Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104510
Name   oriT_STEFF_3|unnamed1 in_silico
Organism   Shigella flexneri strain STEFF_3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055200 (103484..103569 [+], 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_STEFF_3|unnamed1
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   1450 GenBank   WP_000089263
Name   WP_000089263_STEFF_3|unnamed1 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   1451 GenBank   WP_001354030
Name   WP_001354030_STEFF_3|unnamed1 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   3193 GenBank   WP_017901267
Name   traD_HUZ39_RS24425_STEFF_3|unnamed1 insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 82840.44 Da        Isoelectric Point: 5.1644

>WP_017901267.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
IQQHMQRREEVNINVHRERGEDVEPGDDF

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 73068..104137

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ39_RS24425 (HUZ39_24255) 73068..75257 - 2190 WP_017901267 type IV conjugative transfer system coupling protein TraD virb4
HUZ39_RS24430 (HUZ39_24260) 75308..76045 - 738 WP_000199905 hypothetical protein -
HUZ39_RS24435 (HUZ39_24265) 76248..76979 - 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HUZ39_RS24440 (HUZ39_24270) 77028..77513 - 486 WP_000605870 hypothetical protein -
HUZ39_RS24445 (HUZ39_24275) 77529..80351 - 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HUZ39_RS24450 (HUZ39_24280) 80348..81721 - 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HUZ39_RS24455 (HUZ39_24285) 81708..82100 - 393 WP_000660699 F-type conjugal transfer protein TrbF -
HUZ39_RS24460 (HUZ39_24290) 82081..82428 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HUZ39_RS24465 (HUZ39_24295) 82358..82903 - 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ39_RS24470 (HUZ39_24300) 82890..83174 - 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HUZ39_RS24475 (HUZ39_24305) 83293..83637 - 345 WP_000556796 conjugal transfer protein TrbA -
HUZ39_RS24480 (HUZ39_24310) 83651..84394 - 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ39_RS24485 (HUZ39_24315) 84387..84644 - 258 WP_000864353 conjugal transfer protein TrbE -
HUZ39_RS24490 (HUZ39_24320) 84671..86521 - 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ39_RS24495 (HUZ39_24325) 86518..87156 - 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ39_RS24500 (HUZ39_24330) 87165..87470 - 306 WP_000224416 hypothetical protein -
HUZ39_RS24505 (HUZ39_24335) 87500..88492 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HUZ39_RS24510 (HUZ39_24340) 88489..89121 - 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HUZ39_RS24515 (HUZ39_24345) 89118..89504 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HUZ39_RS24520 (HUZ39_24350) 89501..91312 - 1812 Protein_103 type IV secretion system protein TraC -
HUZ39_RS24525 (HUZ39_24355) 91502..93043 + 1542 WP_001298859 IS21-like element ISEc12 family transposase -
HUZ39_RS24530 (HUZ39_24360) 93058..93804 + 747 WP_001016257 IS21-like element ISEc12 family helper ATPase IstB -
HUZ39_RS24535 (HUZ39_24365) 93815..94717 - 903 Protein_106 TraC family protein -
HUZ39_RS24540 (HUZ39_24370) 94843..95190 - 348 WP_000836682 hypothetical protein -
HUZ39_RS24545 (HUZ39_24375) 95218..95436 - 219 WP_000556745 hypothetical protein -
HUZ39_RS24550 (HUZ39_24380) 95516..95998 - 483 WP_204084453 hypothetical protein -
HUZ39_RS24555 (HUZ39_24385) 95991..96404 - 414 WP_000549589 hypothetical protein -
HUZ39_RS24560 (HUZ39_24390) 96397..96618 - 222 WP_001278683 conjugal transfer protein TraR -
HUZ39_RS24565 (HUZ39_24395) 96753..97268 - 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HUZ39_RS24570 (HUZ39_24400) 97265..97585 - 321 WP_001057307 conjugal transfer protein TrbD -
HUZ39_RS24575 (HUZ39_24405) 97572..98138 - 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HUZ39_RS24580 (HUZ39_24410) 98128..99579 - 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HUZ39_RS24585 (HUZ39_24415) 99579..100307 - 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HUZ39_RS24590 (HUZ39_24420) 100294..100860 - 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HUZ39_RS24595 (HUZ39_24425) 100882..101193 - 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HUZ39_RS24600 (HUZ39_24430) 101208..101567 - 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HUZ39_RS24605 (HUZ39_24435) 101600..101827 - 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HUZ39_RS24610 (HUZ39_24440) 101964..102635 - 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HUZ39_RS24615 (HUZ39_24445) 102829..103212 - 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ39_RS24620 (HUZ39_24450) 103535..104137 + 603 WP_000243713 transglycosylase SLT domain-containing protein -
HUZ39_RS24625 (HUZ39_24455) 104434..105255 - 822 WP_001234445 DUF932 domain-containing protein -
HUZ39_RS24630 (HUZ39_24460) 105366..105662 - 297 WP_001272251 hypothetical protein -
HUZ39_RS24635 (HUZ39_24465) 105962..106258 + 297 Protein_126 hypothetical protein -
HUZ39_RS24640 (HUZ39_24470) 106577..106702 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ39_RS24645 106644..106793 - 150 Protein_128 plasmid maintenance protein Mok -
HUZ39_RS24650 (HUZ39_24475) 106815..106994 + 180 WP_001309233 hypothetical protein -
HUZ39_RS24655 (HUZ39_24480) 107015..107734 - 720 WP_001276217 plasmid SOS inhibition protein A -
HUZ39_RS24660 (HUZ39_24485) 107731..108165 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   4949 GenBank   NZ_CP055200
Plasmid name   STEFF_3|unnamed1 Incompatibility group   IncFIB
Plasmid size   137403 bp Coordinate of oriT [Strand]   103484..103569 [+]
Host baterium   Shigella flexneri strain STEFF_3

Cargo genes

Drug resistance gene   tet(M), ant(3'')-Ia, cmlA1, aadA2, dfrA12, floR, blaTEM-30, sul3, aph(3')-Ia, tet(A), sul2, erm(42)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -