Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100387
Name   oriT_TY474p1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_016858 (32927..33185 [-], 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_TY474p1
CTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   458 GenBank   WP_000986921
Name   TraI_TY474p1 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: 7373..30845

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
STM474_RS23650 (STM474_p1005) 6739..6966 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
STM474_RS23655 (STM474_p1006) 6966..7364 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
STM474_RS23660 (STM474_p1007) 7373..9535 - 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
STM474_RS23665 (STM474_p1008) 9912..10643 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
STM474_RS23670 (STM474_p1009) 10679..11173 - 495 WP_010999946 entry exclusion protein -
STM474_RS23675 (STM474_p1010) 11189..14011 - 2823 WP_001007087 conjugal transfer mating-pair stabilization protein TraG traG
STM474_RS23680 (STM474_p1011) 14008..15390 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
STM474_RS23685 (STM474_p1012) 15380..15928 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
STM474_RS23690 (STM474_p1013) 15915..16208 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
STM474_RS23695 (STM474_p1014) 16422..17171 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
STM474_RS23700 (STM474_p1015) 17183..17398 - 216 WP_000700023 conjugal transfer protein TrbE -
STM474_RS23705 (STM474_p1016) 17409..19235 - 1827 WP_000827529 type-F conjugative transfer system mating-pair stabilization protein TraN traN
STM474_RS23710 (STM474_p1017) 19232..19651 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
STM474_RS23715 (STM474_p1018) 19688..20326 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
STM474_RS23720 (STM474_p1019) 20311..20619 - 309 WP_010999945 hypothetical protein -
STM474_RS23725 (STM474_p1020) 20638..21630 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
STM474_RS23730 (STM474_p1021) 21627..22259 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
STM474_RS23735 (STM474_p1022) 22256..22642 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
STM474_RS23740 (STM474_p1023) 22617..25265 - 2649 WP_000793310 type IV secretion system protein TraC virb4
STM474_RS23745 (STM474_p1024) 25281..25544 - 264 WP_001239255 hypothetical protein -
STM474_RS23750 (STM474_p1025) 25661..26128 - 468 WP_000549562 hypothetical protein -
STM474_RS23755 (STM474_p1026) 26121..26342 - 222 WP_001278699 conjugal transfer protein TraR -
STM474_RS23760 (STM474_p1027) 26477..26992 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
STM474_RS23765 (STM474_p1028) 26989..27234 - 246 WP_010999944 DUF2689 domain-containing protein virb4
STM474_RS23770 (STM474_p1029) 27212..27808 - 597 WP_000527897 conjugal transfer pilus-stabilizing protein TraP -
STM474_RS23775 (STM474_p1030) 27798..29219 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
STM474_RS23780 (STM474_p1031) 29219..29959 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
STM474_RS23785 (STM474_p1032) 29946..30512 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
STM474_RS23790 (STM474_p1033) 30534..30845 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
STM474_RS23795 (STM474_p1034) 30860..31222 - 363 WP_001273051 type IV conjugative transfer system pilin TraA -
STM474_RS26265 (STM474_p1035) 31264..31491 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
STM474_RS23800 (STM474_p1036) 31585..32271 - 687 WP_000336297 PAS domain-containing protein -
STM474_RS23805 (STM474_p1037) 32464..32844 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
STM474_RS23810 (STM474_p1038) 33259..33729 + 471 WP_014344446 transglycosylase SLT domain-containing protein -
STM474_RS27365 34040..34858 - 819 Protein_37 DUF932 domain-containing protein -
STM474_RS27290 34961..35119 - 159 WP_001704449 hypothetical protein -
STM474_RS27655 35205..35333 - 129 WP_000372429 hypothetical protein -

Host bacterium

ID   848 GenBank   NC_016858
Plasmid name   TY474p1 Incompatibility group   IncFIB
Plasmid size   93842 bp Coordinate of oriT [Strand]   32927..33185 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

Cargo genes

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