Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104491
Name   oriT_SWHIN_116|unnamed2 in_silico
Organism   Shigella flexneri strain SWHIN_116
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055077 (29854..30205 [+], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      192..198, 206..212  (TATAAAA..TTTTATA)
 104..109, 119..124  (TTTAAA..TTTAAA)
 93..98, 106..111  (GATTTA..TAAATC)
 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_SWHIN_116|unnamed2
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTATCTTTAATATCATTGAGTTGTATTTGTGGATTTATATTGTTTAAATCTGATTTTTTTAAAGCAGCGTCGTTAACGCAGCTACAGCAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGTCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCACTATGAATTCTAGTGTTTCGAAATTAACTTTGTTTTATGTTTAAAAAAGGTAATATCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3253 GenBank   WP_239635735
Name   traI_HUZ90_RS23895_SWHIN_116|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: 191840.50 Da        Isoelectric Point: 5.8404

>WP_239635735.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVREIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   1439 GenBank   WP_001151529
Name   WP_001151529_SWHIN_116|unnamed2 insolico UniProt ID   A0A7I0L277
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14497.49 Da        Isoelectric Point: 4.8662

>WP_001151529.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQAEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSAEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A7I0L277


T4CP

ID   3178 GenBank   WP_000069772
Name   traC_HUZ90_RS23790_SWHIN_116|unnamed2 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99344.15 Da        Isoelectric Point: 6.4096

>WP_000069772.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   3179 GenBank   WP_110046574
Name   traD_HUZ90_RS23890_SWHIN_116|unnamed2 insolico UniProt ID   _
Length   747 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 747 a.a.        Molecular weight: 84969.71 Da        Isoelectric Point: 5.1652

>WP_110046574.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGHQGKQ
QSENEVTGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESG
EVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 29283..57634

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ90_RS23670 (HUZ90_23455) 25273..25707 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HUZ90_RS23675 (HUZ90_23460) 25704..26423 + 720 WP_001276217 plasmid SOS inhibition protein A -
HUZ90_RS23680 (HUZ90_23465) 26444..26623 - 180 WP_001309233 hypothetical protein -
HUZ90_RS23685 26645..26794 + 150 Protein_36 plasmid maintenance protein Mok -
HUZ90_RS23690 (HUZ90_23470) 26736..26861 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ90_RS23695 27162..27458 - 297 Protein_38 hypothetical protein -
HUZ90_RS23700 (HUZ90_23475) 27758..28054 + 297 WP_001272251 hypothetical protein -
HUZ90_RS23705 (HUZ90_23480) 28165..28986 + 822 WP_001234445 DUF932 domain-containing protein -
HUZ90_RS23710 (HUZ90_23485) 29283..29885 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
HUZ90_RS23715 (HUZ90_23490) 30206..30589 + 384 WP_001151529 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ90_RS23720 (HUZ90_23495) 30781..31428 + 648 WP_000332523 transcriptional regulator TraJ family protein -
HUZ90_RS23725 (HUZ90_23500) 31548..31775 + 228 WP_000589556 conjugal transfer relaxosome protein TraY -
HUZ90_RS23730 (HUZ90_23505) 31809..32171 + 363 WP_012881131 type IV conjugative transfer system pilin TraA -
HUZ90_RS23735 (HUZ90_23510) 32186..32497 + 312 WP_000012100 type IV conjugative transfer system protein TraL traL
HUZ90_RS23740 (HUZ90_23515) 32519..33085 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HUZ90_RS23745 (HUZ90_23520) 33072..33800 + 729 WP_001230769 type-F conjugative transfer system secretin TraK traK
HUZ90_RS23750 (HUZ90_23525) 33800..35227 + 1428 WP_012881130 F-type conjugal transfer pilus assembly protein TraB traB
HUZ90_RS23755 (HUZ90_23530) 35217..35807 + 591 WP_012881129 conjugal transfer pilus-stabilizing protein TraP -
HUZ90_RS23760 (HUZ90_23535) 35794..36114 + 321 WP_012881128 conjugal transfer protein TrbD -
HUZ90_RS23765 (HUZ90_23540) 36111..36626 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HUZ90_RS23770 (HUZ90_23545) 36761..36982 + 222 WP_001278683 conjugal transfer protein TraR -
HUZ90_RS23775 (HUZ90_23550) 36975..37451 + 477 WP_012881127 hypothetical protein -
HUZ90_RS23780 (HUZ90_23555) 37550..37768 + 219 WP_000556745 hypothetical protein -
HUZ90_RS23785 (HUZ90_23560) 37796..38143 + 348 WP_000836682 hypothetical protein -
HUZ90_RS23790 (HUZ90_23565) 38269..40899 + 2631 WP_000069772 type IV secretion system protein TraC virb4
HUZ90_RS23795 (HUZ90_23570) 40896..41282 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HUZ90_RS23800 (HUZ90_23575) 41279..41911 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HUZ90_RS23805 (HUZ90_23580) 41908..42900 + 993 WP_000830849 conjugal transfer pilus assembly protein TraU traU
HUZ90_RS23810 (HUZ90_23585) 42930..43235 + 306 WP_000224418 hypothetical protein -
HUZ90_RS23815 (HUZ90_23590) 43244..43882 + 639 WP_015058995 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ90_RS23820 (HUZ90_23595) 43879..45729 + 1851 WP_117389471 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ90_RS23825 (HUZ90_23600) 45756..46013 + 258 WP_000864353 conjugal transfer protein TrbE -
HUZ90_RS23830 (HUZ90_23605) 46006..46749 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ90_RS23835 (HUZ90_23610) 46763..47104 + 342 WP_000556795 conjugal transfer protein TrbA -
HUZ90_RS23840 (HUZ90_23615) 47085..47420 - 336 WP_000736414 hypothetical protein -
HUZ90_RS23845 (HUZ90_23620) 47501..47785 + 285 WP_000624107 type-F conjugative transfer system pilin chaperone TraQ -
HUZ90_RS23850 (HUZ90_23625) 47772..48317 + 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ90_RS23855 (HUZ90_23630) 48247..48594 + 348 WP_011666494 P-type conjugative transfer protein TrbJ -
HUZ90_RS23860 (HUZ90_23635) 48575..48967 + 393 WP_000659962 F-type conjugal transfer protein TrbF -
HUZ90_RS23865 (HUZ90_23640) 48954..50327 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HUZ90_RS23870 (HUZ90_23645) 50324..53149 + 2826 WP_012881124 conjugal transfer mating-pair stabilization protein TraG traG
HUZ90_RS23875 (HUZ90_23650) 53146..53655 + 510 WP_000628111 conjugal transfer entry exclusion protein TraS -
HUZ90_RS23880 (HUZ90_23655) 53669..54400 + 732 WP_012881123 conjugal transfer complement resistance protein TraT -
HUZ90_RS23885 (HUZ90_23660) 54603..55340 + 738 WP_012881122 hypothetical protein -
HUZ90_RS23890 (HUZ90_23665) 55391..57634 + 2244 WP_110046574 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4930 GenBank   NZ_CP055077
Plasmid name   SWHIN_116|unnamed2 Incompatibility group   -
Plasmid size   69050 bp Coordinate of oriT [Strand]   29854..30205 [+]
Host baterium   Shigella flexneri strain SWHIN_116

Cargo genes

Drug resistance gene   erm(B)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -