Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104499
Name   oriT_STEFF_12|unnamed1 in_silico
Organism   Shigella flexneri strain STEFF_12
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055220 (86719..87070 [-], 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_STEFF_12|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3257 GenBank   WP_000986984
Name   traI_HUZ41_RS24735_STEFF_12|unnamed1 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: 192216.86 Da        Isoelectric Point: 6.1142

>WP_000986984.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNMV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAVGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPVTIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNGTLNGLARSGRDVRLYSSLDEPRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPVELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQKTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRSAISEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(969-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   1441 GenBank   WP_001369361
Name   WP_001369361_STEFF_12|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

ID   1442 GenBank   WP_239637167
Name   WP_239637167_STEFF_12|unnamed1 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14503.45 Da        Isoelectric Point: 5.0516

>WP_239637167.1 conjugal transfer relaxosome DNA-binding protein TraM [Shigella flexneri]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGVESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.




T4CP

ID   3181 GenBank   WP_000009364
Name   traD_HUZ41_RS24740_STEFF_12|unnamed1 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: 83567.22 Da        Isoelectric Point: 5.0524

>WP_000009364.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   3182 GenBank   WP_135489858
Name   traC_HUZ41_RS24835_STEFF_12|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: 99165.88 Da        Isoelectric Point: 6.1924

>WP_135489858.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFVLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
VFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVKASWLAKKNQARIDDVVNFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60094..87641

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ41_RS24740 (HUZ41_24520) 60094..62301 - 2208 WP_000009364 type IV conjugative transfer system coupling protein TraD virb4
HUZ41_RS24745 (HUZ41_24525) 62555..63286 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HUZ41_RS24750 (HUZ41_24530) 63300..63809 - 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
HUZ41_RS24755 (HUZ41_24535) 63806..66631 - 2826 WP_239637164 conjugal transfer mating-pair stabilization protein TraG traG
HUZ41_RS24760 (HUZ41_24540) 66628..68001 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HUZ41_RS24765 (HUZ41_24545) 68001..68363 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
HUZ41_RS24770 (HUZ41_24550) 68293..68838 - 546 WP_000052614 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ41_RS24775 (HUZ41_24555) 68825..69109 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HUZ41_RS24780 (HUZ41_24560) 69228..69575 - 348 WP_001287893 conjugal transfer protein TrbA -
HUZ41_RS24785 (HUZ41_24565) 69591..70334 - 744 WP_001030395 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ41_RS24790 (HUZ41_24570) 70399..71096 + 698 WP_094096600 IS1-like element IS1A family transposase -
HUZ41_RS24795 (HUZ41_24575) 71107..71361 - 255 WP_239637179 conjugal transfer protein TrbE -
HUZ41_RS24800 (HUZ41_24580) 71388..73196 - 1809 WP_089645794 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ41_RS24805 (HUZ41_24585) 73193..73831 - 639 WP_239637165 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ41_RS24810 (HUZ41_24590) 73859..74311 - 453 WP_000069428 hypothetical protein -
HUZ41_RS24815 (HUZ41_24595) 74341..74802 - 462 WP_000277841 hypothetical protein -
HUZ41_RS24820 (HUZ41_24600) 74828..75820 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HUZ41_RS24825 (HUZ41_24605) 75817..76449 - 633 WP_239637166 type-F conjugative transfer system protein TraW traW
HUZ41_RS24830 (HUZ41_24610) 76446..76832 - 387 WP_000214094 type-F conjugative transfer system protein TrbI -
HUZ41_RS24835 (HUZ41_24615) 76829..79456 - 2628 WP_135489858 type IV secretion system protein TraC virb4
HUZ41_RS24840 (HUZ41_24620) 79616..79837 - 222 WP_001278685 conjugal transfer protein TraR -
HUZ41_RS24845 (HUZ41_24625) 79972..80487 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HUZ41_RS24850 (HUZ41_24630) 80484..80735 - 252 WP_001038342 conjugal transfer protein TrbG -
HUZ41_RS24855 (HUZ41_24635) 80747..80944 - 198 WP_001324648 conjugal transfer protein TrbD -
HUZ41_RS24860 (HUZ41_24640) 80931..81521 - 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HUZ41_RS24865 (HUZ41_24645) 81511..82938 - 1428 WP_000146649 F-type conjugal transfer pilus assembly protein TraB traB
HUZ41_RS24870 (HUZ41_24650) 82938..83666 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ41_RS24875 (HUZ41_24655) 83653..84219 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ41_RS24880 (HUZ41_24660) 84241..84552 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ41_RS24885 (HUZ41_24665) 84567..84932 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HUZ41_RS24890 (HUZ41_24670) 84965..85360 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ41_RS24895 (HUZ41_24675) 85459..86148 - 690 WP_000283379 conjugal transfer transcriptional regulator TraJ -
HUZ41_RS24900 (HUZ41_24680) 86335..86718 - 384 WP_239637167 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ41_RS24905 (HUZ41_24685) 87051..87641 + 591 WP_222908884 transglycosylase SLT domain-containing protein -
HUZ41_RS24910 (HUZ41_24690) 87938..88759 - 822 WP_001241365 DUF932 domain-containing protein -
HUZ41_RS24915 (HUZ41_24695) 88880..89167 - 288 WP_000107535 hypothetical protein -
HUZ41_RS24920 (HUZ41_24700) 89192..89398 - 207 WP_033804333 hypothetical protein -
HUZ41_RS24925 89468..89641 + 174 Protein_92 hypothetical protein -
HUZ41_RS24930 (HUZ41_24705) 89639..89869 - 231 WP_071845785 hypothetical protein -
HUZ41_RS24935 (HUZ41_24710) 90089..90214 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ41_RS24940 90156..90305 - 150 Protein_95 plasmid maintenance protein Mok -
HUZ41_RS24945 (HUZ41_24715) 90327..90515 + 189 WP_001299721 hypothetical protein -
HUZ41_RS24950 (HUZ41_24720) 90527..91246 - 720 WP_001276240 plasmid SOS inhibition protein A -
HUZ41_RS24955 (HUZ41_24725) 91243..91677 - 435 WP_000845907 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   4938 GenBank   NZ_CP055220
Plasmid name   STEFF_12|unnamed1 Incompatibility group   IncFIB
Plasmid size   118659 bp Coordinate of oriT [Strand]   86719..87070 [-]
Host baterium   Shigella flexneri strain STEFF_12

Cargo genes

Drug resistance gene   -
Virulence gene   exeG, exeE, stcE, nleA/espI
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -