Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113498
Name   oriT_pIMP-1 in_silico
Organism   Leclercia adecarboxylata strain 17YN198
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP106962 (42419..42504 [+], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      34..41, 44..51  (AGTGCGAT..ATCGCACT)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_pIMP-1
TATTTCATTTTTTGTTTTTTTAATCAGTTAGTTAGTGCGATTCATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8648 GenBank   WP_024561907
Name   mobF_OCT50_RS23850_pIMP-1 insolico UniProt ID   H1ZMV6
Length   1072 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1072 a.a.        Molecular weight: 118896.59 Da        Isoelectric Point: 6.4636

>WP_024561907.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSYGHSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPD
TSGTENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARD
VELPQHEHENHQHDHDKEGYGL

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(16-288)

AAA domain (AAA_30)

(480-656)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(855-899)


  Protein structure


Source ID Structure
AlphaFold DB H1ZMV6


T4CP

ID   9995 GenBank   WP_032493179
Name   t4cp2_OCT50_RS23855_pIMP-1 insolico UniProt ID   _
Length   510 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 510 a.a.        Molecular weight: 57912.96 Da        Isoelectric Point: 9.5127

>WP_032493179.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERDHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGTDKRIVLDPNGEYVETFYRPGDVILSPYDKRSPGWSMFNEIRDDFDYDLYAVSIIQ
ESKERSAEEWYRYGRLIYREVSKKLLTLKRSPTMEEVMHWCTIVENEKLKEFVKGTPAEALFIKGAERAT
GSARFVLGDKLAPHLKMPAGDFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTYSQLIERYGINIAETLLGSMRSGIVMGSSRL
GKETLEQMSRALGEIEGEVEHKQGNPFQAGIGNRPRIETRTVRAVTPTEISELKNLTGYVYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(113-492)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15562..25838

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OCT50_RS23675 (OCT50_23665) 11568..12197 + 630 WP_064754415 hypothetical protein -
OCT50_RS23680 (OCT50_23670) 12284..12478 + 195 WP_050136673 hypothetical protein -
OCT50_RS23685 (OCT50_23675) 12550..12882 + 333 WP_045723726 hypothetical protein -
OCT50_RS23690 (OCT50_23680) 13069..13677 + 609 WP_000275218 recombinase family protein -
OCT50_RS23695 (OCT50_23685) 13674..13859 - 186 WP_024562121 ribbon-helix-helix domain-containing protein -
OCT50_RS23700 (OCT50_23690) 14144..14452 - 309 WP_000733764 hypothetical protein -
OCT50_RS23705 (OCT50_23695) 14456..14794 - 339 WP_032493175 hypothetical protein -
OCT50_RS23710 (OCT50_23700) 14791..15141 - 351 WP_024562120 hypothetical protein -
OCT50_RS23715 (OCT50_23705) 15145..15342 - 198 WP_001642194 H-NS family nucleoid-associated regulatory protein -
OCT50_RS23720 (OCT50_23710) 15343..15462 - 120 Protein_27 H-NS histone family protein -
OCT50_RS23725 (OCT50_23715) 15562..16344 + 783 WP_024562119 lytic transglycosylase domain-containing protein virB1
OCT50_RS23730 (OCT50_23720) 16591..16887 + 297 WP_015060075 TrbC/VirB2 family protein virB2
OCT50_RS23735 (OCT50_23725) 16927..17244 + 318 WP_000462629 type IV secretion system protein VirB3 virB3
OCT50_RS23740 (OCT50_23730) 17245..19818 + 2574 WP_032493176 VirB4 family type IV secretion/conjugal transfer ATPase virb4
OCT50_RS23745 (OCT50_23735) 19834..20535 + 702 WP_014014949 type IV secretion system protein virB5
OCT50_RS23750 (OCT50_23740) 20545..20787 + 243 WP_000858958 EexN family lipoprotein -
OCT50_RS23755 (OCT50_23745) 20804..21841 + 1038 WP_014014948 type IV secretion system protein virB6
OCT50_RS24200 21918..22049 + 132 WP_032493177 hypothetical protein -
OCT50_RS23760 (OCT50_23750) 22060..22755 + 696 WP_001208352 type IV secretion system protein virB8
OCT50_RS23765 (OCT50_23755) 22766..23653 + 888 WP_000758230 TrbG/VirB9 family P-type conjugative transfer protein virB9
OCT50_RS23770 (OCT50_23760) 23653..24786 + 1134 WP_000101920 type IV secretion system protein VirB10 virB10
OCT50_RS23775 (OCT50_23765) 24837..25838 + 1002 WP_001076634 ATPase, T2SS/T4P/T4SS family virB11
OCT50_RS23780 (OCT50_23770) 25835..26155 + 321 Protein_40 phospholipase D-like domain-containing protein -
OCT50_RS23785 (OCT50_23775) 26155..26220 + 66 Protein_41 EAL domain-containing protein -
OCT50_RS23790 (OCT50_23780) 26295..27974 + 1680 WP_000179844 Mu transposase C-terminal domain-containing protein -
OCT50_RS23795 (OCT50_23785) 27977..28885 + 909 WP_003155746 TniB family NTP-binding protein -
OCT50_RS23800 (OCT50_23790) 28882..30099 + 1218 WP_006122485 TniQ family protein -
OCT50_RS23805 (OCT50_23795) 30161..30784 + 624 WP_003155741 recombinase family protein -

Host bacterium

ID   13933 GenBank   NZ_CP106962
Plasmid name   pIMP-1 Incompatibility group   IncN3
Plasmid size   42504 bp Coordinate of oriT [Strand]   42419..42504 [+]
Host baterium   Leclercia adecarboxylata strain 17YN198

Cargo genes

Drug resistance gene   aadA6, blaIMP-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -