Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104551
Name   oriT_STLEFF_34|unnamed1 in_silico
Organism   Shigella flexneri strain STLEFF_34
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP058840 (62630..62981 [+], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_STLEFF_34|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3281 GenBank   WP_000986934
Name   traI_HZT26_RS23885_STLEFF_34|unnamed1 insolico UniProt ID   A0A291R9S5
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191764.68 Da        Isoelectric Point: 5.9593

>WP_000986934.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRTEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTEMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

AAA domain (AAA_30)

(968-1156)

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   1468 GenBank   WP_001151524
Name   WP_001151524_STLEFF_34|unnamed1 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22

ID   1469 GenBank   WP_001369361
Name   WP_001369361_STLEFF_34|unnamed1 insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64


T4CP

ID   3216 GenBank   WP_113421867
Name   traC_HZT26_RS23790_STLEFF_34|unnamed1 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: 99470.50 Da        Isoelectric Point: 6.6265

>WP_113421867.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLFPDQFQPLQRDMIGKFGAAKDLWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREGM
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-763)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   3217 GenBank   WP_000009360
Name   traD_HZT26_RS23880_STLEFF_34|unnamed1 insolico UniProt ID   _
Length   732 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 732 a.a.        Molecular weight: 83294.06 Da        Isoelectric Point: 5.1048

>WP_000009360.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHQIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGISTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPVSPAINDKKSDSGVNIPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN
HPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 61989..84893

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HZT26_RS23670 (HZT26_23495) 57955..58389 + 435 WP_000845907 conjugation system SOS inhibitor PsiB -
HZT26_RS23675 (HZT26_23500) 58386..59105 + 720 WP_001276240 plasmid SOS inhibition protein A -
HZT26_RS23680 (HZT26_23505) 59117..59305 - 189 WP_001299721 hypothetical protein -
HZT26_RS23685 59327..59476 + 150 Protein_77 plasmid maintenance protein Mok -
HZT26_RS23690 (HZT26_23510) 59418..59543 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HZT26_RS23695 59763..59993 + 231 WP_071845785 hypothetical protein -
HZT26_RS23700 59991..60164 - 174 Protein_80 hypothetical protein -
HZT26_RS23705 (HZT26_23515) 60234..60440 + 207 WP_063609967 hypothetical protein -
HZT26_RS23710 (HZT26_23520) 60465..60752 + 288 WP_063072995 hypothetical protein -
HZT26_RS23715 (HZT26_23525) 60871..61692 + 822 WP_001241365 DUF932 domain-containing protein -
HZT26_RS23720 (HZT26_23530) 61989..62579 - 591 WP_222908884 transglycosylase SLT domain-containing protein virB1
HZT26_RS23725 (HZT26_23535) 62982..63365 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HZT26_RS23730 (HZT26_23540) 63552..64241 + 690 WP_000283379 conjugal transfer transcriptional regulator TraJ -
HZT26_RS23735 (HZT26_23545) 64340..64735 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HZT26_RS23740 (HZT26_23550) 64768..65133 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HZT26_RS23745 (HZT26_23555) 65148..65459 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HZT26_RS23750 (HZT26_23560) 65481..66047 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HZT26_RS23755 (HZT26_23565) 66034..66762 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HZT26_RS23760 (HZT26_23570) 66762..68189 + 1428 WP_000146638 F-type conjugal transfer pilus assembly protein TraB traB
HZT26_RS23765 (HZT26_23575) 68179..68763 + 585 WP_000002795 conjugal transfer pilus-stabilizing protein TraP -
HZT26_RS23770 (HZT26_23580) 68750..69070 + 321 WP_001057302 conjugal transfer protein TrbD virb4
HZT26_RS23775 (HZT26_23585) 69063..69314 + 252 WP_001038341 conjugal transfer protein TrbG -
HZT26_RS23780 (HZT26_23590) 69311..69826 + 516 WP_000809893 type IV conjugative transfer system lipoprotein TraV traV
HZT26_RS23785 (HZT26_23595) 69961..70182 + 222 WP_072651814 conjugal transfer protein TraR -
HZT26_RS23790 (HZT26_23600) 70342..72969 + 2628 WP_113421867 type IV secretion system protein TraC virb4
HZT26_RS23795 (HZT26_23605) 72966..73352 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
HZT26_RS23800 (HZT26_23610) 73349..73981 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HZT26_RS23805 (HZT26_23615) 73978..74970 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HZT26_RS23810 (HZT26_23620) 75000..75305 + 306 WP_000224411 hypothetical protein -
HZT26_RS23815 (HZT26_23625) 75314..75952 + 639 WP_001080257 type-F conjugative transfer system pilin assembly protein TrbC trbC
HZT26_RS23820 (HZT26_23630) 75949..77757 + 1809 WP_000821863 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HZT26_RS23825 (HZT26_23635) 77784..78041 + 258 WP_000864320 conjugal transfer protein TrbE -
HZT26_RS23830 (HZT26_23640) 78034..78777 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HZT26_RS23835 (HZT26_23645) 78793..79131 + 339 WP_001287905 conjugal transfer protein TrbA -
HZT26_RS23840 (HZT26_23650) 79258..79542 + 285 WP_001448202 type-F conjugative transfer system pilin chaperone TraQ -
HZT26_RS23845 (HZT26_23655) 79529..80074 + 546 WP_000059824 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HZT26_RS23850 (HZT26_23660) 80004..80344 + 341 Protein_110 P-type conjugative transfer protein TrbJ -
HZT26_RS23855 (HZT26_23665) 80325..80717 + 393 WP_000660703 F-type conjugal transfer protein TrbF -
HZT26_RS23860 (HZT26_23670) 80704..82077 + 1374 WP_112901602 conjugal transfer pilus assembly protein TraH traH
HZT26_RS23865 (HZT26_23675) 82074..84893 + 2820 WP_113421866 conjugal transfer mating-pair stabilization protein TraG traG
HZT26_RS23870 (HZT26_23680) 84912..85409 + 498 WP_000605861 hypothetical protein -
HZT26_RS23875 (HZT26_23685) 85441..86172 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
HZT26_RS23880 (HZT26_23690) 86425..88623 + 2199 WP_000009360 type IV conjugative transfer system coupling protein TraD -

Host bacterium

ID   4990 GenBank   NZ_CP058840
Plasmid name   STLEFF_34|unnamed1 Incompatibility group   IncFII
Plasmid size   98962 bp Coordinate of oriT [Strand]   62630..62981 [+]
Host baterium   Shigella flexneri strain STLEFF_34

Cargo genes

Drug resistance gene   cmlA1, qacE, blaCTX-M-14, erm(B), mph(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -