Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113543
Name   oriT_702|unnamed1 in_silico
Organism   Shigella flexneri 4c strain 0702
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP020340 (4621..4704 [+], 84 nt)
oriT length   84 nt
IRs (inverted repeats)      27..32, 38..43  (GCAAAA..TTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      52..53
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 84 nt

>oriT_702|unnamed1
AATTACATGATTTAAAAACTAAATCAGCAAAAACTTGTTTTGCGTAGTGTGTGGTGCTTTTGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   10036 GenBank   WP_087760849
Name   traD_BS653_RS25615_702|unnamed1 insolico UniProt ID   _
Length   759 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 759 a.a.        Molecular weight: 86374.22 Da        Isoelectric Point: 5.1644

>WP_087760849.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEM
EQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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   10037 GenBank   WP_000069777
Name   traC_BS653_RS25710_702|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: 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: 50227..71519

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BS653_RS25615 (BS653_25735) 50227..52506 - 2280 WP_087760849 type IV conjugative transfer system coupling protein TraD prgC
BS653_RS25620 (BS653_25740) 52557..53294 - 738 WP_000199905 hypothetical protein -
BS653_RS25625 (BS653_25745) 53497..54228 - 732 WP_000782451 conjugal transfer complement resistance protein TraT -
BS653_RS25630 (BS653_25750) 54277..54762 - 486 WP_000605870 hypothetical protein -
BS653_RS25635 (BS653_25755) 54778..57600 - 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
BS653_RS25640 (BS653_25760) 57597..58970 - 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
BS653_RS25645 (BS653_25765) 58957..59349 - 393 WP_000660699 F-type conjugal transfer protein TrbF -
BS653_RS25650 (BS653_25770) 59330..59677 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
BS653_RS25655 (BS653_25775) 59607..60152 - 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
BS653_RS25660 (BS653_25780) 60139..60423 - 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
BS653_RS25665 (BS653_25785) 60542..60886 - 345 WP_000556796 conjugal transfer protein TrbA -
BS653_RS25670 (BS653_25790) 60900..61643 - 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
BS653_RS25675 (BS653_25795) 61636..61893 - 258 WP_000864353 conjugal transfer protein TrbE -
BS653_RS25680 (BS653_25800) 61920..63770 - 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
BS653_RS25685 (BS653_25805) 63767..64405 - 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
BS653_RS25690 (BS653_25810) 64414..64719 - 306 WP_000224416 hypothetical protein -
BS653_RS25695 (BS653_25815) 64749..65741 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
BS653_RS25700 (BS653_25820) 65738..66370 - 633 WP_001203728 type-F conjugative transfer system protein TraW traW
BS653_RS25705 (BS653_25825) 66367..66753 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
BS653_RS25710 (BS653_25830) 66750..69380 - 2631 WP_000069777 type IV secretion system protein TraC virb4
BS653_RS26760 69506..69853 - 348 WP_000836682 hypothetical protein -
BS653_RS25720 (BS653_25840) 69881..70099 - 219 WP_000556745 hypothetical protein -
BS653_RS25725 (BS653_25845) 70179..70655 - 477 WP_000549587 hypothetical protein -
BS653_RS25730 (BS653_25850) 70648..70869 - 222 WP_001278683 conjugal transfer protein TraR -
BS653_RS25735 (BS653_25855) 71004..71519 - 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
BS653_RS25740 (BS653_25860) 71516..71836 - 321 WP_001057307 conjugal transfer protein TrbD -
BS653_RS25745 (BS653_25865) 71823..72389 - 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -

Host bacterium

ID   13978 GenBank   NZ_CP020340
Plasmid name   702|unnamed1 Incompatibility group   IncFII
Plasmid size   73096 bp Coordinate of oriT [Strand]   4621..4704 [+]
Host baterium   Shigella flexneri 4c strain 0702

Cargo genes

Drug resistance gene   blaCTX-M-3, blaTEM-1B, fosA3, aac(6')-Ib-cr
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -