Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100798
Name   oriT_pNC983 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain NC983
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP015158 (60644..60902 [-], 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_pNC983
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   870 GenBank   WP_000986921
Name   TraI_pNC983 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: 60100..86456

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
A4H32_RS23820 (A4H32_23815) 55257..57254 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
A4H32_RS23825 (A4H32_23820) 57294..57727 + 434 Protein_74 conjugation system SOS inhibitor PsiB -
A4H32_RS23830 (A4H32_23825) 57724..58461 + 738 WP_000581933 plasmid SOS inhibition protein A -
A4H32_RS26680 58496..58624 + 129 WP_000372429 hypothetical protein -
A4H32_RS26390 58710..58868 + 159 WP_001704449 hypothetical protein -
A4H32_RS26395 58971..59789 + 819 Protein_78 DUF932 domain-containing protein -
A4H32_RS23845 (A4H32_23840) 60100..60570 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
A4H32_RS23850 (A4H32_23845) 60985..61365 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
A4H32_RS23855 (A4H32_23850) 61558..62244 + 687 WP_000336297 PAS domain-containing protein -
A4H32_RS25570 62338..62565 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
A4H32_RS23860 (A4H32_23855) 62607..62969 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
A4H32_RS23865 (A4H32_23860) 62984..63295 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
A4H32_RS23870 (A4H32_23865) 63317..63883 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
A4H32_RS23875 (A4H32_23870) 63870..64610 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
A4H32_RS23880 (A4H32_23875) 64610..66031 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
A4H32_RS23885 (A4H32_23880) 66021..66617 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
A4H32_RS23890 (A4H32_23885) 66595..66840 + 246 WP_010999944 DUF2689 domain-containing protein virb4
A4H32_RS23895 (A4H32_23890) 66837..67352 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
A4H32_RS23900 (A4H32_23895) 67487..67708 + 222 WP_001278699 conjugal transfer protein TraR -
A4H32_RS23905 (A4H32_23900) 67701..68168 + 468 WP_000549562 hypothetical protein -
A4H32_RS23910 (A4H32_23905) 68285..68548 + 264 WP_001239255 hypothetical protein -
A4H32_RS23915 (A4H32_23910) 68564..71212 + 2649 WP_000793310 type IV secretion system protein TraC virb4
A4H32_RS23920 (A4H32_23915) 71187..71573 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
A4H32_RS23925 (A4H32_23920) 71570..72202 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
A4H32_RS23930 (A4H32_23925) 72199..73191 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
A4H32_RS23935 (A4H32_23930) 73210..73518 + 309 WP_010999945 hypothetical protein -
A4H32_RS23940 (A4H32_23935) 73503..74141 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
A4H32_RS23945 (A4H32_23940) 74178..74597 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
A4H32_RS23950 (A4H32_23945) 74594..76420 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
A4H32_RS23955 (A4H32_23950) 76431..76646 + 216 WP_000700023 conjugal transfer protein TrbE -
A4H32_RS23960 (A4H32_23955) 76658..77407 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
A4H32_RS23965 (A4H32_23960) 77621..77914 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
A4H32_RS23970 (A4H32_23965) 77901..78449 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
A4H32_RS23975 (A4H32_23970) 78439..79821 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
A4H32_RS23980 (A4H32_23975) 79818..82640 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
A4H32_RS23985 (A4H32_23980) 82656..83150 + 495 WP_010999946 entry exclusion protein -
A4H32_RS23990 (A4H32_23985) 83186..83917 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
A4H32_RS23995 (A4H32_23990) 84294..86456 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
A4H32_RS24000 (A4H32_23995) 86465..86863 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
A4H32_RS24005 (A4H32_24000) 86863..87090 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1258 GenBank   NZ_CP015158
Plasmid name   pNC983 Incompatibility group   IncFII
Plasmid size   93829 bp Coordinate of oriT [Strand]   60644..60902 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain NC983

Cargo genes

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