Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103166
Name   oriT_pKm38_N in_silico
Organism   Klebsiella michiganensis strain 97_58
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY128484 (56719..56819 [+], 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_pKm38_N
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2369 GenBank   WP_012561166
Name   TrwC_HTK38_RS00295_pKm38_N 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   999 GenBank   WP_001749975
Name   WP_001749975_pKm38_N 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   2112 GenBank   WP_000342688
Name   t4cp2_HTK38_RS00300_pKm38_N 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: 11855..22180

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTK38_RS00045 7700..9133 - 1434 WP_001288432 DNA cytosine methyltransferase -
HTK38_RS00050 9232..9504 + 273 Protein_10 IS1 family transposase -
HTK38_RS00055 9515..9721 - 207 WP_001749967 hypothetical protein -
HTK38_RS00060 9726..10373 - 648 WP_012561184 restriction endonuclease -
HTK38_RS00065 10423..10656 - 234 WP_001191790 hypothetical protein -
HTK38_RS00070 10770..11084 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTK38_RS00075 11081..11425 - 345 WP_001749964 hypothetical protein -
HTK38_RS00080 11441..11812 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTK38_RS00085 11855..12589 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTK38_RS00090 12598..12879 + 282 WP_000440698 transcriptional repressor KorA -
HTK38_RS00095 12889..13182 + 294 WP_001749962 hypothetical protein virB2
HTK38_RS00100 13232..13549 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTK38_RS00105 13549..16149 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTK38_RS00110 16167..16880 + 714 WP_001749960 type IV secretion system protein virB5
HTK38_RS00115 16888..17115 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTK38_RS00120 17131..18171 + 1041 WP_001749958 type IV secretion system protein virB6
HTK38_RS00125 18242..18400 + 159 WP_012561180 hypothetical protein -
HTK38_RS00130 18390..19088 + 699 WP_000646594 type IV secretion system protein virB8
HTK38_RS00135 19099..19983 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTK38_RS00140 19983..21143 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTK38_RS00145 21185..22180 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTK38_RS00150 22180..22713 + 534 WP_000792636 phospholipase D family protein -
HTK38_RS00425 22887..23174 - 288 Protein_31 DUF6710 family protein -
HTK38_RS00160 23441..23620 + 180 Protein_32 helix-turn-helix domain-containing protein -
HTK38_RS00165 23685..24245 + 561 Protein_33 IS6-like element IS26 family transposase -
HTK38_RS00170 24265..26376 - 2112 Protein_34 Tn3-like element Tn3 family transposase -

Host bacterium

ID   3609 GenBank   NZ_KY128484
Plasmid name   pKm38_N Incompatibility group   IncN
Plasmid size   69888 bp Coordinate of oriT [Strand]   56719..56819 [+]
Host baterium   Klebsiella michiganensis strain 97_58

Cargo genes

Drug resistance gene   dfrA14, blaKPC-2, aac(6')-Ib, ant(3'')-Ia, blaOXA-9, blaTEM-1A, aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -