Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106917
Name   oriT_PartC-Senterica-RM8376|unnamed in_silico
Organism   Salmonella enterica subsp. enterica strain PartC-Senterica-RM8376
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP064386 (69210..69479 [-], 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_PartC-Senterica-RM8376|unnamed
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4574 GenBank   WP_000986921
Name   traI_IUJ38_RS23795_PartC-Senterica-RM8376|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   2062 GenBank   WP_001676655
Name   WP_001676655_PartC-Senterica-RM8376|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   2063 GenBank   WP_001151546
Name   WP_001151546_PartC-Senterica-RM8376|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   4661 GenBank   WP_000009320
Name   traD_IUJ38_RS23810_PartC-Senterica-RM8376|unnamed 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.



ID   4662 GenBank   WP_000793310
Name   traC_IUJ38_RS23890_PartC-Senterica-RM8376|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: 43583..70020

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IUJ38_RS23800 (IUJ38_23700) 42949..43176 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
IUJ38_RS23805 (IUJ38_23705) 43176..43574 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
IUJ38_RS23810 (IUJ38_23710) 43583..45826 - 2244 WP_000009320 type IV conjugative transfer system coupling protein TraD prgC
IUJ38_RS23815 (IUJ38_23715) 46203..46934 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
IUJ38_RS23820 (IUJ38_23720) 46970..47464 - 495 WP_010999946 entry exclusion protein -
IUJ38_RS23825 (IUJ38_23725) 47480..50302 - 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
IUJ38_RS23830 (IUJ38_23730) 50299..51681 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
IUJ38_RS23835 (IUJ38_23735) 51671..52219 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IUJ38_RS23840 (IUJ38_23740) 52206..52499 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
IUJ38_RS23845 (IUJ38_23745) 52713..53462 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
IUJ38_RS23850 (IUJ38_23750) 53474..53689 - 216 WP_000700023 conjugal transfer protein TrbE -
IUJ38_RS23855 (IUJ38_23755) 53700..55526 - 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IUJ38_RS23860 (IUJ38_23760) 55523..55942 - 420 WP_001229397 HNH endonuclease signature motif containing protein -
IUJ38_RS23865 (IUJ38_23765) 55979..56617 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
IUJ38_RS23870 (IUJ38_23770) 56602..56910 - 309 WP_010999945 hypothetical protein -
IUJ38_RS23875 (IUJ38_23775) 56929..57921 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
IUJ38_RS23880 (IUJ38_23780) 57918..58550 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
IUJ38_RS23885 (IUJ38_23785) 58547..58933 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
IUJ38_RS23890 (IUJ38_23790) 58908..61556 - 2649 WP_000793310 type IV secretion system protein TraC virb4
IUJ38_RS23895 (IUJ38_23795) 61572..61835 - 264 WP_001239256 hypothetical protein -
IUJ38_RS23900 (IUJ38_23800) 61952..62419 - 468 WP_000549562 hypothetical protein -
IUJ38_RS23905 (IUJ38_23805) 62412..62633 - 222 WP_001278699 conjugal transfer protein TraR -
IUJ38_RS23910 (IUJ38_23810) 62768..63283 - 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
IUJ38_RS23915 (IUJ38_23815) 63280..63525 - 246 WP_010999944 DUF2689 domain-containing protein virb4
IUJ38_RS23920 (IUJ38_23820) 63503..64099 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
IUJ38_RS23925 (IUJ38_23825) 64089..65510 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
IUJ38_RS23930 (IUJ38_23830) 65510..66250 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
IUJ38_RS23935 (IUJ38_23835) 66237..66803 - 567 WP_000399769 type IV conjugative transfer system protein TraE traE
IUJ38_RS23940 (IUJ38_23840) 66825..67136 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
IUJ38_RS23945 (IUJ38_23845) 67151..67513 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
IUJ38_RS23950 (IUJ38_23850) 67555..67782 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
IUJ38_RS23955 (IUJ38_23855) 67876..68562 - 687 WP_000336297 PAS domain-containing protein -
IUJ38_RS23960 (IUJ38_23860) 68755..69135 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
IUJ38_RS23965 (IUJ38_23865) 69550..70020 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
IUJ38_RS23970 (IUJ38_23870) 70543..71149 - 607 Protein_86 DUF932 domain-containing protein -
IUJ38_RS23975 (IUJ38_23875) 71252..71410 - 159 WP_001704449 hypothetical protein -
IUJ38_RS24170 71496..71624 - 129 WP_000372429 hypothetical protein -
IUJ38_RS23980 (IUJ38_23880) 71659..72396 - 738 WP_000581933 plasmid SOS inhibition protein A -
IUJ38_RS23985 (IUJ38_23885) 72393..72827 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
IUJ38_RS23990 (IUJ38_23890) 72867..74864 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   7354 GenBank   NZ_CP064386
Plasmid name   PartC-Senterica-RM8376|unnamed Incompatibility group   IncFIB
Plasmid size   93933 bp Coordinate of oriT [Strand]   69210..69479 [-]
Host baterium   Salmonella enterica subsp. enterica strain PartC-Senterica-RM8376

Cargo genes

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