Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108937
Name   oriT_pB-4515_1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain SCPM-O-B-4515
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP088137 (53102..53163 [-], 62 nt)
oriT length   62 nt
IRs (inverted repeats)      18..25, 28..35  (GCAAAATT..AATTTTGC)
Location of nic site      44..45
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 62 nt

>oriT_pB-4515_1
TTTATAAATAAAAATCAGCAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5991 GenBank   WP_249895813
Name   traI_LRM91_RS22960_pB-4515_1 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: 191327.24 Da        Isoelectric Point: 5.9174

>WP_249895813.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSLEERWAGKGAEQLGVQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLIAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTLHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYREAADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREWLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGSAAGQRERVAELTMMAREQGREVQIIAADRRSQTNLKQDERLSGELITGRR
QLQEGMSFSPGSTVIVDQGEKLSLKETLTLLDGAARHNIQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GGQQTPATVISGPDRNVRYARLAGDFVAAVKAGEESVAQVSGVREQAILAGMIRSELKTQGVLGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKIPVADGERLMVTGKIPGLRVSGGDRLQVSAVNDGMMTVIVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFVSVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVELLTEAKSFAAEGTGFAELGREIDAQ
IKRGDLLHVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVSGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPGSERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWVPENSVTEFSRLQERELVKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPDAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWENHQCALALVDKVYHRIAGISKEDGLITLQDADGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWPVTAVSGDGVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHG
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWTDAINRAAQKGTAHDVLEPKA
DREAMNAERLFSTARELRDVAAGRAVLRNAGLALGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFSGEGRVKGSEEAQFVALQGSRNGESLLADNMQEGVRIARDNPDSGVVVRIAGDGRPW
NPGAITGGRVWGDIPDSSVQPGAVNGEPVTAEILAQRQAEEAVRRETEQRAAEIVRKMAEDKPDLPEEKT
AQAVREIAGQEQDRMTPPERETPLPESVLREPVRERETIREVARENRVRERLQQTEQEMVRDLQKERTPD
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(11-282)

DNA helicase TraI (TraI_C)

(1430-1553)

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

(574-626)

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

(632-711)

AAA domain (AAA_30)

(967-1158)


  Protein structure



No available structure.




Auxiliary protein

ID   3019 GenBank   WP_249895802
Name   WP_249895802_pB-4515_1 insolico UniProt ID   _
Length   126 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 126 a.a.        Molecular weight: 14351.29 Da        Isoelectric Point: 4.7257

>WP_249895802.1 conjugal transfer relaxosome DNA-binding protein TraM [Salmonella enterica]
MAKVQAYVSDEVVEKINAIVEKRRSEGEKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQMEFNRVL
LENVLKTQSSVVKILGIGSISPHVAGNPKFEYANMVEDIKEKVSSEMERFFHENDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   3020 GenBank   WP_032490308
Name   WP_032490308_pB-4515_1 insolico UniProt ID   _
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15514.81 Da        Isoelectric Point: 10.6555

>WP_032490308.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Salmonella]
MSLKRFGTRSATGKMVKLKLPVDVEKLLREASDRSGRSRSFEAVIRLKDHLHRYPKFNRKGNVYGKSLVK
YLTMRLDDETNQLLITAKNRSGWCKTDEAADRVIDHLTKFPDFYNSDIFREANEGKKSTFKER

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(72-119)

TraY domain (TraY)

(17-60)


  Protein structure



No available structure.




T4CP

ID   6477 GenBank   WP_249895805
Name   traC_LRM91_RS22875_pB-4515_1 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: 100529.30 Da        Isoelectric Point: 6.7509

>WP_249895805.1 type IV secretion system protein TraC [Salmonella enterica]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPFRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCIHLMSSQLVGERIEYGLREFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAQAFINIVG
EMINHNPESLHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDHGRNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRRTYEYRAETD

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 52558..71554

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LRM91_RS22770 (LRM91_22770) 47787..48029 + 243 WP_000131519 DUF905 domain-containing protein -
LRM91_RS22775 (LRM91_22775) 48098..50095 + 1998 WP_249895801 ParB/RepB/Spo0J family partition protein -
LRM91_RS22780 (LRM91_22780) 50135..50269 + 135 Protein_65 conjugation system SOS inhibitor PsiB family protein -
LRM91_RS22785 (LRM91_22785) 50263..50919 + 657 Protein_66 plasmid SOS inhibition protein A -
LRM91_RS23090 50954..51082 + 129 WP_000372430 hypothetical protein -
LRM91_RS22790 (LRM91_22790) 51168..51326 + 159 WP_001704449 hypothetical protein -
LRM91_RS22795 (LRM91_22795) 51429..52247 + 819 Protein_69 DUF932 domain-containing protein -
LRM91_RS22800 (LRM91_22800) 52558..53028 - 471 WP_024134052 transglycosylase SLT domain-containing protein virB1
LRM91_RS22805 (LRM91_22805) 53451..53831 + 381 WP_249895802 conjugal transfer relaxosome DNA-binding protein TraM -
LRM91_RS22810 (LRM91_22810) 54026..54715 + 690 WP_249895803 conjugal transfer transcriptional regulator TraJ -
LRM91_RS22815 (LRM91_22815) 54814..55209 + 396 WP_001746564 conjugal transfer relaxosome DNA-bindin protein TraY -
LRM91_RS22820 (LRM91_22820) 55251..55613 + 363 WP_001274202 type IV conjugative transfer system pilin TraA -
LRM91_RS22825 (LRM91_22825) 55628..55939 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
LRM91_RS22830 (LRM91_22830) 55961..56527 + 567 WP_000399760 type IV conjugative transfer system protein TraE traE
LRM91_RS22835 (LRM91_22835) 56514..57254 + 741 WP_015059453 type-F conjugative transfer system secretin TraK traK
LRM91_RS22840 (LRM91_22840) 57254..58675 + 1422 WP_000146698 F-type conjugal transfer pilus assembly protein TraB traB
LRM91_RS22845 (LRM91_22845) 58665..59261 + 597 WP_000527898 conjugal transfer pilus-stabilizing protein TraP -
LRM91_RS22850 (LRM91_22850) 59239..59463 + 225 WP_001746950 DUF2689 domain-containing protein -
LRM91_RS22855 (LRM91_22855) 59460..59975 + 516 WP_001015676 type IV conjugative transfer system lipoprotein TraV traV
LRM91_RS22860 (LRM91_22860) 60110..60331 + 222 WP_001278699 conjugal transfer protein TraR -
LRM91_RS22865 (LRM91_22865) 60324..60791 + 468 WP_249895804 hypothetical protein -
LRM91_RS22870 (LRM91_22870) 60788..61171 + 384 WP_000870325 hypothetical protein -
LRM91_RS22875 (LRM91_22875) 61187..63835 + 2649 WP_249895805 type IV secretion system protein TraC virb4
LRM91_RS22880 (LRM91_22880) 63810..64196 + 387 WP_000102756 type-F conjugative transfer system protein TrbI -
LRM91_RS22885 (LRM91_22885) 64193..64825 + 633 WP_249895806 type-F conjugative transfer system protein TraW traW
LRM91_RS22890 (LRM91_22890) 64822..65814 + 993 WP_249895807 conjugal transfer pilus assembly protein TraU traU
LRM91_RS22895 (LRM91_22895) 65833..66141 + 309 WP_001576663 hypothetical protein -
LRM91_RS22900 (LRM91_22900) 66126..66764 + 639 WP_001576661 type-F conjugative transfer system pilin assembly protein TrbC trbC
LRM91_RS22905 (LRM91_22905) 66801..67220 + 420 WP_001229398 HNH endonuclease -
LRM91_RS22910 (LRM91_22910) 67217..69043 + 1827 WP_249895808 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LRM91_RS22915 (LRM91_22915) 69054..69530 + 477 WP_001746543 hypothetical protein -
LRM91_RS22920 (LRM91_22920) 69541..69756 + 216 WP_001746544 conjugal transfer protein TrbE -
LRM91_RS22925 (LRM91_22925) 69769..70512 + 744 Protein_95 type-F conjugative transfer system pilin assembly protein TraF -
LRM91_RS22930 (LRM91_22930) 70726..71019 + 294 WP_001233883 type-F conjugative transfer system pilin chaperone TraQ -
LRM91_RS22935 (LRM91_22935) 71006..71554 + 549 WP_249895809 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LRM91_RS22940 (LRM91_22940) 71544..72815 + 1272 Protein_98 conjugal transfer pilus assembly protein TraH -
LRM91_RS22945 (LRM91_22945) 74052..74534 + 483 Protein_99 surface exclusion protein -
LRM91_RS22950 (LRM91_22950) 74780..75511 + 732 WP_249895811 conjugal transfer complement resistance protein TraT -

Host bacterium

ID   9372 GenBank   NZ_CP088137
Plasmid name   pB-4515_1 Incompatibility group   IncFII
Plasmid size   86811 bp Coordinate of oriT [Strand]   53102..53163 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain SCPM-O-B-4515

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -