Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102463
Name   oriT_p369 in_silico
Organism   Salmonella enterica strain YAQUESUR001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JARWAY010000074 (54844..55113 [+], 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_p369
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1837 GenBank   WP_000986921
Name   traI_P8599_RS23955_p369 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   753 GenBank   WP_001151546
Name   WP_001151546_p369 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   754 GenBank   WP_001676655
Name   WP_001676655_p369 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   1424 GenBank   WP_000793310
Name   traC_P8599_RS23860_p369 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   1425 GenBank   WP_000009318
Name   traD_P8599_RS23940_p369 insolico UniProt ID   _
Length   720 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 720 a.a.        Molecular weight: 81447.01 Da        Isoelectric Point: 5.1045

>WP_000009318.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Salmonella]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQPTVV
SDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREE
VNINVHRGHGKDEPEPGDDF

  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: 54303..80659

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
P8599_RS23755 (P8599_23745) 49459..51456 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
P8599_RS23760 (P8599_23750) 51496..51930 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
P8599_RS23765 (P8599_23755) 51927..52664 + 738 WP_000581933 plasmid SOS inhibition protein A -
P8599_RS23770 (P8599_23760) 52699..52827 + 129 WP_000372429 hypothetical protein -
P8599_RS23775 (P8599_23765) 52913..53071 + 159 WP_001704449 hypothetical protein -
P8599_RS23780 (P8599_23770) 53174..53992 + 819 Protein_68 DUF932 domain-containing protein -
P8599_RS23785 (P8599_23775) 54303..54773 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
P8599_RS23790 (P8599_23780) 55188..55568 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
P8599_RS23795 (P8599_23785) 55761..56447 + 687 WP_000336297 PAS domain-containing protein -
P8599_RS23800 (P8599_23790) 56541..56768 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
P8599_RS23805 (P8599_23795) 56810..57172 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
P8599_RS23810 (P8599_23800) 57187..57498 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
P8599_RS23815 (P8599_23805) 57520..58086 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
P8599_RS23820 (P8599_23810) 58073..58813 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
P8599_RS23825 (P8599_23815) 58813..60234 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
P8599_RS23830 (P8599_23820) 60224..60820 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
P8599_RS23835 (P8599_23825) 60798..61043 + 246 WP_010999944 DUF2689 domain-containing protein virb4
P8599_RS23840 (P8599_23830) 61040..61555 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
P8599_RS23845 (P8599_23835) 61690..61911 + 222 WP_001278699 conjugal transfer protein TraR -
P8599_RS23850 (P8599_23840) 61904..62371 + 468 WP_000549562 hypothetical protein -
P8599_RS23855 (P8599_23845) 62488..62751 + 264 WP_001239255 hypothetical protein -
P8599_RS23860 (P8599_23850) 62767..65415 + 2649 WP_000793310 type IV secretion system protein TraC virb4
P8599_RS23865 (P8599_23855) 65390..65776 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
P8599_RS23870 (P8599_23860) 65773..66405 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
P8599_RS23875 (P8599_23865) 66402..67394 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
P8599_RS23880 (P8599_23870) 67413..67721 + 309 WP_010999945 hypothetical protein -
P8599_RS23885 (P8599_23875) 67706..68344 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
P8599_RS23890 (P8599_23880) 68381..68800 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
P8599_RS23895 (P8599_23885) 68797..70623 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
P8599_RS23900 (P8599_23890) 70634..70849 + 216 WP_000700023 conjugal transfer protein TrbE -
P8599_RS23905 (P8599_23895) 70861..71610 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
P8599_RS23910 (P8599_23900) 71824..72117 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
P8599_RS23915 (P8599_23905) 72104..72652 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
P8599_RS23920 (P8599_23910) 72642..74024 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
P8599_RS23925 (P8599_23915) 74021..76843 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
P8599_RS23930 (P8599_23920) 76859..77353 + 495 WP_010999946 entry exclusion protein -
P8599_RS23935 (P8599_23925) 77389..78120 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
P8599_RS23940 (P8599_23930) 78497..80659 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
P8599_RS23945 (P8599_23935) 80668..81066 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
P8599_RS23950 (P8599_23940) 81066..81293 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   2907 GenBank   NZ_JARWAY010000074
Plasmid name   p369 Incompatibility group   IncFIB
Plasmid size   91738 bp Coordinate of oriT [Strand]   54844..55113 [+]
Host baterium   Salmonella enterica strain YAQUESUR001

Cargo genes

Drug resistance gene   -
Virulence gene   pefD, pefC, pefA, pefB, spvC, spvB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -