Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104521
Name   oriT_SWHEFF_71|unnamed1 in_silico
Organism   Shigella flexneri strain SWHEFF_71
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055016 (155968..156319 [-], 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_SWHEFF_71|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3270 GenBank   WP_096942428
Name   traI_HUZ78_RS25075_SWHEFF_71|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: 192163.81 Da        Isoelectric Point: 6.0655

>WP_096942428.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNMV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAVGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPVTIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNGTLNGLARSGRDVRLYSSLDEPRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSCASYEAEKSILRHILEGKEAVTPLMERVPVELMEKLTSGQRAATRMI
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   1458 GenBank   WP_001369361
Name   WP_001369361_SWHEFF_71|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   1459 GenBank   WP_001151524
Name   WP_001151524_SWHEFF_71|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


T4CP

ID   3200 GenBank   WP_022630316
Name   traD_HUZ78_RS25080_SWHEFF_71|unnamed1 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: 83920.60 Da        Isoelectric Point: 5.0524

>WP_022630316.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 128798..156890

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ78_RS25080 (HUZ78_24900) 128798..131014 - 2217 WP_022630316 type IV conjugative transfer system coupling protein TraD virb4
HUZ78_RS25085 (HUZ78_24905) 131268..131999 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HUZ78_RS25090 (HUZ78_24910) 132013..132522 - 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
HUZ78_RS25095 (HUZ78_24915) 132519..135344 - 2826 WP_195715507 conjugal transfer mating-pair stabilization protein TraG traG
HUZ78_RS25100 (HUZ78_24920) 135341..136714 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HUZ78_RS25105 (HUZ78_24925) 136714..137076 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
HUZ78_RS25110 (HUZ78_24930) 137006..137551 - 546 WP_000052614 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ78_RS25115 (HUZ78_24935) 137538..137822 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HUZ78_RS25120 (HUZ78_24940) 137941..138288 - 348 WP_001287893 conjugal transfer protein TrbA -
HUZ78_RS25125 (HUZ78_24945) 138304..139047 - 744 WP_001030395 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ78_RS25130 (HUZ78_24950) 139040..139297 - 258 WP_000864311 conjugal transfer protein TrbE -
HUZ78_RS25135 (HUZ78_24955) 139324..141132 - 1809 WP_089645794 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ78_RS25140 (HUZ78_24960) 141129..141767 - 639 WP_122994733 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ78_RS25145 (HUZ78_24965) 141795..142247 - 453 WP_000069428 hypothetical protein -
HUZ78_RS25150 (HUZ78_24970) 142277..142738 - 462 WP_000277841 hypothetical protein -
HUZ78_RS25155 (HUZ78_24975) 142764..143756 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HUZ78_RS25160 (HUZ78_24980) 143753..144385 - 633 WP_001203722 type-F conjugative transfer system protein TraW traW
HUZ78_RS25165 (HUZ78_24985) 144382..144768 - 387 WP_000214094 type-F conjugative transfer system protein TrbI -
HUZ78_RS25170 (HUZ78_24990) 144765..147392 - 2628 WP_205850319 type IV secretion system protein TraC virb4
HUZ78_RS25175 (HUZ78_24995) 147552..147773 - 222 WP_001278685 conjugal transfer protein TraR -
HUZ78_RS25180 (HUZ78_25000) 147908..148423 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HUZ78_RS25185 (HUZ78_25005) 148420..148671 - 252 WP_001038342 conjugal transfer protein TrbG -
HUZ78_RS25190 (HUZ78_25010) 148698..148829 - 132 Protein_160 conjugal transfer protein TrbD -
HUZ78_RS25200 150113..150241 - 129 Protein_162 conjugal transfer protein TrbD -
HUZ78_RS25205 (HUZ78_25020) 150180..150770 - 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HUZ78_RS25210 (HUZ78_25025) 150760..152187 - 1428 WP_000146649 F-type conjugal transfer pilus assembly protein TraB traB
HUZ78_RS25215 (HUZ78_25030) 152187..152915 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ78_RS25220 (HUZ78_25035) 152902..153468 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ78_RS25225 (HUZ78_25040) 153490..153801 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ78_RS25230 (HUZ78_25045) 153816..154181 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HUZ78_RS25235 (HUZ78_25050) 154214..154609 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ78_RS25240 (HUZ78_25055) 154708..155397 - 690 WP_000283379 conjugal transfer transcriptional regulator TraJ -
HUZ78_RS25245 (HUZ78_25060) 155584..155967 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ78_RS25250 (HUZ78_25065) 156300..156890 + 591 WP_222908884 transglycosylase SLT domain-containing protein virB1
HUZ78_RS25255 (HUZ78_25070) 157187..158008 - 822 WP_001241365 DUF932 domain-containing protein -
HUZ78_RS25260 (HUZ78_25075) 158128..158415 - 288 WP_000107535 hypothetical protein -
HUZ78_RS25265 (HUZ78_25080) 158440..158646 - 207 WP_033804333 hypothetical protein -
HUZ78_RS25270 158716..158889 + 174 Protein_176 hypothetical protein -
HUZ78_RS25275 158887..159117 - 231 WP_071845785 hypothetical protein -
HUZ78_RS25280 (HUZ78_25090) 159337..159462 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ78_RS25285 159404..159553 - 150 Protein_179 plasmid maintenance protein Mok -
HUZ78_RS25290 (HUZ78_25095) 159575..159763 + 189 WP_001299721 hypothetical protein -
HUZ78_RS25295 (HUZ78_25100) 159732..160494 - 763 Protein_181 plasmid SOS inhibition protein A -
HUZ78_RS25300 (HUZ78_25105) 160491..160925 - 435 WP_000845895 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   4960 GenBank   NZ_CP055016
Plasmid name   SWHEFF_71|unnamed1 Incompatibility group   IncFIB
Plasmid size   183928 bp Coordinate of oriT [Strand]   155968..156319 [-]
Host baterium   Shigella flexneri strain SWHEFF_71

Cargo genes

Drug resistance gene   tet(A), aadA2, dfrA12, aac(3)-IId, blaTEM-1B, aph(6)-Id, aph(3'')-Ib, sul2, sitABCD
Virulence gene   exeG, exeE, stcE
Metal resistance gene   merR, merT, merP
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -