Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104032
Name   oriT_ER3625|pSLT in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain ER3625
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP067092 (60670..60939 [+], 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_ER3625|pSLT
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2988 GenBank   WP_000986921
Name   traI_JJB80_RS23705_ER3625|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   1257 GenBank   WP_001151546
Name   WP_001151546_ER3625|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   1258 GenBank   WP_001676655
Name   WP_001676655_ER3625|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   2852 GenBank   WP_000793310
Name   traC_JJB80_RS23610_ER3625|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   2853 GenBank   WP_000009320
Name   traD_JJB80_RS23690_ER3625|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: 60129..86566

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JJB80_RS23510 (JJB80_23505) 55285..57282 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
JJB80_RS23515 (JJB80_23510) 57322..57756 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
JJB80_RS23520 (JJB80_23515) 57753..58490 + 738 WP_000581933 plasmid SOS inhibition protein A -
JJB80_RS23985 58525..58653 + 129 WP_000372429 hypothetical protein -
JJB80_RS23525 (JJB80_23520) 58739..58897 + 159 WP_001704449 hypothetical protein -
JJB80_RS23530 (JJB80_23525) 59000..59818 + 819 Protein_79 DUF932 domain-containing protein -
JJB80_RS23535 (JJB80_23530) 60129..60599 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
JJB80_RS23540 (JJB80_23535) 61014..61394 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
JJB80_RS23545 (JJB80_23540) 61587..62273 + 687 WP_000336297 PAS domain-containing protein -
JJB80_RS23550 (JJB80_23545) 62367..62594 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
JJB80_RS23555 (JJB80_23550) 62636..62998 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
JJB80_RS23560 (JJB80_23555) 63013..63324 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
JJB80_RS23565 (JJB80_23560) 63346..63912 + 567 WP_000399769 type IV conjugative transfer system protein TraE traE
JJB80_RS23570 (JJB80_23565) 63899..64639 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
JJB80_RS23575 (JJB80_23570) 64639..66060 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
JJB80_RS23580 (JJB80_23575) 66050..66646 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
JJB80_RS23585 (JJB80_23580) 66624..66869 + 246 WP_010999944 DUF2689 domain-containing protein virb4
JJB80_RS23590 (JJB80_23585) 66866..67381 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
JJB80_RS23595 (JJB80_23590) 67516..67737 + 222 WP_001278699 conjugal transfer protein TraR -
JJB80_RS23600 (JJB80_23595) 67730..68197 + 468 WP_000549562 hypothetical protein -
JJB80_RS23605 (JJB80_23600) 68314..68577 + 264 WP_001239256 hypothetical protein -
JJB80_RS23610 (JJB80_23605) 68593..71241 + 2649 WP_000793310 type IV secretion system protein TraC virb4
JJB80_RS23615 (JJB80_23610) 71216..71602 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
JJB80_RS23620 (JJB80_23615) 71599..72231 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
JJB80_RS23625 (JJB80_23620) 72228..73220 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
JJB80_RS23630 (JJB80_23625) 73239..73547 + 309 WP_010999945 hypothetical protein -
JJB80_RS23635 (JJB80_23630) 73532..74170 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
JJB80_RS23640 (JJB80_23635) 74207..74626 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
JJB80_RS23645 (JJB80_23640) 74623..76449 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JJB80_RS23650 (JJB80_23645) 76460..76675 + 216 WP_000700023 conjugal transfer protein TrbE -
JJB80_RS23655 (JJB80_23650) 76687..77436 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
JJB80_RS23660 (JJB80_23655) 77650..77943 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
JJB80_RS23665 (JJB80_23660) 77930..78478 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JJB80_RS23670 (JJB80_23665) 78468..79850 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
JJB80_RS23675 (JJB80_23670) 79847..82669 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
JJB80_RS23680 (JJB80_23675) 82685..83179 + 495 WP_010999946 entry exclusion protein -
JJB80_RS23685 (JJB80_23680) 83215..83946 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
JJB80_RS23690 (JJB80_23685) 84323..86566 + 2244 WP_000009320 type IV conjugative transfer system coupling protein TraD prgC
JJB80_RS23695 (JJB80_23690) 86575..86973 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
JJB80_RS23700 (JJB80_23695) 86973..87200 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   4471 GenBank   NZ_CP067092
Plasmid name   ER3625|pSLT Incompatibility group   IncFII
Plasmid size   93939 bp Coordinate of oriT [Strand]   60670..60939 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain ER3625

Cargo genes

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