Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100788
Name   oriT_pSTY1-2011K-1702 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2011K-1702 isolate USDA-ARS-USMARC-1910
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014968 (60732..60990 [-], 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_pSTY1-2011K-1702
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   860 GenBank   WP_058683854
Name   TraI_pSTY1-2011K-1702 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191738.74 Da        Isoelectric Point: 5.9319

>WP_058683854.1 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
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVERENRGRERLQQMEQEMVRDLQKEKTPG
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: 60188..86644

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AX06_RS24130 (AX06_00360) 55344..57341 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
AX06_RS24135 (AX06_00365) 57381..57815 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
AX06_RS24140 (AX06_00370) 57812..58549 + 738 WP_000581933 plasmid SOS inhibition protein A -
AX06_RS27050 58584..58712 + 129 WP_000372429 hypothetical protein -
AX06_RS26730 58798..58956 + 159 WP_001704449 hypothetical protein -
AX06_RS26735 59059..59877 + 819 Protein_80 DUF932 domain-containing protein -
AX06_RS24155 (AX06_00385) 60188..60658 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
AX06_RS24160 (AX06_00390) 61073..61453 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
AX06_RS24165 (AX06_00395) 61646..62332 + 687 WP_000336297 PAS domain-containing protein -
AX06_RS25850 62427..62654 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
AX06_RS24170 (AX06_00400) 62696..63058 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
AX06_RS24175 (AX06_00405) 63073..63384 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
AX06_RS24180 (AX06_00410) 63406..63972 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
AX06_RS24185 (AX06_00415) 63959..64699 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
AX06_RS24190 (AX06_00420) 64699..66120 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
AX06_RS24195 (AX06_00425) 66110..66706 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
AX06_RS24200 (AX06_00430) 66684..66929 + 246 WP_010999944 DUF2689 domain-containing protein virb4
AX06_RS24205 (AX06_00435) 66926..67441 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
AX06_RS24210 (AX06_00440) 67576..67797 + 222 WP_001278699 conjugal transfer protein TraR -
AX06_RS24215 (AX06_00445) 67790..68257 + 468 WP_000549562 hypothetical protein -
AX06_RS24220 (AX06_00450) 68374..68637 + 264 WP_001239256 hypothetical protein -
AX06_RS24225 (AX06_00455) 68653..71301 + 2649 WP_000793310 type IV secretion system protein TraC virb4
AX06_RS24230 (AX06_00460) 71276..71662 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
AX06_RS24235 (AX06_00465) 71659..72291 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
AX06_RS24240 (AX06_00470) 72288..73280 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
AX06_RS24245 (AX06_00475) 73299..73607 + 309 WP_010999945 hypothetical protein -
AX06_RS24250 (AX06_00480) 73592..74230 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
AX06_RS24255 (AX06_00485) 74267..74686 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
AX06_RS24260 (AX06_00490) 74683..76509 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AX06_RS24265 (AX06_00495) 76520..76735 + 216 WP_000700023 conjugal transfer protein TrbE -
AX06_RS24270 (AX06_00500) 76747..77496 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
AX06_RS24275 (AX06_00505) 77710..78003 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
AX06_RS24280 (AX06_00510) 77990..78538 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AX06_RS24285 (AX06_00515) 78528..79910 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
AX06_RS24290 (AX06_00520) 79907..82729 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
AX06_RS24295 (AX06_00525) 82745..83239 + 495 WP_010999946 entry exclusion protein -
AX06_RS24300 (AX06_00530) 83275..84006 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
AX06_RS24305 (AX06_00535) 84383..86644 + 2262 WP_022743189 type IV conjugative transfer system coupling protein TraD prgC
AX06_RS24310 (AX06_00540) 86653..87051 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
AX06_RS24315 (AX06_00545) 87051..87278 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1248 GenBank   NZ_CP014968
Plasmid name   pSTY1-2011K-1702 Incompatibility group   IncFII
Plasmid size   94016 bp Coordinate of oriT [Strand]   60732..60990 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2011K-1702 isolate USDA-ARS-USMARC-1910

Cargo genes

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