Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113593
Name   oriT_p2013C-3749-1 in_silico
Organism   Shigella flexneri strain 2013C-3749
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP034932 (62473..62558 [+], 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_p2013C-3749-1
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   10076 GenBank   WP_000009330
Name   traD_EPD86_RS23730_p2013C-3749-1 insolico UniProt ID   _
Length   744 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 744 a.a.        Molecular weight: 84607.33 Da        Isoelectric Point: 5.1644

>WP_000009330.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVV
DMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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   10077 GenBank   WP_000069777
Name   traC_EPD86_RS23825_p2013C-3749-1 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: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  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: 35010..63126

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EPD86_RS23730 35010..37244 - 2235 WP_000009330 type IV conjugative transfer system coupling protein TraD virb4
EPD86_RS23735 37295..38032 - 738 WP_000199905 hypothetical protein -
EPD86_RS23740 38235..38966 - 732 WP_000782451 conjugal transfer complement resistance protein TraT -
EPD86_RS23745 39015..39500 - 486 WP_000605870 hypothetical protein -
EPD86_RS23750 39516..42338 - 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
EPD86_RS23755 42335..43708 - 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
EPD86_RS23760 43695..44087 - 393 WP_000660699 F-type conjugal transfer protein TrbF -
EPD86_RS23765 44068..44415 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
EPD86_RS23770 44345..44890 - 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
EPD86_RS23775 44877..45161 - 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
EPD86_RS23780 45280..45624 - 345 WP_000556796 conjugal transfer protein TrbA -
EPD86_RS23785 45638..46381 - 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
EPD86_RS23790 46374..46631 - 258 WP_000864353 conjugal transfer protein TrbE -
EPD86_RS23795 46658..48508 - 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
EPD86_RS23800 48505..49143 - 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
EPD86_RS23805 49152..49457 - 306 WP_000224416 hypothetical protein -
EPD86_RS23810 49487..50479 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
EPD86_RS23815 50476..51108 - 633 WP_001203728 type-F conjugative transfer system protein TraW traW
EPD86_RS23820 51105..51491 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
EPD86_RS23825 51488..54118 - 2631 WP_000069777 type IV secretion system protein TraC virb4
EPD86_RS23830 54244..54591 - 348 WP_000836682 hypothetical protein -
EPD86_RS23835 54619..54837 - 219 WP_000556745 hypothetical protein -
EPD86_RS23840 54917..55393 - 477 WP_000549587 hypothetical protein -
EPD86_RS23845 55386..55607 - 222 WP_001278683 conjugal transfer protein TraR -
EPD86_RS23850 55742..56257 - 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
EPD86_RS23855 56254..56574 - 321 WP_001057307 conjugal transfer protein TrbD -
EPD86_RS23860 56561..57127 - 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
EPD86_RS23865 57117..58568 - 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
EPD86_RS23870 58568..59296 - 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
EPD86_RS23875 59283..59849 - 567 WP_000399780 type IV conjugative transfer system protein TraE traE
EPD86_RS23880 59871..60182 - 312 WP_000012113 type IV conjugative transfer system protein TraL traL
EPD86_RS23885 60197..60556 - 360 WP_001098992 type IV conjugative transfer system pilin TraA -
EPD86_RS23890 60589..60816 - 228 WP_000089263 conjugal transfer relaxosome protein TraY -
EPD86_RS23895 60953..61624 - 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
EPD86_RS23900 61818..62201 - 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
EPD86_RS23905 62536..63126 + 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
EPD86_RS23910 63423..64244 - 822 WP_001234445 DUF932 domain-containing protein -
EPD86_RS23915 64355..64651 - 297 WP_001272251 hypothetical protein -
EPD86_RS26015 64951..65247 + 297 Protein_80 hypothetical protein -
EPD86_RS23930 65566..65691 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
EPD86_RS26020 65633..65782 - 150 Protein_82 plasmid maintenance protein Mok -
EPD86_RS23935 65804..65983 + 180 WP_001309233 hypothetical protein -
EPD86_RS23940 66004..66723 - 720 WP_001276217 plasmid SOS inhibition protein A -
EPD86_RS23945 66720..67154 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   14028 GenBank   NZ_CP034932
Plasmid name   p2013C-3749-1 Incompatibility group   IncFII
Plasmid size   71053 bp Coordinate of oriT [Strand]   62473..62558 [+]
Host baterium   Shigella flexneri strain 2013C-3749

Cargo genes

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