Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100351
Name   oriT_pSLT-BT in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_013437 (80458..80716 [-], 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_pSLT-BT
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   422 GenBank   YP_003264475
Name   TraI_pSLT-BT insolico UniProt ID   H9L4G8
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

>YP_003264475.1 conjugal transfer nickase/helicase TraI (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
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: 79914..106270

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXF88_RS00455 (pSLTBT_p078) 75070..77067 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
HXF88_RS00460 (pSLTBT_p079) 77107..77541 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
HXF88_RS00465 (pSLTBT_p080) 77538..78275 + 738 WP_000581933 plasmid SOS inhibition protein A -
HXF88_RS00470 78512..78682 + 171 WP_000229547 hypothetical protein -
HXF88_RS00475 78785..79603 + 819 Protein_94 DUF945 domain-containing protein -
HXF88_RS00480 (pSLTBT_p081) 79914..80384 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
HXF88_RS00485 (pSLTBT_p082) 80799..81179 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
HXF88_RS00490 (pSLTBT_p083) 81372..82058 + 687 WP_000336297 PAS domain-containing protein -
HXF88_RS00495 (pSLTBT_p084) 82152..82379 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
HXF88_RS00500 (pSLTBT_p085) 82421..82783 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
HXF88_RS00505 (pSLTBT_p086) 82798..83109 + 312 WP_012825259 type IV conjugative transfer system protein TraL traL
HXF88_RS00510 (pSLTBT_p087) 83131..83697 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
HXF88_RS00515 (pSLTBT_p088) 83684..84424 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
HXF88_RS00520 (pSLTBT_p089) 84424..85845 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
HXF88_RS00525 (pSLTBT_p090) 85835..86431 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
HXF88_RS00530 (pSLTBT_p091) 86409..86654 + 246 WP_010999944 DUF2689 domain-containing protein virb4
HXF88_RS00535 (pSLTBT_p092) 86651..87166 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
HXF88_RS00540 (pSLTBT_p093) 87301..87522 + 222 WP_001278699 conjugal transfer protein TraR -
HXF88_RS00545 (pSLTBT_p094) 87515..87982 + 468 WP_000549562 hypothetical protein -
HXF88_RS00550 (pSLTBT_p095) 88099..88362 + 264 WP_001239255 hypothetical protein -
HXF88_RS00555 (pSLTBT_p096) 88378..91026 + 2649 WP_012825260 type IV secretion system protein TraC virb4
HXF88_RS00560 (pSLTBT_p097) 91001..91387 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
HXF88_RS00565 (pSLTBT_p098) 91384..92016 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
HXF88_RS00570 (pSLTBT_p099) 92013..93005 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
HXF88_RS00575 (pSLTBT_p100) 93024..93332 + 309 WP_010999945 hypothetical protein -
HXF88_RS00580 (pSLTBT_p101) 93317..93955 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
HXF88_RS00585 (pSLTBT_p102) 93992..94411 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
HXF88_RS00590 (pSLTBT_p103) 94408..96234 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HXF88_RS00595 (pSLTBT_p104) 96245..96460 + 216 WP_000700023 conjugal transfer protein TrbE -
HXF88_RS00600 (pSLTBT_p105) 96472..97221 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
HXF88_RS00605 (pSLTBT_p106) 97435..97728 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
HXF88_RS00610 (pSLTBT_p107) 97715..98263 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HXF88_RS00615 (pSLTBT_p108) 98253..99635 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
HXF88_RS00620 (pSLTBT_p109) 99632..102454 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
HXF88_RS00625 (pSLTBT_p110) 102470..102964 + 495 WP_010999946 entry exclusion protein -
HXF88_RS00630 (pSLTBT_p111) 103000..103731 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
HXF88_RS00635 (pSLTBT_p112) 104108..106270 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
HXF88_RS00640 106279..106677 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
HXF88_RS00645 106677..106904 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   812 GenBank   NC_013437
Plasmid name   pSLT-BT Incompatibility group   IncFIB
Plasmid size   117047 bp Coordinate of oriT [Strand]   80458..80716 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

Cargo genes

Drug resistance gene   streptomycin resistance; aminoglycoside resistance; quaternary ammonium compound-resistance
Virulence gene   plasmid virulence genes spvDCBAR
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -