Detailed information of oriT

oriT


The information of the oriT region


oriTDB ID   104974
Name   oriT_pSalMiami in_silico
Organism   Salmonella enterica subsp. enterica strain BAA-1586
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP023469 (61541..61810 [+], 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)
 31..38, 41..48  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site  
 
 _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 270 nt

>oriT_pSalMiami
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTGCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase


ID   3494 GenBank   WP_117338900
Name   traI_COO54_RS24070_pSalMiami insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191392.56 Da        Isoelectric Point: 5.8093

>WP_117338900.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSLEERWAGKGAEQLGLQGAVDKEVFTRELEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEAMASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTLHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYREAADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGRR
QLQEGMTFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGVREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVAAQSHSLTLRDAQRGTQMVRISALDSS
WSLFRPEKIPVADGERLMVTGKIPGLLVSGGDRLQVSAVNDGMMTVIVPGRAELASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKISRHPSFTVVSEQIK
ARAGEVSLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSQVELLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRATTRMIL
ETKDRFTVVQGYAGGGKTTQFRAVMSAVNLLPENERPHVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQIPRLKGVWAPENSVTEFSRLQERELAEAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPDAREQTLIVTHLNADRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHG
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMMNAERLFRIARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFSGEGRVKGSEEAQFVVLQGSRNGESLLADNMQEGVRIARDNPDSGVVVRIAGDGRPW
NPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEILAQRQAEEAVCRETEQRAAEIVRKMAEDKPDLPEEKT
AQAVREIAGQEQDRMTPPERETPLPESVLREPVRERETIREVARENRVRERLQQMEQEMVRDLQKEKTPG
GD

  Protein domains


Predicted by InterproScan.

(574-626)

(967-1157)

(11-282)

(632-711)

(1430-1553)


  Protein structure



No available structure.




Auxiliary protein


ID   1554 GenBank   WP_001151546
Name   WP_001151546_pSalMiami 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.

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB Q93GP1

ID   1555 GenBank   WP_001676655
Name   WP_001676655_pSalMiami 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.

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB H3JT82


T4CP


ID   3441 GenBank   WP_117338895
Name   traC_COO54_RS23985_pSalMiami 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: 100386.16 Da        Isoelectric Point: 6.6137

>WP_117338895.1 type IV secretion system protein TraC [Salmonella enterica]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLREFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRTDILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESLHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQMRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD

  Protein domains


Predicted by InterproScan.

(289-446)

(468-770)

(38-276)

  Protein structure



No available structure.



ID   3442 GenBank   WP_117338899
Name   traD_COO54_RS24065_pSalMiami insolico UniProt ID   _
Length   730 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 730 a.a.        Molecular weight: 82666.30 Da        Isoelectric Point: 5.2394

>WP_117338899.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEGRQMSSLFEPDTEAVAPAAAEAQAEQPQQPQQPQQ
PQQPQQPTVVSDKKSAAAGTAANTSAGGVGQELKMKQEDEEQPLPPGINASGEVVDMAVYERWRQEQELN
TQQQMQRREEVNINVHRGHGKDEPEPGDHF

  Protein domains


Predicted by InterproScan.

(173-560)

(32-128)

  Protein structure



No available structure.




T4SS


T4SS were predicted by using oriTfinder2.

