Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100793
Name   oriT_pSTY1-H2662 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. CDC H2662
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014980 (60768..61026 [-], 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-H2662
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   865 GenBank   WP_022743192
Name   Relaxase_pSTY1-H2662 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: 60224..86662

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AX03_RS25400 (AX03_24110) 55380..57377 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
AX03_RS25405 (AX03_24115) 57417..57851 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
AX03_RS25410 (AX03_24120) 57848..58585 + 738 WP_000581933 plasmid SOS inhibition protein A -
AX03_RS26420 58620..58748 + 129 WP_000372429 hypothetical protein -
AX03_RS26080 58834..58992 + 159 WP_001704449 hypothetical protein -
AX03_RS26085 59095..59913 + 819 Protein_80 DUF932 domain-containing protein -
AX03_RS25430 (AX03_24135) 60224..60694 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
AX03_RS25440 (AX03_24140) 61109..61489 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
AX03_RS25445 (AX03_24145) 61682..62368 + 687 WP_000336297 PAS domain-containing protein -
AX03_RS25450 (AX03_25935) 62463..62690 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
AX03_RS25455 (AX03_24150) 62732..63094 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
AX03_RS25460 (AX03_24155) 63109..63420 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
AX03_RS25465 (AX03_24160) 63442..64008 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
AX03_RS25470 (AX03_24165) 63995..64735 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
AX03_RS25475 (AX03_24170) 64735..66156 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
AX03_RS25480 (AX03_24175) 66146..66742 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
AX03_RS25485 (AX03_24180) 66720..66965 + 246 WP_010999944 DUF2689 domain-containing protein virb4
AX03_RS25490 (AX03_24185) 66962..67477 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
AX03_RS25495 (AX03_24190) 67612..67833 + 222 WP_001278699 conjugal transfer protein TraR -
AX03_RS25500 (AX03_24195) 67826..68293 + 468 WP_000549562 hypothetical protein -
AX03_RS25505 (AX03_24200) 68410..68673 + 264 WP_001239256 hypothetical protein -
AX03_RS25510 (AX03_24205) 68689..71337 + 2649 WP_000793310 type IV secretion system protein TraC virb4
AX03_RS25515 (AX03_24210) 71312..71698 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
AX03_RS25520 (AX03_24215) 71695..72327 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
AX03_RS25525 (AX03_24220) 72324..73316 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
AX03_RS25530 (AX03_24225) 73335..73643 + 309 WP_010999945 hypothetical protein -
AX03_RS25535 (AX03_24230) 73628..74266 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
AX03_RS25540 (AX03_24235) 74303..74722 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
AX03_RS25545 (AX03_24240) 74719..76545 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AX03_RS25550 (AX03_24245) 76556..76771 + 216 WP_000700023 conjugal transfer protein TrbE -
AX03_RS25555 (AX03_24250) 76783..77532 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
AX03_RS25560 (AX03_24255) 77746..78039 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
AX03_RS25565 (AX03_24260) 78026..78574 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AX03_RS25570 (AX03_24265) 78564..79946 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
AX03_RS25575 (AX03_24270) 79943..82765 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
AX03_RS25580 (AX03_24275) 82781..83275 + 495 WP_010999946 entry exclusion protein -
AX03_RS25585 (AX03_24280) 83311..84042 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
AX03_RS25590 (AX03_24285) 84419..86662 + 2244 WP_031608981 type IV conjugative transfer system coupling protein TraD prgC
AX03_RS25595 (AX03_24290) 86671..87069 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
AX03_RS25600 (AX03_24295) 87069..87296 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1253 GenBank   NZ_CP014980
Plasmid name   pSTY1-H2662 Incompatibility group   IncFII
Plasmid size   94034 bp Coordinate of oriT [Strand]   60768..61026 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. CDC H2662

Cargo genes

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