Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200279
Name   oriT_ICEKpnRJF999-2 in_silico
Organism   Klebsiella pneumoniae subsp. pneumoniae strain RJF999
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP014010 (80813..80936 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      95..102, 106..113  (GTCGCGCG..CGCGCGAC)
 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_ICEKpnRJF999-2
CCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCCATTTTTTCGAGCTTGCGAAGAAAAAATAGGCTAAACGCGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGCGCGACGGTGTGCCGCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   16802 GenBank   AMA31185
Name   t4cp2_RJF9_17320_ICEKpnRJF999-2 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: 103084.02 Da        Isoelectric Point: 7.4625

>AMA31185.1 ATPase [Klebsiella pneumoniae subsp. pneumoniae]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGNAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
GKRDKAPWGDAMALLRTPSGDGYYINLHNTLADKDEFNEKNPASTCILGTNGSGKTMLMTFFEIMQQKYG
REDSFSPDAKTKRLTTVYLDKDRGAEMNIRALGGRYYRVISGESTGWNPFSLPATKRNINFIKQLMKILC
TRNGSTISPRDERRLSDAVNAVMNDEPQYRVYGITRMLENLPEPATKEAQENGLSIRLSQWAQGGEFGWV
FDNESDTFDISNCDNFGIDGTEFLDDASVCAPISFYLLYRITSLLDGRRLVIFMDEFWKWLRDPVFKDFA
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)

TraG P-loop domain (P-loop_TraG)

(535-813)

  Protein structure



No available structure.



ID   16803 GenBank   AMA31195
Name   t4cp2_RJF9_17375_ICEKpnRJF999-2 insolico UniProt ID   _
Length   579 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 579 a.a.        Molecular weight: 65588.83 Da        Isoelectric Point: 8.0425

>AMA31195.1 molybdopterin-guanine dinucleotide biosynthesis protein MobB [Klebsiella pneumoniae subsp. pneumoniae]
MGSHLMQRLNAFADAFSFFLLWLQNSPVILSLFAGLTLPFIVNLPREERKNAPFWLKSVACVSIFFFIFG
TISPLTIQGLSYFFKLLDNNILFRIPLWIMTVTFTTAGLFFHIAARRLLAGEIDNLKHRMIKKTKLERNT
RTDVRKVKELLPESIEYNPLDYIDLKKGAFIGLNKNDQPQYITIKEFKTQHAAIIGTTGSGKSVTAAILL
YQAILAGEAVFVEDPKDDEWAPHVLREACKKAGKKFTLINLNKPNFQLDLLADISHEQLEELFNAGFSLA
KKGEASDFYRISDRRAARNTSAIYEKGMTLYDLFNTDFVQSLRQAAPAFFGELEEVALVNSINATNGFSL
KEVFDEGGCCYIIGSTRNQKIISAQRMILTRLIQIAETRDRINSTPRTVAIFLDELKYHLSRPALEGLGT
ARDKGVHIFMAFQAIDDLRDCPSDLNGDAVIGAIIENAKFKLIYKIQNPETAEWAAKMTGSILVDDEMRK
VRTDLSLTEKMDTDRMIRQAESYYVDSNMFLNLPEKVGFVFTTKELAKATKMSPILVKKKHIELLSFENP
QSEQPQTEINEQNKPSINL

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(174-227)

TraM recognition site of TraD and TraG (TraG-D_C)

(399-490)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3539804..3553651

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RJF9_17285 3536830..3537264 + 435 AMA33093 hypothetical protein -
RJF9_17290 3537404..3537589 + 186 AMA31179 DNA-binding protein -
RJF9_17295 3537778..3538359 + 582 AMA31180 hypothetical protein -
RJF9_17300 3538801..3538929 + 129 AMA31181 transcriptional regulator -
RJF9_17305 3539498..3539731 + 234 AMA31182 ATP-binding protein -
RJF9_17310 3539804..3540514 + 711 AMA31183 type VI secretion protein virB1
RJF9_17315 3540514..3540807 + 294 AMA31184 TriB protein virB2
RJF9_17320 3540820..3543558 + 2739 AMA31185 ATPase virb4
RJF9_17325 3543576..3544283 + 708 AMA31186 type IV secretion system protein VirB5 -
RJF9_17330 3544537..3545610 + 1074 AMA31187 conjugal transfer protein TrbL virB6
RJF9_17335 3545683..3545802 - 120 AMA31188 hypothetical protein -
RJF9_17340 3545832..3546515 + 684 AMA31189 hypothetical protein virB8
RJF9_17345 3546515..3547420 + 906 AMA33094 type VI secretion protein virB9
RJF9_17350 3547464..3548708 + 1245 AMA31190 type VI secretion protein virB10
RJF9_17355 3548720..3549040 + 321 AMA31191 hypothetical protein -
RJF9_17360 3549030..3550055 + 1026 AMA31192 P-type DNA transfer ATPase VirB11 virB11
RJF9_17365 3550484..3550786 + 303 AMA31193 conjugal transfer protein -
RJF9_17370 3550829..3551134 + 306 AMA31194 dpoa decarboxylase -
RJF9_17375 3551912..3553651 + 1740 AMA31195 molybdopterin-guanine dinucleotide biosynthesis protein MobB virb4
RJF9_17380 3553660..3554424 + 765 AMA31196 molybdopterin-guanine dinucleotide biosynthesis protein MobC -
RJF9_17385 3555694..3556206 - 513 AMA31197 hypothetical protein -
RJF9_17390 3556241..3556810 - 570 AMA33095 thioesterase -
RJF9_17395 3556956..3558461 - 1506 AMA31198 serine hydrolase -

Host bacterium

ID   256 Element type   ICE (Integrative and conjugative element)
Element name   ICEKpnRJF999-2 GenBank   CP014010
Element size   5461919 bp Coordinate of oriT [Strand]   80813..80936 [+]
Host bacterium   Klebsiella pneumoniae subsp. pneumoniae strain RJF999 Coordinate of element   3470664..3608386

Cargo genes

Drug resistance gene   -
Virulence gene   ybtS, ybtX, ybtQ, ybtP, ybtA, irp2, irp1, ybtU, ybtT, ybtE, fyuA, clbS, clbQ, clbP, clbO, clbN, clbM, clbL, clbJ, clbI, clbH, clbG, clbF, clbE, clbD, clbC, clbB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -