Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100791
Name   oriT_pSTY2-1898 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014973 (60668..60926 [-], 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_pSTY2-1898
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   863 GenBank   WP_000986921
Name   TraI_pSTY2-1898 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: 60124..86588

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AX01_RS25195 (AX01_23360) 55280..57277 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
AX01_RS25200 (AX01_23365) 57317..57751 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
AX01_RS25205 (AX01_23370) 57748..58485 + 738 WP_000581933 plasmid SOS inhibition protein A -
AX01_RS26275 58520..58648 + 129 WP_000372429 hypothetical protein -
AX01_RS25940 58734..58892 + 159 WP_001704449 hypothetical protein -
AX01_RS25945 58995..59813 + 819 Protein_79 DUF932 domain-containing protein -
AX01_RS25225 (AX01_23385) 60124..60594 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
AX01_RS25235 (AX01_23390) 61009..61389 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
AX01_RS25240 (AX01_23395) 61582..62268 + 687 WP_000336297 PAS domain-containing protein -
AX01_RS25245 (AX01_25895) 62362..62589 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
AX01_RS25250 (AX01_23400) 62631..62993 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
AX01_RS25255 (AX01_23405) 63008..63319 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
AX01_RS25260 (AX01_23410) 63341..63907 + 567 WP_000399769 type IV conjugative transfer system protein TraE traE
AX01_RS25265 (AX01_23415) 63894..64634 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
AX01_RS25270 (AX01_23420) 64634..66055 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
AX01_RS25275 (AX01_23425) 66045..66641 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
AX01_RS25280 (AX01_23430) 66619..66864 + 246 WP_010999944 DUF2689 domain-containing protein virb4
AX01_RS25285 (AX01_23435) 66861..67376 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
AX01_RS25290 (AX01_23440) 67511..67732 + 222 WP_001278699 conjugal transfer protein TraR -
AX01_RS25295 (AX01_23445) 67725..68192 + 468 WP_000549562 hypothetical protein -
AX01_RS25300 (AX01_23450) 68309..68572 + 264 WP_001239256 hypothetical protein -
AX01_RS25305 (AX01_23455) 68588..71236 + 2649 WP_000793310 type IV secretion system protein TraC virb4
AX01_RS25310 (AX01_23460) 71211..71597 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
AX01_RS25315 (AX01_23465) 71594..72226 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
AX01_RS25320 (AX01_23470) 72223..73215 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
AX01_RS25325 (AX01_23475) 73234..73542 + 309 WP_010999945 hypothetical protein -
AX01_RS25330 (AX01_23480) 73527..74165 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
AX01_RS25335 (AX01_23485) 74202..74621 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
AX01_RS25340 (AX01_23490) 74618..76444 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AX01_RS25345 (AX01_23495) 76455..76670 + 216 WP_000700023 conjugal transfer protein TrbE -
AX01_RS25350 (AX01_23500) 76682..77431 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
AX01_RS25355 (AX01_23505) 77645..77938 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
AX01_RS25360 (AX01_23510) 77925..78473 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AX01_RS25365 (AX01_23515) 78463..79845 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
AX01_RS25370 (AX01_23520) 79842..82664 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
AX01_RS25375 (AX01_23525) 82680..83174 + 495 WP_010999946 entry exclusion protein -
AX01_RS25380 (AX01_23530) 83210..83941 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
AX01_RS25385 (AX01_23535) 84318..86588 + 2271 WP_054175269 type IV conjugative transfer system coupling protein TraD prgC
AX01_RS25390 (AX01_23540) 86597..86995 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
AX01_RS25395 (AX01_23545) 86995..87222 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1251 GenBank   NZ_CP014973
Plasmid name   pSTY2-1898 Incompatibility group   IncFII
Plasmid size   93960 bp Coordinate of oriT [Strand]   60668..60926 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073

Cargo genes

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