Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104565
Name   oriT_SWHEFF_49|unnamed1 in_silico
Organism   Shigella dysenteriae strain SWHEFF_49
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055056 (80863..81214 [-], 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_49|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGTGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTCTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3291 GenBank   WP_109954974
Name   traI_HUZ68_RS24460_SWHEFF_49|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: 192003.76 Da        Isoelectric Point: 5.8849

>WP_109954974.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LRETGFDIRAYRDAEDQRAETRTQAPGPASPDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDLLQVASVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ESGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEIDA
QIKRGDLLYVDVAKDYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYNLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVMEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRHGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGSRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDNPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVRDVARENLLQERLQQMERDMVRALQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   1476 GenBank   WP_001369361
Name   WP_001369361_SWHEFF_49|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   1477 GenBank   WP_001151522
Name   WP_001151522_SWHEFF_49|unnamed1 insolico UniProt ID   A0A8B5LTD0
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14577.58 Da        Isoelectric Point: 5.0516

>WP_001151522.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVFGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A8B5LTD0


T4CP

ID   3230 GenBank   WP_001332348
Name   traD_HUZ68_RS24465_SWHEFF_49|unnamed1 insolico UniProt ID   _
Length   720 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 720 a.a.        Molecular weight: 81800.33 Da        Isoelectric Point: 5.0524

>WP_001332348.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPVS
PAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRRE
EVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.



ID   3231 GenBank   WP_000069755
Name   traC_HUZ68_RS24545_SWHEFF_49|unnamed1 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: 99278.95 Da        Isoelectric Point: 5.8486

>WP_000069755.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(468-772)

TraC protein (TraC_F_IV)

(39-277)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 54665..81785

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ68_RS24465 (HUZ68_24245) 54665..56827 - 2163 WP_001332348 type IV conjugative transfer system coupling protein TraD virb4
HUZ68_RS24470 (HUZ68_24250) 57079..57810 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HUZ68_RS24475 (HUZ68_24255) 57824..58333 - 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
HUZ68_RS24480 (HUZ68_24260) 58330..61155 - 2826 WP_001007030 conjugal transfer mating-pair stabilization protein TraG traG
HUZ68_RS24485 (HUZ68_24265) 61152..62525 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HUZ68_RS24490 (HUZ68_24270) 62525..62887 - 363 WP_074149687 P-type conjugative transfer protein TrbJ -
HUZ68_RS24495 (HUZ68_24275) 62817..63362 - 546 WP_000052614 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ68_RS24500 (HUZ68_24280) 63349..63633 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HUZ68_RS24505 (HUZ68_24285) 63752..64098 - 347 Protein_58 conjugal transfer protein TrbA -
HUZ68_RS24510 (HUZ68_24290) 64114..64857 - 744 WP_063073478 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ68_RS24515 (HUZ68_24295) 64850..65107 - 258 WP_000864325 conjugal transfer protein TrbE -
HUZ68_RS24520 (HUZ68_24300) 65134..66942 - 1809 WP_001567342 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ68_RS24525 (HUZ68_24305) 66939..67577 - 639 WP_089541249 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ68_RS24530 (HUZ68_24310) 67586..68578 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HUZ68_RS24535 (HUZ68_24315) 68575..69207 - 633 WP_001749440 type-F conjugative transfer system protein TraW traW
HUZ68_RS24540 (HUZ68_24320) 69204..69590 - 387 WP_000099690 type-F conjugative transfer system protein TrbI -
HUZ68_RS24545 (HUZ68_24325) 69587..72217 - 2631 WP_000069755 type IV secretion system protein TraC virb4
HUZ68_RS24550 (HUZ68_24330) 72343..72705 - 363 WP_000836675 hypothetical protein -
HUZ68_RS24555 (HUZ68_24335) 72733..72948 - 216 WP_000556747 hypothetical protein -
HUZ68_RS24560 (HUZ68_24340) 73028..73501 - 474 WP_194161624 hypothetical protein -
HUZ68_RS24565 (HUZ68_24345) 73494..73907 - 414 WP_000549581 hypothetical protein -
HUZ68_RS24570 (HUZ68_24350) 73900..74121 - 222 WP_001278695 conjugal transfer protein TraR -
HUZ68_RS24575 (HUZ68_24355) 74256..74771 - 516 WP_000809874 type IV conjugative transfer system lipoprotein TraV traV
HUZ68_RS24580 (HUZ68_24360) 74768..75088 - 321 WP_001057307 conjugal transfer protein TrbD -
HUZ68_RS24585 (HUZ68_24365) 75075..75665 - 591 WP_000002784 conjugal transfer pilus-stabilizing protein TraP -
HUZ68_RS24590 (HUZ68_24370) 75655..77082 - 1428 WP_000146657 F-type conjugal transfer pilus assembly protein TraB traB
HUZ68_RS24595 (HUZ68_24375) 77082..77810 - 729 WP_214673585 type-F conjugative transfer system secretin TraK traK
HUZ68_RS24600 (HUZ68_24380) 77797..78363 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ68_RS24605 (HUZ68_24385) 78385..78696 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ68_RS24610 (HUZ68_24390) 78711..79070 - 360 WP_000994781 type IV conjugative transfer system pilin TraA -
HUZ68_RS24615 (HUZ68_24395) 79103..79498 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ68_RS24620 (HUZ68_24400) 79597..80286 - 690 WP_000283383 conjugal transfer transcriptional regulator TraJ -
HUZ68_RS24625 (HUZ68_24405) 80479..80862 - 384 WP_001151522 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ68_RS24630 (HUZ68_24410) 81183..81785 + 603 WP_077633622 transglycosylase SLT domain-containing protein -
HUZ68_RS24635 (HUZ68_24415) 82082..82902 - 821 Protein_84 DUF932 domain-containing protein -
HUZ68_RS24640 (HUZ68_24420) 83021..83308 - 288 WP_000107535 hypothetical protein -
HUZ68_RS24645 83333..83539 - 207 WP_000547968 hypothetical protein -
HUZ68_RS24650 83609..83782 + 174 Protein_87 hypothetical protein -
HUZ68_RS24655 83780..84010 - 231 WP_001426396 hypothetical protein -
HUZ68_RS24660 (HUZ68_24425) 84230..84355 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ68_RS24665 84297..84446 - 150 Protein_90 plasmid maintenance protein Mok -
HUZ68_RS24670 (HUZ68_24430) 84468..84656 + 189 WP_001299721 hypothetical protein -
HUZ68_RS24675 (HUZ68_24435) 84668..85387 - 720 WP_239594264 plasmid SOS inhibition protein A -
HUZ68_RS24680 (HUZ68_24440) 85384..85818 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   5004 GenBank   NZ_CP055056
Plasmid name   SWHEFF_49|unnamed1 Incompatibility group   IncFIB
Plasmid size   117256 bp Coordinate of oriT [Strand]   80863..81214 [-]
Host baterium   Shigella dysenteriae strain SWHEFF_49

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -