Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100464
Name   oriT_pSal8934b in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019109 (35716..35974 [-], 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_pSal8934b
CTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   535 GenBank   YP_006955336
Name   TraI_pSal8934b 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_006955336.1 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: 10162..36518

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS794_RS00050 9528..9755 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
HS794_RS00055 9755..10153 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
HS794_RS00060 (p8934bo011) 10162..12324 - 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
HS794_RS00065 (p8934bo012) 12701..13432 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
HS794_RS00070 (p8934bo013) 13468..13962 - 495 WP_010999946 entry exclusion protein -
HS794_RS00075 (p8934bo014) 13978..16800 - 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
HS794_RS00080 (p8934bo015) 16797..18179 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
HS794_RS00085 (p8934bo016) 18169..18717 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS794_RS00090 (p8934bo017) 18704..18997 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
HS794_RS00095 (p8934bo018) 19211..19960 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
HS794_RS00100 (p8934bo019) 19972..20187 - 216 WP_000700023 conjugal transfer protein TrbE -
HS794_RS00105 (p8934bo020) 20198..22024 - 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS794_RS00110 (p8934bo021) 22021..22440 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
HS794_RS00115 (p8934bo022) 22477..23115 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS794_RS00120 (p8934bo023) 23100..23408 - 309 WP_010999945 hypothetical protein -
HS794_RS00125 (p8934bo024) 23427..24419 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
HS794_RS00130 (p8934bo025) 24416..25048 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
HS794_RS00135 (p8934bo026) 25045..25431 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
HS794_RS00140 (p8934bo027) 25406..28054 - 2649 WP_000793310 type IV secretion system protein TraC virb4
HS794_RS00145 (p8934bo028) 28070..28333 - 264 WP_001239255 hypothetical protein -
HS794_RS00150 (p8934bo029) 28450..28917 - 468 WP_000549562 hypothetical protein -
HS794_RS00155 (p8934bo030) 28910..29131 - 222 WP_001278699 conjugal transfer protein TraR -
HS794_RS00160 (p8934bo031) 29266..29781 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
HS794_RS00165 (p8934bo032) 29778..30023 - 246 WP_010999944 DUF2689 domain-containing protein virb4
HS794_RS00170 (p8934bo033) 30001..30597 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
HS794_RS00175 (p8934bo034) 30587..32008 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
HS794_RS00180 (p8934bo035) 32008..32748 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
HS794_RS00185 (p8934bo036) 32735..33301 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
HS794_RS00190 (p8934bo037) 33323..33634 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
HS794_RS00195 (p8934bo038) 33649..34011 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
HS794_RS00200 (p8934bo039) 34053..34280 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
HS794_RS00205 (p8934bo040) 34374..35060 - 687 WP_000336297 PAS domain-containing protein -
HS794_RS00210 (p8934bo041) 35253..35633 - 381 WP_013307857 conjugal transfer relaxosome DNA-binding protein TraM -
HS794_RS00215 (p8934bo042) 36048..36518 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
HS794_RS00220 36829..37647 - 819 Protein_43 DUF945 domain-containing protein -
HS794_RS00225 37750..37920 - 171 WP_000229547 hypothetical protein -
HS794_RS00230 (p8934bo045) 38157..38894 - 738 WP_000581933 plasmid SOS inhibition protein A -
HS794_RS00235 (p8934bo046) 38891..39325 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
HS794_RS00240 (p8934bo047) 39365..41362 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   925 GenBank   NC_019109
Plasmid name   pSal8934b Incompatibility group   IncFII
Plasmid size   133216 bp Coordinate of oriT [Strand]   35716..35974 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium

Cargo genes

Drug resistance gene   tetracycline resistance
Virulence gene   virulence protein SpvR, SpvA, SpvB, SpvC, SpvD, VsdF
Metal resistance gene   mercury resistance
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -