Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104024
Name   oriT_ATCC 14028|unnamed in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP043905 (65524..65793 [-], 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_ATCC 14028|unnamed
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2982 GenBank   WP_000986921
Name   traI_F1727_RS00235_ATCC 14028|unnamed 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   1249 GenBank   WP_001676655
Name   WP_001676655_ATCC 14028|unnamed 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   1250 GenBank   WP_001151546
Name   WP_001151546_ATCC 14028|unnamed 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   2843 GenBank   WP_000793310
Name   traC_F1727_RS00330_ATCC 14028|unnamed 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: 43794..66334

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
F1727_RS00240 (F1727_00255) 39345..39572 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
F1727_RS00245 (F1727_00260) 39572..39970 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
F1727_RS00250 (F1727_00265) 39979..42140 - 2162 Protein_51 type IV conjugative transfer system coupling protein TraD -
F1727_RS00255 (F1727_00270) 42517..43248 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
F1727_RS00260 (F1727_00275) 43284..43778 - 495 WP_010999946 entry exclusion protein -
F1727_RS00265 (F1727_00280) 43794..46616 - 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
F1727_RS00270 (F1727_00285) 46613..47995 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
F1727_RS00275 (F1727_00290) 47985..48533 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
F1727_RS00280 (F1727_00295) 48520..48813 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
F1727_RS00285 (F1727_00300) 49027..49776 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
F1727_RS00290 (F1727_00305) 49788..50003 - 216 WP_000700023 conjugal transfer protein TrbE -
F1727_RS00295 (F1727_00310) 50014..51840 - 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
F1727_RS00300 (F1727_00315) 51837..52256 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
F1727_RS00305 (F1727_00320) 52293..52931 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
F1727_RS00310 (F1727_00325) 52916..53224 - 309 WP_010999945 hypothetical protein -
F1727_RS00315 (F1727_00330) 53243..54235 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
F1727_RS00320 (F1727_00335) 54232..54864 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
F1727_RS00325 (F1727_00340) 54861..55247 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
F1727_RS00330 (F1727_00345) 55222..57870 - 2649 WP_000793310 type IV secretion system protein TraC virb4
F1727_RS00335 (F1727_00350) 57886..58149 - 264 WP_001239255 hypothetical protein -
F1727_RS00340 (F1727_00355) 58266..58733 - 468 WP_000549562 hypothetical protein -
F1727_RS00345 (F1727_00360) 58726..58947 - 222 WP_001278699 conjugal transfer protein TraR -
F1727_RS00350 (F1727_00365) 59082..59597 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
F1727_RS00355 (F1727_00370) 59594..59839 - 246 WP_010999944 DUF2689 domain-containing protein virb4
F1727_RS00360 (F1727_00375) 59817..60413 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
F1727_RS00365 (F1727_00380) 60403..61824 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
F1727_RS00370 (F1727_00385) 61824..62564 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
F1727_RS00375 (F1727_00390) 62551..63117 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
F1727_RS00380 (F1727_00395) 63139..63450 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
F1727_RS00385 (F1727_00400) 63465..63827 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
F1727_RS00390 (F1727_00405) 63869..64096 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
F1727_RS00395 (F1727_00410) 64190..64876 - 687 WP_000336297 PAS domain-containing protein -
F1727_RS00400 (F1727_00415) 65069..65449 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
F1727_RS00405 (F1727_00425) 65864..66334 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
F1727_RS00410 66645..67463 - 819 Protein_83 DUF932 domain-containing protein -
F1727_RS00415 67566..67724 - 159 WP_001704449 hypothetical protein -
F1727_RS24655 67810..67938 - 129 WP_000372429 hypothetical protein -
F1727_RS00420 (F1727_00440) 67973..68710 - 738 WP_000581933 plasmid SOS inhibition protein A -
F1727_RS00425 (F1727_00445) 68707..69141 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
F1727_RS00430 (F1727_00450) 69181..71178 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   4464 GenBank   NZ_CP043905
Plasmid name   ATCC 14028|unnamed Incompatibility group   IncFIB
Plasmid size   93830 bp Coordinate of oriT [Strand]   65524..65793 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028

Cargo genes

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