Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107521
Name   oriT_pSTY1-1899 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1899
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP014962 (60663..60932 [+], 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_pSTY1-1899
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5045 GenBank   WP_000986921
Name   traI_AX02_RS00565_pSTY1-1899 insolico UniProt ID   Q93GL4
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  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


Source ID Structure
AlphaFold DB Q93GL4


Auxiliary protein

ID   2313 GenBank   WP_001717252
Name   WP_001717252_pSTY1-1899 insolico UniProt ID   A0A1S6L5E8
Length   115 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 115 a.a.        Molecular weight: 12887.74 Da        Isoelectric Point: 8.4665

>WP_001717252.1 conjugal transfer relaxosome DNA-binding protein TraM, partial [Salmonella enterica]
MAKVNVYISNEVHNKITAIVEKRRQEGARDKDISFSGTSSMLLELGLRVYEAQMERKESPFNQTEFNKVL
LENVLKTQSSVAKILGIGSLSPHVAGNPKFEYANMVEDIKEKVSS

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-115)


  Protein structure


Source ID Structure
AlphaFold DB A0A1S6L5E8

ID   2314 GenBank   WP_001676655
Name   WP_001676655_pSTY1-1899 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   5262 GenBank   WP_000793310
Name   traC_AX02_RS00470_pSTY1-1899 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   5263 GenBank   WP_000009318
Name   traD_AX02_RS00550_pSTY1-1899 insolico UniProt ID   _
Length   720 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 720 a.a.        Molecular weight: 81447.01 Da        Isoelectric Point: 5.1045

>WP_000009318.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Salmonella]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQPTVV
SDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREE
VNINVHRGHGKDEPEPGDDF

  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: 60122..86478

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AX02_RS00365 (AX02_51235) 55278..57275 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
AX02_RS00370 (AX02_51240) 57315..57749 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
AX02_RS00375 (AX02_51245) 57746..58483 + 738 WP_000581933 plasmid SOS inhibition protein A -
AX02_RS00590 58518..58646 + 129 WP_000372429 hypothetical protein -
AX02_RS00380 58720..58890 + 171 WP_000229547 hypothetical protein -
AX02_RS00385 58993..59811 + 819 Protein_79 DUF932 domain-containing protein -
AX02_RS00390 (AX02_51265) 60122..60592 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
AX02_RS00400 (AX02_51275) 61007..61354 + 348 WP_001717252 conjugal transfer relaxosome DNA-binding protein TraM -
AX02_RS00405 (AX02_51280) 61580..62266 + 687 WP_000336297 PAS domain-containing protein -
AX02_RS00410 (AX02_51285) 62360..62587 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
AX02_RS00415 (AX02_51290) 62629..62991 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
AX02_RS00420 (AX02_51295) 63006..63317 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
AX02_RS00425 (AX02_51300) 63339..63905 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
AX02_RS00430 (AX02_51305) 63892..64632 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
AX02_RS00435 (AX02_51310) 64632..66053 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
AX02_RS00440 (AX02_51315) 66043..66639 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
AX02_RS00445 (AX02_51320) 66617..66862 + 246 WP_010999944 DUF2689 domain-containing protein virb4
AX02_RS00450 (AX02_51325) 66859..67374 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
AX02_RS00455 (AX02_51330) 67509..67730 + 222 WP_001278699 conjugal transfer protein TraR -
AX02_RS00460 (AX02_51335) 67723..68190 + 468 WP_000549562 hypothetical protein -
AX02_RS00465 (AX02_51340) 68307..68570 + 264 WP_001239255 hypothetical protein -
AX02_RS00470 (AX02_51345) 68586..71234 + 2649 WP_000793310 type IV secretion system protein TraC virb4
AX02_RS00475 (AX02_51350) 71209..71595 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
AX02_RS00480 (AX02_51355) 71592..72224 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
AX02_RS00485 (AX02_51360) 72221..73213 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
AX02_RS00490 (AX02_51365) 73232..73540 + 309 WP_010999945 hypothetical protein -
AX02_RS00495 (AX02_51370) 73525..74163 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
AX02_RS00500 (AX02_51375) 74200..74619 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
AX02_RS00505 (AX02_51380) 74616..76442 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AX02_RS00510 (AX02_51385) 76453..76668 + 216 WP_000700023 conjugal transfer protein TrbE -
AX02_RS00515 (AX02_51390) 76680..77429 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
AX02_RS00520 (AX02_51395) 77643..77936 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
AX02_RS00525 (AX02_51400) 77923..78471 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AX02_RS00530 (AX02_51405) 78461..79843 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
AX02_RS00535 (AX02_51410) 79840..82662 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
AX02_RS00540 (AX02_51415) 82678..83172 + 495 WP_010999946 entry exclusion protein -
AX02_RS00545 (AX02_51420) 83208..83939 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
AX02_RS00550 (AX02_51425) 84316..86478 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
AX02_RS00555 (AX02_51430) 86487..86885 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
AX02_RS00560 (AX02_51435) 86885..87112 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   7956 GenBank   NZ_CP014962
Plasmid name   pSTY1-1899 Incompatibility group   IncFII
Plasmid size   93850 bp Coordinate of oriT [Strand]   60663..60932 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1899

Cargo genes

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