Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103347
Name   oriT_pYUW043 in_silico
Organism   Salmonella enterica strain W043
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK778454 (37629..37752 [+], 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_pYUW043
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2505 GenBank   WP_061093447
Name   traI_HTX42_RS00450_pYUW043 insolico UniProt ID   A0A2Z4I1F4
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192119.90 Da        Isoelectric Point: 6.0788

>WP_061093447.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   1071 GenBank   WP_000124981
Name   WP_000124981_pYUW043 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   1072 GenBank   WP_001254386
Name   WP_001254386_pYUW043 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   2278 GenBank   WP_015059012
Name   traC_HTX42_RS00340_pYUW043 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   2279 GenBank   WP_059274178
Name   traD_HTX42_RS00445_pYUW043 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: 83906.57 Da        Isoelectric Point: 5.0504

>WP_059274178.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 37057..65236

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTX42_RS00235 33029..33463 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTX42_RS00240 33460..34179 + 720 WP_001276217 plasmid SOS inhibition protein A -
HTX42_RS00505 34401..34550 + 150 Protein_48 plasmid maintenance protein Mok -
HTX42_RS00245 34492..34617 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTX42_RS00485 34936..35232 - 297 Protein_50 hypothetical protein -
HTX42_RS00260 35532..35828 + 297 WP_001272251 hypothetical protein -
HTX42_RS00265 35939..36760 + 822 WP_001234445 DUF932 domain-containing protein -
HTX42_RS00270 37057..37704 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
HTX42_RS00275 37981..38364 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HTX42_RS00280 38555..39241 + 687 WP_015059009 PAS domain-containing protein -
HTX42_RS00285 39335..39562 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTX42_RS00290 39596..39961 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
HTX42_RS00295 39976..40287 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTX42_RS00300 40309..40875 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
HTX42_RS00305 40862..41590 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTX42_RS00310 41590..43017 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
HTX42_RS00315 43007..43597 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HTX42_RS00320 43584..43781 + 198 WP_001324648 conjugal transfer protein TrbD -
HTX42_RS00325 43793..44044 + 252 WP_001038341 conjugal transfer protein TrbG -
HTX42_RS00330 44041..44556 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
HTX42_RS00335 44691..44912 + 222 WP_001278692 conjugal transfer protein TraR -
HTX42_RS00340 45072..47699 + 2628 WP_015059012 type IV secretion system protein TraC virb4
HTX42_RS00345 47696..48082 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
HTX42_RS00350 48079..48711 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
HTX42_RS00355 48708..49700 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTX42_RS00360 49727..50035 + 309 WP_000412447 hypothetical protein -
HTX42_RS00365 50098..50619 + 522 WP_015059014 hypothetical protein -
HTX42_RS00370 50646..51284 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTX42_RS00375 51281..51652 + 372 WP_000056336 hypothetical protein -
HTX42_RS00380 51678..52100 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
HTX42_RS00385 52097..53947 + 1851 WP_172694668 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTX42_RS00390 53974..54231 + 258 WP_053913405 conjugal transfer protein TrbE -
HTX42_RS00395 54224..54967 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
HTX42_RS00400 55083..55364 + 282 WP_000549793 type-F conjugative transfer system pilin chaperone TraQ -
HTX42_RS00405 55351..55896 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTX42_RS00410 55886..56200 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
HTX42_RS00415 56154..56546 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
HTX42_RS00420 56533..57906 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
HTX42_RS00425 57903..60719 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
HTX42_RS00430 60752..61273 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
HTX42_RS00435 61298..62029 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
HTX42_RS00440 62232..62969 + 738 WP_015059020 hypothetical protein -
HTX42_RS00445 63020..65236 + 2217 WP_059274178 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3790 GenBank   NZ_MK778454
Plasmid name   pYUW043 Incompatibility group   IncFII
Plasmid size   74227 bp Coordinate of oriT [Strand]   37629..37752 [+]
Host baterium   Salmonella enterica strain W043

Cargo genes

Drug resistance gene   blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -