Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119509
Name   oriT_pC9_003 in_silico
Organism   Klebsiella aerogenes strain C9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP042533 (37487..37587 [+], 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_pC9_003
TATTTATTTTTTTATCTTTTAAATCAGTACGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12324 GenBank   WP_012561142
Name   mobF_FR830_RS26290_pC9_003 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   7018 GenBank   WP_001749975
Name   WP_001749975_pC9_003 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   14472 GenBank   WP_000342688
Name   t4cp2_FR830_RS26295_pC9_003 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: 19056..36920

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FR830_RS26155 (FR830_26150) 14901..16334 - 1434 WP_001288432 DNA cytosine methyltransferase -
FR830_RS26160 (FR830_26155) 16433..16705 + 273 Protein_16 IS1 family transposase -
FR830_RS26165 (FR830_26160) 16716..16922 - 207 WP_001749967 hypothetical protein -
FR830_RS26170 (FR830_26165) 16927..17568 - 642 WP_012561158 restriction endonuclease -
FR830_RS26175 (FR830_26170) 17624..17935 - 312 WP_013279382 hypothetical protein -
FR830_RS26180 (FR830_26175) 17971..18285 - 315 WP_016338363 TrbM/KikA/MpfK family conjugal transfer protein -
FR830_RS26185 (FR830_26180) 18282..18626 - 345 WP_012561155 hypothetical protein -
FR830_RS26190 (FR830_26185) 18642..19019 - 378 WP_193567606 H-NS family nucleoid-associated regulatory protein -
FR830_RS26195 (FR830_26190) 19056..19793 + 738 WP_013279384 lytic transglycosylase domain-containing protein virB1
FR830_RS26200 (FR830_26195) 19802..20083 + 282 WP_016338364 transcriptional repressor KorA -
FR830_RS26205 (FR830_26200) 20093..20386 + 294 WP_001749962 hypothetical protein virB2
FR830_RS26210 (FR830_26205) 20436..20753 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
FR830_RS26215 (FR830_26210) 20753..23353 + 2601 WP_012561149 VirB4 family type IV secretion/conjugal transfer ATPase virb4
FR830_RS26220 (FR830_26215) 23371..24084 + 714 WP_001749960 type IV secretion system protein virB5
FR830_RS26225 (FR830_26220) 24092..24319 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
FR830_RS26230 (FR830_26225) 24335..25375 + 1041 WP_001749958 type IV secretion system protein virB6
FR830_RS26895 (FR830_26230) 25476..25604 + 129 WP_071882546 conjugal transfer protein TraN -
FR830_RS26240 (FR830_26235) 25594..26292 + 699 WP_000646594 virB8 family protein virB8
FR830_RS26245 (FR830_26240) 26303..27187 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
FR830_RS26250 (FR830_26245) 27187..28347 + 1161 WP_012561145 type IV secretion system protein VirB10 virB10
FR830_RS26255 (FR830_26250) 28389..29384 + 996 WP_012561144 ATPase, T2SS/T4P/T4SS family virB11
FR830_RS26260 (FR830_26255) 29384..29917 + 534 WP_000792636 phospholipase D family protein -
FR830_RS26265 (FR830_26260) 30090..30404 - 315 WP_000091613 hypothetical protein -
FR830_RS26270 (FR830_26265) 30659..31015 - 357 WP_000215515 cupin domain-containing protein -
FR830_RS26275 (FR830_26270) 31005..31406 - 402 WP_001293886 DUF86 domain-containing protein -
FR830_RS26280 (FR830_26275) 31403..31693 - 291 WP_001247892 nucleotidyltransferase family protein -
FR830_RS26285 (FR830_26280) 31757..32155 - 399 WP_012561143 DUF6710 family protein -
FR830_RS26290 (FR830_26285) 32155..35391 - 3237 WP_012561142 MobF family relaxase -
FR830_RS26295 (FR830_26290) 35391..36920 - 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
FR830_RS26300 (FR830_26295) 36922..37338 - 417 WP_001749975 hypothetical protein -
FR830_RS26305 (FR830_26300) 37895..38281 + 387 WP_013279398 plasmid stabilization protein StbA -
FR830_RS26310 (FR830_26305) 38290..39006 + 717 WP_012561139 StbB family protein -
FR830_RS26315 (FR830_26310) 39008..39376 + 369 WP_012561138 plasmid stabilization protein StbC -
FR830_RS26320 (FR830_26315) 39577..39921 + 345 WP_012561137 hypothetical protein -
FR830_RS26325 (FR830_26320) 40383..40562 - 180 WP_012561134 protein CcgAI -
FR830_RS26330 (FR830_26325) 41393..41902 - 510 WP_012561131 antirestriction protein ArdA -

Host bacterium

ID   19939 GenBank   NZ_CP042533
Plasmid name   pC9_003 Incompatibility group   IncN
Plasmid size   51987 bp Coordinate of oriT [Strand]   37487..37587 [+]
Host baterium   Klebsiella aerogenes strain C9

Cargo genes

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