Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100858
Name   oriT_pSARA13 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. SARA13 strain SGSC 2193
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP017729 (45873..46131 [-], 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_pSARA13
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   930 GenBank   WP_000986921
Name   TraI_pSARA13 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: 48213..71685

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SEETRA13_RS25945 43725..43853 + 129 WP_000372429 hypothetical protein -
SEETRA13_RS25680 43939..44097 + 159 WP_001704449 hypothetical protein -
SEETRA13_RS25685 44200..45018 + 819 Protein_57 DUF932 domain-containing protein -
SEETRA13_RS23580 (SEETRA13_023580) 45329..45799 - 471 WP_014344446 transglycosylase SLT domain-containing protein -
SEETRA13_RS23585 (SEETRA13_023585) 46214..46594 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
SEETRA13_RS23590 (SEETRA13_023590) 46787..47473 + 687 WP_000336297 PAS domain-containing protein -
SEETRA13_RS25445 47567..47794 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
SEETRA13_RS23595 (SEETRA13_023595) 47836..48198 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
SEETRA13_RS23600 (SEETRA13_023600) 48213..48524 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
SEETRA13_RS23605 (SEETRA13_023605) 48546..49112 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
SEETRA13_RS23610 (SEETRA13_023610) 49099..49839 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
SEETRA13_RS23615 (SEETRA13_023615) 49839..51260 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
SEETRA13_RS23620 (SEETRA13_023620) 51250..51846 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
SEETRA13_RS23625 (SEETRA13_023625) 51824..52069 + 246 WP_010999944 DUF2689 domain-containing protein virb4
SEETRA13_RS23630 (SEETRA13_023630) 52066..52581 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
SEETRA13_RS23635 (SEETRA13_023635) 52716..52937 + 222 WP_001278699 conjugal transfer protein TraR -
SEETRA13_RS23640 (SEETRA13_023640) 52930..53397 + 468 WP_023198173 conjugative transfer protein -
SEETRA13_RS23645 (SEETRA13_023645) 53514..53777 + 264 WP_001239255 hypothetical protein -
SEETRA13_RS23650 (SEETRA13_023650) 53793..56441 + 2649 WP_000793310 type IV secretion system protein TraC virb4
SEETRA13_RS23655 (SEETRA13_023655) 56416..56802 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
SEETRA13_RS23660 (SEETRA13_023660) 56799..57431 + 633 WP_023139304 type-F conjugative transfer system protein TraW traW
SEETRA13_RS23665 (SEETRA13_023665) 57428..58420 + 993 WP_023198135 conjugal transfer pilus assembly protein TraU traU
SEETRA13_RS23670 (SEETRA13_023670) 58439..58747 + 309 WP_010999945 hypothetical protein -
SEETRA13_RS23675 (SEETRA13_023675) 58732..59370 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
SEETRA13_RS23680 (SEETRA13_023680) 59407..59826 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
SEETRA13_RS23685 (SEETRA13_023685) 59823..61649 + 1827 WP_023198136 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SEETRA13_RS23690 (SEETRA13_023690) 61660..61875 + 216 WP_000700023 conjugal transfer protein TrbE -
SEETRA13_RS23695 (SEETRA13_023695) 61887..62636 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
SEETRA13_RS23700 (SEETRA13_023700) 62850..63143 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
SEETRA13_RS23705 (SEETRA13_023705) 63130..63678 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SEETRA13_RS23710 (SEETRA13_023710) 63668..65050 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
SEETRA13_RS23715 (SEETRA13_023715) 65047..67869 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
SEETRA13_RS23720 (SEETRA13_023720) 67885..68379 + 495 WP_010999946 entry exclusion protein -
SEETRA13_RS23725 (SEETRA13_023725) 68415..69146 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
SEETRA13_RS23730 (SEETRA13_023730) 69523..71685 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
SEETRA13_RS23735 (SEETRA13_023735) 71694..72092 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
SEETRA13_RS23740 (SEETRA13_023740) 72092..72319 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1318 GenBank   NZ_CP017729
Plasmid name   pSARA13 Incompatibility group   IncFIB
Plasmid size   93826 bp Coordinate of oriT [Strand]   45873..46131 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. SARA13 strain SGSC 2193

Cargo genes

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