Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104037
Name   oriT_psLT in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain LB5000
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP067398 (60669..60938 [+], 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_psLT
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2992 GenBank   WP_000986921
Name   traI_JJB81_RS23680_psLT 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   1261 GenBank   WP_001151546
Name   WP_001151546_psLT 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   1262 GenBank   WP_001676655
Name   WP_001676655_psLT 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   2858 GenBank   WP_000793310
Name   traC_JJB81_RS23585_psLT 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   2859 GenBank   WP_000009320
Name   traD_JJB81_RS23665_psLT insolico UniProt ID   _
Length   747 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 747 a.a.        Molecular weight: 84627.41 Da        Isoelectric Point: 5.1045

>WP_000009320.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGE
VVDMAAYERWRQEQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60128..86565

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JJB81_RS23485 (JJB81_23480) 55284..57281 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
JJB81_RS23490 (JJB81_23485) 57321..57755 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
JJB81_RS23495 (JJB81_23490) 57752..58489 + 738 WP_000581933 plasmid SOS inhibition protein A -
JJB81_RS23960 58524..58652 + 129 WP_000372429 hypothetical protein -
JJB81_RS23500 (JJB81_23495) 58738..58896 + 159 WP_001704449 hypothetical protein -
JJB81_RS23505 (JJB81_23500) 58999..59817 + 819 Protein_79 DUF932 domain-containing protein -
JJB81_RS23510 (JJB81_23505) 60128..60598 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
JJB81_RS23515 (JJB81_23510) 61013..61393 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
JJB81_RS23520 (JJB81_23515) 61586..62272 + 687 WP_000336297 PAS domain-containing protein -
JJB81_RS23525 (JJB81_23520) 62366..62593 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
JJB81_RS23530 (JJB81_23525) 62635..62997 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
JJB81_RS23535 (JJB81_23530) 63012..63323 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
JJB81_RS23540 (JJB81_23535) 63345..63911 + 567 WP_000399769 type IV conjugative transfer system protein TraE traE
JJB81_RS23545 (JJB81_23540) 63898..64638 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
JJB81_RS23550 (JJB81_23545) 64638..66059 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
JJB81_RS23555 (JJB81_23550) 66049..66645 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
JJB81_RS23560 (JJB81_23555) 66623..66868 + 246 WP_010999944 DUF2689 domain-containing protein virb4
JJB81_RS23565 (JJB81_23560) 66865..67380 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
JJB81_RS23570 (JJB81_23565) 67515..67736 + 222 WP_001278699 conjugal transfer protein TraR -
JJB81_RS23575 (JJB81_23570) 67729..68196 + 468 WP_000549562 hypothetical protein -
JJB81_RS23580 (JJB81_23575) 68313..68576 + 264 WP_001239256 hypothetical protein -
JJB81_RS23585 (JJB81_23580) 68592..71240 + 2649 WP_000793310 type IV secretion system protein TraC virb4
JJB81_RS23590 (JJB81_23585) 71215..71601 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
JJB81_RS23595 (JJB81_23590) 71598..72230 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
JJB81_RS23600 (JJB81_23595) 72227..73219 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
JJB81_RS23605 (JJB81_23600) 73238..73546 + 309 WP_010999945 hypothetical protein -
JJB81_RS23610 (JJB81_23605) 73531..74169 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
JJB81_RS23615 (JJB81_23610) 74206..74625 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
JJB81_RS23620 (JJB81_23615) 74622..76448 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JJB81_RS23625 (JJB81_23620) 76459..76674 + 216 WP_000700023 conjugal transfer protein TrbE -
JJB81_RS23630 (JJB81_23625) 76686..77435 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
JJB81_RS23635 (JJB81_23630) 77649..77942 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
JJB81_RS23640 (JJB81_23635) 77929..78477 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JJB81_RS23645 (JJB81_23640) 78467..79849 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
JJB81_RS23650 (JJB81_23645) 79846..82668 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
JJB81_RS23655 (JJB81_23650) 82684..83178 + 495 WP_010999946 entry exclusion protein -
JJB81_RS23660 (JJB81_23655) 83214..83945 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
JJB81_RS23665 (JJB81_23660) 84322..86565 + 2244 WP_000009320 type IV conjugative transfer system coupling protein TraD prgC
JJB81_RS23670 (JJB81_23665) 86574..86972 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
JJB81_RS23675 (JJB81_23670) 86972..87199 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   4476 GenBank   NZ_CP067398
Plasmid name   psLT Incompatibility group   IncFII
Plasmid size   93938 bp Coordinate of oriT [Strand]   60669..60938 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain LB5000

Cargo genes

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