Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100368
Name   oriT_pYT1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_014476 (76552..76810 [-], 259 nt)
oriT length   259 nt
IRs (inverted repeats)      115..128, 134..147  (ATAGCGGTGCCGGC..GCCTGCACCGCTAT)
Location of nic site      241..242
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 259 nt

>oriT_pYT1
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   439 GenBank   YP_003864254
Name   Nickase_pYT1 insolico UniProt ID   H9L4G8
Length   1752 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191683.72 Da        Isoelectric Point: 5.9311

>YP_003864254.1 conjugative transfer oriT nicking-unwinding protein (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
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



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 76008..102364

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXC32_RS00430 (D645_p14109) 71167..73164 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
HXC32_RS00435 (D645_p14097) 73204..73638 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
HXC32_RS00440 (D645_p14098) 73635..74372 + 738 WP_000581933 plasmid SOS inhibition protein A -
HXC32_RS00445 74609..74779 + 171 WP_000229547 hypothetical protein -
HXC32_RS00450 74882..75700 + 819 Protein_89 DUF945 domain-containing protein -
HXC32_RS00455 (D645_p14106) 76008..76478 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
HXC32_RS00460 (D645_p14065) 76893..77273 + 381 WP_013307857 conjugal transfer relaxosome DNA-binding protein TraM -
HXC32_RS00465 (D645_p14071) 77466..78152 + 687 WP_000336297 PAS domain-containing protein -
HXC32_RS00470 (D645_p14053) 78246..78473 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
HXC32_RS00475 (D645_p14075) 78515..78877 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
HXC32_RS00480 (D645_p14066) 78892..79203 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
HXC32_RS00485 (D645_p14073) 79225..79791 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
HXC32_RS00490 (D645_p14069) 79778..80518 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
HXC32_RS00495 (D645_p14074) 80518..81939 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
HXC32_RS00500 (D645_p14062) 81929..82525 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
HXC32_RS00505 (D645_p14052) 82503..82748 + 246 WP_010999944 DUF2689 domain-containing protein virb4
HXC32_RS00510 (D645_p14055) 82745..83260 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
HXC32_RS00515 (D645_p14056) 83395..83616 + 222 WP_001278699 conjugal transfer protein TraR -
HXC32_RS00520 (D645_p14112) 83609..84076 + 468 WP_000549562 hypothetical protein -
HXC32_RS00525 (D645_p14113) 84193..84456 + 264 WP_001239255 hypothetical protein -
HXC32_RS00530 (D645_p14076) 84472..87120 + 2649 WP_000793310 type IV secretion system protein TraC virb4
HXC32_RS00535 (D645_p14054) 87095..87481 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
HXC32_RS00540 (D645_p14060) 87478..88110 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
HXC32_RS00545 (D645_p14064) 88107..89099 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
HXC32_RS00550 (D645_p14114) 89118..89426 + 309 WP_010999945 hypothetical protein -
HXC32_RS00555 (D645_p14059) 89411..90049 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
HXC32_RS00560 (D645_p14115) 90086..90505 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
HXC32_RS00565 (D645_p14072) 90502..92328 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HXC32_RS00570 (D645_p14058) 92339..92554 + 216 WP_000700023 conjugal transfer protein TrbE -
HXC32_RS00575 (D645_p14080) 92566..93315 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
HXC32_RS00580 (D645_p14070) 93529..93822 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
HXC32_RS00585 (D645_p14061) 93809..94357 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HXC32_RS00590 (D645_p14078) 94347..95729 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
HXC32_RS00595 (D645_p14079) 95726..98548 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
HXC32_RS00600 (D645_p14068) 98564..99058 + 495 WP_010999946 entry exclusion protein -
HXC32_RS00605 (D645_p14067) 99094..99825 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
HXC32_RS00610 (D645_p14082) 100202..102364 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
HXC32_RS00615 102373..102771 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
HXC32_RS00620 102771..102998 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   829 GenBank   NC_014476
Plasmid name   pYT1 Incompatibility group   IncFII
Plasmid size   112670 bp Coordinate of oriT [Strand]   76552..76810 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium

Cargo genes

Drug resistance gene   tetracycline resistance; sulfonamide resistance; aminoglycoside resistance
Virulence gene   Salmonella plasmid virulence protein
Metal resistance gene   mercury resistance
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -