Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105370
Name   oriT_p28321b-2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain CVM 28321-b
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051364 (15745..16014 [+], 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_p28321b-2
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3664 GenBank   WP_022743192
Name   traI_HFS62_RS24025_p28321b-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   1653 GenBank   WP_001151546
Name   WP_001151546_p28321b-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   1654 GenBank   WP_001676655
Name   WP_001676655_p28321b-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   3637 GenBank   WP_000793310
Name   traC_HFS62_RS23930_p28321b-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   3638 GenBank   WP_022743189
Name   traD_HFS62_RS24010_p28321b-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: 15204..41660

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFS62_RS23830 (HFS62_23820) 10360..12357 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
HFS62_RS23835 (HFS62_23825) 12397..12831 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
HFS62_RS23840 (HFS62_23830) 12828..13565 + 738 WP_000581933 plasmid SOS inhibition protein A -
HFS62_RS24670 13600..13728 + 129 WP_000372429 hypothetical protein -
HFS62_RS23845 (HFS62_23835) 13814..13972 + 159 WP_001704449 hypothetical protein -
HFS62_RS23850 (HFS62_23840) 14075..14893 + 819 Protein_23 DUF932 domain-containing protein -
HFS62_RS23855 (HFS62_23845) 15204..15674 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
HFS62_RS23860 (HFS62_23850) 16089..16469 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
HFS62_RS23865 (HFS62_23855) 16662..17348 + 687 WP_000336297 PAS domain-containing protein -
HFS62_RS23870 (HFS62_23860) 17443..17670 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
HFS62_RS23875 (HFS62_23865) 17712..18074 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
HFS62_RS23880 (HFS62_23870) 18089..18400 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
HFS62_RS23885 (HFS62_23875) 18422..18988 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
HFS62_RS23890 (HFS62_23880) 18975..19715 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
HFS62_RS23895 (HFS62_23885) 19715..21136 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
HFS62_RS23900 (HFS62_23890) 21126..21722 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
HFS62_RS23905 (HFS62_23895) 21700..21945 + 246 WP_010999944 DUF2689 domain-containing protein virb4
HFS62_RS23910 (HFS62_23900) 21942..22457 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
HFS62_RS23915 (HFS62_23905) 22592..22813 + 222 WP_001278699 conjugal transfer protein TraR -
HFS62_RS23920 (HFS62_23910) 22806..23273 + 468 WP_000549562 hypothetical protein -
HFS62_RS23925 (HFS62_23915) 23390..23653 + 264 WP_001239256 hypothetical protein -
HFS62_RS23930 (HFS62_23920) 23669..26317 + 2649 WP_000793310 type IV secretion system protein TraC virb4
HFS62_RS23935 (HFS62_23925) 26292..26678 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
HFS62_RS23940 (HFS62_23930) 26675..27307 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
HFS62_RS23945 (HFS62_23935) 27304..28296 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
HFS62_RS23950 (HFS62_23940) 28315..28623 + 309 WP_010999945 hypothetical protein -
HFS62_RS23955 (HFS62_23945) 28608..29246 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
HFS62_RS23960 (HFS62_23950) 29283..29702 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
HFS62_RS23965 (HFS62_23955) 29699..31525 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HFS62_RS23970 (HFS62_23960) 31536..31751 + 216 WP_000700023 conjugal transfer protein TrbE -
HFS62_RS23975 (HFS62_23965) 31763..32512 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
HFS62_RS23980 (HFS62_23970) 32726..33019 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
HFS62_RS23985 (HFS62_23975) 33006..33554 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HFS62_RS23990 (HFS62_23980) 33544..34926 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
HFS62_RS23995 (HFS62_23985) 34923..37745 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
HFS62_RS24000 (HFS62_23990) 37761..38255 + 495 WP_010999946 entry exclusion protein -
HFS62_RS24005 (HFS62_23995) 38291..39022 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
HFS62_RS24010 (HFS62_24000) 39399..41660 + 2262 WP_022743189 type IV conjugative transfer system coupling protein TraD prgC
HFS62_RS24015 (HFS62_24005) 41669..42067 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
HFS62_RS24020 (HFS62_24010) 42067..42294 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   5808 GenBank   NZ_CP051364
Plasmid name   p28321b-2 Incompatibility group   IncFII
Plasmid size   107602 bp Coordinate of oriT [Strand]   15745..16014 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain CVM 28321-b

Cargo genes

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