Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100390
Name   oriT_pSTUK-100 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_016864 (42458..42716 [-], 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_pSTUK-100
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   461 GenBank   WP_000986921
Name   TraI_pSTUK-100 insolico UniProt ID   _
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: 41914..68270

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
STMUK_RS23470 (STMUK_p041) 37070..39067 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
STMUK_RS23475 (STMUK_p042) 39107..39541 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
STMUK_RS23480 (STMUK_p043) 39538..40275 + 738 WP_000581933 plasmid SOS inhibition protein A -
STMUK_RS26490 40310..40438 + 129 WP_000372429 hypothetical protein -
STMUK_RS26140 40524..40682 + 159 WP_001704449 hypothetical protein -
STMUK_RS26210 40785..41603 + 819 Protein_54 DUF932 domain-containing protein -
STMUK_RS23495 (STMUK_p044) 41914..42384 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
STMUK_RS23500 (STMUK_p045) 42799..43179 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
STMUK_RS23505 (STMUK_p046) 43372..44058 + 687 WP_000336297 PAS domain-containing protein -
STMUK_RS25350 (STMUK_p047) 44152..44379 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
STMUK_RS23510 (STMUK_p048) 44421..44783 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
STMUK_RS23515 (STMUK_p049) 44798..45109 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
STMUK_RS23520 (STMUK_p050) 45131..45697 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
STMUK_RS23525 (STMUK_p051) 45684..46424 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
STMUK_RS23530 (STMUK_p052) 46424..47845 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
STMUK_RS23535 (STMUK_p053) 47835..48431 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
STMUK_RS23540 (STMUK_p054) 48409..48654 + 246 WP_010999944 DUF2689 domain-containing protein virb4
STMUK_RS23545 (STMUK_p055) 48651..49166 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
STMUK_RS23550 (STMUK_p056) 49301..49522 + 222 WP_001278699 conjugal transfer protein TraR -
STMUK_RS23555 (STMUK_p057) 49515..49982 + 468 WP_000549562 hypothetical protein -
STMUK_RS23560 50099..50362 + 264 WP_001239255 hypothetical protein -
STMUK_RS23565 (STMUK_p058) 50378..53026 + 2649 WP_000793310 type IV secretion system protein TraC virb4
STMUK_RS23570 (STMUK_p059) 53001..53387 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
STMUK_RS23575 (STMUK_p060) 53384..54016 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
STMUK_RS23580 (STMUK_p061) 54013..55005 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
STMUK_RS23585 (STMUK_p062) 55024..55332 + 309 WP_010999945 hypothetical protein -
STMUK_RS23590 (STMUK_p063) 55317..55955 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
STMUK_RS23595 55992..56411 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
STMUK_RS23600 (STMUK_p064) 56408..58234 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
STMUK_RS23605 (STMUK_p065) 58245..58460 + 216 WP_000700023 conjugal transfer protein TrbE -
STMUK_RS23610 (STMUK_p066) 58472..59221 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
STMUK_RS23615 (STMUK_p067) 59435..59728 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
STMUK_RS23620 (STMUK_p068) 59715..60263 + 549 WP_000055839 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
STMUK_RS23625 (STMUK_p069) 60253..61635 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
STMUK_RS23630 (STMUK_p070) 61632..64454 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
STMUK_RS23635 (STMUK_p071) 64470..64964 + 495 WP_010999946 entry exclusion protein -
STMUK_RS23640 (STMUK_p072) 65000..65731 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
STMUK_RS23645 (STMUK_p073) 66108..68270 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
STMUK_RS23650 (STMUK_p075) 68279..68677 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
STMUK_RS23655 (STMUK_p076) 68677..68904 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   851 GenBank   NC_016864
Plasmid name   pSTUK-100 Incompatibility group   IncFII
Plasmid size   93277 bp Coordinate of oriT [Strand]   42458..42716 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1

Cargo genes

Drug resistance gene   -
Virulence gene   spvC, spvB, rck, pefD, pefC, pefA, pefB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -