Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106336
Name   oriT_NCCP16345|unnamed in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain NCCP16345
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP068697 (2873..3142 [+], 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_NCCP16345|unnamed
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4237 GenBank   WP_000986921
Name   traI_JKV46_RS24145_NCCP16345|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   1887 GenBank   WP_235176211
Name   WP_235176211_NCCP16345|unnamed insolico UniProt ID   _
Length   126 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 126 a.a.        Molecular weight: 14408.38 Da        Isoelectric Point: 5.7236

>WP_235176211.1 conjugal transfer relaxosome DNA-binding protein TraM [Salmonella enterica]
MAKVNVYISNEVHNKITAIVEKRRQEVARDKDISFSGTSSMLLELGLRVYEAQMERKESPFNQTEFNKVL
LENVLKTQSSVAKILGIGSLSPHVAGNPKFEYANMVEDIKEKVSSEMERFFHENEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   1888 GenBank   WP_001676655
Name   WP_001676655_NCCP16345|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


T4CP

ID   4258 GenBank   WP_235176212
Name   traC_JKV46_RS24050_NCCP16345|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: 100363.15 Da        Isoelectric Point: 6.8524

>WP_235176212.1 type IV secretion system protein TraC [Salmonella enterica]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLRKFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESIHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCHDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVTNLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(468-763)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.



ID   4259 GenBank   WP_000009318
Name   traD_JKV46_RS24130_NCCP16345|unnamed 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: 2332..28688

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JKV46_RS24580 728..856 + 129 WP_000372429 hypothetical protein -
JKV46_RS23965 (JKV46_23840) 942..1100 + 159 WP_001704449 hypothetical protein -
JKV46_RS23970 (JKV46_23845) 1203..2021 + 819 Protein_3 DUF932 domain-containing protein -
JKV46_RS23975 (JKV46_23850) 2332..2802 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
JKV46_RS23980 (JKV46_23855) 3217..3597 + 381 WP_235176211 conjugal transfer relaxosome DNA-binding protein TraM -
JKV46_RS23985 (JKV46_23860) 3790..4476 + 687 WP_000336297 PAS domain-containing protein -
JKV46_RS23990 (JKV46_23865) 4570..4797 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
JKV46_RS23995 (JKV46_23870) 4839..5201 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
JKV46_RS24000 (JKV46_23875) 5216..5527 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
JKV46_RS24005 (JKV46_23880) 5549..6115 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
JKV46_RS24010 (JKV46_23885) 6102..6842 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
JKV46_RS24015 (JKV46_23890) 6842..8263 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
JKV46_RS24020 (JKV46_23895) 8253..8849 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
JKV46_RS24025 (JKV46_23900) 8827..9072 + 246 WP_010999944 DUF2689 domain-containing protein virb4
JKV46_RS24030 (JKV46_23905) 9069..9584 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
JKV46_RS24035 (JKV46_23910) 9719..9940 + 222 WP_001278699 conjugal transfer protein TraR -
JKV46_RS24040 (JKV46_23915) 9933..10400 + 468 WP_000549562 hypothetical protein -
JKV46_RS24045 (JKV46_23920) 10517..10780 + 264 WP_001239255 hypothetical protein -
JKV46_RS24050 (JKV46_23925) 10796..13444 + 2649 WP_235176212 type IV secretion system protein TraC virb4
JKV46_RS24055 (JKV46_23930) 13419..13805 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
JKV46_RS24060 (JKV46_23935) 13802..14434 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
JKV46_RS24065 (JKV46_23940) 14431..15423 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
JKV46_RS24070 (JKV46_23945) 15442..15750 + 309 WP_010999945 hypothetical protein -
JKV46_RS24075 (JKV46_23950) 15735..16373 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
JKV46_RS24080 (JKV46_23955) 16410..16829 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
JKV46_RS24085 (JKV46_23960) 16826..18652 + 1827 WP_146471649 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JKV46_RS24090 (JKV46_23965) 18663..18878 + 216 WP_000700023 conjugal transfer protein TrbE -
JKV46_RS24095 (JKV46_23970) 18890..19639 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
JKV46_RS24100 (JKV46_23975) 19853..20146 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
JKV46_RS24105 (JKV46_23980) 20133..20681 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JKV46_RS24110 (JKV46_23985) 20671..22053 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
JKV46_RS24115 (JKV46_23990) 22050..24872 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
JKV46_RS24120 (JKV46_23995) 24888..25382 + 495 WP_010999946 entry exclusion protein -
JKV46_RS24125 (JKV46_24000) 25418..26149 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
JKV46_RS24130 (JKV46_24005) 26526..28688 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
JKV46_RS24135 (JKV46_24010) 28697..29095 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
JKV46_RS24140 (JKV46_24015) 29095..29322 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   6773 GenBank   NZ_CP068697
Plasmid name   NCCP16345|unnamed Incompatibility group   IncFII
Plasmid size   93874 bp Coordinate of oriT [Strand]   2873..3142 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain NCCP16345

Cargo genes

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