Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103102
Name   oriT_p80-547 in_silico
Organism   Shigella dysenteriae strain 80-547
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT754160 (68008..68131 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 57..62, 70..75  (TGATTT..AAATCA)
 41..48, 61..68  (AAAAACAA..TTGTTTTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_p80-547
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTAAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2324 GenBank   WP_171265027
Name   traI_HPF59_RS00555_p80-547 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192245.06 Da        Isoelectric Point: 6.0277

>WP_171265027.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSASMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAVSVKAGEESVAQVSGVREQAMLTQTIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVFGGDRLQVSSVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMHSAGVDAQTLASFLHDT
QLQQRSGEIPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTEQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVNNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRLGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRMIRPAQERVEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVMAEVQAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRTAITEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   984 GenBank   WP_001541914
Name   WP_001541914_p80-547 insolico UniProt ID   A0A142CLH0
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14544.56 Da        Isoelectric Point: 5.0359

>WP_001541914.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A142CLH0

ID   985 GenBank   WP_001254386
Name   WP_001254386_p80-547 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   2048 GenBank   WP_001064245
Name   traC_HPF59_RS00470_p80-547 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.



ID   2049 GenBank   WP_000009363
Name   traD_HPF59_RS00550_p80-547 insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84259.95 Da        Isoelectric Point: 5.0504

>WP_000009363.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 67436..93086

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPF59_RS00760 62815..63591 + 777 WP_201799183 hypothetical protein -
HPF59_RS00365 64005..64430 + 426 WP_001198918 antirestriction protein -
HPF59_RS00370 64477..64899 + 423 WP_000271685 DUF1380 family protein -
HPF59_RS00375 64896..65083 + 188 Protein_77 hypothetical protein -
HPF59_RS00380 65053..65610 - 558 WP_201799181 hypothetical protein -
HPF59_RS00390 65913..66200 + 288 WP_171265023 hypothetical protein -
HPF59_RS00395 66319..67140 + 822 Protein_80 DUF932 domain-containing protein -
HPF59_RS00400 67436..68038 - 603 WP_326305067 transglycosylase SLT domain-containing protein -
HPF59_RS00405 68360..68743 + 384 WP_001541914 conjugal transfer relaxosome DNA-binding protein TraM -
HPF59_RS00410 68928..69614 + 687 WP_000332492 PAS domain-containing protein -
HPF59_RS00415 69708..69935 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HPF59_RS00420 69969..70334 + 366 WP_000340270 type IV conjugative transfer system pilin TraA -
HPF59_RS00425 70349..70660 + 312 WP_064221663 type IV conjugative transfer system protein TraL traL
HPF59_RS00430 70682..71248 + 567 WP_000399797 type IV conjugative transfer system protein TraE traE
HPF59_RS00435 71235..71963 + 729 WP_001230766 type-F conjugative transfer system secretin TraK traK
HPF59_RS00440 71963..73390 + 1428 WP_000146655 F-type conjugal transfer pilus assembly protein TraB traB
HPF59_RS00445 73380..73970 + 591 WP_001523507 conjugal transfer pilus-stabilizing protein TraP -
HPF59_RS00450 73957..74154 + 198 WP_001454499 conjugal transfer protein TrbD -
HPF59_RS00455 74166..74417 + 252 WP_001038342 conjugal transfer protein TrbG -
HPF59_RS00460 74414..74929 + 516 WP_171265024 type IV conjugative transfer system lipoprotein TraV traV
HPF59_RS00465 75064..75285 + 222 WP_001278689 conjugal transfer protein TraR -
HPF59_RS00470 75445..78072 + 2628 WP_001064245 type IV secretion system protein TraC virb4
HPF59_RS00475 78069..78455 + 387 WP_000099689 type-F conjugative transfer system protein TrbI -
HPF59_RS00480 78452..79084 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HPF59_RS00485 79081..80073 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HPF59_RS00490 80082..80720 + 639 WP_171265032 type-F conjugative transfer system pilin assembly protein TrbC trbC
HPF59_RS00495 80717..82525 + 1809 WP_171265025 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HPF59_RS00500 82552..82809 + 258 WP_000864325 conjugal transfer protein TrbE -
HPF59_RS00505 82802..83545 + 744 WP_001030376 type-F conjugative transfer system pilin assembly protein TraF traF
HPF59_RS00510 83561..83908 + 348 WP_025269861 conjugal transfer protein TrbA -
HPF59_RS00515 84027..84311 + 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HPF59_RS00520 84298..84843 + 546 WP_171265026 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HPF59_RS00525 84773..85135 + 363 WP_001443292 P-type conjugative transfer protein TrbJ -
HPF59_RS00530 85135..86508 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HPF59_RS00535 86505..89327 + 2823 WP_001007026 conjugal transfer mating-pair stabilization protein TraG traG
HPF59_RS00540 89342..89845 + 504 WP_061583830 surface exclusion protein -
HPF59_RS00545 89877..90608 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HPF59_RS00550 90861..93086 + 2226 WP_000009363 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3545 GenBank   NZ_KT754160
Plasmid name   p80-547 Incompatibility group   IncFIB
Plasmid size   129841 bp Coordinate of oriT [Strand]   68008..68131 [+]
Host baterium   Shigella dysenteriae strain 80-547

Cargo genes

Drug resistance gene   blaTEM-1B, sul1, qacE, ant(3'')-Ia, catA1, tet(B)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -