Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103050
Name   oriT_pIMP-GZ1058 in_silico
Organism   Escherichia coli strain CRE1058
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU051709 (13790..13890 [-], 101 nt)
oriT length   101 nt
IRs (inverted repeats)      80..85, 91..96  (AAAAAA..TTTTTT)
 20..26, 38..44  (TAAATCA..TGATTTA)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 101 nt

>oriT_pIMP-GZ1058
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2281 GenBank   WP_012561166
Name   TrwC_HTG37_RS00110_pIMP-GZ1058 insolico UniProt ID   D7RU03
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120141.30 Da        Isoelectric Point: 6.5229

>WP_012561166.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure


Source ID Structure
AlphaFold DB D7RU03


Auxiliary protein

ID   940 GenBank   WP_001749975
Name   WP_001749975_pIMP-GZ1058 insolico UniProt ID   A0A5C2CVS6
Length   138 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15332.60 Da        Isoelectric Point: 5.9670

>WP_001749975.1 MULTISPECIES: hypothetical protein [Gammaproteobacteria]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A5C2CVS6


T4CP

ID   1984 GenBank   WP_000342688
Name   t4cp2_HTG37_RS00105_pIMP-GZ1058 insolico UniProt ID   _
Length   509 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 509 a.a.        Molecular weight: 57762.87 Da        Isoelectric Point: 9.6551

>WP_000342688.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(113-489)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 27874..38199

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTG37_RS00145 22996..23610 + 615 WP_014839983 recombinase family protein -
HTG37_RS00150 23929..24585 - 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
HTG37_RS00155 24980..25611 + 632 Protein_30 transposase -
HTG37_RS00160 25665..26369 - 705 WP_001067855 IS6-like element IS26 family transposase -
HTG37_RS00165 26434..26613 - 180 Protein_32 helix-turn-helix domain-containing protein -
HTG37_RS00355 26880..27167 + 288 Protein_33 DUF6710 family protein -
HTG37_RS00175 27341..27874 - 534 WP_000792636 phospholipase D family protein -
HTG37_RS00180 27874..28869 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTG37_RS00185 28911..30071 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTG37_RS00190 30071..30955 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTG37_RS00195 30966..31664 - 699 WP_000646594 type IV secretion system protein virB8
HTG37_RS00200 31654..31812 - 159 WP_012561180 hypothetical protein -
HTG37_RS00205 31883..32923 - 1041 WP_001749958 type IV secretion system protein virB6
HTG37_RS00210 32939..33166 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTG37_RS00215 33174..33938 - 765 WP_013149461 type IV secretion system protein virB5
HTG37_RS00220 33905..36505 - 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTG37_RS00225 36505..36822 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTG37_RS00230 36872..37165 - 294 WP_001749962 hypothetical protein virB2
HTG37_RS00235 37175..37456 - 282 WP_000440698 transcriptional repressor KorA -
HTG37_RS00240 37465..38199 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTG37_RS00245 38242..38613 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTG37_RS00250 38629..38973 + 345 WP_001749964 hypothetical protein -
HTG37_RS00255 38970..39284 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTG37_RS00260 39398..39631 + 234 WP_001191790 hypothetical protein -
HTG37_RS00265 39681..40328 + 648 WP_015344958 restriction endonuclease -
HTG37_RS00270 40333..40539 + 207 WP_001749967 hypothetical protein -
HTG37_RS00275 40550..40822 - 273 Protein_54 IS1 family transposase -
HTG37_RS00280 40921..42354 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   3493 GenBank   NZ_KU051709
Plasmid name   pIMP-GZ1058 Incompatibility group   IncN
Plasmid size   51600 bp Coordinate of oriT [Strand]   13790..13890 [-]
Host baterium   Escherichia coli strain CRE1058

Cargo genes

Drug resistance gene   qnrS1, blaIMP-4
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -