Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100524
Name   oriT_pSTU288-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. U288
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_021155 (143487..143596 [+], 110 nt)
oriT length   110 nt
IRs (inverted repeats)      IR1: 24..31, 35..42  (GTCGGGGC..GCCCTGAC)
 IR2: 49..65, 72..88  (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC)
Location of nic site      96..97
Conserved sequence flanking the
  nic site    		  CATCCTG|T
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 110 nt

>oriT_pSTU288-1
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   595 GenBank   WP_000986921
Name   TraI_pSTU288-1 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: 50562..77017

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
STU288_RS23780 (STU288_1p00355) 49928..50155 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
STU288_RS23785 (STU288_1p00360) 50155..50553 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
STU288_RS23790 (STU288_1p00365) 50562..52823 - 2262 WP_015589607 type IV conjugative transfer system coupling protein TraD prgC
STU288_RS23795 (STU288_1p00370) 53200..53931 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
STU288_RS23800 (STU288_1p00375) 53967..54461 - 495 WP_010999946 entry exclusion protein -
STU288_RS23805 (STU288_1p00380) 54477..57299 - 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
STU288_RS23810 (STU288_1p00385) 57296..58678 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
STU288_RS23815 (STU288_1p00390) 58668..59216 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
STU288_RS23820 (STU288_1p00395) 59203..59496 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
STU288_RS23825 (STU288_1p00400) 59710..60459 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
STU288_RS23830 (STU288_1p00405) 60471..60686 - 216 WP_000700023 conjugal transfer protein TrbE -
STU288_RS23835 (STU288_1p00410) 60697..62523 - 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
STU288_RS23840 (STU288_1p00415) 62520..62939 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
STU288_RS23845 (STU288_1p00420) 62976..63614 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
STU288_RS23850 (STU288_1p00425) 63599..63907 - 309 WP_010999945 hypothetical protein -
STU288_RS23855 (STU288_1p00430) 63926..64918 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
STU288_RS23860 (STU288_1p00435) 64915..65547 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
STU288_RS23865 (STU288_1p00440) 65544..65930 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
STU288_RS23870 (STU288_1p00445) 65905..68553 - 2649 WP_000793310 type IV secretion system protein TraC virb4
STU288_RS23875 (STU288_1p00450) 68569..68832 - 264 WP_001239256 hypothetical protein -
STU288_RS23880 (STU288_1p00460) 68949..69416 - 468 WP_000549562 hypothetical protein -
STU288_RS23885 (STU288_1p00465) 69409..69630 - 222 WP_001278699 conjugal transfer protein TraR -
STU288_RS23890 (STU288_1p00470) 69765..70280 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
STU288_RS23895 (STU288_1p00475) 70277..70522 - 246 WP_010999944 DUF2689 domain-containing protein virb4
STU288_RS23900 (STU288_1p00480) 70500..71096 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
STU288_RS23905 (STU288_1p00485) 71086..72507 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
STU288_RS23910 (STU288_1p00490) 72507..73247 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
STU288_RS23915 (STU288_1p00495) 73234..73800 - 567 WP_000399769 type IV conjugative transfer system protein TraE traE
STU288_RS23920 (STU288_1p00500) 73822..74133 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
STU288_RS23925 (STU288_1p00505) 74148..74510 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
STU288_RS23930 (STU288_1p00510) 74552..74779 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
STU288_RS23935 (STU288_1p00515) 74873..75559 - 687 WP_000336297 PAS domain-containing protein -
STU288_RS23940 (STU288_1p00520) 75752..76132 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
STU288_RS23945 (STU288_1p00525) 76547..77017 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
STU288_RS27435 77329..78147 - 819 Protein_96 DUF945 domain-containing protein -
STU288_RS27345 (STU288_1p00545) 78250..78408 - 159 WP_001704449 hypothetical protein -
STU288_RS23960 (STU288_1p00555) 78657..79394 - 738 WP_000581933 plasmid SOS inhibition protein A -
STU288_RS23965 (STU288_1p00560) 79391..79825 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
STU288_RS23970 (STU288_1p00565) 79865..81862 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   985 GenBank   NC_021155
Plasmid name   pSTU288-1 Incompatibility group   IncFIB
Plasmid size   148711 bp Coordinate of oriT [Strand]   143487..143596 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. U288

Cargo genes

Drug resistance gene   -
Virulence gene   Salmonella plasmid virulence protein
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -