Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100637
Name   oriT_pSTM in_silico
Organism   Salmonella enterica subsp. enterica strain SA972816
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP007489 (60689..60947 [-], 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_pSTM
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   709 GenBank   WP_022743192
Name   Relaxase_pSTM insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191680.70 Da        Isoelectric Point: 5.9879

>WP_022743192.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR
QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMKNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW
NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1158)

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

(632-711)

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

(574-626)

TrwC relaxase (TrwC)

(11-282)

DNA helicase TraI (TraI_C)

(1430-1553)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60145..86592

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CO44_RS24790 (CO44_25365) 55301..57298 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
CO44_RS24795 (CO44_25370) 57338..57772 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
CO44_RS24800 (CO44_25375) 57769..58506 + 738 WP_000581933 plasmid SOS inhibition protein A -
CO44_RS27810 58541..58669 + 129 WP_000372429 hypothetical protein -
CO44_RS27470 58755..58913 + 159 WP_001704449 hypothetical protein -
CO44_RS27475 59016..59834 + 819 Protein_79 DUF932 domain-containing protein -
CO44_RS24815 (CO44_25400) 60145..60615 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
CO44_RS24820 (CO44_25405) 61030..61410 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
CO44_RS24825 (CO44_25410) 61603..62289 + 687 WP_000336297 PAS domain-containing protein -
CO44_RS26570 62384..62611 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
CO44_RS24830 (CO44_25415) 62653..63015 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
CO44_RS24835 (CO44_25420) 63030..63341 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
CO44_RS24840 (CO44_25425) 63363..63929 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
CO44_RS24845 (CO44_25430) 63916..64656 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
CO44_RS24850 (CO44_25435) 64656..66077 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
CO44_RS24855 (CO44_25440) 66067..66663 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
CO44_RS24860 (CO44_25445) 66641..66886 + 246 WP_010999944 DUF2689 domain-containing protein virb4
CO44_RS24865 (CO44_25450) 66883..67398 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
CO44_RS24870 (CO44_25455) 67533..67754 + 222 WP_001278699 conjugal transfer protein TraR -
CO44_RS24875 (CO44_25460) 67747..68214 + 468 WP_000549562 hypothetical protein -
CO44_RS24880 (CO44_25470) 68331..68594 + 264 WP_001239256 hypothetical protein -
CO44_RS24885 (CO44_25475) 68610..71258 + 2649 WP_000793310 type IV secretion system protein TraC virb4
CO44_RS24890 (CO44_25480) 71233..71619 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
CO44_RS24895 (CO44_25485) 71616..72248 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
CO44_RS24900 (CO44_25490) 72245..73237 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
CO44_RS24905 (CO44_25495) 73256..73564 + 309 WP_010999945 hypothetical protein -
CO44_RS24910 (CO44_25500) 73549..74187 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
CO44_RS24915 (CO44_25505) 74224..74643 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
CO44_RS24920 (CO44_25510) 74640..76466 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CO44_RS24925 (CO44_25515) 76477..76692 + 216 WP_000700023 conjugal transfer protein TrbE -
CO44_RS24930 (CO44_25520) 76704..77453 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
CO44_RS24935 (CO44_25525) 77667..77960 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
CO44_RS24940 (CO44_25530) 77947..78495 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CO44_RS24945 (CO44_25535) 78485..79867 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
CO44_RS24950 (CO44_25540) 79864..82686 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
CO44_RS24955 (CO44_25545) 82702..83196 + 495 WP_010999946 entry exclusion protein -
CO44_RS24960 (CO44_25550) 83232..83963 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
CO44_RS24965 (CO44_25555) 84340..86592 + 2253 WP_058657852 type IV conjugative transfer system coupling protein TraD prgC
CO44_RS24970 (CO44_25560) 86601..86999 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
CO44_RS24975 (CO44_25565) 86999..87226 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1097 GenBank   NZ_CP007489
Plasmid name   pSTM Incompatibility group   IncFII
Plasmid size   93965 bp Coordinate of oriT [Strand]   60689..60947 [-]
Host baterium   Salmonella enterica subsp. enterica strain SA972816

Cargo genes

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