Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103974
Name   oriT_pST-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain ST113
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050727 (89089..89212 [-], 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_pST-1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2955 GenBank   WP_015059123
Name   traI_HEC93_RS24650_pST-1 insolico UniProt ID   I1WZQ7
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191914.74 Da        Isoelectric Point: 6.1060

>WP_015059123.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKISGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

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

(575-627)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   1227 GenBank   WP_001254386
Name   WP_001254386_pST-1 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   1228 GenBank   WP_000124981
Name   WP_000124981_pST-1 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


T4CP

ID   2814 GenBank   WP_022630316
Name   traD_HEC93_RS24655_pST-1 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: 83920.60 Da        Isoelectric Point: 5.0524

>WP_022630316.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
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.



ID   2815 GenBank   WP_000069764
Name   traC_HEC93_RS24735_pST-1 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: 99302.93 Da        Isoelectric Point: 5.8486

>WP_000069764.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 62944..89784

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HEC93_RS24655 (HEC93_24655) 62944..65160 - 2217 WP_022630316 type IV conjugative transfer system coupling protein TraD virb4
HEC93_RS24660 (HEC93_24660) 65413..66144 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HEC93_RS24665 (HEC93_24665) 66158..66667 - 510 WP_031943494 conjugal transfer entry exclusion protein TraS -
HEC93_RS24670 (HEC93_24670) 66664..69489 - 2826 WP_001007045 conjugal transfer mating-pair stabilization protein TraG traG
HEC93_RS24675 (HEC93_24675) 69486..70862 - 1377 WP_029400169 conjugal transfer pilus assembly protein TraH traH
HEC93_RS24680 (HEC93_24680) 70859..71221 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
HEC93_RS24685 (HEC93_24685) 71151..71696 - 546 WP_000059821 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HEC93_RS24690 (HEC93_24690) 71683..71967 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HEC93_RS24695 (HEC93_24695) 72086..72433 - 348 WP_001287891 conjugal transfer protein TrbA -
HEC93_RS24700 (HEC93_24700) 72449..73192 - 744 WP_001430248 type-F conjugative transfer system pilin assembly protein TraF traF
HEC93_RS24705 (HEC93_24705) 73185..73442 - 258 WP_000864352 conjugal transfer protein TrbE -
HEC93_RS24710 (HEC93_24710) 73469..75277 - 1809 WP_000821821 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HEC93_RS24715 (HEC93_24715) 75274..75912 - 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
HEC93_RS24720 (HEC93_24720) 75921..76913 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HEC93_RS24725 (HEC93_24725) 76910..77542 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HEC93_RS24730 (HEC93_24730) 77539..77925 - 387 WP_000214092 type-F conjugative transfer system protein TrbI -
HEC93_RS24735 (HEC93_24735) 77922..80552 - 2631 WP_000069764 type IV secretion system protein TraC virb4
HEC93_RS24740 (HEC93_24740) 80678..81040 - 363 WP_000836675 hypothetical protein -
HEC93_RS24745 (HEC93_24745) 81068..81282 - 215 Protein_97 hypothetical protein -
HEC93_RS24750 (HEC93_24750) 81362..81838 - 477 WP_015059129 hypothetical protein -
HEC93_RS24755 (HEC93_24755) 81831..82052 - 222 WP_001278695 conjugal transfer protein TraR -
HEC93_RS24760 (HEC93_24760) 82187..82702 - 516 WP_015059130 type IV conjugative transfer system lipoprotein TraV traV
HEC93_RS24765 (HEC93_24765) 82699..82950 - 252 WP_001038342 conjugal transfer protein TrbG -
HEC93_RS24770 (HEC93_24770) 82943..83263 - 321 WP_001057287 conjugal transfer protein TrbD virb4
HEC93_RS24775 (HEC93_24775) 83250..83840 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
HEC93_RS24780 (HEC93_24780) 83830..85257 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HEC93_RS24785 (HEC93_24785) 85257..85985 - 729 WP_001230813 type-F conjugative transfer system secretin TraK traK
HEC93_RS24790 (HEC93_24790) 85972..86538 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HEC93_RS24795 (HEC93_24795) 86560..86871 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HEC93_RS24800 (HEC93_24800) 86886..87245 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
HEC93_RS24805 (HEC93_24805) 87279..87506 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HEC93_RS24810 (HEC93_24810) 87600..88286 - 687 WP_000332484 PAS domain-containing protein -
HEC93_RS24815 (HEC93_24815) 88477..88860 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HEC93_RS24820 (HEC93_24820) 89137..89784 + 648 WP_031943493 transglycosylase SLT domain-containing protein virB1
HEC93_RS24825 (HEC93_24825) 90081..90902 - 822 WP_001234469 DUF932 domain-containing protein -
HEC93_RS24830 (HEC93_24830) 91020..91307 - 288 WP_000107544 hypothetical protein -
HEC93_RS25505 91332..91538 - 207 WP_000547968 hypothetical protein -
HEC93_RS25510 91608..91781 + 174 Protein_116 hypothetical protein -
HEC93_RS25515 91779..92009 - 231 WP_001426396 hypothetical protein -
HEC93_RS24840 (HEC93_24840) 92229..92354 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HEC93_RS25520 92296..92445 - 150 Protein_119 plasmid maintenance protein Mok -
HEC93_RS24845 (HEC93_24845) 92667..93386 - 720 WP_013362833 plasmid SOS inhibition protein A -
HEC93_RS24850 (HEC93_24850) 93383..93817 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   4414 GenBank   NZ_CP050727
Plasmid name   pST-1 Incompatibility group   IncA/C2
Plasmid size   147578 bp Coordinate of oriT [Strand]   89089..89212 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain ST113

Cargo genes

Drug resistance gene   blaTEM-1B, mcr-3.1, aac(3)-IId, qnrS1, blaCTX-M-55, catA2, sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR
Virulence gene   -
Metal resistance gene   merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -