Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104501
Name   oriT_STIN_92|unnamed2 in_silico
Organism   Shigella flexneri strain STIN_92
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP054979 (106360..106445 [+], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..13, 21..26  (TGATTT..AAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_STIN_92|unnamed2
AATTACATGATTTAAAACACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3259 GenBank   WP_239636838
Name   traI_HUZ60_RS24880_STIN_92|unnamed2 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: 192064.90 Da        Isoelectric Point: 5.8166

>WP_239636838.1 conjugative transfer relaxase/helicase TraI [Shigella flexneri]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQDETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
DRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   1443 GenBank   WP_001352842
Name   WP_001352842_STIN_92|unnamed2 insolico UniProt ID   A0A6Y3H4U0
Length   71 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 71 a.a.        Molecular weight: 8117.19 Da        Isoelectric Point: 9.9216

>WP_001352842.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MSRGRTRAAPGNKVLLILDETTNQKLLAARDRSGRTKTNEVFIRLKDHLNRFPDFYNASLVKEEAESIDD
I

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A6Y3H4U0

ID   1444 GenBank   WP_001063020
Name   WP_001063020_STIN_92|unnamed2 insolico UniProt ID   A0A6Y3HD60
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14442.54 Da        Isoelectric Point: 5.3125

>WP_001063020.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]
MAKIQVYVNDHVSEKINAIAVQRRAEGAKEKDVSYSSIASMLLELGLRVYEAQMERKESAFNQAEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGKPKFEYANMVEDIREKVSVEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A6Y3HD60


T4CP

ID   3184 GenBank   WP_000009324
Name   traD_HUZ60_RS24895_STIN_92|unnamed2 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81528.14 Da        Isoelectric Point: 5.1126

>WP_000009324.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRREEVN
INVHRERGEDVEPGDDF

  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   3185 GenBank   WP_001064245
Name   traC_HUZ60_RS24985_STIN_92|unnamed2 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: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
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)

(467-771)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 80791..107013

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ60_RS24885 (HUZ60_24565) 80157..80384 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
HUZ60_RS24890 (HUZ60_24570) 80384..80782 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HUZ60_RS24895 (HUZ60_24575) 80791..82944 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HUZ60_RS24900 (HUZ60_24580) 83197..83928 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
HUZ60_RS24905 (HUZ60_24585) 83960..84457 - 498 WP_000605857 entry exclusion protein -
HUZ60_RS24910 (HUZ60_24590) 84473..87295 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
HUZ60_RS24915 (HUZ60_24595) 87292..88665 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
HUZ60_RS24920 (HUZ60_24600) 88665..89045 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
HUZ60_RS24925 (HUZ60_24605) 89032..89373 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HUZ60_RS24930 (HUZ60_24610) 89303..89848 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ60_RS24935 (HUZ60_24615) 89835..90119 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HUZ60_RS24940 (HUZ60_24620) 90200..90514 + 315 WP_001324103 hypothetical protein -
HUZ60_RS24945 (HUZ60_24625) 90516..90863 - 348 WP_001287910 conjugal transfer protein TrbA -
HUZ60_RS24950 (HUZ60_24630) 90879..91622 - 744 WP_001030377 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ60_RS24955 (HUZ60_24635) 91615..91872 - 258 WP_000864318 conjugal transfer protein TrbE -
HUZ60_RS24960 (HUZ60_24640) 91899..93707 - 1809 WP_000821838 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ60_RS24965 (HUZ60_24645) 93704..94342 - 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ60_RS24970 (HUZ60_24650) 94351..95343 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
HUZ60_RS24975 (HUZ60_24655) 95340..95972 - 633 WP_001203717 type-F conjugative transfer system protein TraW traW
HUZ60_RS24980 (HUZ60_24660) 95969..96355 - 387 WP_000099691 type-F conjugative transfer system protein TrbI -
HUZ60_RS24985 (HUZ60_24665) 96352..98979 - 2628 WP_001064245 type IV secretion system protein TraC virb4
HUZ60_RS24990 (HUZ60_24670) 99139..99360 - 222 WP_001278689 conjugal transfer protein TraR -
HUZ60_RS24995 (HUZ60_24675) 99495..100010 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
HUZ60_RS25000 (HUZ60_24680) 100007..100258 - 252 WP_001038342 conjugal transfer protein TrbG -
HUZ60_RS25005 (HUZ60_24685) 100270..100467 - 198 WP_024179215 conjugal transfer protein TrbD -
HUZ60_RS25010 (HUZ60_24690) 100454..101044 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
HUZ60_RS25015 (HUZ60_24695) 101034..102461 - 1428 WP_000146684 F-type conjugal transfer pilus assembly protein TraB traB
HUZ60_RS25020 (HUZ60_24700) 102461..103189 - 729 WP_001230813 type-F conjugative transfer system secretin TraK traK
HUZ60_RS25025 (HUZ60_24705) 103176..103742 - 567 WP_000399790 type IV conjugative transfer system protein TraE traE
HUZ60_RS25030 (HUZ60_24710) 103764..104075 - 312 WP_239636833 type IV conjugative transfer system protein TraL traL
HUZ60_RS25035 (HUZ60_24715) 104090..104455 - 366 WP_000340282 type IV conjugative transfer system pilin TraA -
HUZ60_RS25040 (HUZ60_24720) 104498..104713 - 216 WP_001352842 conjugal transfer relaxosome protein TraY -
HUZ60_RS25045 (HUZ60_24725) 104849..105496 - 648 WP_000332520 conjugal transfer transcriptional regulator TraJ -
HUZ60_RS25050 (HUZ60_24730) 105688..106071 - 384 WP_001063020 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ60_RS25055 (HUZ60_24735) 106411..107013 + 603 WP_077248356 transglycosylase SLT domain-containing protein -
HUZ60_RS25060 (HUZ60_24740) 107308..108129 - 822 WP_001234475 DUF932 domain-containing protein -
HUZ60_RS25065 (HUZ60_24745) 108248..108535 - 288 WP_000107546 hypothetical protein -
HUZ60_RS25070 (HUZ60_24750) 108560..108766 - 207 WP_000547965 hypothetical protein -
HUZ60_RS25075 (HUZ60_24755) 108836..109132 + 297 Protein_114 hypothetical protein -
HUZ60_RS25080 (HUZ60_24760) 109433..109558 - 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
HUZ60_RS25085 109500..109649 - 150 Protein_116 DUF5431 family protein -
HUZ60_RS25090 (HUZ60_24765) 109823..110585 - 763 Protein_117 plasmid SOS inhibition protein A -
HUZ60_RS25095 (HUZ60_24770) 110582..111016 - 435 WP_000845928 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   4940 GenBank   NZ_CP054979
Plasmid name   STIN_92|unnamed2 Incompatibility group   IncFIB
Plasmid size   157162 bp Coordinate of oriT [Strand]   106360..106445 [+]
Host baterium   Shigella flexneri strain STIN_92

Cargo genes

Drug resistance gene   sitABCD
Virulence gene   iroB, iroC, iroD, iroE, iroN, vat, iutA, iucC, iucB, iucA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -