Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105961
Name   oriT_pPIR00538 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain PIR00538
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP025556 (8032..8301 [+], 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_pPIR00538
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4016 GenBank   WP_000986921
Name   traI_C0Z08_RS25260_pPIR00538 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   1773 GenBank   WP_001151546
Name   WP_001151546_pPIR00538 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   1774 GenBank   WP_001676655
Name   WP_001676655_pPIR00538 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   4024 GenBank   WP_000793310
Name   traC_C0Z08_RS25165_pPIR00538 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   4025 GenBank   WP_000009318
Name   traD_C0Z08_RS25245_pPIR00538 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: 7491..33847

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C0Z08_RS25065 (C0Z08_25040) 2647..4644 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
C0Z08_RS25070 (C0Z08_25045) 4684..5118 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
C0Z08_RS25075 (C0Z08_25050) 5115..5852 + 738 WP_000581933 plasmid SOS inhibition protein A -
C0Z08_RS26035 5887..6015 + 129 WP_000372429 hypothetical protein -
C0Z08_RS25760 6101..6259 + 159 WP_001704449 hypothetical protein -
C0Z08_RS25765 (C0Z08_25055) 6362..7180 + 819 Protein_10 DUF932 domain-containing protein -
C0Z08_RS25085 (C0Z08_25060) 7491..7961 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
C0Z08_RS25095 (C0Z08_25070) 8376..8756 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
C0Z08_RS25100 (C0Z08_25075) 8949..9635 + 687 WP_000336297 PAS domain-containing protein -
C0Z08_RS25105 (C0Z08_25080) 9729..9956 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
C0Z08_RS25110 (C0Z08_25085) 9998..10360 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
C0Z08_RS25115 (C0Z08_25090) 10375..10686 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
C0Z08_RS25120 (C0Z08_25095) 10708..11274 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
C0Z08_RS25125 (C0Z08_25100) 11261..12001 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
C0Z08_RS25130 (C0Z08_25105) 12001..13422 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
C0Z08_RS25135 (C0Z08_25110) 13412..14008 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
C0Z08_RS25140 (C0Z08_25115) 13986..14231 + 246 WP_010999944 DUF2689 domain-containing protein virb4
C0Z08_RS25145 (C0Z08_25120) 14228..14743 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
C0Z08_RS25150 (C0Z08_25125) 14878..15099 + 222 WP_001278699 conjugal transfer protein TraR -
C0Z08_RS25155 (C0Z08_25130) 15092..15559 + 468 WP_000549562 hypothetical protein -
C0Z08_RS25160 (C0Z08_25135) 15676..15939 + 264 WP_001239255 hypothetical protein -
C0Z08_RS25165 (C0Z08_25140) 15955..18603 + 2649 WP_000793310 type IV secretion system protein TraC virb4
C0Z08_RS25170 (C0Z08_25145) 18578..18964 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
C0Z08_RS25175 (C0Z08_25150) 18961..19593 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
C0Z08_RS25180 (C0Z08_25155) 19590..20582 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
C0Z08_RS25185 (C0Z08_25160) 20601..20909 + 309 WP_010999945 hypothetical protein -
C0Z08_RS25190 (C0Z08_25165) 20894..21532 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
C0Z08_RS25195 (C0Z08_25170) 21569..21988 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
C0Z08_RS25200 (C0Z08_25175) 21985..23811 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
C0Z08_RS25205 (C0Z08_25180) 23822..24037 + 216 WP_000700023 conjugal transfer protein TrbE -
C0Z08_RS25210 (C0Z08_25185) 24049..24798 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
C0Z08_RS25215 (C0Z08_25190) 25012..25305 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
C0Z08_RS25220 (C0Z08_25195) 25292..25840 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
C0Z08_RS25225 (C0Z08_25200) 25830..27212 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
C0Z08_RS25230 (C0Z08_25205) 27209..30031 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
C0Z08_RS25235 (C0Z08_25210) 30047..30541 + 495 WP_010999946 entry exclusion protein -
C0Z08_RS25240 (C0Z08_25215) 30577..31308 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
C0Z08_RS25245 (C0Z08_25220) 31685..33847 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
C0Z08_RS25250 (C0Z08_25225) 33856..34254 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
C0Z08_RS25255 (C0Z08_25230) 34254..34481 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   6398 GenBank   NZ_CP025556
Plasmid name   pPIR00538 Incompatibility group   IncFII
Plasmid size   93832 bp Coordinate of oriT [Strand]   8032..8301 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain PIR00538

Cargo genes

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