Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100386
Name   oriT_plasmid_14028S in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_016855 (60647..60905 [-], 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_plasmid_14028S
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   457 GenBank   WP_000986921
Name   TraI_plasmid_14028S insolico UniProt ID   A0A0F6AWB4
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

>WP_000986921.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Salmonella]
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: 60103..86459

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
STM14_RS00355 (STM14_5589) 55259..57256 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
STM14_RS00360 (STM14_5590) 57296..57730 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
STM14_RS00365 (STM14_5591) 57727..58464 + 738 WP_000581933 plasmid SOS inhibition protein A -
STM14_RS26910 58499..58627 + 129 WP_000372429 hypothetical protein -
STM14_RS26580 58713..58871 + 159 WP_001704449 hypothetical protein -
STM14_RS26605 58974..59792 + 819 Protein_78 DUF932 domain-containing protein -
STM14_RS00380 (STM14_5592) 60103..60573 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
STM14_RS00385 (STM14_5593) 60988..61368 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
STM14_RS00390 (STM14_5595) 61561..62247 + 687 WP_000336297 PAS domain-containing protein -
STM14_RS24325 (STM14_5596) 62341..62568 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
STM14_RS00395 (STM14_5597) 62610..62972 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
STM14_RS00400 (STM14_5598) 62987..63298 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
STM14_RS00405 (STM14_5599) 63320..63886 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
STM14_RS00410 (STM14_5600) 63873..64613 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
STM14_RS00415 (STM14_5601) 64613..66034 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
STM14_RS00420 (STM14_5602) 66024..66620 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
STM14_RS00425 (STM14_5603) 66598..66843 + 246 WP_010999944 DUF2689 domain-containing protein virb4
STM14_RS00430 (STM14_5604) 66840..67355 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
STM14_RS00435 (STM14_5605) 67490..67711 + 222 WP_001278699 conjugal transfer protein TraR -
STM14_RS00440 (STM14_5606) 67704..68171 + 468 WP_000549562 hypothetical protein -
STM14_RS00445 68288..68551 + 264 WP_001239255 hypothetical protein -
STM14_RS00450 (STM14_5607) 68567..71215 + 2649 WP_000793310 type IV secretion system protein TraC virb4
STM14_RS00455 (STM14_5608) 71190..71576 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
STM14_RS00460 (STM14_5609) 71573..72205 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
STM14_RS00465 (STM14_5610) 72202..73194 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
STM14_RS00470 (STM14_5611) 73213..73521 + 309 WP_010999945 hypothetical protein -
STM14_RS00475 (STM14_5612) 73506..74144 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
STM14_RS00480 74181..74600 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
STM14_RS00485 (STM14_5613) 74597..76423 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
STM14_RS00490 (STM14_5614) 76434..76649 + 216 WP_000700023 conjugal transfer protein TrbE -
STM14_RS00495 (STM14_5615) 76661..77410 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
STM14_RS00500 (STM14_5616) 77624..77917 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
STM14_RS00505 (STM14_5617) 77904..78452 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
STM14_RS00510 (STM14_5618) 78442..79824 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
STM14_RS00515 (STM14_5619) 79821..82643 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
STM14_RS00520 (STM14_5620) 82659..83153 + 495 WP_010999946 entry exclusion protein -
STM14_RS00525 (STM14_5621) 83189..83920 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
STM14_RS00530 (STM14_5622) 84297..86459 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
STM14_RS00535 (STM14_5624) 86468..86866 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
STM14_RS00540 (STM14_5625) 86866..87093 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   847 GenBank   NC_016855
Plasmid name   plasmid_14028S Incompatibility group   IncFII
Plasmid size   93832 bp Coordinate of oriT [Strand]   60647..60905 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Cargo genes

Drug resistance gene   -
Virulence gene   Salmonella plasmid virulence protein
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -