Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100463
Name   oriT_pSal6919a in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019108 (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_pSal6919a
CTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   534 GenBank   YP_006955196
Name   TraI_pSal6919a 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

>YP_006955196.1 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
HS789_RS00050 9528..9755 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
HS789_RS00055 9755..10153 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
HS789_RS00060 (p6919o011) 10162..12324 - 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
HS789_RS00065 (p6919o012) 12701..13432 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
HS789_RS00070 (p6919o013) 13468..13962 - 495 WP_010999946 entry exclusion protein -
HS789_RS00075 (p6919o014) 13978..16800 - 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
HS789_RS00080 (p6919o015) 16797..18179 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
HS789_RS00085 (p6919o016) 18169..18717 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS789_RS00090 (p6919o017) 18704..18997 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
HS789_RS00095 (p6919o018) 19211..19960 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
HS789_RS00100 (p6919o019) 19972..20187 - 216 WP_000700023 conjugal transfer protein TrbE -
HS789_RS00105 (p6919o020) 20198..22024 - 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS789_RS00110 (p6919o021) 22021..22440 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
HS789_RS00115 (p6919o022) 22477..23115 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS789_RS00120 (p6919o023) 23100..23408 - 309 WP_010999945 hypothetical protein -
HS789_RS00125 (p6919o024) 23427..24419 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
HS789_RS00130 (p6919o025) 24416..25048 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
HS789_RS00135 (p6919o026) 25045..25431 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
HS789_RS00140 (p6919o027) 25406..28054 - 2649 WP_000793310 type IV secretion system protein TraC virb4
HS789_RS00145 (p6919o028) 28070..28333 - 264 WP_001239255 hypothetical protein -
HS789_RS00150 (p6919o029) 28450..28917 - 468 WP_000549562 hypothetical protein -
HS789_RS00155 (p6919o030) 28910..29131 - 222 WP_001278699 conjugal transfer protein TraR -
HS789_RS00160 (p6919o031) 29266..29781 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
HS789_RS00165 (p6919o032) 29778..30023 - 246 WP_010999944 DUF2689 domain-containing protein virb4
HS789_RS00170 (p6919o033) 30001..30597 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
HS789_RS00175 (p6919o034) 30587..32008 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
HS789_RS00180 (p6919o035) 32008..32748 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
HS789_RS00185 (p6919o036) 32735..33301 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
HS789_RS00190 (p6919o037) 33323..33634 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
HS789_RS00195 (p6919o038) 33649..34011 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
HS789_RS00200 (p6919o039) 34053..34280 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
HS789_RS00205 (p6919o040) 34374..35060 - 687 WP_000336297 PAS domain-containing protein -
HS789_RS00210 (p6919o041) 35253..35633 - 381 WP_013307857 conjugal transfer relaxosome DNA-binding protein TraM -
HS789_RS00215 (p6919o042) 36048..36518 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
HS789_RS00220 36829..37647 - 819 Protein_43 DUF945 domain-containing protein -
HS789_RS00225 37750..37908 - 159 WP_001704449 hypothetical protein -
HS789_RS00230 (p6919o045) 38157..38894 - 738 WP_000581933 plasmid SOS inhibition protein A -
HS789_RS00235 (p6919o046) 38891..39325 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
HS789_RS00240 (p6919o047) 39365..41362 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   924 GenBank   NC_019108
Plasmid name   pSal6919a Incompatibility group   IncFII
Plasmid size   112673 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 SpvA, SpvB, SpvD, VsdF
Metal resistance gene   mercury resistance
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -