Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118391
Name   oriT_p1RM9976 in_silico
Organism   Escherichia albertii strain RM9976
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP043265 (135088..135173 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..13, 21..26  (TGATTT..AAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_p1RM9976
AATTACATGATTTAAAACGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   6741 GenBank   WP_059257118
Name   WP_059257118_p1RM9976 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14535.58 Da        Isoelectric Point: 5.0277

>WP_059257118.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia albertii]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISLSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDKE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.



ID   6742 GenBank   WP_072247434
Name   WP_072247434_p1RM9976 insolico UniProt ID   _
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8556.84 Da        Isoelectric Point: 10.7978

>WP_072247434.1 conjugal transfer relaxosome protein TraY [Escherichia albertii]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLRRFPDFYNIDSIKEGTGKTDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-57)


  Protein structure



No available structure.




T4CP

ID   13675 GenBank   WP_265463417
Name   traC_FYK19_RS26245_p1RM9976 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: 99097.76 Da        Isoelectric Point: 6.0492

>WP_265463417.1 type IV secretion system protein TraC [Escherichia albertii]
MNNPLEAVTQAVNSLVTALKLPDESAKANDVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFINIVG
EMINHNPDSLYPKRHQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGG
LRQRLGSGQSAVVSYFLNITAFCRDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAARDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-770)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.



ID   13676 GenBank   WP_265463465
Name   traD_FYK19_RS26615_p1RM9976 insolico UniProt ID   _
Length   732 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 732 a.a.        Molecular weight: 83256.09 Da        Isoelectric Point: 5.1657

>WP_265463465.1 type IV conjugative transfer system coupling protein TraD [Escherichia albertii]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLMAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKSAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPREINPEMENRLSAVLAAREAEGRQMASLFEPDMPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPVSPVINDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMVAYEAWQQEN
HPGIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 134520..152161

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FYK19_RS26145 (FYK19_26650) 130875..131309 + 435 WP_001603648 conjugation system SOS inhibitor PsiB -
FYK19_RS26150 (FYK19_26655) 131306..132068 + 763 Protein_139 plasmid SOS inhibition protein A -
FYK19_RS26155 132242..132391 + 150 Protein_140 plasmid maintenance protein Mok -
FYK19_RS26160 (FYK19_26660) 132333..132458 + 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
FYK19_RS26165 132759..133017 - 259 Protein_142 hypothetical protein -
FYK19_RS26170 (FYK19_26675) 133066..133285 + 220 Protein_143 hypothetical protein -
FYK19_RS26175 (FYK19_26680) 133404..134224 + 821 Protein_144 DUF932 domain-containing protein -
FYK19_RS26180 (FYK19_26685) 134520..135077 - 558 WP_262939981 transglycosylase SLT domain-containing protein virB1
FYK19_RS26185 (FYK19_26695) 135445..135828 + 384 WP_059257118 conjugal transfer relaxosome DNA-binding protein TraM -
FYK19_RS26190 (FYK19_26700) 136023..136694 + 672 WP_059257109 conjugal transfer transcriptional regulator TraJ -
FYK19_RS26195 (FYK19_26705) 136832..137059 + 228 WP_072247434 conjugal transfer relaxosome protein TraY -
FYK19_RS26200 (FYK19_26710) 137092..137451 + 360 WP_059257108 type IV conjugative transfer system pilin TraA -
FYK19_RS26205 (FYK19_26715) 137466..137777 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
FYK19_RS26210 (FYK19_26720) 137799..138365 + 567 WP_059257107 type IV conjugative transfer system protein TraE traE
FYK19_RS26215 (FYK19_26725) 138352..139080 + 729 WP_059257106 type-F conjugative transfer system secretin TraK traK
FYK19_RS26220 (FYK19_26730) 139080..140507 + 1428 WP_059257105 F-type conjugal transfer pilus assembly protein TraB traB
FYK19_RS26225 (FYK19_26735) 140497..141081 + 585 WP_059257104 conjugal transfer pilus-stabilizing protein TraP -
FYK19_RS26230 (FYK19_26740) 141068..141388 + 321 WP_059257103 conjugal transfer protein TrbD -
FYK19_RS26235 (FYK19_26745) 141385..141900 + 516 WP_059257102 type IV conjugative transfer system lipoprotein TraV traV
FYK19_RS26240 (FYK19_26750) 142035..142256 + 222 WP_001278692 conjugal transfer protein TraR -
FYK19_RS26245 (FYK19_26755) 142416..145043 + 2628 WP_265463417 type IV secretion system protein TraC virb4
FYK19_RS26250 (FYK19_26760) 145040..145426 + 387 WP_059257100 type-F conjugative transfer system protein TrbI -
FYK19_RS26255 (FYK19_26765) 145423..146055 + 633 WP_059257099 type-F conjugative transfer system protein TraW traW
FYK19_RS26260 (FYK19_26770) 146052..147044 + 993 WP_059257098 conjugal transfer pilus assembly protein TraU traU
FYK19_RS26265 (FYK19_26775) 147085..147407 + 323 Protein_162 hypothetical protein -
FYK19_RS26270 (FYK19_26780) 147400..147852 + 453 WP_059257097 hypothetical protein -
FYK19_RS26275 (FYK19_26785) 147880..148518 + 639 WP_059257096 type-F conjugative transfer system pilin assembly protein TrbC trbC
FYK19_RS26280 (FYK19_26790) 148515..148886 + 372 WP_059257095 hypothetical protein -
FYK19_RS26285 (FYK19_26795) 148911..149333 + 423 WP_059257094 HNH endonuclease -
FYK19_RS26290 (FYK19_26800) 149330..151138 + 1809 WP_059257093 type-F conjugative transfer system mating-pair stabilization protein TraN traN
FYK19_RS26295 (FYK19_26805) 151165..151425 + 261 WP_000864323 conjugal transfer protein TrbE -
FYK19_RS26300 (FYK19_26810) 151418..152161 + 744 WP_059257092 type-F conjugative transfer system pilin assembly protein TraF traF
FYK19_RS26305 (FYK19_26815) 152175..152516 + 342 WP_023181031 conjugal transfer protein TrbA -
FYK19_RS26310 (FYK19_26820) 152497..152832 - 336 WP_059257091 hypothetical protein -
FYK19_RS26315 (FYK19_26825) 152914..153198 + 285 WP_059257090 type-F conjugative transfer system pilin chaperone TraQ -
FYK19_RS26320 (FYK19_26830) 153515..154162 - 648 WP_265463426 helix-turn-helix domain-containing protein -
FYK19_RS26325 (FYK19_26835) 154331..154567 + 237 WP_000989761 helix-turn-helix domain-containing protein -
FYK19_RS26330 (FYK19_26840) 154567..156609 + 2043 WP_265463428 Mu transposase C-terminal domain-containing protein -

Host bacterium

ID   18824 GenBank   NZ_CP043265
Plasmid name   p1RM9976 Incompatibility group   IncFII
Plasmid size   200522 bp Coordinate of oriT [Strand]   135088..135173 [-]
Host baterium   Escherichia albertii strain RM9976

Cargo genes

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