Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102921
Name   oriT_pQJDsal2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Pullorum strain QJ-2D-Sal
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP022965 (67734..67795 [+], 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_pQJDsal2
TTTATAAATAAAAATCAGCAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2193 GenBank   WP_079786986
Name   traI_CJD41_RS24650_pQJDsal2 insolico UniProt ID   _
Length   1659 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1659 a.a.        Molecular weight: 181111.70 Da        Isoelectric Point: 5.5011

>WP_079786986.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSLEERWAGKGAEQLGVQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLIAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTLHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYREAADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISRERLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGSAAGQRERVADLTMMAREQGREVQIIAADRRSQTNLKQDERLSGELITGRR
QLQEGMSFSPGSTVIVDQGEKLSLKETLTLLDGAARHNIQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GGQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGVREQAILAGMIRSELKTQGVLGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKIPVADGERLMVTGKIPGLRVSGGDRLQVSAVNDGMMTVIVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFVSVTQMAMDNATLNGLARSGRDVWLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVELLTEAKSFAAEVTGFAELGREIDAQ
IKRGDLLHVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVSGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVSKTTQFRAVMSAVNLLPGSERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWVPENSVTEFSRLQERELVKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPDAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWENHQCALALVDKVYHRIAGISKEDGLITLQDADGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWPVTAVSGDGVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHG
AQGASETFAIALEGTEGGRKQMAGFESAYVALPAFDRNGKSAGIWLNPLTTDDGAGLRGFSGEGRVKGSE
EAQFVALQGSRNGESLLADNMQEGVRIARDNPDSGVVVRIAGDGRPWNPGAITGGRVWGDIPDSSVQPGA
VNGEPVTAEILAQRQAEEAVRRETEQRAAEIVRKMAEDKPDLPEEKTAQAVREIAGQEQDRMTPPERETP
LPESVLREPVRERETIREVARENRVRERLQQTEQEMVRDLQKERTPDGD

  Protein domains


Predicted by InterproScan.

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

(574-626)

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

(632-711)

TrwC relaxase (TrwC)

(11-282)

AAA domain (AAA_30)

(967-1158)

DNA helicase TraI (TraI_C)

(1425-1460)


  Protein structure



No available structure.




Auxiliary protein

ID   895 GenBank   WP_032490308
Name   WP_032490308_pQJDsal2 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.



ID   896 GenBank   WP_001151568
Name   WP_001151568_pQJDsal2 insolico UniProt ID   Q8L369
Length   126 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 126 a.a.        Molecular weight: 14293.25 Da        Isoelectric Point: 4.8463

>WP_001151568.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Salmonella]
MAKVQAYVSDEVVEKINAIVEKRRSEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQMEFNRVL
LENVLKTQSSVVKILGIGSISPHVAGNPKFEYANMVEDIKEKVSSEMERFFHENDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB Q8L369


T4CP

ID   1868 GenBank   WP_023212018
Name   traD_CJD41_RS24655_pQJDsal2 insolico UniProt ID   _
Length   750 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 750 a.a.        Molecular weight: 84921.70 Da        Isoelectric Point: 5.2353

>WP_023212018.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILTPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEGRQMSSLFEPDTEAVAPAAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAANTSAGGVGQELKMKQEDEEQPLPPGINA
AGEVVDMAAYERWRQEQEVNTQQQMQRREEVNINVHHGHGKDEPEPGDHF

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42758..68339

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CJD41_RS24650 (CJD41_24840) 37779..42758 - 4980 WP_079786986 conjugative transfer relaxase/helicase TraI -
CJD41_RS24655 (CJD41_24845) 42758..45010 - 2253 WP_023212018 type IV conjugative transfer system coupling protein TraD prgC
CJD41_RS24665 (CJD41_24850) 45387..46118 - 732 WP_000850404 conjugal transfer complement resistance protein TraT -
CJD41_RS24670 (CJD41_24855) 46364..46846 - 483 WP_000787664 hypothetical protein -
CJD41_RS25630 48083..49354 - 1272 Protein_56 conjugal transfer pilus assembly protein TraH -
CJD41_RS24680 (CJD41_24865) 49344..49892 - 549 WP_000055842 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CJD41_RS24685 (CJD41_24870) 49879..50172 - 294 WP_001233883 type-F conjugative transfer system pilin chaperone TraQ -
CJD41_RS24690 (CJD41_24875) 50386..51129 - 744 WP_001746545 type-F conjugative transfer system pilin assembly protein TraF traF
CJD41_RS24695 (CJD41_24880) 51142..51357 - 216 WP_001746544 conjugal transfer protein TrbE -
CJD41_RS24700 (CJD41_24885) 51368..51844 - 477 WP_001746543 hypothetical protein -
CJD41_RS24705 (CJD41_24890) 51855..53681 - 1827 WP_001746541 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CJD41_RS24710 (CJD41_24895) 53678..54097 - 420 WP_001229398 HNH endonuclease -
CJD41_RS24715 (CJD41_24900) 54134..54772 - 639 WP_079786993 type-F conjugative transfer system pilin assembly protein TrbC trbC
CJD41_RS24720 (CJD41_24905) 54757..55065 - 309 WP_001576663 hypothetical protein -
CJD41_RS24725 (CJD41_24910) 55084..56076 - 993 WP_015059450 conjugal transfer pilus assembly protein TraU traU
CJD41_RS24730 (CJD41_24915) 56073..56705 - 633 WP_015059451 type-F conjugative transfer system protein TraW traW
CJD41_RS24735 (CJD41_24920) 56702..57088 - 387 WP_000102756 type-F conjugative transfer system protein TrbI -
CJD41_RS24740 (CJD41_24925) 57063..59710 - 2648 Protein_69 type IV secretion system protein TraC -
CJD41_RS24745 (CJD41_24930) 59726..60109 - 384 WP_000870325 hypothetical protein -
CJD41_RS24750 (CJD41_24935) 60106..60573 - 468 WP_000549559 hypothetical protein -
CJD41_RS24755 (CJD41_24940) 60566..60787 - 222 WP_001278699 conjugal transfer protein TraR -
CJD41_RS24760 (CJD41_24945) 60922..61437 - 516 WP_001746951 type IV conjugative transfer system lipoprotein TraV traV
CJD41_RS24765 (CJD41_24950) 61434..61658 - 225 WP_001746950 DUF2689 domain-containing protein -
CJD41_RS24770 (CJD41_24955) 61636..62232 - 597 WP_000527898 conjugal transfer pilus-stabilizing protein TraP -
CJD41_RS24775 (CJD41_24960) 62222..63643 - 1422 WP_000146698 F-type conjugal transfer pilus assembly protein TraB traB
CJD41_RS24780 (CJD41_24965) 63643..64383 - 741 WP_015059453 type-F conjugative transfer system secretin TraK traK
CJD41_RS24785 (CJD41_24970) 64370..64936 - 567 WP_000399760 type IV conjugative transfer system protein TraE traE
CJD41_RS24790 (CJD41_24975) 64958..65269 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
CJD41_RS24795 (CJD41_24980) 65284..65646 - 363 WP_001274202 type IV conjugative transfer system pilin TraA -
CJD41_RS24800 (CJD41_24985) 65688..66083 - 396 WP_001746564 conjugal transfer relaxosome DNA-bindin protein TraY -
CJD41_RS24805 (CJD41_24990) 66182..66871 - 690 WP_001746563 conjugal transfer transcriptional regulator TraJ -
CJD41_RS24810 (CJD41_24995) 67066..67446 - 381 WP_001151568 conjugal transfer relaxosome DNA-binding protein TraM -
CJD41_RS24815 (CJD41_25000) 67869..68339 + 471 WP_120116676 transglycosylase SLT domain-containing protein virB1
CJD41_RS24820 68650..69468 - 819 Protein_85 DUF932 domain-containing protein -
CJD41_RS25735 69814..69942 - 129 WP_001746558 hypothetical protein -
CJD41_RS24825 (CJD41_25020) 69977..70633 - 657 Protein_87 plasmid SOS inhibition protein A -
CJD41_RS24830 (CJD41_25025) 70627..70761 - 135 Protein_88 conjugation system SOS inhibitor PsiB family protein -
CJD41_RS24835 (CJD41_25030) 70801..72784 - 1984 Protein_89 ParB/RepB/Spo0J family partition protein -
CJD41_RS24840 (CJD41_25035) 72853..72993 - 141 Protein_90 DUF905 family protein -
CJD41_RS24845 (CJD41_25040) 72995..73309 - 315 Protein_91 single-stranded DNA-binding protein SSB2 -

Host bacterium

ID   3364 GenBank   NZ_CP022965
Plasmid name   pQJDsal2 Incompatibility group   IncFII
Plasmid size   86369 bp Coordinate of oriT [Strand]   67734..67795 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Pullorum strain QJ-2D-Sal

Cargo genes

Drug resistance gene   -
Virulence gene   spvB, spvC, faeI, faeH
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -