Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103896
Name   oriT_pRSE04 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain RSE04
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP034720 (50604..50873 [-], 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_pRSE04
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2898 GenBank   WP_000986921
Name   traI_ELZ71_RS23920_pRSE04 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   1194 GenBank   WP_001676655
Name   WP_001676655_pRSE04 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   1195 GenBank   WP_001151546
Name   WP_001151546_pRSE04 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   2742 GenBank   WP_000009319
Name   traD_ELZ71_RS23935_pRSE04 insolico UniProt ID   _
Length   744 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 744 a.a.        Molecular weight: 84274.03 Da        Isoelectric Point: 5.1045

>WP_000009319.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVD
MAAYERWRQEQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

  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   2743 GenBank   WP_000793310
Name   traC_ELZ71_RS24015_pRSE04 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: 24986..51414

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELZ71_RS23925 (ELZ71_23925) 24352..24579 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
ELZ71_RS23930 (ELZ71_23930) 24579..24977 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
ELZ71_RS23935 (ELZ71_23935) 24986..27220 - 2235 WP_000009319 type IV conjugative transfer system coupling protein TraD virb4
ELZ71_RS23940 (ELZ71_23940) 27597..28328 - 732 WP_022743186 conjugal transfer complement resistance protein TraT -
ELZ71_RS23945 (ELZ71_23945) 28364..28858 - 495 WP_010999946 entry exclusion protein -
ELZ71_RS23950 (ELZ71_23950) 28874..31696 - 2823 WP_127201233 conjugal transfer mating-pair stabilization protein TraG traG
ELZ71_RS23955 (ELZ71_23955) 31693..33075 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
ELZ71_RS23960 (ELZ71_23960) 33065..33613 - 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ELZ71_RS23965 (ELZ71_23965) 33600..33893 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
ELZ71_RS23970 (ELZ71_23970) 34107..34856 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
ELZ71_RS23975 (ELZ71_23975) 34868..35083 - 216 WP_000700023 conjugal transfer protein TrbE -
ELZ71_RS23980 (ELZ71_23980) 35094..36920 - 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ELZ71_RS23985 (ELZ71_23985) 36917..37336 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
ELZ71_RS23990 (ELZ71_23990) 37373..38011 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
ELZ71_RS23995 (ELZ71_23995) 37996..38304 - 309 WP_010999945 hypothetical protein -
ELZ71_RS24000 (ELZ71_24000) 38323..39315 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
ELZ71_RS24005 (ELZ71_24005) 39312..39944 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
ELZ71_RS24010 (ELZ71_24010) 39941..40327 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
ELZ71_RS24015 (ELZ71_24015) 40302..42950 - 2649 WP_000793310 type IV secretion system protein TraC virb4
ELZ71_RS24020 (ELZ71_24020) 42966..43229 - 264 WP_001239256 hypothetical protein -
ELZ71_RS24025 (ELZ71_24025) 43346..43813 - 468 WP_000549562 hypothetical protein -
ELZ71_RS24030 (ELZ71_24030) 43806..44027 - 222 WP_001278699 conjugal transfer protein TraR -
ELZ71_RS24035 (ELZ71_24035) 44162..44677 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
ELZ71_RS24040 (ELZ71_24040) 44674..44919 - 246 WP_010999944 DUF2689 domain-containing protein virb4
ELZ71_RS24045 (ELZ71_24045) 44897..45493 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
ELZ71_RS24050 (ELZ71_24050) 45483..46904 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
ELZ71_RS24055 (ELZ71_24055) 46904..47644 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
ELZ71_RS24060 (ELZ71_24060) 47631..48197 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
ELZ71_RS24065 (ELZ71_24065) 48219..48530 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
ELZ71_RS24070 (ELZ71_24070) 48545..48907 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
ELZ71_RS24075 (ELZ71_24075) 48949..49176 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
ELZ71_RS24080 (ELZ71_24080) 49270..49956 - 687 WP_000336297 PAS domain-containing protein -
ELZ71_RS24085 (ELZ71_24085) 50149..50529 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
ELZ71_RS24095 (ELZ71_24095) 50944..51414 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
ELZ71_RS24100 (ELZ71_24100) 51725..52543 - 819 Protein_61 DUF932 domain-containing protein -
ELZ71_RS24425 52646..52804 - 159 WP_001704449 hypothetical protein -
ELZ71_RS24730 52890..53018 - 129 WP_000372429 hypothetical protein -
ELZ71_RS24105 (ELZ71_24105) 53053..53790 - 738 WP_000581933 plasmid SOS inhibition protein A -
ELZ71_RS24110 (ELZ71_24110) 53787..54221 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
ELZ71_RS24115 (ELZ71_24115) 54261..56258 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   4336 GenBank   NZ_CP034720
Plasmid name   pRSE04 Incompatibility group   IncFIB
Plasmid size   93964 bp Coordinate of oriT [Strand]   50604..50873 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain RSE04

Cargo genes

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