Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103206
Name   oriT_2020CK-00200|unnamed5 in_silico
Organism   Klebsiella oxytoca strain 2020CK-00200
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP115684 (44699..44799 [+], 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_2020CK-00200|unnamed5
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2400 GenBank   WP_001749977
Name   TrwC_PF584_RS00255_2020CK-00200|unnamed5 insolico UniProt ID   A0A5C2CVP7
Length   1080 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1080 a.a.        Molecular weight: 120419.59 Da        Isoelectric Point: 6.5483

>WP_001749977.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLSQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEHEEGGHEI

  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 A0A5C2CVP7


Auxiliary protein

ID   1014 GenBank   WP_001749975
Name   WP_001749975_2020CK-00200|unnamed5 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   2158 GenBank   WP_001749976
Name   t4cp2_PF584_RS00260_2020CK-00200|unnamed5 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: 57679.73 Da        Isoelectric Point: 9.5788

>WP_001749976.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Gammaproteobacteria]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVSARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELRDI

  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: 24023..44132

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PF584_RS00120 (PF584_34105) 20174..20878 + 705 WP_001067855 IS6-like element IS26 family transposase -
PF584_RS00125 (PF584_34110) 20884..22197 + 1314 WP_073520341 HAMP domain-containing methyl-accepting chemotaxis protein -
PF584_RS00130 (PF584_34115) 22591..22824 - 234 WP_001191790 hypothetical protein -
PF584_RS00135 (PF584_34120) 22938..23252 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
PF584_RS00140 (PF584_34125) 23249..23593 - 345 WP_001749964 hypothetical protein -
PF584_RS00145 (PF584_34130) 23609..23980 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
PF584_RS00150 (PF584_34135) 24023..24757 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
PF584_RS00155 (PF584_34140) 24766..25047 + 282 WP_000440698 transcriptional repressor KorA -
PF584_RS00160 (PF584_34145) 25057..25350 + 294 WP_001749962 hypothetical protein virB2
PF584_RS00165 (PF584_34150) 25400..25717 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
PF584_RS00170 (PF584_34155) 25717..28317 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
PF584_RS00175 (PF584_34160) 28335..29048 + 714 WP_001749960 type IV secretion system protein virB5
PF584_RS00180 (PF584_34165) 29056..29283 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
PF584_RS00185 (PF584_34170) 29299..30339 + 1041 WP_001749958 type IV secretion system protein virB6
PF584_RS00190 30410..30568 + 159 WP_012561180 hypothetical protein -
PF584_RS00195 (PF584_34175) 30558..31256 + 699 WP_000646594 type IV secretion system protein virB8
PF584_RS00200 (PF584_34180) 31267..32151 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
PF584_RS00205 (PF584_34185) 32151..33311 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
PF584_RS00210 (PF584_34190) 33353..34348 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
PF584_RS00215 (PF584_34195) 34348..34881 + 534 WP_000792636 phospholipase D family protein -
PF584_RS00220 (PF584_34200) 35055..35240 - 186 WP_315970982 DUF6710 family protein -
PF584_RS00225 (PF584_34205) 35445..35768 - 324 WP_226331933 DUF6710 family protein -
PF584_RS00230 (PF584_34210) 36079..36321 + 243 WP_000844627 transposase -
PF584_RS00235 (PF584_34215) 36353..37003 - 651 WP_000164043 tetracycline resistance transcriptional repressor TetR(A) -
PF584_RS00240 (PF584_34220) 37109..38308 + 1200 WP_012579085 tetracycline efflux MFS transporter Tet(A) -
PF584_RS00245 (PF584_34225) 38340..38993 - 654 Protein_48 EamA family transporter -
PF584_RS00250 (PF584_34230) 39188..39361 - 174 WP_001749978 hypothetical protein -
PF584_RS00255 (PF584_34235) 39361..42603 - 3243 WP_001749977 MobF family relaxase -
PF584_RS00260 (PF584_34240) 42603..44132 - 1530 WP_001749976 type IV secretion system DNA-binding domain-containing protein virb4
PF584_RS00265 (PF584_34245) 44134..44550 - 417 WP_001749975 hypothetical protein -
PF584_RS00270 (PF584_34250) 45041..45460 + 420 WP_001749974 plasmid stabilization protein StbA -
PF584_RS00275 (PF584_34255) 45469..46185 + 717 WP_001749973 StbB family protein -
PF584_RS00280 (PF584_34260) 46187..46555 + 369 WP_000414913 plasmid stabilization protein StbC -
PF584_RS00285 (PF584_34265) 46737..47069 + 333 WP_272487262 hypothetical protein -
PF584_RS00290 (PF584_34270) 47180..47500 - 321 WP_001749971 protein CcgAII -
PF584_RS00295 (PF584_34275) 47555..47734 - 180 WP_000214483 protein CcgAI -
PF584_RS00300 (PF584_34280) 48461..48970 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   3649 GenBank   NZ_CP115684
Plasmid name   2020CK-00200|unnamed5 Incompatibility group   IncN
Plasmid size   57856 bp Coordinate of oriT [Strand]   44699..44799 [+]
Host baterium   Klebsiella oxytoca strain 2020CK-00200

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, blaOXA-1, catB3, qacE, sul1, qnrS1, blaLAP-2, tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -