Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100781
Name   oriT_pRM9437 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain RM9437
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014577 (60665..60923 [-], 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_pRM9437
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   853 GenBank   WP_022743192
Name   Relaxase_pRM9437 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191680.70 Da        Isoelectric Point: 5.9879

>WP_022743192.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR
QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMKNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW
NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1158)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(632-711)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(574-626)

TrwC relaxase (TrwC)

(11-282)

DNA helicase TraI (TraI_C)

(1430-1553)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60121..82662

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SEETMRM9437_RS24480 (SEETMRM9437_23780) 55277..57274 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
SEETMRM9437_RS24485 (SEETMRM9437_23785) 57314..57748 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
SEETMRM9437_RS24490 (SEETMRM9437_23790) 57745..58482 + 738 WP_000581933 plasmid SOS inhibition protein A -
SEETMRM9437_RS24495 58992..59393 + 402 Protein_81 DUF945 domain-containing protein -
SEETMRM9437_RS27080 59455..59810 + 356 Protein_82 DUF945 domain-containing protein -
SEETMRM9437_RS24505 (SEETMRM9437_23795) 60121..60591 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
SEETMRM9437_RS26285 60808..61013 + 206 Protein_84 hypothetical protein -
SEETMRM9437_RS24510 (SEETMRM9437_23800) 61006..61386 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
SEETMRM9437_RS24515 (SEETMRM9437_23805) 61579..62265 + 687 WP_000336297 PAS domain-containing protein -
SEETMRM9437_RS26290 62360..62587 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
SEETMRM9437_RS24520 (SEETMRM9437_23810) 62629..62991 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
SEETMRM9437_RS24525 (SEETMRM9437_23815) 63006..63317 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
SEETMRM9437_RS24530 (SEETMRM9437_23820) 63339..63905 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
SEETMRM9437_RS24535 (SEETMRM9437_23825) 63892..64632 + 741 WP_063503128 type-F conjugative transfer system secretin TraK traK
SEETMRM9437_RS24540 (SEETMRM9437_23830) 64632..66053 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
SEETMRM9437_RS24545 (SEETMRM9437_23835) 66043..66639 + 597 Protein_93 conjugal transfer protein TraP -
SEETMRM9437_RS24550 (SEETMRM9437_23840) 66617..66862 + 246 WP_010999944 DUF2689 domain-containing protein virb4
SEETMRM9437_RS24555 (SEETMRM9437_23845) 66859..67374 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
SEETMRM9437_RS24560 (SEETMRM9437_23850) 67509..67730 + 222 WP_001278699 conjugal transfer protein TraR -
SEETMRM9437_RS24565 (SEETMRM9437_23855) 67723..68190 + 468 WP_000549562 hypothetical protein -
SEETMRM9437_RS24570 68307..68570 + 264 WP_001239256 hypothetical protein -
SEETMRM9437_RS24575 (SEETMRM9437_23860) 68586..71234 + 2649 WP_000793310 type IV secretion system protein TraC virb4
SEETMRM9437_RS24580 (SEETMRM9437_23865) 71209..71595 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
SEETMRM9437_RS24585 (SEETMRM9437_23870) 71592..72224 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
SEETMRM9437_RS24590 (SEETMRM9437_23875) 72221..73213 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
SEETMRM9437_RS24595 (SEETMRM9437_23880) 73232..73540 + 309 WP_010999945 hypothetical protein -
SEETMRM9437_RS24600 (SEETMRM9437_23885) 73525..74163 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
SEETMRM9437_RS24605 (SEETMRM9437_23890) 74200..74619 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
SEETMRM9437_RS24610 (SEETMRM9437_23895) 74616..76442 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SEETMRM9437_RS24615 (SEETMRM9437_23900) 76453..76668 + 216 WP_000700023 conjugal transfer protein TrbE -
SEETMRM9437_RS24620 (SEETMRM9437_23905) 76680..77429 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
SEETMRM9437_RS24625 (SEETMRM9437_23910) 77643..77936 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
SEETMRM9437_RS24630 (SEETMRM9437_23915) 77923..78471 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SEETMRM9437_RS24635 (SEETMRM9437_23920) 78461..79843 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
SEETMRM9437_RS24640 (SEETMRM9437_23925) 79840..82662 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
SEETMRM9437_RS24645 (SEETMRM9437_23930) 82678..83172 + 495 WP_010999946 entry exclusion protein -
SEETMRM9437_RS24650 (SEETMRM9437_23935) 83208..83939 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
SEETMRM9437_RS24655 (SEETMRM9437_23960) 84316..86557 + 2242 Protein_115 type IV conjugative transfer system coupling protein TraD -
SEETMRM9437_RS24660 86566..86964 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
SEETMRM9437_RS24665 86964..87194 - 231 WP_001526804 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1241 GenBank   NZ_CP014577
Plasmid name   pRM9437 Incompatibility group   IncFII
Plasmid size   93930 bp Coordinate of oriT [Strand]   60665..60923 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain RM9437

Cargo genes

Drug resistance gene   -
Virulence gene   Salmonella plasmid virulence
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -