Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113556
Name   oriT_p183660 in_silico
Organism   Shigella sonnei strain 183660
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX008967 (61724..61809 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_p183660
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   10044 GenBank   WP_171264644
Name   traC_HPF68_RS00500_p183660 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: 99169.82 Da        Isoelectric Point: 6.1126

>WP_171264644.1 type IV secretion system protein TraC [Shigella sonnei]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGAEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 61156..84766

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPF68_RS00385 57128..57562 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HPF68_RS00390 57559..58278 + 720 WP_001276217 plasmid SOS inhibition protein A -
HPF68_RS00610 58500..58649 + 150 Protein_74 plasmid maintenance protein Mok -
HPF68_RS00395 58591..58716 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HPF68_RS00595 59035..59331 - 297 Protein_76 hypothetical protein -
HPF68_RS00410 59631..59927 + 297 WP_001272251 hypothetical protein -
HPF68_RS00415 60038..60859 + 822 WP_001234445 DUF932 domain-containing protein -
HPF68_RS00420 61156..61758 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
HPF68_RS00425 62081..62464 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HPF68_RS00430 62658..63329 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HPF68_RS00435 63466..63693 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HPF68_RS00440 63726..64085 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HPF68_RS00445 64100..64411 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HPF68_RS00450 64433..64999 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HPF68_RS00455 64986..65714 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HPF68_RS00460 65714..67165 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HPF68_RS00465 67155..67721 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HPF68_RS00470 67708..68028 + 321 WP_001057307 conjugal transfer protein TrbD -
HPF68_RS00475 68025..68540 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HPF68_RS00480 68675..68896 + 222 WP_001278683 conjugal transfer protein TraR -
HPF68_RS00485 68889..69365 + 477 WP_000549587 hypothetical protein -
HPF68_RS00490 69445..69663 + 219 WP_000556745 hypothetical protein -
HPF68_RS00495 69691..70038 + 348 WP_000836682 hypothetical protein -
HPF68_RS00500 70164..72794 + 2631 WP_171264644 type IV secretion system protein TraC virb4
HPF68_RS00505 72791..73177 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HPF68_RS00510 73174..73806 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HPF68_RS00515 73803..74795 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HPF68_RS00520 74825..75130 + 306 WP_000224416 hypothetical protein -
HPF68_RS00525 75139..75777 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HPF68_RS00530 75774..77624 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HPF68_RS00535 77651..77908 + 258 WP_000864353 conjugal transfer protein TrbE -
HPF68_RS00540 77901..78644 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HPF68_RS00545 78658..79002 + 345 WP_000556796 conjugal transfer protein TrbA -
HPF68_RS00550 79121..79405 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HPF68_RS00555 79392..79937 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HPF68_RS00560 79867..80214 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HPF68_RS00565 80195..80587 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HPF68_RS00570 80574..81947 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HPF68_RS00575 81944..84766 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HPF68_RS00580 84782..85267 + 486 WP_000605870 hypothetical protein -
HPF68_RS00585 85316..86047 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HPF68_RS00590 86250..86987 + 738 WP_000199905 hypothetical protein -

Host bacterium

ID   13991 GenBank   NZ_KX008967
Plasmid name   p183660 Incompatibility group   IncFII
Plasmid size   88976 bp Coordinate of oriT [Strand]   61724..61809 [-]
Host baterium   Shigella sonnei strain 183660

Cargo genes

Drug resistance gene   blaTEM-1B, aadA5, qacE, sul1, mph(A), erm(B), blaCTX-M-27
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -