Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111546
Name   oriT_pATCC14028 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP034231 (9725..9994 [+], 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_pATCC14028
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7500 GenBank   WP_000986921
Name   traI_EIL76_RS24650_pATCC14028 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   4131 GenBank   WP_001151546
Name   WP_001151546_pATCC14028 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   4132 GenBank   WP_001676655
Name   WP_001676655_pATCC14028 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   8541 GenBank   WP_000793310
Name   traC_EIL76_RS24555_pATCC14028 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   8542 GenBank   WP_000009318
Name   traD_EIL76_RS24635_pATCC14028 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9184..35540

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EIL76_RS24455 (EIL76_24455) 4340..6337 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
EIL76_RS24460 (EIL76_24460) 6377..6811 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
EIL76_RS24465 (EIL76_24465) 6808..7545 + 738 WP_000581933 plasmid SOS inhibition protein A -
EIL76_RS25390 7580..7708 + 129 WP_000372429 hypothetical protein -
EIL76_RS25090 7794..7952 + 159 WP_001704449 hypothetical protein -
EIL76_RS24470 (EIL76_24470) 8055..8873 + 819 Protein_11 DUF932 domain-containing protein -
EIL76_RS24475 (EIL76_24475) 9184..9654 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
EIL76_RS24485 (EIL76_24485) 10069..10449 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
EIL76_RS24490 (EIL76_24490) 10642..11328 + 687 WP_000336297 PAS domain-containing protein -
EIL76_RS24495 (EIL76_24495) 11422..11649 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
EIL76_RS24500 (EIL76_24500) 11691..12053 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
EIL76_RS24505 (EIL76_24505) 12068..12379 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
EIL76_RS24510 (EIL76_24510) 12401..12967 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
EIL76_RS24515 (EIL76_24515) 12954..13694 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
EIL76_RS24520 (EIL76_24520) 13694..15115 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
EIL76_RS24525 (EIL76_24525) 15105..15701 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
EIL76_RS24530 (EIL76_24530) 15679..15924 + 246 WP_010999944 DUF2689 domain-containing protein virb4
EIL76_RS24535 (EIL76_24535) 15921..16436 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
EIL76_RS24540 (EIL76_24540) 16571..16792 + 222 WP_001278699 conjugal transfer protein TraR -
EIL76_RS24545 (EIL76_24545) 16785..17252 + 468 WP_000549562 hypothetical protein -
EIL76_RS24550 (EIL76_24550) 17369..17632 + 264 WP_001239255 hypothetical protein -
EIL76_RS24555 (EIL76_24555) 17648..20296 + 2649 WP_000793310 type IV secretion system protein TraC virb4
EIL76_RS24560 (EIL76_24560) 20271..20657 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
EIL76_RS24565 (EIL76_24565) 20654..21286 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
EIL76_RS24570 (EIL76_24570) 21283..22275 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
EIL76_RS24575 (EIL76_24575) 22294..22602 + 309 WP_010999945 hypothetical protein -
EIL76_RS24580 (EIL76_24580) 22587..23225 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
EIL76_RS24585 (EIL76_24585) 23262..23681 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
EIL76_RS24590 (EIL76_24590) 23678..25504 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
EIL76_RS24595 (EIL76_24595) 25515..25730 + 216 WP_000700023 conjugal transfer protein TrbE -
EIL76_RS24600 (EIL76_24600) 25742..26491 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
EIL76_RS24605 (EIL76_24605) 26705..26998 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
EIL76_RS24610 (EIL76_24610) 26985..27533 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
EIL76_RS24615 (EIL76_24615) 27523..28905 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
EIL76_RS24620 (EIL76_24620) 28902..31724 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
EIL76_RS24625 (EIL76_24625) 31740..32234 + 495 WP_010999946 entry exclusion protein -
EIL76_RS24630 (EIL76_24630) 32270..33001 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
EIL76_RS24635 (EIL76_24635) 33378..35540 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
EIL76_RS24640 (EIL76_24640) 35549..35947 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
EIL76_RS24645 (EIL76_24645) 35947..36174 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   11981 GenBank   NZ_CP034231
Plasmid name   pATCC14028 Incompatibility group   IncFII
Plasmid size   95924 bp Coordinate of oriT [Strand]   9725..9994 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -