Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107730
Name   oriT_pSC-09-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CFSAN067216
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP028319 (61502..61771 [-], 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_pSC-09-1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5194 GenBank   WP_022743192
Name   traI_C0X15_RS24860_pSC-09-1 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   2364 GenBank   WP_001676655
Name   WP_001676655_pSC-09-1 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

ID   2365 GenBank   WP_001151546
Name   WP_001151546_pSC-09-1 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


T4CP

ID   5440 GenBank   WP_022743189
Name   traD_C0X15_RS24875_pSC-09-1 insolico UniProt ID   _
Length   753 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 753 a.a.        Molecular weight: 85281.12 Da        Isoelectric Point: 5.0447

>WP_022743189.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFCSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPG
INASGEVVDMAAYERWRQEQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

  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.



ID   5441 GenBank   WP_000793310
Name   traC_C0X15_RS24955_pSC-09-1 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 35856..62312

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C0X15_RS24865 (C0X15_25405) 35222..35449 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
C0X15_RS24870 (C0X15_25410) 35449..35847 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
C0X15_RS24875 (C0X15_25415) 35856..38117 - 2262 WP_022743189 type IV conjugative transfer system coupling protein TraD prgC
C0X15_RS24880 (C0X15_25420) 38494..39225 - 732 WP_022743186 conjugal transfer complement resistance protein TraT -
C0X15_RS24885 (C0X15_25425) 39261..39755 - 495 WP_010999946 entry exclusion protein -
C0X15_RS24890 (C0X15_25430) 39771..42593 - 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
C0X15_RS24895 (C0X15_25435) 42590..43972 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
C0X15_RS24900 (C0X15_25440) 43962..44510 - 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
C0X15_RS24905 (C0X15_25445) 44497..44790 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
C0X15_RS24910 (C0X15_25450) 45004..45753 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
C0X15_RS24915 (C0X15_25455) 45765..45980 - 216 WP_000700023 conjugal transfer protein TrbE -
C0X15_RS24920 (C0X15_25460) 45991..47817 - 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
C0X15_RS24925 (C0X15_25465) 47814..48233 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
C0X15_RS24930 (C0X15_25470) 48270..48908 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
C0X15_RS24935 (C0X15_25475) 48893..49201 - 309 WP_010999945 hypothetical protein -
C0X15_RS24940 (C0X15_25480) 49220..50212 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
C0X15_RS24945 (C0X15_25485) 50209..50841 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
C0X15_RS24950 (C0X15_25490) 50838..51224 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
C0X15_RS24955 (C0X15_25495) 51199..53847 - 2649 WP_000793310 type IV secretion system protein TraC virb4
C0X15_RS24960 (C0X15_25500) 53863..54126 - 264 WP_001239256 hypothetical protein -
C0X15_RS24965 (C0X15_25505) 54243..54710 - 468 WP_000549562 hypothetical protein -
C0X15_RS24970 (C0X15_25510) 54703..54924 - 222 WP_001278699 conjugal transfer protein TraR -
C0X15_RS24975 (C0X15_25515) 55059..55574 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
C0X15_RS24980 (C0X15_25520) 55571..55816 - 246 WP_010999944 DUF2689 domain-containing protein virb4
C0X15_RS24985 (C0X15_25525) 55794..56390 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
C0X15_RS24990 (C0X15_25530) 56380..57801 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
C0X15_RS24995 (C0X15_25535) 57801..58541 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
C0X15_RS25000 (C0X15_25540) 58528..59094 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
C0X15_RS25005 (C0X15_25545) 59116..59427 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
C0X15_RS25010 (C0X15_25550) 59442..59804 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
C0X15_RS25015 (C0X15_25555) 59846..60073 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
C0X15_RS25020 (C0X15_25560) 60168..60854 - 687 WP_000336297 PAS domain-containing protein -
C0X15_RS25025 (C0X15_25565) 61047..61427 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
C0X15_RS25035 (C0X15_25575) 61842..62312 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
C0X15_RS25400 (C0X15_25580) 62835..63441 - 607 Protein_79 DUF932 domain-containing protein -
C0X15_RS25405 63544..63702 - 159 WP_001704449 hypothetical protein -
C0X15_RS25815 63788..63916 - 129 WP_000372429 hypothetical protein -
C0X15_RS25045 (C0X15_25585) 63951..64688 - 738 WP_000581933 plasmid SOS inhibition protein A -
C0X15_RS25050 (C0X15_25590) 64685..65119 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
C0X15_RS25055 (C0X15_25595) 65159..67156 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   8165 GenBank   NZ_CP028319
Plasmid name   pSC-09-1 Incompatibility group   IncFIB
Plasmid size   94045 bp Coordinate of oriT [Strand]   61502..61771 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CFSAN067216

Cargo genes

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