Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114164
Name   oriT_p6904-27 in_silico
Organism   Shigella sonnei strain 6904.27
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP045525 (24459..24544 [+], 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_p6904-27
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   5307 GenBank   WP_000089263
Name   WP_000089263_p6904-27 insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9

ID   5308 GenBank   WP_001354030
Name   WP_001354030_p6904-27 insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3


T4CP

ID   10540 GenBank   WP_000069777
Name   traC_GE168_RS24200_p6904-27 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   10541 GenBank   WP_000009330
Name   traD_GE168_RS24610_p6904-27 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1502..25112

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GE168_RS24115 (GE168_25175) 221..952 - 732 WP_000782451 conjugal transfer complement resistance protein TraT -
GE168_RS24120 (GE168_25180) 1001..1486 - 486 WP_000605870 hypothetical protein -
GE168_RS24125 (GE168_24330) 1502..4324 - 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
GE168_RS24130 (GE168_24335) 4321..5694 - 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
GE168_RS24135 (GE168_24340) 5681..6073 - 393 WP_000660699 F-type conjugal transfer protein TrbF -
GE168_RS24140 (GE168_24345) 6054..6401 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
GE168_RS24145 (GE168_24350) 6331..6876 - 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
GE168_RS24150 (GE168_24355) 6863..7147 - 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
GE168_RS24155 (GE168_24360) 7266..7610 - 345 WP_000556796 conjugal transfer protein TrbA -
GE168_RS24160 (GE168_24365) 7624..8367 - 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
GE168_RS24165 (GE168_24370) 8360..8617 - 258 WP_000864353 conjugal transfer protein TrbE -
GE168_RS24170 (GE168_24375) 8644..10494 - 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
GE168_RS24175 (GE168_24380) 10491..11129 - 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
GE168_RS24180 (GE168_24385) 11138..11443 - 306 WP_000224416 hypothetical protein -
GE168_RS24185 (GE168_24390) 11473..12465 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
GE168_RS24190 (GE168_24395) 12462..13094 - 633 WP_001203728 type-F conjugative transfer system protein TraW traW
GE168_RS24195 (GE168_24400) 13091..13477 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
GE168_RS24200 (GE168_24405) 13474..16104 - 2631 WP_000069777 type IV secretion system protein TraC virb4
GE168_RS24205 (GE168_24410) 16230..16577 - 348 WP_000836682 hypothetical protein -
GE168_RS24210 (GE168_24415) 16605..16823 - 219 WP_000556745 hypothetical protein -
GE168_RS24215 (GE168_24420) 16903..17379 - 477 WP_000549587 hypothetical protein -
GE168_RS24220 (GE168_24425) 17372..17593 - 222 WP_001278683 conjugal transfer protein TraR -
GE168_RS24225 (GE168_24430) 17728..18243 - 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
GE168_RS24230 (GE168_24435) 18240..18560 - 321 WP_001057307 conjugal transfer protein TrbD -
GE168_RS24235 (GE168_24440) 18547..19113 - 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
GE168_RS24240 (GE168_24445) 19103..20554 - 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
GE168_RS24245 (GE168_24450) 20554..21282 - 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
GE168_RS24250 (GE168_24455) 21269..21835 - 567 WP_000399780 type IV conjugative transfer system protein TraE traE
GE168_RS24255 (GE168_24460) 21857..22168 - 312 WP_000012113 type IV conjugative transfer system protein TraL traL
GE168_RS24260 (GE168_24465) 22183..22542 - 360 WP_001098992 type IV conjugative transfer system pilin TraA -
GE168_RS24265 (GE168_24470) 22575..22802 - 228 WP_000089263 conjugal transfer relaxosome protein TraY -
GE168_RS24270 (GE168_24475) 22939..23610 - 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
GE168_RS24275 (GE168_24480) 23804..24187 - 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
GE168_RS24280 (GE168_24490) 24522..25112 + 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
GE168_RS24285 (GE168_24495) 25409..26230 - 822 WP_001234445 DUF932 domain-containing protein -
GE168_RS24290 (GE168_24500) 26341..26637 - 297 WP_001272251 hypothetical protein -
GE168_RS24295 26937..27233 + 297 Protein_36 hypothetical protein -
GE168_RS24300 (GE168_24520) 27552..27677 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
GE168_RS24305 27619..27768 - 150 Protein_38 plasmid maintenance protein Mok -
GE168_RS24310 (GE168_25185) 27790..27969 + 180 WP_001309233 hypothetical protein -
GE168_RS24315 (GE168_24525) 27990..28709 - 720 WP_001276217 plasmid SOS inhibition protein A -
GE168_RS24320 (GE168_24530) 28706..29140 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   14599 GenBank   NZ_CP045525
Plasmid name   p6904-27 Incompatibility group   IncFII
Plasmid size   83273 bp Coordinate of oriT [Strand]   24459..24544 [+]
Host baterium   Shigella sonnei strain 6904.27

Cargo genes

Drug resistance gene   blaCTX-M-15, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -