Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104382
Name   oriT_pL2395_NDM in_silico
Organism   Citrobacter koseri strain L2395
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP118928 (54670..54770 [+], 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_pL2395_NDM
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3203 GenBank   WP_012561166
Name   mobF_PX343_RS23095_pL2395_NDM 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   1403 GenBank   WP_001749975
Name   WP_001749975_pL2395_NDM 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   3117 GenBank   WP_021740568
Name   t4cp2_PX343_RS23100_pL2395_NDM 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: 57738.89 Da        Isoelectric Point: 9.6550

>WP_021740568.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacteriaceae]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVILWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
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: 4709..15034

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PX343_RS22745 (PX343_22745) 1..720 + 720 WP_001749982 replication initiation protein -
PX343_RS22750 (PX343_22750) 1896..2450 - 555 Protein_1 recombinase family protein -
PX343_RS22755 (PX343_22755) 2500..3204 - 705 WP_001067855 IS6-like element IS26 family transposase -
PX343_RS22760 (PX343_22760) 3269..3448 - 180 Protein_3 helix-turn-helix domain-containing protein -
PX343_RS23600 3715..4002 + 288 Protein_4 DUF6710 family protein -
PX343_RS22770 (PX343_22770) 4176..4709 - 534 WP_000792636 phospholipase D family protein -
PX343_RS22775 (PX343_22775) 4709..5704 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
PX343_RS22780 (PX343_22780) 5746..6906 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
PX343_RS22785 (PX343_22785) 6906..7790 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
PX343_RS22790 (PX343_22790) 7801..8499 - 699 WP_000646594 type IV secretion system protein virB8
PX343_RS23605 8489..8647 - 159 WP_012561180 hypothetical protein -
PX343_RS22795 (PX343_22795) 8718..9758 - 1041 WP_001749958 type IV secretion system protein virB6
PX343_RS22800 (PX343_22800) 9774..10001 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
PX343_RS22805 (PX343_22805) 10009..10722 - 714 WP_001749960 type IV secretion system protein virB5
PX343_RS22810 (PX343_22810) 10740..13208 - 2469 WP_224743086 VirB4 family type IV secretion/conjugal transfer ATPase virb4
PX343_RS22815 (PX343_22815) 13340..13657 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
PX343_RS22820 (PX343_22820) 13707..14000 - 294 WP_001749962 hypothetical protein virB2
PX343_RS22825 (PX343_22825) 14010..14291 - 282 WP_000440698 transcriptional repressor KorA -
PX343_RS22830 (PX343_22830) 14300..15034 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
PX343_RS22835 (PX343_22835) 15077..15448 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
PX343_RS22840 (PX343_22840) 15464..15808 + 345 WP_001749964 hypothetical protein -
PX343_RS22845 (PX343_22845) 15805..16119 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
PX343_RS22850 (PX343_22850) 16155..16466 + 312 WP_001452736 hypothetical protein -
PX343_RS22855 (PX343_22855) 16516..17085 + 570 WP_275055905 restriction endonuclease -
PX343_RS22865 (PX343_22865) 18393..18599 + 207 WP_001749967 hypothetical protein -
PX343_RS22870 (PX343_22870) 18610..18882 - 273 Protein_26 IS1 family transposase -

Host bacterium

ID   4821 GenBank   NZ_CP118928
Plasmid name   pL2395_NDM Incompatibility group   IncN
Plasmid size   67839 bp Coordinate of oriT [Strand]   54670..54770 [+]
Host baterium   Citrobacter koseri strain L2395

Cargo genes

Drug resistance gene   dfrA14, qnrS1, blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -