Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105379
Name   oriT_p24362-2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain CVM 24362
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051377 (13063..13332 [+], 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_p24362-2
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3672 GenBank   WP_022743192
Name   traI_HFS07_RS00280_p24362-2 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   1659 GenBank   WP_001151546
Name   WP_001151546_p24362-2 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   1660 GenBank   WP_001676655
Name   WP_001676655_p24362-2 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   3648 GenBank   WP_000793310
Name   traC_HFS07_RS00185_p24362-2 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   3649 GenBank   WP_022743189
Name   traD_HFS07_RS00265_p24362-2 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 12522..38978

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFS07_RS00085 (HFS07_00100) 7678..9675 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
HFS07_RS00090 (HFS07_00105) 9715..10149 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
HFS07_RS00095 (HFS07_00110) 10146..10883 + 738 WP_000581933 plasmid SOS inhibition protein A -
HFS07_RS25780 10918..11046 + 129 WP_000372429 hypothetical protein -
HFS07_RS00100 (HFS07_00115) 11132..11290 + 159 WP_001704449 hypothetical protein -
HFS07_RS00105 (HFS07_00120) 11393..12211 + 819 Protein_20 DUF932 domain-containing protein -
HFS07_RS00110 (HFS07_00125) 12522..12992 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
HFS07_RS00115 (HFS07_00130) 13407..13787 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
HFS07_RS00120 (HFS07_00135) 13980..14666 + 687 WP_000336297 PAS domain-containing protein -
HFS07_RS00125 (HFS07_00140) 14761..14988 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
HFS07_RS00130 (HFS07_00145) 15030..15392 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
HFS07_RS00135 (HFS07_00150) 15407..15718 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
HFS07_RS00140 (HFS07_00155) 15740..16306 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
HFS07_RS00145 (HFS07_00160) 16293..17033 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
HFS07_RS00150 (HFS07_00165) 17033..18454 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
HFS07_RS00155 (HFS07_00170) 18444..19040 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
HFS07_RS00160 (HFS07_00175) 19018..19263 + 246 WP_010999944 DUF2689 domain-containing protein virb4
HFS07_RS00165 (HFS07_00180) 19260..19775 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
HFS07_RS00170 (HFS07_00185) 19910..20131 + 222 WP_001278699 conjugal transfer protein TraR -
HFS07_RS00175 (HFS07_00190) 20124..20591 + 468 WP_000549562 hypothetical protein -
HFS07_RS00180 (HFS07_00195) 20708..20971 + 264 WP_001239256 hypothetical protein -
HFS07_RS00185 (HFS07_00200) 20987..23635 + 2649 WP_000793310 type IV secretion system protein TraC virb4
HFS07_RS00190 (HFS07_00205) 23610..23996 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
HFS07_RS00195 (HFS07_00210) 23993..24625 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
HFS07_RS00200 (HFS07_00215) 24622..25614 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
HFS07_RS00205 (HFS07_00220) 25633..25941 + 309 WP_010999945 hypothetical protein -
HFS07_RS00210 (HFS07_00225) 25926..26564 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
HFS07_RS00215 (HFS07_00230) 26601..27020 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
HFS07_RS00220 (HFS07_00235) 27017..28843 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HFS07_RS00225 (HFS07_00240) 28854..29069 + 216 WP_000700023 conjugal transfer protein TrbE -
HFS07_RS00230 (HFS07_00245) 29081..29830 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
HFS07_RS00235 (HFS07_00250) 30044..30337 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
HFS07_RS00240 (HFS07_00255) 30324..30872 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HFS07_RS00245 (HFS07_00260) 30862..32244 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
HFS07_RS00250 (HFS07_00265) 32241..35063 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
HFS07_RS00255 (HFS07_00270) 35079..35573 + 495 WP_010999946 entry exclusion protein -
HFS07_RS00260 (HFS07_00275) 35609..36340 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
HFS07_RS00265 (HFS07_00280) 36717..38978 + 2262 WP_022743189 type IV conjugative transfer system coupling protein TraD prgC
HFS07_RS00270 (HFS07_00285) 38987..39385 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
HFS07_RS00275 (HFS07_00290) 39385..39612 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   5817 GenBank   NZ_CP051377
Plasmid name   p24362-2 Incompatibility group   IncFII
Plasmid size   94046 bp Coordinate of oriT [Strand]   13063..13332 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain CVM 24362

Cargo genes

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