Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120369
Name   oriT_pNDM1-CBG in_silico
Organism   Enterobacter cloacae strain CBG15936
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP046118 (49494..49594 [+], 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_pNDM1-CBG
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12817 GenBank   WP_012561166
Name   mobF_GJ694_RS24635_pNDM1-CBG 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   7234 GenBank   WP_001749975
Name   WP_001749975_pNDM1-CBG 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   15060 GenBank   WP_021740568
Name   t4cp2_GJ694_RS24640_pNDM1-CBG 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: 57738.89 Da        Isoelectric Point: 9.6550

>WP_021740568.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacteriaceae]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVILWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
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: 12340..22665

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GJ694_RS24405 (GJ694_24405) 8185..9618 - 1434 WP_001288432 DNA cytosine methyltransferase -
GJ694_RS24410 (GJ694_24410) 9717..9989 + 273 Protein_10 IS1 family transposase -
GJ694_RS24415 (GJ694_24415) 10000..10206 - 207 WP_001749967 hypothetical protein -
GJ694_RS24420 (GJ694_24420) 10211..10858 - 648 WP_015344958 restriction endonuclease -
GJ694_RS24425 (GJ694_24425) 10908..11219 - 312 WP_001452736 hypothetical protein -
GJ694_RS24430 (GJ694_24430) 11255..11569 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
GJ694_RS24435 (GJ694_24435) 11566..11910 - 345 WP_001749964 hypothetical protein -
GJ694_RS24440 (GJ694_24440) 11926..12297 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
GJ694_RS24445 (GJ694_24445) 12340..13074 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
GJ694_RS24450 (GJ694_24450) 13083..13364 + 282 WP_000440698 transcriptional repressor KorA -
GJ694_RS24455 (GJ694_24455) 13374..13667 + 294 WP_001749962 hypothetical protein virB2
GJ694_RS24460 (GJ694_24460) 13717..14034 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
GJ694_RS24465 (GJ694_24465) 14034..16634 + 2601 WP_154694013 VirB4 family type IV secretion/conjugal transfer ATPase virb4
GJ694_RS24470 (GJ694_24470) 16652..17365 + 714 WP_001749960 type IV secretion system protein virB5
GJ694_RS24475 (GJ694_24475) 17373..17600 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
GJ694_RS24480 (GJ694_24480) 17616..18656 + 1041 WP_001749958 type IV secretion system protein virB6
GJ694_RS25075 18757..18885 + 129 WP_071882546 conjugal transfer protein TraN -
GJ694_RS24485 (GJ694_24485) 18875..19573 + 699 WP_000646594 virB8 family protein virB8
GJ694_RS24490 (GJ694_24490) 19584..20468 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
GJ694_RS24495 (GJ694_24495) 20468..21628 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
GJ694_RS24500 (GJ694_24500) 21670..22665 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
GJ694_RS24505 (GJ694_24505) 22665..23198 + 534 WP_000792636 phospholipase D family protein -
GJ694_RS25080 23372..23659 - 288 Protein_31 DUF6710 family protein -
GJ694_RS24510 (GJ694_24510) 23926..24105 + 180 Protein_32 helix-turn-helix domain-containing protein -
GJ694_RS24515 (GJ694_24515) 24170..24874 + 705 WP_001067855 IS6-like element IS26 family transposase -
GJ694_RS24520 (GJ694_24520) 24928..25559 - 632 Protein_34 transposase -
GJ694_RS24525 (GJ694_24525) 25954..26610 + 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
GJ694_RS24530 (GJ694_24530) 26929..27543 - 615 WP_014839983 recombinase family protein -

Host bacterium

ID   20798 GenBank   NZ_CP046118
Plasmid name   pNDM1-CBG Incompatibility group   IncN
Plasmid size   62663 bp Coordinate of oriT [Strand]   49494..49594 [+]
Host baterium   Enterobacter cloacae strain CBG15936

Cargo genes

Drug resistance gene   dfrA14, qnrS1, blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -