Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200205
Name   oriT_ICEKpn1084-1 in_silico
Organism   Klebsiella pneumoniae subsp. pneumoniae 1084
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_018522 (194207..194330 [-], 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_ICEKpn1084-1
CCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCCATTTTTTCGAGCTTGCGAAGAAAAAATAGGCTAAACGCGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGCGCGACGGTGTGCCGCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   16679 GenBank   WP_004175309
Name   t4cp2_A79E_RS08645_ICEKpn1084-1 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

>WP_004175309.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
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.



ID   16680 GenBank   WP_001096398
Name   t4cp2_A79E_RS08700_ICEKpn1084-1 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: 103084.02 Da        Isoelectric Point: 7.4625

>WP_001096398.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacterales]
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1800472..1814319

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
A79E_RS08620 (A79E_1678) 1796095..1796817 + 723 WP_000065646 colibactin biosynthesis thioesterase ClbQ -
A79E_RS08625 1796852..1797364 + 513 WP_004175305 colibactin self-protection protein ClbS -
A79E_RS08635 (A79E_1681) 1798636..1799604 - 969 WP_004225014 IS5 family transposase -
A79E_RS08640 (A79E_1682) 1799699..1800463 - 765 WP_004175307 MobC family replication-relaxation protein -
A79E_RS08645 (A79E_1684) 1800472..1802211 - 1740 WP_004175309 type IV secretion system DNA-binding domain-containing protein virb4
A79E_RS08650 1802989..1803294 - 306 WP_012131835 hypothetical protein -
A79E_RS08655 1803337..1803640 - 304 Protein_1668 TrbM/KikA/MpfK family conjugal transfer protein -
A79E_RS26640 1803674..1804072 - 399 WP_012131837 cag pathogenicity island Cag12 family protein -
A79E_RS08660 (A79E_1686) 1804069..1805094 - 1026 WP_004175311 P-type DNA transfer ATPase VirB11 virB11
A79E_RS08665 (A79E_1687) 1805084..1805404 - 321 WP_004175313 hypothetical protein -
A79E_RS08670 (A79E_1688) 1805416..1806660 - 1245 WP_012131839 VirB10/TraB/TrbI family type IV secretion system protein virB10
A79E_RS08675 (A79E_1689) 1806704..1807612 - 909 WP_000976328 P-type conjugative transfer protein VirB9 virB9
A79E_RS08680 (A79E_1690) 1807609..1808292 - 684 WP_000003229 type IV secretion system protein virB8
A79E_RS08690 (A79E_1692) 1808514..1809587 - 1074 WP_001593439 type IV secretion system protein virB6
A79E_RS26645 1809591..1809827 - 237 WP_032173000 EexN family lipoprotein -
A79E_RS08695 (A79E_1693) 1809840..1810547 - 708 WP_000857358 type IV secretion system protein -
A79E_RS08700 (A79E_1694) 1810565..1813303 - 2739 WP_001096398 VirB3 family type IV secretion system protein virb4
A79E_RS08705 1813316..1813609 - 294 WP_000600171 TrbC/VirB2 family protein virB2
A79E_RS08710 (A79E_1696) 1813609..1814319 - 711 WP_001593436 lytic transglycosylase domain-containing protein virB1
A79E_RS08715 (A79E_1697) 1814392..1814625 - 234 WP_001231171 hypothetical protein -
A79E_RS27690 (A79E_1698) 1815194..1815343 - 150 Protein_1682 Hha/YmoA family nucleoid-associated regulatory protein -
A79E_RS26655 1815565..1815774 - 210 WP_001112403 TraR/DksA family transcriptional regulator -
A79E_RS08730 (A79E_1699) 1815764..1816345 - 582 WP_000937857 DUF2857 domain-containing protein -
A79E_RS26660 1816330..1816513 - 184 Protein_1685 hypothetical protein -
A79E_RS08735 1816535..1816720 - 186 WP_000205185 AlpA family transcriptional regulator -
A79E_RS29090 1816859..1817785 - 927 Protein_1687 hypothetical protein -

Host bacterium

ID   193 Element type   ICE (Integrative and conjugative element)
Element name   ICEKpn1084-1 GenBank   NC_018522
Element size   5386705 bp Coordinate of oriT [Strand]   194207..194330 [-]
Host bacterium   Klebsiella pneumoniae subsp. pneumoniae 1084 Coordinate of element   1608318..1882592

Cargo genes

Drug resistance gene   -
Virulence gene   cpsACP, wzi, wza, wzc, wzx, wcsS, wcsT, gmd, wcaG, wcaH, wcaJ, gnd, manC, manB, ugd, wzm, wbbM, glf, wbbN, wbbO, kfoC, clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbI, clbJ, clbK, clbL, clbM, clbN, clbO, clbP, clbQ, clbS, fyuA, ybtE, ybtT, ybtU, irp1, irp2, ybtA, ybtP, ybtQ, ybtX, ybtS
Metal resistance gene   mdtC/yegO, mdtB/yegN, mdtA/yegM
Degradation gene   -
Symbiosis gene   noeL
Anti-CRISPR   -