Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101022
Name   oriT_pKPHS2 experimental
Organism   Klebsiella pneumoniae subsp. pneumoniae HS11286
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   CP003224 (79857..79906 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      6..14, 17..25  (TGCAAAATT..AATTTTGCG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  GATTTTGTGG
Note   

  oriT sequence  


Download         Length: 50 nt

>oriT_pKPHS2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Jianfeng Zhang et al. (2023) Mobilizable plasmids drive the spread of antimicrobial resistance genes and virulence genes in Klebsiella pneumoniae. Genome medicine. 15(1):106. [PMID:38041146]


Relaxase

ID   1079 GenBank   YP_005229687
Name   TraI_pKPHS2 experimental UniProt ID   A0A0H3H1C0
Length   1752 a.a. PDB ID   
Note   

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190459.18 Da        Isoelectric Point: 6.1353

>YP_005229687.1 conjugal transfer nickase/helicase TraI (plasmid) [Klebsiella pneumoniae subsp. pneumoniae HS11286]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREATDARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGINAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVTF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRASTRM
ILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPHVIGLGPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSISPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDLHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(634-713)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1155)


  Protein structure


Source ID Structure
AlphaFold DB A0A0H3H1C0

  Reference


[1] Jianfeng Zhang et al. (2023) Mobilizable plasmids drive the spread of antimicrobial resistance genes and virulence genes in Klebsiella pneumoniae. Genome medicine. 15(1):106. [PMID:38041146]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 52012..80464

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KPHS_p200720 52012..54291 - 2280 AEW92121 conjugal transfer protein TraD virb4
KPHS_p200730 54418..55107 - 690 AEW92122 hypothetical protein -
KPHS_p200740 55300..56031 - 732 AEW92123 conjugal transfer surface exclusion protein TraT -
KPHS_p200750 56217..56750 - 534 AEW92124 conjugal transfer entry exclusion protein TraS -
KPHS_p200760 56753..59602 - 2850 AEW92125 conjugal transfer mating pair stabilization protein TraG traG
KPHS_p200770 59602..60981 - 1380 AEW92126 conjugal transfer pilus assembly protein TraH traH
KPHS_p200780 60959..61402 - 444 AEW92127 conjugal transfer protein TrbF -
KPHS_p200790 61448..62005 - 558 AEW92128 conjugal transfer protein TrbB traF
KPHS_p200800 61977..62216 - 240 AEW92129 conjugal transfer pilin chaperone TraQ -
KPHS_p200810 62227..62979 - 753 AEW92130 conjugal pilus assembly protein TraF traF
KPHS_p200820 63000..63326 - 327 AEW92131 hypothetical protein -
KPHS_p200830 63339..63587 - 249 AEW92132 hypothetical protein -
KPHS_p200840 63565..63819 - 255 AEW92133 conjugal transfer protein TrbE -
KPHS_p200850 63851..65806 - 1956 AEW92134 conjugal transfer mating pair stabilization protein TraN traN
KPHS_p200860 65865..66503 - 639 AEW92135 cconjugal transfer pilus assembly protein TrbC trbC
KPHS_p200870 66516..67505 - 990 AEW92136 conjugal transfer pilus assembly protein TraU traU
KPHS_p200880 67502..67903 - 402 AEW92137 hypothetical protein -
KPHS_p200890 67938..68573 - 636 AEW92138 conjugal transfer pilus assembly protein TraW traW
KPHS_p200900 68573..68962 - 390 AEW92139 conjugal transfer protein TrbI -
KPHS_p200910 68962..71601 - 2640 AEW92140 conjugal transfer ATP-binding protein TraC virb4
KPHS_p200920 71673..72071 - 399 AEW92141 hypothetical protein -
KPHS_p200930 72255..72461 + 207 AEW92142 hypothetical protein -
KPHS_p200940 72448..72852 - 405 AEW92143 hypothetical protein -
KPHS_p200950 72919..73230 - 312 AEW92144 hypothetical protein -
KPHS_p200960 73231..73449 - 219 AEW92145 hypothetical protein -
KPHS_p200970 73515..73640 + 126 AEW92146 hypothetical protein -
KPHS_p200980 73772..74356 - 585 AEW92147 conjugal transfer protein TraV traV
KPHS_p200990 74428..75852 - 1425 AEW92148 conjugal transfer pilus assembly protein TraB traB
KPHS_p201000 75852..76592 - 741 AEW92149 conjugal transfer protein TraK traK
KPHS_p201010 76579..77145 - 567 AEW92150 conjugal transfer pilus assembly protein TraE traE
KPHS_p201020 77165..77470 - 306 AEW92151 conjugal transfer pilus assembly protein TraL traL
KPHS_p201030 77484..77852 - 369 AEW92152 conjugal transfer pilin subunit TraA -
KPHS_p201040 77914..78084 - 171 AEW92153 conjugal transfer protein TraY -
KPHS_p201050 78235..78972 - 738 AEW92154 conjugal transfer transcriptional regulator TraJ -
KPHS_p201060 79172..79588 - 417 AEW92155 conjugal transfer protein TraM -
KPHS_p201070 79979..80464 + 486 AEW92156 putative lytic transglycosylase virB1
KPHS_p201080 80497..80826 - 330 AEW92157 hypothetical protein -
KPHS_p201090 80859..81680 - 822 AEW92158 hypothetical protein -
KPHS_p201100 81791..82132 - 342 AEW92159 hypothetical protein -
KPHS_p201110 82398..82613 + 216 AEW92160 hypothetical protein -
KPHS_p201120 82617..82895 - 279 AEW92161 XRE-like antitoxin protein -
KPHS_p201130 82885..83205 - 321 AEW92162 RelE-like toxin protein -
KPHS_p201140 83286..83510 - 225 AEW92163 hypothetical protein -
KPHS_p201150 83521..83733 - 213 AEW92164 hypothetical protein -
KPHS_p201160 83794..84150 - 357 AEW92165 hypothetical protein -
KPHS_p201170 84147..84272 - 126 AEW92166 single-strand binding protein -
KPHS_p201180 84408..84584 - 177 AEW92167 hypothetical protein -
KPHS_p201190 84728..84862 - 135 AEW92168 hypothetical protein -
KPHS_p201200 84992..85309 - 318 AEW92169 hypothetical protein -

Host bacterium

ID   1483 GenBank   CP003224
Plasmid name   pKPHS2 Incompatibility group   IncFII
Plasmid size   111195 bp Coordinate of oriT [Strand]   79857..79906 [+]
Host baterium   Klebsiella pneumoniae subsp. pneumoniae HS11286

Cargo genes

Drug resistance gene   resistance to amoxicillin, amoxicillin+clavulanic_acid, ampicillin, ampicillin+clavulanic_acid, aztreonam, cefepime, cefotaxime, cefoxitin, ceftazidime, ertapenem, imipenem, meropenem, piperacillin, piperacillin+tazobactam, ticarcillin, ticarcillin+clavulanic_acid and cephalothin
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9