Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113336
Name   oriT_Sflex 21-42|unnamed4 in_silico
Organism   Shigella flexneri 2a strain Sflex 21-42
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP121221 (60173..60524 [+], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..46, 51..57  (GCAAAAA..TTTTTGC)
 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_Sflex 21-42|unnamed4
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAATTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATCATTTTATATTAGGGGCGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGTATTATGAATTTTAGTGTTCCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8551 GenBank   WP_001545323
Name   traI_P5F89_RS00695_Sflex 21-42|unnamed4 insolico UniProt ID   A0A9Q7V3L1
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191854.42 Da        Isoelectric Point: 5.6444

>WP_001545323.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVES
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGMFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELAMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWVDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRSAISEREAALPESVLRESQREQEAVREVARENLLQERLQQMERDMVRDLQKE
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)

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

(575-626)

AAA domain (AAA_30)

(968-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   4941 GenBank   WP_001151538
Name   WP_001151538_Sflex 21-42|unnamed4 insolico UniProt ID   A0A8B3KK21
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14559.51 Da        Isoelectric Point: 4.8662

>WP_001151538.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVNLYISNDAYEKINSIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A8B3KK21

ID   4942 GenBank   WP_001369361
Name   WP_001369361_Sflex 21-42|unnamed4 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   9871 GenBank   WP_001545324
Name   traD_P5F89_RS00690_Sflex 21-42|unnamed4 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83966.64 Da        Isoelectric Point: 5.1048

>WP_001545324.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEMNINVHRERGEDVEPGDDF

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 59602..89790

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
P5F89_RS00460 (P5F89_00455) 55594..56028 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
P5F89_RS00465 (P5F89_00460) 56025..56744 + 720 WP_001276217 plasmid SOS inhibition protein A -
P5F89_RS00470 (P5F89_00465) 56765..56944 - 180 WP_001309233 hypothetical protein -
P5F89_RS00475 (P5F89_00470) 56966..57115 + 150 Protein_79 plasmid maintenance protein Mok -
P5F89_RS00480 (P5F89_00475) 57057..57182 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
P5F89_RS00485 (P5F89_00480) 57483..57779 - 297 Protein_81 hypothetical protein -
P5F89_RS00490 (P5F89_00485) 58079..58375 + 297 WP_001272251 hypothetical protein -
P5F89_RS00495 (P5F89_00490) 58485..59306 + 822 WP_001234445 DUF932 domain-containing protein -
P5F89_RS00500 (P5F89_00495) 59602..60111 - 510 WP_000759173 transglycosylase SLT domain-containing protein virB1
P5F89_RS00505 (P5F89_00500) 60525..60908 + 384 WP_001151538 conjugal transfer relaxosome DNA-binding protein TraM -
P5F89_RS00510 (P5F89_00505) 61095..61784 + 690 WP_000283387 conjugal transfer transcriptional regulator TraJ -
P5F89_RS00515 (P5F89_00510) 61883..62278 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
P5F89_RS00520 (P5F89_00515) 62311..62670 + 360 WP_001099001 type IV conjugative transfer system pilin TraA -
P5F89_RS00525 (P5F89_00520) 62685..62996 + 312 WP_000012100 type IV conjugative transfer system protein TraL traL
P5F89_RS00530 (P5F89_00525) 63018..63584 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
P5F89_RS00535 (P5F89_00530) 63571..64299 + 729 WP_001230767 type-F conjugative transfer system secretin TraK traK
P5F89_RS00540 (P5F89_00535) 64299..65750 + 1452 WP_000146663 F-type conjugal transfer pilus assembly protein TraB traB
P5F89_RS00545 (P5F89_00540) 65740..66306 + 567 WP_000896598 conjugal transfer pilus-stabilizing protein TraP -
P5F89_RS00550 (P5F89_00545) 66293..66610 + 318 WP_001057297 conjugal transfer protein TrbD -
P5F89_RS00555 (P5F89_00550) 66610..67125 + 516 WP_000809872 type IV conjugative transfer system lipoprotein TraV traV
P5F89_RS00560 (P5F89_00555) 67260..67481 + 222 WP_001278695 conjugal transfer protein TraR -
P5F89_RS00565 (P5F89_00560) 67474..67887 + 414 WP_000549574 hypothetical protein -
P5F89_RS00570 (P5F89_00565) 67880..68353 + 474 WP_000549566 hypothetical protein -
P5F89_RS00575 (P5F89_00570) 68433..68651 + 219 WP_000556746 hypothetical protein -
P5F89_RS25470 68679..68892 + 214 Protein_100 hypothetical protein -
P5F89_RS00580 (P5F89_00575) 69018..71647 + 2630 Protein_101 type IV secretion system protein TraC -
P5F89_RS00585 (P5F89_00580) 71644..72029 + 386 Protein_102 type-F conjugative transfer system protein TrbI -
P5F89_RS00590 (P5F89_00585) 72026..72658 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
P5F89_RS00595 (P5F89_00590) 72655..73647 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
P5F89_RS00600 (P5F89_00595) 73674..73982 + 309 WP_000412445 hypothetical protein -
P5F89_RS00605 (P5F89_00600) 74045..74563 + 519 WP_000009088 hypothetical protein -
P5F89_RS00610 (P5F89_00605) 74590..75228 + 639 WP_000087539 type-F conjugative transfer system pilin assembly protein TrbC trbC
P5F89_RS00615 (P5F89_00610) 75225..75596 + 372 WP_000174465 hypothetical protein -
P5F89_RS00620 (P5F89_00615) 75621..76043 + 423 WP_001229309 HNH endonuclease -
P5F89_RS00625 (P5F89_00620) 76040..77890 + 1851 WP_000826177 type-F conjugative transfer system mating-pair stabilization protein TraN traN
P5F89_RS00630 (P5F89_00625) 77917..78174 + 258 WP_000864310 conjugal transfer protein TrbE -
P5F89_RS00635 (P5F89_00630) 78167..78910 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
P5F89_RS00640 (P5F89_00635) 78924..79265 + 342 WP_000556795 conjugal transfer protein TrbA -
P5F89_RS00645 (P5F89_00640) 79662..79946 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
P5F89_RS00650 (P5F89_00645) 79933..80478 + 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
P5F89_RS00655 (P5F89_00650) 80468..80782 + 315 WP_001336805 P-type conjugative transfer protein TrbJ -
P5F89_RS00660 (P5F89_00655) 80736..81128 + 393 WP_000138369 F-type conjugal transfer protein TrbF -
P5F89_RS00665 (P5F89_00660) 81115..82488 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
P5F89_RS00670 (P5F89_00665) 82485..85304 + 2820 WP_001537571 conjugal transfer mating-pair stabilization protein TraG traG
P5F89_RS00675 (P5F89_00670) 85323..85820 + 498 WP_000605862 entry exclusion protein -
P5F89_RS00680 (P5F89_00675) 85852..86583 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
P5F89_RS00685 (P5F89_00680) 86786..87523 + 738 WP_000199901 hypothetical protein -
P5F89_RS00690 (P5F89_00685) 87574..89790 + 2217 WP_001545324 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   13771 GenBank   NZ_CP121221
Plasmid name   Sflex 21-42|unnamed4 Incompatibility group   IncFIC
Plasmid size   96218 bp Coordinate of oriT [Strand]   60173..60524 [+]
Host baterium   Shigella flexneri 2a strain Sflex 21-42

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib, sul2, tet(A), blaOXA-1, aac(6')-Ib-cr
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -