Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116787
Name   oriT_A39|unnamed1 in_silico
Organism   Salmonella sp. A39
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084195 (80197..80466 [-], 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_A39|unnamed1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10710 GenBank   WP_000986921
Name   traI_LDO68_RS24190_A39|unnamed1 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   6303 GenBank   WP_001676655
Name   WP_001676655_A39|unnamed1 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   6304 GenBank   WP_001151546
Name   WP_001151546_A39|unnamed1 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   12508 GenBank   WP_000009318
Name   traD_LDO68_RS24205_A39|unnamed1 insolico UniProt ID   _
Length   720 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 720 a.a.        Molecular weight: 81447.01 Da        Isoelectric Point: 5.1045

>WP_000009318.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Salmonella]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQPTVV
SDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREE
VNINVHRGHGKDEPEPGDDF

  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   12509 GenBank   WP_080247908
Name   traC_LDO68_RS24285_A39|unnamed1 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: 100329.15 Da        Isoelectric Point: 6.8164

>WP_080247908.1 MULTISPECIES: type IV secretion system protein TraC [Salmonella]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLRKFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESIHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVTNLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWC
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(468-763)

TraC protein (TraC_F_IV)

(38-276)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 54650..81007

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDO68_RS24195 54016..54243 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
LDO68_RS24200 54243..54641 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
LDO68_RS24205 54650..56812 - 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
LDO68_RS24210 57189..57920 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
LDO68_RS24215 57956..58450 - 495 WP_010999946 entry exclusion protein -
LDO68_RS24220 58466..61288 - 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
LDO68_RS24225 61285..62667 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
LDO68_RS24230 62657..63205 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LDO68_RS24235 63192..63485 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
LDO68_RS24240 63699..64448 - 750 WP_080247907 type-F conjugative transfer system pilin assembly protein TraF traF
LDO68_RS24245 64460..64675 - 216 WP_000700023 conjugal transfer protein TrbE -
LDO68_RS24250 64686..66513 - 1828 Protein_74 type-F conjugative transfer system mating-pair stabilization protein TraN -
LDO68_RS24255 66510..66929 - 420 WP_001229397 HNH endonuclease -
LDO68_RS24260 66966..67604 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
LDO68_RS24265 67589..67897 - 309 WP_010999945 hypothetical protein -
LDO68_RS24270 67916..68908 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
LDO68_RS24275 68905..69537 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
LDO68_RS24280 69534..69920 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
LDO68_RS24285 69895..72543 - 2649 WP_080247908 type IV secretion system protein TraC virb4
LDO68_RS24290 72559..72822 - 264 WP_001239255 hypothetical protein -
LDO68_RS24295 72939..73406 - 468 WP_000549562 hypothetical protein -
LDO68_RS24300 73399..73620 - 222 WP_001278699 conjugal transfer protein TraR -
LDO68_RS24305 73755..74270 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
LDO68_RS24310 74267..74512 - 246 WP_010999944 DUF2689 domain-containing protein virb4
LDO68_RS24315 74490..75086 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
LDO68_RS24320 75076..76497 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
LDO68_RS24325 76497..77237 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
LDO68_RS24330 77224..77790 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
LDO68_RS24335 77812..78123 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
LDO68_RS24340 78138..78500 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
LDO68_RS24345 78542..78769 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
LDO68_RS24350 78863..79549 - 687 WP_000336297 PAS domain-containing protein -
LDO68_RS24355 79742..80122 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
LDO68_RS24360 80537..81007 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
LDO68_RS24365 81318..82136 - 819 Protein_97 DUF932 domain-containing protein -
LDO68_RS24370 82239..82397 - 159 WP_001704449 hypothetical protein -
LDO68_RS24375 82646..83383 - 738 WP_080247910 plasmid SOS inhibition protein A -
LDO68_RS24380 83380..83814 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
LDO68_RS24385 83854..85851 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   17220 GenBank   NZ_CP084195
Plasmid name   A39|unnamed1 Incompatibility group   IncFIB
Plasmid size   93861 bp Coordinate of oriT [Strand]   80197..80466 [-]
Host baterium   Salmonella sp. A39

Cargo genes

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