Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113927
Name   oriT_pP10159-2 in_silico
Organism   Citrobacter freundii strain P10159
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MF072962 (38125..38225 [+], 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_pP10159-2
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8941 GenBank   WP_012561166
Name   mobF_HTN40_RS00225_pP10159-2 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   5230 GenBank   WP_001749975
Name   WP_001749975_pP10159-2 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   10385 GenBank   WP_000342688
Name   t4cp2_HTN40_RS00230_pP10159-2 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: 14048..24373

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTN40_RS00060 9893..11326 - 1434 WP_001288432 DNA cytosine methyltransferase -
HTN40_RS00065 11425..11697 + 273 Protein_13 IS1 family transposase -
HTN40_RS00070 11708..11914 - 207 WP_001749967 hypothetical protein -
HTN40_RS00075 11919..12566 - 648 WP_015344958 restriction endonuclease -
HTN40_RS00080 12616..12849 - 234 WP_001191790 hypothetical protein -
HTN40_RS00085 12963..13277 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTN40_RS00090 13274..13618 - 345 WP_001749964 hypothetical protein -
HTN40_RS00095 13634..14005 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTN40_RS00100 14048..14782 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTN40_RS00105 14791..15072 + 282 WP_000440698 transcriptional repressor KorA -
HTN40_RS00110 15082..15375 + 294 WP_001749962 hypothetical protein virB2
HTN40_RS00115 15425..15742 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTN40_RS00120 15742..18342 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTN40_RS00125 18360..19073 + 714 WP_001749960 type IV secretion system protein virB5
HTN40_RS00130 19081..19308 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTN40_RS00135 19324..20364 + 1041 WP_001749958 type IV secretion system protein virB6
HTN40_RS00140 20435..20593 + 159 WP_012561180 hypothetical protein -
HTN40_RS00145 20583..21281 + 699 WP_000646594 virB8 family protein virB8
HTN40_RS00150 21292..22176 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTN40_RS00155 22176..23336 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTN40_RS00160 23378..24373 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTN40_RS00165 24373..24906 + 534 WP_000792636 phospholipase D family protein -
HTN40_RS00350 25080..25367 - 288 Protein_34 DUF6710 family protein -
HTN40_RS00175 25634..25813 + 180 Protein_35 helix-turn-helix domain-containing protein -
HTN40_RS00180 25878..26582 + 705 WP_001067855 IS6-like element IS26 family transposase -
HTN40_RS00185 26636..27267 - 632 Protein_37 transposase -
HTN40_RS00190 27662..28318 + 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
HTN40_RS00195 28637..29251 - 615 WP_014839983 recombinase family protein -

Host bacterium

ID   14362 GenBank   NZ_MF072962
Plasmid name   pP10159-2 Incompatibility group   IncN
Plasmid size   51104 bp Coordinate of oriT [Strand]   38125..38225 [+]
Host baterium   Citrobacter freundii strain P10159

Cargo genes

Drug resistance gene   blaIMP-4, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -