Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103938
Name   oriT_NCCP 16207|unnamed1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain NCCP 16207
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP041974 (23031..23300 [+], 270 nt)
oriT length   270 nt
IRs (inverted repeats)      245..253, 262..270  (CACCCCTGG..CCAGGGGTG)
 92..98, 111..117  (ATTTAAT..ATTAAAT)
 103..108, 111..116  (TTTAAT..ATTAAA)
 33..38, 41..46  (AAAATT..AATTTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 270 nt

>oriT_NCCP 16207|unnamed1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2930 GenBank   WP_022743192
Name   traI_FPL16_RS00325_NCCP 16207|unnamed1 insolico UniProt ID   A0A484WVL1
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  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.




Auxiliary protein

ID   1205 GenBank   WP_001151546
Name   WP_001151546_NCCP 16207|unnamed1 insolico UniProt ID   Q93GP1
Length   126 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 126 a.a.        Molecular weight: 14366.30 Da        Isoelectric Point: 5.7236

>WP_001151546.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Salmonella]
MAKVNVYISNEVHNKITAIVEKRRQEGARDKDISFSGTSSMLLELGLRVYEAQMERKESPFNQTEFNKVL
LENVLKTQSSVAKILGIGSLSPHVAGNPKFEYANMVEDIKEKVSSEMERFFHENEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB Q93GP1

ID   1206 GenBank   WP_001676655
Name   WP_001676655_NCCP 16207|unnamed1 insolico UniProt ID   H3JT82
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9147.26 Da        Isoelectric Point: 9.6183

>WP_001676655.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Salmonella]
MRRRNAREGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRYPDFYNEEIFREVIEETES
TFKEI

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB H3JT82


T4CP

ID   2784 GenBank   WP_000793310
Name   traC_FPL16_RS00230_NCCP 16207|unnamed1 insolico UniProt ID   _
Length   882 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 882 a.a.        Molecular weight: 100382.20 Da        Isoelectric Point: 6.9316

>WP_000793310.1 MULTISPECIES: type IV secretion system protein TraC [Salmonella]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLRKFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESIHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVTNLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(468-763)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   2785 GenBank   WP_110029902
Name   traD_FPL16_RS00310_NCCP 16207|unnamed1 insolico UniProt ID   _
Length   759 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 759 a.a.        Molecular weight: 85987.87 Da        Isoelectric Point: 5.0447

>WP_110029902.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFCSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEE
QPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 22490..48964

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FPL16_RS00130 (FPL16_00145) 17646..19643 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
FPL16_RS00135 (FPL16_00150) 19683..20117 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
FPL16_RS00140 (FPL16_00155) 20114..20851 + 738 WP_000581933 plasmid SOS inhibition protein A -
FPL16_RS25435 20886..21014 + 129 WP_000372429 hypothetical protein -
FPL16_RS25025 21100..21258 + 159 WP_001704449 hypothetical protein -
FPL16_RS25030 21361..22179 + 819 Protein_31 DUF932 domain-containing protein -
FPL16_RS00155 (FPL16_00170) 22490..22960 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
FPL16_RS00160 (FPL16_00180) 23375..23755 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
FPL16_RS00165 (FPL16_00185) 23948..24634 + 687 WP_000336297 PAS domain-containing protein -
FPL16_RS00170 (FPL16_00190) 24729..24956 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
FPL16_RS00175 (FPL16_00195) 24998..25360 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
FPL16_RS00180 (FPL16_00200) 25375..25686 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
FPL16_RS00185 (FPL16_00205) 25708..26274 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
FPL16_RS00190 (FPL16_00210) 26261..27001 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
FPL16_RS00195 (FPL16_00215) 27001..28422 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
FPL16_RS00200 (FPL16_00220) 28412..29008 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
FPL16_RS00205 (FPL16_00225) 28986..29231 + 246 WP_010999944 DUF2689 domain-containing protein virb4
FPL16_RS00210 (FPL16_00230) 29228..29743 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
FPL16_RS00215 (FPL16_00235) 29878..30099 + 222 WP_001278699 conjugal transfer protein TraR -
FPL16_RS00220 (FPL16_00240) 30092..30559 + 468 WP_000549562 hypothetical protein -
FPL16_RS00225 (FPL16_00245) 30676..30939 + 264 WP_001239256 hypothetical protein -
FPL16_RS00230 (FPL16_00250) 30955..33603 + 2649 WP_000793310 type IV secretion system protein TraC virb4
FPL16_RS00235 (FPL16_00255) 33578..33964 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
FPL16_RS00240 (FPL16_00260) 33961..34593 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
FPL16_RS00245 (FPL16_00265) 34590..35582 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
FPL16_RS00250 (FPL16_00270) 35601..35909 + 309 WP_010999945 hypothetical protein -
FPL16_RS00255 (FPL16_00275) 35894..36532 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
FPL16_RS00260 (FPL16_00280) 36569..36988 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
FPL16_RS00265 (FPL16_00285) 36985..38811 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
FPL16_RS00270 (FPL16_00290) 38822..39037 + 216 WP_000700023 conjugal transfer protein TrbE -
FPL16_RS00275 (FPL16_00295) 39049..39798 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
FPL16_RS00280 (FPL16_00300) 40012..40305 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
FPL16_RS00285 (FPL16_00305) 40292..40840 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
FPL16_RS00290 (FPL16_00310) 40830..42212 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
FPL16_RS00295 (FPL16_00315) 42209..45031 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
FPL16_RS00300 (FPL16_00320) 45047..45541 + 495 WP_010999946 entry exclusion protein -
FPL16_RS00305 (FPL16_00325) 45577..46308 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
FPL16_RS00310 (FPL16_00330) 46685..48964 + 2280 WP_110029902 type IV conjugative transfer system coupling protein TraD prgC
FPL16_RS00315 (FPL16_00335) 48973..49371 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
FPL16_RS00320 (FPL16_00340) 49371..49598 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   4378 GenBank   NZ_CP041974
Plasmid name   NCCP 16207|unnamed1 Incompatibility group   IncFII
Plasmid size   113858 bp Coordinate of oriT [Strand]   23031..23300 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain NCCP 16207

Cargo genes

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