Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121582
Name   oriT_pKOX101_3 in_silico
Organism   Klebsiella michiganensis strain Kox101
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP089410 (63481..63581 [-], 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_pKOX101_3
TATTTATTTTTTTATCTTTTAAATCAGTACGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13609 GenBank   WP_012561142
Name   mobF_LUW94_RS30790_pKOX101_3 insolico UniProt ID   A0A1S6KKJ9
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120195.37 Da        Isoelectric Point: 6.5230

>WP_012561142.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKADMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

AAA domain (AAA_30)

(477-653)

TrwC relaxase (TrwC)

(16-287)


  Protein structure


Source ID Structure
AlphaFold DB A0A1S6KKJ9


Auxiliary protein

ID   7500 GenBank   WP_001749975
Name   WP_001749975_pKOX101_3 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   15908 GenBank   WP_000342688
Name   t4cp2_LUW94_RS31170_pKOX101_3 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: 20900..31228

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LUW94_RS30880 (LUW94_30880) 16177..17013 - 837 WP_040119816 branched-chain amino acid ABC transporter permease -
LUW94_RS30885 (LUW94_30885) 17027..18181 - 1155 WP_049101017 substrate-binding protein -
LUW94_RS30890 (LUW94_30890) 18178..19092 - 915 WP_049101016 nitrilase family protein -
LUW94_RS31255 19430..19678 - 249 WP_305955805 hypothetical protein -
LUW94_RS30895 (LUW94_30895) 19660..20640 - 981 WP_032216024 IS5-like element ISKpn26 family transposase -
LUW94_RS30900 (LUW94_30900) 20754..20900 - 147 Protein_23 phospholipase D family protein -
LUW94_RS30905 (LUW94_30905) 20900..21895 - 996 WP_012561144 ATPase, T2SS/T4P/T4SS family virB11
LUW94_RS30910 (LUW94_30910) 21937..23097 - 1161 WP_012561145 type IV secretion system protein VirB10 virB10
LUW94_RS30915 (LUW94_30915) 23097..23981 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
LUW94_RS30920 (LUW94_30920) 23992..24690 - 699 WP_000646594 virB8 family protein virB8
LUW94_RS31260 24680..24838 - 159 WP_012561180 hypothetical protein -
LUW94_RS30925 (LUW94_30925) 24909..25949 - 1041 WP_001749958 type IV secretion system protein virB6
LUW94_RS30930 (LUW94_30930) 25965..26192 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
LUW94_RS30935 (LUW94_30935) 26200..26913 - 714 WP_001749960 type IV secretion system protein virB5
LUW94_RS30940 (LUW94_30940) 26931..29531 - 2601 WP_012561149 VirB4 family type IV secretion/conjugal transfer ATPase virb4
LUW94_RS30945 (LUW94_30945) 29531..29848 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
LUW94_RS30950 (LUW94_30950) 29898..30191 - 294 WP_001749962 hypothetical protein virB2
LUW94_RS30955 (LUW94_30955) 30201..30482 - 282 WP_016338364 transcriptional repressor KorA -
LUW94_RS30960 (LUW94_30960) 30491..31228 - 738 WP_013279384 lytic transglycosylase domain-containing protein virB1
LUW94_RS30965 (LUW94_30965) 31337..31642 + 306 WP_012561154 H-NS family nucleoid-associated regulatory protein -
LUW94_RS30970 (LUW94_30970) 31658..32002 + 345 WP_012561155 hypothetical protein -
LUW94_RS30975 (LUW94_30975) 31999..32313 + 315 WP_016338363 TrbM/KikA/MpfK family conjugal transfer protein -
LUW94_RS30980 (LUW94_30980) 32349..32660 + 312 WP_013279382 hypothetical protein -
LUW94_RS30985 (LUW94_30985) 32716..33357 + 642 WP_012561158 restriction endonuclease -
LUW94_RS30990 (LUW94_30990) 33362..33568 + 207 WP_001749967 hypothetical protein -
LUW94_RS30995 (LUW94_30995) 33579..33851 - 273 Protein_43 IS1 family transposase -
LUW94_RS31000 (LUW94_31000) 33950..35383 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   22009 GenBank   NZ_CP089410
Plasmid name   pKOX101_3 Incompatibility group   IncN
Plasmid size   66593 bp Coordinate of oriT [Strand]   63481..63581 [-]
Host baterium   Klebsiella michiganensis strain Kox101

Cargo genes

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