Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107517
Name   oriT_p893916 in_silico
Organism   Shigella sonnei strain 893916
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MW396858 (45522..45607 [-], 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_p893916
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   5255 GenBank   WP_000069777
Name   traC_J5X06_RS00390_p893916 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.



ID   5256 GenBank   WP_207954088
Name   traD_J5X06_RS00485_p893916 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83828.51 Da        Isoelectric Point: 5.2308

>WP_207954088.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQGLKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 44954..73052

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J5X06_RS00280 (LAGLCMAM_00053) 40926..41360 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
J5X06_RS00285 (LAGLCMAM_00054) 41357..42076 + 720 WP_001276217 plasmid SOS inhibition protein A -
J5X06_RS00540 (LAGLCMAM_00055) 42298..42447 + 150 Protein_56 plasmid maintenance protein Mok -
J5X06_RS00290 (LAGLCMAM_00055) 42389..42514 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
J5X06_RS00295 42833..43129 - 297 Protein_58 hypothetical protein -
J5X06_RS00300 (LAGLCMAM_00056) 43429..43725 + 297 WP_001272251 hypothetical protein -
J5X06_RS00305 (LAGLCMAM_00057) 43836..44657 + 822 WP_001234445 DUF932 domain-containing protein -
J5X06_RS00310 (LAGLCMAM_00058) 44954..45556 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
J5X06_RS00315 (LAGLCMAM_00059) 45879..46262 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
J5X06_RS00320 (LAGLCMAM_00060) 46456..47127 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
J5X06_RS00325 47264..47491 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
J5X06_RS00330 (LAGLCMAM_00061) 47524..47883 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
J5X06_RS00335 (LAGLCMAM_00062) 47898..48209 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
J5X06_RS00340 (LAGLCMAM_00063) 48231..48797 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
J5X06_RS00345 (LAGLCMAM_00064) 48784..49512 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
J5X06_RS00350 (LAGLCMAM_00065) 49512..50963 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
J5X06_RS00355 (LAGLCMAM_00066) 50953..51519 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
J5X06_RS00360 (LAGLCMAM_00067) 51506..51826 + 321 WP_001057307 conjugal transfer protein TrbD -
J5X06_RS00365 (LAGLCMAM_00068) 51823..52338 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
J5X06_RS00370 52473..52694 + 222 WP_001278683 conjugal transfer protein TraR -
J5X06_RS00375 (LAGLCMAM_00069) 52687..53163 + 477 WP_000549587 hypothetical protein -
J5X06_RS00380 (LAGLCMAM_00070) 53243..53461 + 219 WP_000556745 hypothetical protein -
J5X06_RS00385 (LAGLCMAM_00071) 53489..53836 + 348 WP_000836682 hypothetical protein -
J5X06_RS00390 (LAGLCMAM_00072) 53962..56592 + 2631 WP_000069777 type IV secretion system protein TraC virb4
J5X06_RS00395 (LAGLCMAM_00073) 56589..56975 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
J5X06_RS00400 (LAGLCMAM_00074) 56972..57604 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
J5X06_RS00405 (LAGLCMAM_00075) 57601..58593 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
J5X06_RS00410 (LAGLCMAM_00076) 58623..58928 + 306 WP_000224416 hypothetical protein -
J5X06_RS00415 (LAGLCMAM_00077) 58937..59575 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
J5X06_RS00420 (LAGLCMAM_00078) 59572..61422 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
J5X06_RS00425 (LAGLCMAM_00079) 61449..61706 + 258 WP_000864353 conjugal transfer protein TrbE -
J5X06_RS00430 (LAGLCMAM_00080) 61699..62442 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
J5X06_RS00435 (LAGLCMAM_00081) 62456..62800 + 345 WP_000556796 conjugal transfer protein TrbA -
J5X06_RS00440 (LAGLCMAM_00082) 62919..63203 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
J5X06_RS00445 (LAGLCMAM_00083) 63190..63735 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
J5X06_RS00450 63665..64012 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
J5X06_RS00455 (LAGLCMAM_00084) 63993..64385 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
J5X06_RS00460 (LAGLCMAM_00085) 64372..65745 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
J5X06_RS00465 (LAGLCMAM_00086) 65742..68564 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
J5X06_RS00470 (LAGLCMAM_00087) 68580..69065 + 486 WP_000605870 hypothetical protein -
J5X06_RS00475 (LAGLCMAM_00088) 69114..69845 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
J5X06_RS00480 (LAGLCMAM_00089) 70048..70785 + 738 WP_000199905 hypothetical protein -
J5X06_RS00485 (LAGLCMAM_00090) 70836..73052 + 2217 WP_207954088 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   7952 GenBank   NZ_MW396858
Plasmid name   p893916 Incompatibility group   IncFII
Plasmid size   83397 bp Coordinate of oriT [Strand]   45522..45607 [-]
Host baterium   Shigella sonnei strain 893916

Cargo genes

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