Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100420
Name   oriT_pSLT_SL1344 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_017720 (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_pSLT_SL1344
CTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   491 GenBank   WP_000986921
Name   TraI_pSLT_SL1344 insolico UniProt ID   A0A0H3NX93
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
SL1344_RS23655 6739..6966 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
SL1344_RS23660 6966..7364 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
SL1344_RS23665 (SL1344_P1_0007) 7373..9535 - 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
SL1344_RS23670 (SL1344_P1_0008) 9912..10643 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
SL1344_RS23675 (SL1344_P1_0009) 10679..11173 - 495 WP_010999946 entry exclusion protein -
SL1344_RS23680 (SL1344_P1_0010) 11189..14011 - 2823 WP_001007087 conjugal transfer mating-pair stabilization protein TraG traG
SL1344_RS23685 (SL1344_P1_0011) 14008..15390 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
SL1344_RS23690 (SL1344_P1_0012) 15380..15928 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SL1344_RS23695 (SL1344_P1_0013) 15915..16208 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
SL1344_RS23700 (SL1344_P1_0014) 16422..17171 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
SL1344_RS23705 (SL1344_P1_0015) 17183..17398 - 216 WP_000700023 conjugal transfer protein TrbE -
SL1344_RS23710 (SL1344_P1_0016) 17409..19235 - 1827 WP_000827529 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SL1344_RS23715 19232..19651 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
SL1344_RS23720 (SL1344_P1_0017) 19688..20326 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
SL1344_RS23725 (SL1344_P1_0018) 20311..20619 - 309 WP_010999945 hypothetical protein -
SL1344_RS23730 (SL1344_P1_0019) 20638..21630 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
SL1344_RS23735 (SL1344_P1_0020) 21627..22259 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
SL1344_RS23740 (SL1344_P1_0021) 22256..22642 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
SL1344_RS23745 (SL1344_P1_0022) 22617..25265 - 2649 WP_000793310 type IV secretion system protein TraC virb4
SL1344_RS23750 25281..25544 - 264 WP_001239255 hypothetical protein -
SL1344_RS23755 (SL1344_P1_0023) 25661..26128 - 468 WP_000549562 hypothetical protein -
SL1344_RS23760 (SL1344_P1_0024) 26121..26342 - 222 WP_001278699 conjugal transfer protein TraR -
SL1344_RS23765 (SL1344_P1_0025) 26477..26992 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
SL1344_RS23770 (SL1344_P1_0026) 26989..27234 - 246 WP_010999944 DUF2689 domain-containing protein virb4
SL1344_RS23775 (SL1344_P1_0027) 27212..27808 - 597 WP_000527897 conjugal transfer pilus-stabilizing protein TraP -
SL1344_RS23780 (SL1344_P1_0028) 27798..29219 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
SL1344_RS23785 (SL1344_P1_0029) 29219..29959 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
SL1344_RS23790 (SL1344_P1_0030) 29946..30512 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
SL1344_RS23795 (SL1344_P1_0031) 30534..30845 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
SL1344_RS23800 (SL1344_P1_0032) 30860..31222 - 363 WP_001273051 type IV conjugative transfer system pilin TraA -
SL1344_RS26285 (SL1344_P1_0033) 31264..31491 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
SL1344_RS23805 (SL1344_P1_0034) 31585..32271 - 687 WP_000336297 PAS domain-containing protein -
SL1344_RS23810 (SL1344_P1_0035) 32464..32844 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
SL1344_RS23815 (SL1344_P1_0036) 33259..33729 + 471 WP_014344446 transglycosylase SLT domain-containing protein -
SL1344_RS27530 34040..34858 - 819 Protein_37 DUF932 domain-containing protein -
SL1344_RS27480 34961..35119 - 159 WP_001704449 hypothetical protein -
SL1344_RS27885 35205..35333 - 129 WP_000372429 hypothetical protein -

Host bacterium

ID   881 GenBank   NC_017720
Plasmid name   pSLT_SL1344 Incompatibility group   IncFIB
Plasmid size   93842 bp Coordinate of oriT [Strand]   32927..33185 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Cargo genes

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