Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104559
Name   oriT_pST1539 in_silico
Organism   Salmonella enterica subsp. enterica strain ST1539
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP035302 (61017..61286 [-], 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_pST1539
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3286 GenBank   WP_000986921
Name   traI_ST1539_RS24360_pST1539 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   1472 GenBank   WP_001676655
Name   WP_001676655_pST1539 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   1473 GenBank   WP_001151546
Name   WP_001151546_pST1539 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   3224 GenBank   WP_000009318
Name   traD_ST1539_RS24375_pST1539 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.



ID   3225 GenBank   WP_000793310
Name   traC_ST1539_RS24455_pST1539 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: 35471..61827

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ST1539_RS24365 (ST1539_p034) 34837..35064 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
ST1539_RS24370 (ST1539_p035) 35064..35462 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
ST1539_RS24375 (ST1539_p036) 35471..37633 - 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
ST1539_RS24380 (ST1539_p037) 38010..38741 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
ST1539_RS24385 (ST1539_p038) 38777..39271 - 495 WP_010999946 entry exclusion protein -
ST1539_RS24390 39287..42109 - 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
ST1539_RS24395 (ST1539_p039) 42106..43488 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
ST1539_RS24400 (ST1539_p040) 43478..44026 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ST1539_RS24405 44013..44306 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
ST1539_RS24410 (ST1539_p041) 44520..45269 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
ST1539_RS24415 (ST1539_p042) 45281..45496 - 216 WP_000700023 conjugal transfer protein TrbE -
ST1539_RS24420 (ST1539_p043) 45507..47333 - 1827 WP_146471649 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ST1539_RS24425 (ST1539_p044) 47330..47749 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
ST1539_RS24430 (ST1539_p045) 47786..48424 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
ST1539_RS24435 (ST1539_p046) 48409..48717 - 309 WP_010999945 hypothetical protein -
ST1539_RS24440 (ST1539_p047) 48736..49728 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
ST1539_RS24445 49725..50357 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
ST1539_RS24450 (ST1539_p048) 50354..50740 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
ST1539_RS24455 50715..53363 - 2649 WP_000793310 type IV secretion system protein TraC virb4
ST1539_RS24460 (ST1539_p049) 53379..53642 - 264 WP_001239255 hypothetical protein -
ST1539_RS24465 (ST1539_p050) 53759..54226 - 468 WP_000549562 hypothetical protein -
ST1539_RS24470 (ST1539_p051) 54219..54440 - 222 WP_001278699 conjugal transfer protein TraR -
ST1539_RS24475 (ST1539_p052) 54575..55090 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
ST1539_RS24480 (ST1539_p053) 55087..55332 - 246 WP_010999944 DUF2689 domain-containing protein virb4
ST1539_RS24485 (ST1539_p054) 55310..55906 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
ST1539_RS24490 (ST1539_p055) 55896..57317 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
ST1539_RS24495 (ST1539_p056) 57317..58057 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
ST1539_RS24500 (ST1539_p057) 58044..58610 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
ST1539_RS24505 (ST1539_p058) 58632..58943 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
ST1539_RS24510 (ST1539_p059) 58958..59320 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
ST1539_RS24515 59362..59589 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
ST1539_RS24520 (ST1539_p060) 59683..60369 - 687 WP_000336297 PAS domain-containing protein -
ST1539_RS24525 (ST1539_p061) 60562..60942 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
ST1539_RS24535 (ST1539_p062) 61357..61827 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
ST1539_RS24895 62138..62956 - 819 Protein_78 DUF932 domain-containing protein -
ST1539_RS24815 (ST1539_p065) 63059..63217 - 159 WP_001704449 hypothetical protein -
ST1539_RS25245 63303..63431 - 129 WP_000372429 hypothetical protein -
ST1539_RS24550 (ST1539_p066) 63466..64203 - 738 WP_000581933 plasmid SOS inhibition protein A -
ST1539_RS24555 (ST1539_p067) 64200..64634 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
ST1539_RS24560 (ST1539_p068) 64674..66671 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   4998 GenBank   NZ_CP035302
Plasmid name   pST1539 Incompatibility group   IncFIB
Plasmid size   93876 bp Coordinate of oriT [Strand]   61017..61286 [-]
Host baterium   Salmonella enterica subsp. enterica strain ST1539

Cargo genes

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