW
I5Z93_RS00095 13948..14334 - 387 WP_015059013 type-F conjugative transfer system protein TrbI -
I5Z93_RS00100 14331..16958 - 2628 WP_015059012 type IV secretion system protein TraC virb4
I5Z93_RS00105 17118..17339 - 222 WP_001278692 conjugal transfer protein TraR -
I5Z93_RS00110 17474..17989 - 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
I5Z93_RS00115 17986..18237 - 252 WP_001038341 conjugal transfer protein TrbG -
I5Z93_RS00120 18249..18446 - 198 WP_001324648 conjugal transfer protein TrbD -
I5Z93_RS00125 18433..19023 - 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
I5Z93_RS00130 19013..20440 - 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
I5Z93_RS00135 20440..21168 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
I5Z93_RS00140 21155..21721 - 567 WP_000399794 type IV conjugative transfer system protein TraE traE
I5Z93_RS00145 21743..22054 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
I5Z93_RS00150 22069..22434 - 366 WP_021519752 type IV conjugative transfer system pilin TraA -
I5Z93_RS00155 22468..22695 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
I5Z93_RS00160 22789..23475 - 687 WP_015059009 PAS domain-containing protein -
I5Z93_RS00165 23666..24049 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
I5Z93_RS00170 24326..24973 + 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
I5Z93_RS00175 25270..26091 - 822 WP_001234445 DUF932 domain-containing protein -
I5Z93_RS00180 26202..26498 - 297 WP_001272251 hypothetical protein -
I5Z93_RS00185 26798..27094 + 297 Protein_36 hypothetical protein -
I5Z93_RS00190 27413..27538 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
I5Z93_RS00925 27480..27629 - 150 Protein_38 plasmid maintenance protein Mok -
I5Z93_RS00195 27851..28570 - 720 WP_001276217 plasmid SOS inhibition protein A -
I5Z93_RS00200 28567..29001 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   21598 GenBank   NZ_MT657397
Plasmid name   pS13D Incompatibility group   ColE10
Plasmid size   167286 bp Coordinate of oriT [Strand]   24278..24401 [-]
Host baterium   Salmonella sp. S13 strain DS13

Cargo genes

Drug resistance gene   blaCTX-M-55, blaTEM-1B, qnrS1, tet(M), ant(3'')-Ia, cmlA1, aadA2, dfrA12, oqxA, oqxB
Virulence gene   -
Metal resistance gene   silP, silA, silB, silF, silC, silR, silS, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -