Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113231
Name   oriT_pRM096_1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain RM096
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP117358 (50530..50799 [-], 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_pRM096_1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8490 GenBank   WP_000986921
Name   traI_PQQ15_RS23785_pRM096_1 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   4889 GenBank   WP_001676655
Name   WP_001676655_pRM096_1 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   4890 GenBank   WP_001151546
Name   WP_001151546_pRM096_1 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   9795 GenBank   WP_084568444
Name   traD_PQQ15_RS23800_pRM096_1 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: 81404.92 Da        Isoelectric Point: 5.1045

>WP_084568444.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQPTVV
SDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREE
GNINVHRGHGKDEPEPGDDF

  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.



ID   9796 GenBank   WP_274882989
Name   traC_PQQ15_RS23880_pRM096_1 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: 100400.23 Da        Isoelectric Point: 6.9316

>WP_274882989.1 type IV secretion system protein TraC [Salmonella enterica]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLRKFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESIHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVTNLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLMNQYT
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: 24985..51340

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PQQ15_RS23790 (PQQ15_23790) 24351..24578 + 228 WP_000450265 toxin-antitoxin system antitoxin VapB -
PQQ15_RS23795 (PQQ15_23795) 24578..24976 + 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
PQQ15_RS23800 (PQQ15_23800) 24985..27147 - 2163 WP_084568444 type IV conjugative transfer system coupling protein TraD virb4
PQQ15_RS23805 (PQQ15_23805) 27524..28255 - 732 WP_000782438 conjugal transfer complement resistance protein TraT -
PQQ15_RS23810 (PQQ15_23810) 28291..28785 - 495 WP_010999946 entry exclusion protein -
PQQ15_RS23815 (PQQ15_23815) 28801..31623 - 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
PQQ15_RS23820 (PQQ15_23820) 31620..33002 - 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
PQQ15_RS23825 (PQQ15_23825) 32992..33540 - 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
PQQ15_RS23830 (PQQ15_23830) 33527..33820 - 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
PQQ15_RS23835 (PQQ15_23835) 34034..34783 - 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
PQQ15_RS23840 (PQQ15_23840) 34795..35010 - 216 WP_000700023 conjugal transfer protein TrbE -
PQQ15_RS23845 (PQQ15_23845) 35021..36847 - 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
PQQ15_RS23850 (PQQ15_23850) 36844..37263 - 420 WP_001229397 HNH endonuclease -
PQQ15_RS23855 (PQQ15_23855) 37300..37938 - 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
PQQ15_RS23860 (PQQ15_23860) 37923..38230 - 308 Protein_41 hypothetical protein -
PQQ15_RS23865 (PQQ15_23865) 38249..39241 - 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
PQQ15_RS23870 (PQQ15_23870) 39238..39870 - 633 WP_000871995 type-F conjugative transfer system protein TraW traW
PQQ15_RS23875 (PQQ15_23875) 39867..40253 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
PQQ15_RS23880 (PQQ15_23880) 40228..42876 - 2649 WP_274882989 type IV secretion system protein TraC virb4
PQQ15_RS23885 (PQQ15_23885) 42892..43155 - 264 WP_001239255 hypothetical protein -
PQQ15_RS23890 (PQQ15_23890) 43272..43739 - 468 WP_000549562 hypothetical protein -
PQQ15_RS23895 (PQQ15_23895) 43732..43953 - 222 WP_001278699 conjugal transfer protein TraR -
PQQ15_RS23900 (PQQ15_23900) 44088..44603 - 516 WP_274882992 type IV conjugative transfer system lipoprotein TraV traV
PQQ15_RS23905 (PQQ15_23905) 44600..44845 - 246 WP_010999944 DUF2689 domain-containing protein virb4
PQQ15_RS23910 (PQQ15_23910) 44823..45419 - 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
PQQ15_RS23915 (PQQ15_23915) 45409..46830 - 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
PQQ15_RS23920 (PQQ15_23920) 46830..47570 - 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
PQQ15_RS23925 (PQQ15_23925) 47557..48123 - 567 WP_000399768 type IV conjugative transfer system protein TraE traE
PQQ15_RS23930 (PQQ15_23930) 48145..48456 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
PQQ15_RS23935 (PQQ15_23935) 48471..48833 - 363 WP_001274201 type IV conjugative transfer system pilin TraA -
PQQ15_RS23940 (PQQ15_23940) 48875..49102 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
PQQ15_RS23945 (PQQ15_23945) 49196..49882 - 687 WP_000336297 PAS domain-containing protein -
PQQ15_RS23950 (PQQ15_23950) 50075..50455 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
PQQ15_RS23955 (PQQ15_23955) 50870..51340 + 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
PQQ15_RS23960 (PQQ15_23960) 51651..52469 - 819 Protein_61 DUF932 domain-containing protein -
PQQ15_RS23965 (PQQ15_23965) 52572..52730 - 159 WP_001704449 hypothetical protein -
PQQ15_RS23970 (PQQ15_23970) 52816..52944 - 129 WP_000372429 hypothetical protein -
PQQ15_RS23975 (PQQ15_23975) 52979..53716 - 738 WP_000581933 plasmid SOS inhibition protein A -
PQQ15_RS23980 (PQQ15_23980) 53713..54147 - 435 WP_010999943 conjugation system SOS inhibitor PsiB -
PQQ15_RS23985 (PQQ15_23985) 54187..56184 - 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -

Host bacterium

ID   13666 GenBank   NZ_CP117358
Plasmid name   pRM096_1 Incompatibility group   IncFIB
Plasmid size   93864 bp Coordinate of oriT [Strand]   50530..50799 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain RM096

Cargo genes

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