Region 1: 61000..87387

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
COO54_RS23885 (COO54_23775) 56156..58153 + 1998 WP_117338888 ParB/RepB/Spo0J family partition protein -
COO54_RS23890 (COO54_23780) 58193..58627 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
COO54_RS23895 (COO54_23785) 58624..59361 + 738 WP_117338889 plasmid SOS inhibition protein A -
COO54_RS24255 59610..59768 + 159 WP_001704449 hypothetical protein -
COO54_RS23900 (COO54_23790) 59871..60689 + 819 Protein_71 DUF932 domain-containing protein -
COO54_RS23905 (COO54_23795) 61000..61470 - 471 WP_042828200 transglycosylase SLT domain-containing protein virB1
COO54_RS23915 (COO54_23805) 61886..62266 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
COO54_RS23920 (COO54_23810) 62459..63145 + 687 WP_085376305 PAS domain-containing protein -
COO54_RS23925 (COO54_23815) 63239..63466 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
COO54_RS23930 (COO54_23820) 63508..63870 + 363 WP_001274202 type IV conjugative transfer system pilin TraA -
COO54_RS23935 (COO54_23825) 63885..64196 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
COO54_RS23940 (COO54_23830) 64218..64784 + 567 WP_058215155 type IV conjugative transfer system protein TraE traE
COO54_RS23945 (COO54_23835) 64771..65511 + 741 WP_117338891 type-F conjugative transfer system secretin TraK traK
COO54_RS23950 (COO54_23840) 65511..66932 + 1422 WP_117338892 F-type conjugal transfer pilus assembly protein TraB traB
COO54_RS23955 (COO54_23845) 66922..67518 + 597 WP_047593686 conjugal transfer pilus-stabilizing protein TraP -
COO54_RS23960 (COO54_23850) 67496..67741 + 246 WP_117338893 DUF2689 domain-containing protein virb4
COO54_RS23965 (COO54_23855) 67738..68253 + 516 WP_085376303 type IV conjugative transfer system lipoprotein TraV traV
COO54_RS23970 (COO54_23860) 68388..68609 + 222 WP_001278699 conjugal transfer protein TraR -
COO54_RS23975 (COO54_23865) 68602..69069 + 468 WP_000549562 hypothetical protein -
COO54_RS23980 (COO54_23870) 69066..69449 + 384 WP_117338894 hypothetical protein -
COO54_RS23985 (COO54_23875) 69465..72113 + 2649 WP_117338895 type IV secretion system protein TraC virb4
COO54_RS23990 (COO54_23880) 72088..72474 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
COO54_RS23995 (COO54_23885) 72471..73103 + 633 WP_079967495 type-F conjugative transfer system protein TraW traW
COO54_RS24000 (COO54_23890) 73100..74092 + 993 WP_000833319 conjugal transfer pilus assembly protein TraU traU
COO54_RS24005 (COO54_23895) 74111..74419 + 309 WP_080235917 hypothetical protein -
COO54_RS24010 (COO54_23900) 74404..75042 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
COO54_RS24015 (COO54_23905) 75079..75498 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
COO54_RS24020 (COO54_23910) 75495..77321 + 1827 WP_117338896 type-F conjugative transfer system mating-pair stabilization protein TraN traN
COO54_RS24025 (COO54_23915) 77332..77547 + 216 WP_000700023 conjugal transfer protein TrbE -
COO54_RS24030 (COO54_23920) 77559..78308 + 750 WP_117338897 type-F conjugative transfer system pilin assembly protein TraF traF
COO54_RS24035 (COO54_23925) 78522..78815 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
COO54_RS24040 (COO54_23930) 78802..79350 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
COO54_RS24045 (COO54_23935) 79340..80722 + 1383 WP_117338898 conjugal transfer pilus assembly protein TraH traH
COO54_RS24050 (COO54_23940) 80719..83541 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
COO54_RS24055 (COO54_23945) 83557..84051 + 495 WP_077916534 entry exclusion protein -
COO54_RS24060 (COO54_23950) 84087..84818 + 732 WP_031608647 conjugal transfer complement resistance protein TraT -
COO54_RS24065 (COO54_23955) 85195..87387 + 2193 WP_117338899 type IV conjugative transfer system coupling protein TraD virb4


Host bacterium


ID   5412 GenBank   NZ_CP023469
Plasmid name   pSalMiami Incompatibility group   IncFII
Plasmid size   94044 bp Coordinate of oriT [Strand]   61541..61810 [+]
Host baterium   Salmonella enterica subsp. enterica strain BAA-1586

Cargo genes


Drug resistance gene   -
Virulence gene   paa, faeC, faeD, faeE, faeF, faeH, faeI
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -