Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   109982
Name   oriT_pCY16A in_silico
Organism   Salmonella enterica subsp. enterica strain CY16
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP126324 (56559..56620 [-], 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_pCY16A
TTTATAAATAAAAATCAGCAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   6590 GenBank   WP_015059446
Name   traI_QN087_RS22750_pCY16A insolico UniProt ID   H9ACC1
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191399.30 Da        Isoelectric Point: 5.9179

>WP_015059446.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSLEERWAGKGAEQLGVQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLIAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTLHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYREAADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISRERLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGSAAGQRERVADLTMMAREQGREVQIIAADRRSQTNLKQDERLSGELITGRR
QLQEGMSFSPGSTVIVDQGEKLSLKETLTLLDGAARHNIQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GGQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGVREQAILAGMIRSELKTQGVLGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKIPVADGERLMVTGKIPGLRVSGGDRLQVSAVNDGMMTVIVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFVSVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVELLTEAKSFAAEVTGFAELGREIDAQ
IKRGDLLHVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVSGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVSKTTQFRAVMSAVNLLPGSERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWVPENSVTEFSRLQERELVKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPDAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWENHQCALALVDKVYHRIAGISKEDGLITLQDADGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWPVTAVSGDGVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHG
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWTDAINRAAQKGTAHDVLEPKA
DREAMNAERLFSTARELRDVAAGRAVLRNAGLALGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFSGEGRVKGSEEAQFAALQGSRNGESLLADNMQEGVRIARDNPDSGVVVRIAGDGRPW
NPGAITGGRVWGDIPDSSVQPGAVNGEPVTAEILAQRQAEEAVRRETEQRAAEIVRKMAEDKPDLPEEKT
AQAVREIAGQEQDRMTPPERETPLPESVLREPVRERETIREVARENRVRERLQQTEQEMVRDLQKERTPD
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(11-282)

AAA domain (AAA_30)

(967-1158)

DNA helicase TraI (TraI_C)

(1430-1553)

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

(632-711)

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

(574-626)


  Protein structure



No available structure.




Auxiliary protein

ID   3540 GenBank   WP_001151568
Name   WP_001151568_pCY16A 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

ID   3541 GenBank   WP_032490308
Name   WP_032490308_pCY16A 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   7277 GenBank   WP_001747308
Name   traD_QN087_RS23290_pCY16A insolico UniProt ID   _
Length   744 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 744 a.a.        Molecular weight: 84214.94 Da        Isoelectric Point: 5.2353

>WP_001747308.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILTPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEGRQMSSLFEPDTEAVAPAAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAANTSAGGVGQELKMKQEDEEQPLPPGINAAGEVVD
MAAYERWRQEQEVNTQQQMQRREEVNINVHHGHGKDEPEPGDHF

  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: 56015..81578

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QN087_RS23095 (QN087_23095) 51044..51358 + 315 Protein_71 single-stranded DNA-binding protein SSB2 -
QN087_RS23100 (QN087_23100) 51360..51500 + 141 Protein_72 DUF905 family protein -
QN087_RS23105 (QN087_23105) 51569..53552 + 1984 Protein_73 ParB/RepB/Spo0J family partition protein -
QN087_RS23110 (QN087_23110) 53592..53726 + 135 Protein_74 conjugation system SOS inhibitor PsiB family protein -
QN087_RS23115 (QN087_23115) 53720..54376 + 657 Protein_75 plasmid SOS inhibition protein A -
QN087_RS23120 (QN087_23120) 54411..54539 + 129 WP_001746558 hypothetical protein -
QN087_RS23125 (QN087_23125) 54625..54783 + 159 WP_001704449 hypothetical protein -
QN087_RS23130 (QN087_23130) 54886..55704 + 819 Protein_78 DUF932 domain-containing protein -
QN087_RS23135 (QN087_23135) 56015..56485 - 471 WP_024134052 transglycosylase SLT domain-containing protein virB1
QN087_RS23140 (QN087_23140) 56908..57288 + 381 WP_001151568 conjugal transfer relaxosome DNA-binding protein TraM -
QN087_RS23145 (QN087_23145) 57483..58172 + 690 WP_001746563 conjugal transfer transcriptional regulator TraJ -
QN087_RS23150 (QN087_23150) 58271..58666 + 396 WP_001746564 conjugal transfer relaxosome DNA-bindin protein TraY -
QN087_RS23155 (QN087_23155) 58708..59070 + 363 WP_001274202 type IV conjugative transfer system pilin TraA -
QN087_RS23160 (QN087_23160) 59085..59396 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
QN087_RS23165 (QN087_23165) 59418..59984 + 567 WP_000399760 type IV conjugative transfer system protein TraE traE
QN087_RS23170 (QN087_23170) 59971..60711 + 741 WP_015059453 type-F conjugative transfer system secretin TraK traK
QN087_RS23175 (QN087_23175) 60711..62132 + 1422 WP_000146698 F-type conjugal transfer pilus assembly protein TraB traB
QN087_RS23180 (QN087_23180) 62122..62718 + 597 WP_000527898 conjugal transfer pilus-stabilizing protein TraP -
QN087_RS23185 (QN087_23185) 62696..62920 + 225 WP_001746950 DUF2689 domain-containing protein -
QN087_RS23190 (QN087_23190) 62917..63432 + 516 WP_001746951 type IV conjugative transfer system lipoprotein TraV traV
QN087_RS23195 (QN087_23195) 63567..63788 + 222 WP_001278699 conjugal transfer protein TraR -
QN087_RS23200 (QN087_23200) 63781..64248 + 468 WP_000549559 hypothetical protein -
QN087_RS23205 (QN087_23205) 64245..64628 + 384 WP_000870325 hypothetical protein -
QN087_RS23210 (QN087_23210) 64644..67291 + 2648 Protein_94 type IV secretion system protein TraC -
QN087_RS23215 (QN087_23215) 67266..67652 + 387 WP_000102756 type-F conjugative transfer system protein TrbI -
QN087_RS23220 (QN087_23220) 67649..68281 + 633 WP_015059451 type-F conjugative transfer system protein TraW traW
QN087_RS23225 (QN087_23225) 68278..69270 + 993 WP_015059450 conjugal transfer pilus assembly protein TraU traU
QN087_RS23230 (QN087_23230) 69289..69597 + 309 WP_001576663 hypothetical protein -
QN087_RS23235 (QN087_23235) 69582..70220 + 639 WP_001576661 type-F conjugative transfer system pilin assembly protein TrbC trbC
QN087_RS23240 (QN087_23240) 70257..70676 + 420 WP_001229398 HNH endonuclease -
QN087_RS23245 (QN087_23245) 70673..72499 + 1827 WP_001746541 type-F conjugative transfer system mating-pair stabilization protein TraN traN
QN087_RS23250 (QN087_23250) 72510..72986 + 477 WP_001746543 hypothetical protein -
QN087_RS23255 (QN087_23255) 72997..73212 + 216 WP_001746544 conjugal transfer protein TrbE -
QN087_RS23260 (QN087_23260) 73225..73968 + 744 WP_001746545 type-F conjugative transfer system pilin assembly protein TraF traF
QN087_RS23265 (QN087_23265) 74182..74475 + 294 WP_001233883 type-F conjugative transfer system pilin chaperone TraQ -
QN087_RS23270 (QN087_23270) 74462..75010 + 549 WP_000055842 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
QN087_RS23275 (QN087_23275) 75000..76271 + 1272 Protein_107 conjugal transfer pilus assembly protein TraH -
QN087_RS23280 (QN087_23280) 77508..77990 + 483 WP_000787664 hypothetical protein -
QN087_RS23285 (QN087_23285) 78236..78967 + 732 WP_000850404 conjugal transfer complement resistance protein TraT -
QN087_RS23290 (QN087_23290) 79344..81578 + 2235 WP_001747308 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   10417 GenBank   NZ_CP126324
Plasmid name   pCY16A Incompatibility group   IncFII
Plasmid size   86649 bp Coordinate of oriT [Strand]   56559..56620 [-]
Host baterium   Salmonella enterica subsp. enterica strain CY16

Cargo genes

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