Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104027
Name   oriT_C_cip|pSLT in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain C_cip
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP074099 (60664..60933 [+], 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_C_cip|pSLT
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2983 GenBank   WP_000986921
Name   traI_KFV01_RS24010_C_cip|pSLT 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   1251 GenBank   WP_001151546
Name   WP_001151546_C_cip|pSLT 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   1252 GenBank   WP_001676655
Name   WP_001676655_C_cip|pSLT 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   2844 GenBank   WP_000793310
Name   traC_KFV01_RS23915_C_cip|pSLT 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   2845 GenBank   WP_000009320
Name   traD_KFV01_RS23995_C_cip|pSLT 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60123..86560

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KFV01_RS23815 (KFV01_23820) 55279..57276 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
KFV01_RS23820 (KFV01_23825) 57316..57750 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
KFV01_RS23825 (KFV01_23830) 57747..58484 + 738 WP_000581933 plasmid SOS inhibition protein A -
KFV01_RS24290 58519..58647 + 129 WP_000372429 hypothetical protein -
KFV01_RS23830 (KFV01_23835) 58733..58891 + 159 WP_001704449 hypothetical protein -
KFV01_RS23835 (KFV01_23840) 58994..59812 + 819 Protein_79 DUF932 domain-containing protein -
KFV01_RS23840 (KFV01_23845) 60123..60593 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
KFV01_RS23845 (KFV01_23850) 61008..61388 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
KFV01_RS23850 (KFV01_23855) 61581..62267 + 687 WP_000336297 PAS domain-containing protein -
KFV01_RS23855 (KFV01_23860) 62361..62588 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
KFV01_RS23860 (KFV01_23865) 62630..62992 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
KFV01_RS23865 (KFV01_23870) 63007..63318 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
KFV01_RS23870 (KFV01_23875) 63340..63906 + 567 WP_000399769 type IV conjugative transfer system protein TraE traE
KFV01_RS23875 (KFV01_23880) 63893..64633 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
KFV01_RS23880 (KFV01_23885) 64633..66054 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
KFV01_RS23885 (KFV01_23890) 66044..66640 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
KFV01_RS23890 (KFV01_23895) 66618..66863 + 246 WP_010999944 DUF2689 domain-containing protein virb4
KFV01_RS23895 (KFV01_23900) 66860..67375 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
KFV01_RS23900 (KFV01_23905) 67510..67731 + 222 WP_001278699 conjugal transfer protein TraR -
KFV01_RS23905 (KFV01_23910) 67724..68191 + 468 WP_000549562 hypothetical protein -
KFV01_RS23910 (KFV01_23915) 68308..68571 + 264 WP_001239256 hypothetical protein -
KFV01_RS23915 (KFV01_23920) 68587..71235 + 2649 WP_000793310 type IV secretion system protein TraC virb4
KFV01_RS23920 (KFV01_23925) 71210..71596 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
KFV01_RS23925 (KFV01_23930) 71593..72225 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
KFV01_RS23930 (KFV01_23935) 72222..73214 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
KFV01_RS23935 (KFV01_23940) 73233..73541 + 309 WP_010999945 hypothetical protein -
KFV01_RS23940 (KFV01_23945) 73526..74164 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
KFV01_RS23945 (KFV01_23950) 74201..74620 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
KFV01_RS23950 (KFV01_23955) 74617..76443 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KFV01_RS23955 (KFV01_23960) 76454..76669 + 216 WP_000700023 conjugal transfer protein TrbE -
KFV01_RS23960 (KFV01_23965) 76681..77430 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
KFV01_RS23965 (KFV01_23970) 77644..77937 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
KFV01_RS23970 (KFV01_23975) 77924..78472 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KFV01_RS23975 (KFV01_23980) 78462..79844 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
KFV01_RS23980 (KFV01_23985) 79841..82663 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
KFV01_RS23985 (KFV01_23990) 82679..83173 + 495 WP_010999946 entry exclusion protein -
KFV01_RS23990 (KFV01_23995) 83209..83940 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
KFV01_RS23995 (KFV01_24000) 84317..86560 + 2244 WP_000009320 type IV conjugative transfer system coupling protein TraD prgC
KFV01_RS24000 (KFV01_24005) 86569..86967 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
KFV01_RS24005 (KFV01_24010) 86967..87194 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   4466 GenBank   NZ_CP074099
Plasmid name   C_cip|pSLT Incompatibility group   IncFII
Plasmid size   93933 bp Coordinate of oriT [Strand]   60664..60933 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain C_cip

Cargo genes

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