Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200273
Name   oriT_ICEKpnPMK1-1 in_silico
Organism   Klebsiella pneumoniae strain PMK1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP008929 (68368..68491 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      40..47, 59..66  (ATTTTTTC..GAAAAAAT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_ICEKpnPMK1-1
CCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCCATTTTTTCGAGCTTGCGAAGAAAAAATAGGCTAAACGCGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGGGCGACGGTGTGCTGCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   16790 GenBank   AIT04299
Name   virB4_PMK1_04870_ICEKpnPMK1-1 insolico UniProt ID   _
Length   912 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 912 a.a.        Molecular weight: 103112.03 Da        Isoelectric Point: 7.4626

>AIT04299.1 Type IV secretion system protein virB4 [Klebsiella pneumoniae]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGNAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
GKRDKAPWGDAMALLRTPSGDGYYINLHNTLADKDEFNEKNPASTCILGTNGSGKTMLMTFFEIMQQKYG
REDSFSPDAKTKRLTTVYLDKDRGAEMNIRALGGRYYRVISGESTGWNPFSLPATKRNINFIKQLMKILC
TRNGSTISPRDERRLSDAVNAVMNDEPQYRVYGITRMLENLPEPATKEAQENGLSIRLSQWAQGGEFGWV
FDNESDTFDISNCDNFGIDGTEFLDDASVCAPISFYLLYRITSLLDGRRLVIFMDEFWRWLRDPVFKDFA
YNKLKTIRKLNGMLVVGTQSPAEIIKDDIAPAVIEQCGTQILAANPNADRAHYVDGMKFEPEVFDVVKGL
DPQARQYVVVKNQFKRGDTKRFAARVTLDLSGIGRYTKVMSGDAPNLEIFESIYREGMQPHEWLDTYLAK
AL

  Protein domains


Predicted by InterproScan.

Type IV secretory pathway, VirB3-like protein (VirB3)

(3-79)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(269-470)

  Protein structure



No available structure.



ID   16791 GenBank   AIT04309
Name   t4cp2_PMK1_04880_ICEKpnPMK1-1 insolico UniProt ID   _
Length   619 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 619 a.a.        Molecular weight: 69752.68 Da        Isoelectric Point: 5.7361

>AIT04309.1 conjugative coupling factor TraD, SXT/TOL subfamily [Klebsiella pneumoniae]
MILNKLTASLSPIVNGMLALLAFVQQQQLILALLAGLTMPFFTSMKSDERQKAPLWKKLIIAFSLLCFIS
GTMAPIVIGSFQWLYKIRLTSDNTVLAWAVRITFTVTGIIFHIMLRRVFTPELDRIKKRLVKKTTLEREL
RTDVRTVKSLLPETLHYNPLDYIDLNKGIFTGMDSEKEPLYLPLKDWQKQHADIIGTTGAGKGVAAGILL
YQSILAGEGVFVMDPKDDEWAPHLYRKACEDAGKPFALIDLRKQQYQLNLIEDITPDELEELFVAGFSLA
EKGQESDFYRIDDRKAARMAAQFVSDNPSATLRDVYNGDYVQSIAEKIKAFFGKIEELALLNAINSPEGF
SLQQMFDEGGCCYVIGSMRNSKIITTQRMLLVRLYQLAERRDRVTNVPRSIAIYLSELKYHLSRPALEGL
GAARDKGVHIIMDHQSIADLKDCPADLKGDAVVGAVVENAKFKLVYRVMDPDTAEWVARMSGTILVDDEL
RKAKTDNMLTETIDSERTIRQAERYFIDSNMILNLHDFVSFIFTTKTLPSASLISPIKIRKRQLKIFSVS
PDIAASAAPVKIALDFDEDDKPSIQDVMTTHPDLFFNESEVQPAEPQPDEGEHLSPLDF

  Protein domains


Predicted by InterproScan.

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

(291-541)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 5233353..5243278

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PMK1_04863 5229887..5230813 + 927 AIT04292 hypothetical protein -
PMK1_04864 5230953..5231138 + 186 AIT04293 putative transcriptional regulator -
PMK1_04865 5231160..5231342 + 183 AIT04294 hypothetical protein -
PMK1_04866 5231327..5231908 + 582 AIT04295 hypothetical protein -
PMK1_04867 5233047..5233280 + 234 AIT04296 hypothetical protein -
PMK1_04868 5233353..5234063 + 711 AIT04297 Type IV secretion system protein virB1 virB1
PMK1_04869 5234063..5234356 + 294 AIT04298 Pertussis toxin liberation protein A virB2
PMK1_04870 5234369..5237107 + 2739 AIT04299 Type IV secretion system protein virB4 virb4
PMK1_04871 5237125..5237832 + 708 AIT04300 P-type DNA transfer protein VirB5 -
PMK1_04872 5237840..5238082 + 243 AIT04301 hypothetical protein -
PMK1_04873 5238086..5239159 + 1074 AIT04302 TrbL/VirB6 plasmid conjugal transfer protein virB6
PMK1_04874 5239251..5239388 + 138 AIT04303 hypothetical protein -
PMK1_04875 5239381..5240064 + 684 AIT04304 Pertussis toxin liberation protein E virB8
PMK1_04876 5240064..5240969 + 906 AIT04305 Type IV secretion system protein virB9 precursor virB9
PMK1_04877 5241013..5242263 + 1251 AIT04306 Type IV secretion system protein virB10 virB10
PMK1_04878 5242253..5243278 + 1026 AIT04307 Type IV secretion system protein VirB11 virB11
PMK1_04879 5244048..5244353 + 306 AIT04308 hypothetical protein -
PMK1_04880 5245063..5246922 + 1860 AIT04309 conjugative coupling factor TraD, SXT/TOL subfamily -
PMK1_04881 5246932..5247678 + 747 AIT04310 hypothetical protein -

Host bacterium

ID   250 Element type   ICE (Integrative and conjugative element)
Element name   ICEKpnPMK1-1 GenBank   CP008929
Element size   5317001 bp Coordinate of oriT [Strand]   68368..68491 [+]
Host bacterium   Klebsiella pneumoniae strain PMK1 Coordinate of element   5176327..5297023

Cargo genes

Drug resistance gene   -
Virulence gene   ybtS, ybtX, ybtQ, ybtP, ybtA, irp2, irp1, ybtU, ybtT, ybtE, fyuA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -