Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103075
Name   oriT_p3099-85 in_silico
Organism   Shigella dysenteriae
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT754164 (71656..71779 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      92..99, 113..120  (ATAATGTA..TACATTAT)
 90..95, 107..112  (AAATAA..TTATTT)
 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_p3099-85
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTACTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2302 GenBank   WP_171265033
Name   traI_HPF53_RS00235_p3099-85 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: 191678.40 Da        Isoelectric Point: 5.9040

>WP_171265033.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFPPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTEAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDEPRTAEKLARHPSFTVVSDQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSNGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGTSETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGRGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRTASSERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

AAA domain (AAA_30)

(968-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   960 GenBank   WP_001254388
Name   WP_001254388_p3099-85 insolico UniProt ID   W9A0Z2
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9072.20 Da        Isoelectric Point: 10.2071

>WP_001254388.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacterales]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB W9A0Z2

ID   961 GenBank   WP_001151566
Name   WP_001151566_p3099-85 insolico UniProt ID   A0A142CMX1
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14476.46 Da        Isoelectric Point: 4.8498

>WP_001151566.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYETQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPENDEG

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A142CMX1


T4CP

ID   2017 GenBank   WP_021547900
Name   traD_HPF53_RS00240_p3099-85 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83494.17 Da        Isoelectric Point: 5.1657

>WP_021547900.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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   2018 GenBank   WP_001064258
Name   traC_HPF53_RS00345_p3099-85 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: 99195.72 Da        Isoelectric Point: 5.8689

>WP_001064258.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLKSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNYKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFQPLQRDMIGKFGAARDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
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)

(467-763)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42249..72351

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPF53_RS00240 42249..44456 - 2208 WP_021547900 type IV conjugative transfer system coupling protein TraD virb4
HPF53_RS00245 44453..45232 - 780 WP_000199914 hypothetical protein -
HPF53_RS00250 45435..46148 - 714 WP_033550797 conjugal transfer complement resistance protein TraT -
HPF53_RS00255 46197..46694 - 498 WP_000605862 entry exclusion protein -
HPF53_RS00260 46713..49532 - 2820 WP_171265034 conjugal transfer mating-pair stabilization protein TraG traG
HPF53_RS00265 49529..50902 - 1374 WP_000944328 conjugal transfer pilus assembly protein TraH traH
HPF53_RS00270 50889..51281 - 393 WP_000659962 F-type conjugal transfer protein TrbF -
HPF53_RS00275 51262..51609 - 348 WP_071571857 P-type conjugative transfer protein TrbJ -
HPF53_RS00280 51539..52084 - 546 WP_000059829 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HPF53_RS00285 52071..52355 - 285 WP_001617873 type-F conjugative transfer system pilin chaperone TraQ -
HPF53_RS00290 52482..52802 - 321 WP_001348757 conjugal transfer protein TrbA -
HPF53_RS00300 53702..54682 - 981 WP_000019450 IS5-like element ISKpn26 family transposase -
HPF53_RS00305 54812..55555 - 744 WP_001030401 type-F conjugative transfer system pilin assembly protein TraF traF
HPF53_RS00310 55548..55805 - 258 WP_000864347 conjugal transfer protein TrbE -
HPF53_RS00315 55832..57682 - 1851 WP_000821866 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HPF53_RS00320 57679..58317 - 639 WP_001080259 type-F conjugative transfer system pilin assembly protein TrbC trbC
HPF53_RS00325 58326..58631 - 306 WP_000224413 hypothetical protein -
HPF53_RS00330 58661..59653 - 993 WP_000830190 conjugal transfer pilus assembly protein TraU traU
HPF53_RS00335 59650..60282 - 633 WP_001203727 type-F conjugative transfer system protein TraW traW
HPF53_RS00340 60279..60665 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HPF53_RS00345 60662..63289 - 2628 WP_001064258 type IV secretion system protein TraC virb4
HPF53_RS00350 63449..63670 - 222 WP_001278694 conjugal transfer protein TraR -
HPF53_RS00355 63805..64320 - 516 WP_000809886 type IV conjugative transfer system lipoprotein TraV traV
HPF53_RS00360 64320..64631 - 312 WP_001057272 conjugal transfer protein TrbD -
HPF53_RS00365 64618..65184 - 567 WP_000896601 conjugal transfer pilus-stabilizing protein TraP -
HPF53_RS00370 65174..66625 - 1452 WP_000146687 F-type conjugal transfer pilus assembly protein TraB traB
HPF53_RS00375 66625..67353 - 729 WP_001230808 type-F conjugative transfer system secretin TraK traK
HPF53_RS00380 67340..67768 - 429 Protein_75 type IV conjugative transfer system protein TraE -
HPF53_RS00390 69029..69175 - 147 Protein_77 TraE/TraK family type IV conjugative transfer system protein -
HPF53_RS00395 69197..69508 - 312 WP_000012107 type IV conjugative transfer system protein TraL traL
HPF53_RS00400 69513..69875 - 363 WP_000338606 type IV conjugative transfer system pilin TraA -
HPF53_RS00405 69909..70136 - 228 WP_001254388 conjugal transfer relaxosome protein TraY -
HPF53_RS00410 70224..70901 - 678 WP_001348626 PAS domain-containing protein -
HPF53_RS00415 71035..71418 - 384 WP_001151566 conjugal transfer relaxosome DNA-binding protein TraM -
HPF53_RS00420 71749..72351 + 603 WP_000243712 transglycosylase SLT domain-containing protein virB1
HPF53_RS00425 72648..73469 - 822 WP_001234469 DUF932 domain-containing protein -
HPF53_RS00430 73588..73875 - 288 WP_000107535 hypothetical protein -
HPF53_RS00435 73900..74106 - 207 WP_000275859 hypothetical protein -
HPF53_RS00655 74176..74349 + 174 Protein_87 hypothetical protein -
HPF53_RS00660 74347..74577 - 231 WP_001426396 hypothetical protein -
HPF53_RS00445 74667..75092 + 426 WP_000422741 transposase -
HPF53_RS00450 75089..75439 + 351 WP_000624722 IS66 family insertion sequence element accessory protein TnpB -
HPF53_RS00455 75470..77083 + 1614 WP_000080195 IS66-like element ISEc23 family transposase -

Host bacterium

ID   3518 GenBank   NZ_KT754164
Plasmid name   p3099-85 Incompatibility group   IncFII
Plasmid size   111227 bp Coordinate of oriT [Strand]   71656..71779 [-]
Host baterium   Shigella dysenteriae

Cargo genes

Drug resistance gene   tet(B), catA1, blaOXA-1, ant(3'')-Ia, qacE, sul1
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -