Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105407
Name   oriT_p24350-2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain CVM 24350
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051388 (93818..94169 [+], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      192..198, 206..212  (TATAAAA..TTTTATA)
 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: 352 nt

>oriT_p24350-2
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   1666 GenBank   WP_001151528
Name   WP_001151528_p24350-2 insolico UniProt ID   A0A731UEV6
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14577.51 Da        Isoelectric Point: 5.0517

>WP_001151528.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LEYVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A731UEV6

ID   1667 GenBank   WP_223195105
Name   WP_223195105_p24350-2 insolico UniProt ID   _
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15423.73 Da        Isoelectric Point: 9.9240

>WP_223195105.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Enterobacteriaceae]
MLLKRFGTRSATGKMVKLKLPLDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure



No available structure.




T4CP

ID   3670 GenBank   WP_001064265
Name   traC_HFR97_RS24895_p24350-2 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: 99296.07 Da        Isoelectric Point: 6.3032

>WP_001064265.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
AGGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.



ID   3671 GenBank   WP_000009324
Name   traD_HFR97_RS24985_p24350-2 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: 81528.14 Da        Isoelectric Point: 5.1126

>WP_000009324.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRREEVN
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: 93247..119705

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFR97_RS24800 (HFR97_24870) 89175..90544 + 1370 WP_085947770 IS3-like element IS150 family transposase -
HFR97_RS25235 90586..90735 + 150 Protein_103 plasmid maintenance protein Mok -
HFR97_RS24805 (HFR97_24875) 90677..90802 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HFR97_RS25390 (HFR97_24880) 91022..91251 + 230 Protein_105 hypothetical protein -
HFR97_RS25240 91249..91422 - 174 Protein_106 hypothetical protein -
HFR97_RS25245 91492..91698 + 207 WP_015059635 hypothetical protein -
HFR97_RS24815 (HFR97_24885) 91723..92009 + 287 Protein_108 hypothetical protein -
HFR97_RS24820 (HFR97_24890) 92129..92950 + 822 WP_001234423 DUF932 domain-containing protein -
HFR97_RS24825 (HFR97_24895) 93247..93837 - 591 WP_023565181 transglycosylase SLT domain-containing protein -
HFR97_RS24830 (HFR97_24900) 94170..94553 + 384 WP_001151528 conjugal transfer relaxosome DNA-binding protein TraM -
HFR97_RS24835 (HFR97_24905) 94740..95429 + 690 WP_000283383 conjugal transfer transcriptional regulator TraJ -
HFR97_RS24840 (HFR97_24910) 95528..95923 + 396 WP_001366159 conjugal transfer relaxosome DNA-bindin protein TraY -
HFR97_RS24845 (HFR97_24915) 95956..96318 + 363 WP_000994784 type IV conjugative transfer system pilin TraA -
HFR97_RS24850 (HFR97_24920) 96323..96634 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HFR97_RS24855 (HFR97_24925) 96656..97222 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HFR97_RS24860 (HFR97_24930) 97209..97937 + 729 WP_001230805 type-F conjugative transfer system secretin TraK traK
HFR97_RS24865 (HFR97_24935) 97937..99388 + 1452 WP_000146659 F-type conjugal transfer pilus assembly protein TraB traB
HFR97_RS24870 (HFR97_24940) 99378..99938 + 561 WP_000896605 conjugal transfer pilus-stabilizing protein TraP -
HFR97_RS24875 (HFR97_24945) 99925..100245 + 321 WP_001057304 conjugal transfer protein TrbD virb4
HFR97_RS24880 (HFR97_24950) 100238..100489 + 252 WP_001038331 conjugal transfer protein TrbG -
HFR97_RS24885 (HFR97_24955) 100486..101001 + 516 WP_000809885 type IV conjugative transfer system lipoprotein TraV traV
HFR97_RS24890 (HFR97_24960) 101136..101357 + 222 WP_001278686 conjugal transfer protein TraR -
HFR97_RS24895 (HFR97_24965) 101517..104144 + 2628 WP_001064265 type IV secretion system protein TraC virb4
HFR97_RS24900 (HFR97_24970) 104141..104527 + 387 WP_000099693 type-F conjugative transfer system protein TrbI -
HFR97_RS24905 (HFR97_24975) 104524..105156 + 633 WP_001203750 type-F conjugative transfer system protein TraW traW
HFR97_RS24910 (HFR97_24980) 105153..106145 + 993 WP_000830835 conjugal transfer pilus assembly protein TraU traU
HFR97_RS24915 (HFR97_24985) 106154..106792 + 639 WP_000777690 type-F conjugative transfer system pilin assembly protein TrbC trbC
HFR97_RS24920 (HFR97_24990) 106789..108597 + 1809 WP_000821840 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HFR97_RS24925 (HFR97_24995) 108624..108881 + 258 WP_000864318 conjugal transfer protein TrbE -
HFR97_RS24930 (HFR97_25000) 108874..109617 + 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
HFR97_RS24935 (HFR97_25005) 109633..109980 + 348 WP_001287910 conjugal transfer protein TrbA -
HFR97_RS24940 (HFR97_25010) 109982..110296 - 315 WP_000415566 protein ArtA -
HFR97_RS24945 (HFR97_25015) 110377..110661 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HFR97_RS24950 (HFR97_25020) 110648..111193 + 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HFR97_RS24955 (HFR97_25025) 111123..111464 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HFR97_RS24960 (HFR97_25030) 111451..111831 + 381 WP_001366201 F-type conjugal transfer protein TrbF -
HFR97_RS24965 (HFR97_25035) 111828..113204 + 1377 WP_000982840 conjugal transfer pilus assembly protein TraH traH
HFR97_RS24970 (HFR97_25040) 113201..116023 + 2823 WP_001007016 conjugal transfer mating-pair stabilization protein TraG traG
HFR97_RS24975 (HFR97_25045) 116039..116536 + 498 WP_000605859 entry exclusion protein -
HFR97_RS24980 (HFR97_25050) 116568..117299 + 732 WP_023565183 conjugal transfer complement resistance protein TraT -
HFR97_RS24985 (HFR97_25055) 117552..119705 + 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HFR97_RS24990 (HFR97_25060) 119714..120112 - 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HFR97_RS24995 (HFR97_25065) 120112..120339 - 228 WP_000450520 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   5845 GenBank   NZ_CP051388
Plasmid name   p24350-2 Incompatibility group   IncFIB
Plasmid size   120420 bp Coordinate of oriT [Strand]   93818..94169 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain CVM 24350

Cargo genes

Drug resistance gene   sul2, aph(3')-Ia, aph(6)-Id, aph(3'')-Ib, tet(B), sitABCD
Virulence gene   iucA, iucB, iucC, iutA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -