Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108349
Name   oriT_pS1380-118kb in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain S1380
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OM048934 (83982..84251 [+], 270 nt)
oriT length   270 nt
IRs (inverted repeats)      245..253, 262..270  (CACCCCTGG..CCAGGGGTG)
 92..98, 111..117  (ATTTAAT..ATTAAAT)
 103..108, 111..116  (TTTAAT..ATTAAA)
 33..38, 41..46  (AAAATT..AATTTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 270 nt

>oriT_pS1380-118kb
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCACCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5584 GenBank   WP_000986921
Name   traI_M5E05_RS00730_pS1380-118kb insolico UniProt ID   Q93GL4
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191683.72 Da        Isoelectric Point: 5.9311

>WP_000986921.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Salmonella]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR
QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMMNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW
NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1158)

TrwC relaxase (TrwC)

(11-282)

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

(632-711)

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

(574-626)

DNA helicase TraI (TraI_C)

(1430-1553)


  Protein structure


Source ID Structure
AlphaFold DB Q93GL4


Auxiliary protein

ID   2680 GenBank   WP_001151546
Name   WP_001151546_pS1380-118kb insolico UniProt ID   Q93GP1
Length   126 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 126 a.a.        Molecular weight: 14366.30 Da        Isoelectric Point: 5.7236

>WP_001151546.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Salmonella]
MAKVNVYISNEVHNKITAIVEKRRQEGARDKDISFSGTSSMLLELGLRVYEAQMERKESPFNQTEFNKVL
LENVLKTQSSVAKILGIGSLSPHVAGNPKFEYANMVEDIKEKVSSEMERFFHENEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB Q93GP1

ID   2681 GenBank   WP_001676655
Name   WP_001676655_pS1380-118kb insolico UniProt ID   H3JT82
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9147.26 Da        Isoelectric Point: 9.6183

>WP_001676655.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Salmonella]
MRRRNAREGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRYPDFYNEEIFREVIEETES
TFKEI

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB H3JT82


T4CP

ID   5960 GenBank   WP_000793310
Name   traC_M5E05_RS00635_pS1380-118kb insolico UniProt ID   _
Length   882 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 882 a.a.        Molecular weight: 100382.20 Da        Isoelectric Point: 6.9316

>WP_000793310.1 MULTISPECIES: type IV secretion system protein TraC [Salmonella]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLRKFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESIHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVTNLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(468-763)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   5961 GenBank   WP_053299623
Name   traD_M5E05_RS00715_pS1380-118kb insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83213.90 Da        Isoelectric Point: 5.1045

>WP_053299623.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQ
EQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

  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: 83441..109842

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
M5E05_RS00535 (BNIPNGOD_00118) 78596..80593 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
M5E05_RS00540 (BNIPNGOD_00119) 80633..81067 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
M5E05_RS00545 (BNIPNGOD_00120) 81064..81801 + 738 WP_000581933 plasmid SOS inhibition protein A -
M5E05_RS00775 81836..81964 + 129 WP_000372429 hypothetical protein -
M5E05_RS00550 82038..82208 + 171 WP_000229547 hypothetical protein -
M5E05_RS00555 82311..83130 + 820 Protein_113 DUF932 domain-containing protein -
M5E05_RS00560 (BNIPNGOD_00123) 83441..83911 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
M5E05_RS00565 84326..84706 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
M5E05_RS00570 (BNIPNGOD_00124) 84899..85585 + 687 WP_000336297 PAS domain-containing protein -
M5E05_RS00575 (BNIPNGOD_00125) 85679..85906 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
M5E05_RS00580 (BNIPNGOD_00126) 85948..86310 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
M5E05_RS00585 (BNIPNGOD_00127) 86325..86636 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
M5E05_RS00590 (BNIPNGOD_00128) 86658..87224 + 567 WP_000399769 type IV conjugative transfer system protein TraE traE
M5E05_RS00595 (BNIPNGOD_00129) 87211..87951 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
M5E05_RS00600 (BNIPNGOD_00130) 87951..89372 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
M5E05_RS00605 (BNIPNGOD_00131) 89362..89958 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
M5E05_RS00610 (BNIPNGOD_00132) 89936..90181 + 246 WP_010999944 DUF2689 domain-containing protein virb4
M5E05_RS00615 (BNIPNGOD_00133) 90178..90693 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
M5E05_RS00620 (BNIPNGOD_00134) 90828..91049 + 222 WP_001278699 conjugal transfer protein TraR -
M5E05_RS00625 (BNIPNGOD_00135) 91042..91509 + 468 WP_000549562 hypothetical protein -
M5E05_RS00630 (BNIPNGOD_00137) 91626..91889 + 264 WP_001239256 hypothetical protein -
M5E05_RS00635 (BNIPNGOD_00138) 91905..94553 + 2649 WP_000793310 type IV secretion system protein TraC virb4
M5E05_RS00640 (BNIPNGOD_00139) 94528..94914 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
M5E05_RS00645 (BNIPNGOD_00140) 94911..95543 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
M5E05_RS00650 (BNIPNGOD_00141) 95540..96532 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
M5E05_RS00655 (BNIPNGOD_00142) 96551..96859 + 309 WP_010999945 hypothetical protein -
M5E05_RS00660 (BNIPNGOD_00143) 96844..97482 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
M5E05_RS00665 (BNIPNGOD_00144) 97519..97938 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
M5E05_RS00670 (BNIPNGOD_00145) 97935..99761 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
M5E05_RS00675 (BNIPNGOD_00146) 99772..99987 + 216 WP_000700023 conjugal transfer protein TrbE -
M5E05_RS00680 (BNIPNGOD_00147) 99999..100748 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
M5E05_RS00685 (BNIPNGOD_00148) 100962..101255 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
M5E05_RS00690 (BNIPNGOD_00149) 101242..101790 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
M5E05_RS00695 (BNIPNGOD_00150) 101780..103162 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
M5E05_RS00700 (BNIPNGOD_00151) 103159..105981 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
M5E05_RS00705 (BNIPNGOD_00152) 105997..106491 + 495 WP_010999946 entry exclusion protein -
M5E05_RS00710 (BNIPNGOD_00153) 106527..107258 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
M5E05_RS00715 (BNIPNGOD_00154) 107635..109842 + 2208 WP_053299623 type IV conjugative transfer system coupling protein TraD virb4
M5E05_RS00720 (BNIPNGOD_00155) 109851..110249 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
M5E05_RS00725 (BNIPNGOD_00156) 110249..110476 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   8784 GenBank   NZ_OM048934
Plasmid name   pS1380-118kb Incompatibility group   -
Plasmid size   118931 bp Coordinate of oriT [Strand]   83982..84251 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain S1380

Cargo genes

Drug resistance gene   aac(3)-IId, mph(A), aph(3')-Ia
Virulence gene   spvB, spvC
Metal resistance gene   merP, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -