Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114798
Name   oriT_254_1_EW_B|plas1 in_silico
Organism   Escherichia albertii strain 254_1_EW_B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099869 (40220..40343 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 88..93, 105..110  (ATAAAT..ATTTAT)
 41..48, 61..68  (AAAAACAA..TTGTTTTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_254_1_EW_B|plas1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTGAATCATTAGCTTATGTTATAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   5561 GenBank   WP_001254385
Name   WP_001254385_254_1_EW_B|plas1 insolico UniProt ID   A0A1Q9L2K4
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8975.08 Da        Isoelectric Point: 10.1422

>WP_001254385.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVAEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A1Q9L2K4

ID   5562 GenBank   WP_000124979
Name   WP_000124979_254_1_EW_B|plas1 insolico UniProt ID   Q5JBL6
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14456.50 Da        Isoelectric Point: 5.2973

>WP_000124979.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB Q5JBL6


T4CP

ID   11036 GenBank   WP_153449148
Name   traD_NIZ25_RS23575_254_1_EW_B|plas1 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: 83934.58 Da        Isoelectric Point: 5.0504

>WP_153449148.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Escherichia]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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   11037 GenBank   WP_001064248
Name   traC_NIZ25_RS23665_254_1_EW_B|plas1 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99269.03 Da        Isoelectric Point: 6.1932

>WP_001064248.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 14190..40915

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NIZ25_RS23575 (NIZ25_23555) 14190..16406 - 2217 WP_153449148 type IV conjugative transfer system coupling protein TraD virb4
NIZ25_RS23580 (NIZ25_23560) 16659..17390 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
NIZ25_RS23585 (NIZ25_23565) 17422..17925 - 504 WP_000605510 hypothetical protein -
NIZ25_RS23590 (NIZ25_23570) 17940..20762 - 2823 WP_011251382 conjugal transfer mating-pair stabilization protein TraG traG
NIZ25_RS23595 (NIZ25_23575) 20759..22132 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
NIZ25_RS23600 (NIZ25_23580) 22132..22494 - 363 WP_001443292 P-type conjugative transfer protein TrbJ -
NIZ25_RS23605 (NIZ25_23585) 22424..22969 - 546 WP_000059847 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NIZ25_RS23610 (NIZ25_23590) 22956..23240 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
NIZ25_RS23615 (NIZ25_23595) 23359..23706 - 348 WP_001287895 conjugal transfer protein TrbA -
NIZ25_RS23620 (NIZ25_23600) 23722..24465 - 744 WP_001030376 type-F conjugative transfer system pilin assembly protein TraF traF
NIZ25_RS23625 (NIZ25_23605) 24458..24715 - 258 WP_000864325 conjugal transfer protein TrbE -
NIZ25_RS23630 (NIZ25_23610) 24742..26550 - 1809 WP_000821818 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NIZ25_RS23635 (NIZ25_23615) 26547..27185 - 639 WP_001104248 type-F conjugative transfer system pilin assembly protein TrbC trbC
NIZ25_RS23640 (NIZ25_23620) 27213..27665 - 453 WP_000069427 hypothetical protein -
NIZ25_RS23645 (NIZ25_23625) 27695..28156 - 462 WP_000277845 hypothetical protein -
NIZ25_RS23650 (NIZ25_23630) 28182..29174 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
NIZ25_RS23655 (NIZ25_23635) 29171..29803 - 633 WP_001203745 type-F conjugative transfer system protein TraW traW
NIZ25_RS23660 (NIZ25_23640) 29800..30186 - 387 WP_000214096 type-F conjugative transfer system protein TrbI -
NIZ25_RS23665 (NIZ25_23645) 30183..32810 - 2628 WP_001064248 type IV secretion system protein TraC virb4
NIZ25_RS23670 (NIZ25_23650) 32970..33191 - 222 WP_001278689 conjugal transfer protein TraR -
NIZ25_RS23675 (NIZ25_23655) 33325..33840 - 516 WP_000809906 type IV conjugative transfer system lipoprotein TraV traV
NIZ25_RS23680 (NIZ25_23660) 33837..34088 - 252 WP_001038341 conjugal transfer protein TrbG -
NIZ25_RS23685 (NIZ25_23665) 34085..34402 - 318 WP_001057292 conjugal transfer protein TrbD virb4
NIZ25_RS23690 (NIZ25_23670) 34399..34971 - 573 WP_000002794 conjugal transfer pilus-stabilizing protein TraP -
NIZ25_RS23695 (NIZ25_23675) 34961..36388 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
NIZ25_RS23700 (NIZ25_23680) 36388..37116 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
NIZ25_RS23705 (NIZ25_23685) 37103..37669 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
NIZ25_RS23710 (NIZ25_23690) 37691..38002 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
NIZ25_RS23715 (NIZ25_23695) 38017..38376 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
NIZ25_RS23720 (NIZ25_23700) 38410..38637 - 228 WP_001254385 conjugal transfer relaxosome protein TraY -
NIZ25_RS23725 (NIZ25_23705) 38731..39417 - 687 WP_000332493 PAS domain-containing protein -
NIZ25_RS23730 (NIZ25_23710) 39608..39991 - 384 WP_000124979 conjugal transfer relaxosome DNA-binding protein TraM -
NIZ25_RS23735 (NIZ25_23715) 40268..40915 + 648 WP_256876177 transglycosylase SLT domain-containing protein virB1
NIZ25_RS23740 (NIZ25_23720) 41212..42033 - 822 WP_001234469 DUF932 domain-containing protein -
NIZ25_RS23745 (NIZ25_23725) 42153..42440 - 288 WP_000107535 hypothetical protein -
NIZ25_RS23750 (NIZ25_23730) 42465..42671 - 207 WP_000547971 hypothetical protein -
NIZ25_RS23755 (NIZ25_23735) 42741..42914 + 174 Protein_48 hypothetical protein -
NIZ25_RS23760 (NIZ25_23740) 42912..43142 - 231 WP_256876178 hypothetical protein -
NIZ25_RS23765 (NIZ25_23745) 43362..43487 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
NIZ25_RS23770 (NIZ25_23750) 43429..43578 - 150 Protein_51 plasmid maintenance protein Mok -
NIZ25_RS23775 (NIZ25_23755) 43600..43788 + 189 WP_001299721 hypothetical protein -
NIZ25_RS23780 (NIZ25_23760) 43757..44519 - 763 Protein_53 plasmid SOS inhibition protein A -
NIZ25_RS23785 (NIZ25_23765) 44516..44950 - 435 WP_000845873 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   15233 GenBank   NZ_CP099869
Plasmid name   254_1_EW_B|plas1 Incompatibility group   IncFII
Plasmid size   105541 bp Coordinate of oriT [Strand]   40220..40343 [-]
Host baterium   Escherichia albertii strain 254_1_EW_B

Cargo genes

Drug resistance gene   -
Virulence gene   espL2
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -