Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120013
Name   oriT_pKqs_12A476_1 in_silico
Organism   Klebsiella quasipneumoniae subsp. similipneumoniae strain 12A476
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084780 (206444..206493 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pKqs_12A476_1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12615 GenBank   WP_226680527
Name   traI_LGM27_RS25615_pKqs_12A476_1 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190323.86 Da        Isoelectric Point: 5.9136

>WP_226680527.1 conjugative transfer relaxase/helicase TraI [Klebsiella quasipneumoniae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVIGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQLELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

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

(576-628)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   14813 GenBank   WP_023329042
Name   traD_LGM27_RS25620_pKqs_12A476_1 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85943.90 Da        Isoelectric Point: 5.0577

>WP_023329042.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEARESEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRATEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 177807..207051

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LGM27_RS25620 (LGM27_25620) 177807..180116 - 2310 WP_023329042 type IV conjugative transfer system coupling protein TraD virb4
LGM27_RS25625 (LGM27_25625) 180474..181205 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
LGM27_RS25630 (LGM27_25630) 181395..181922 - 528 WP_029498351 conjugal transfer protein TraS -
LGM27_RS25635 (LGM27_25635) 181928..184777 - 2850 WP_023329044 conjugal transfer mating-pair stabilization protein TraG traG
LGM27_RS25640 (LGM27_25640) 184777..186156 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
LGM27_RS25645 (LGM27_25645) 186134..186577 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
LGM27_RS25650 (LGM27_25650) 186623..187180 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LGM27_RS25655 (LGM27_25655) 187152..187391 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
LGM27_RS25660 (LGM27_25660) 187402..188154 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
LGM27_RS25665 (LGM27_25665) 188175..188501 - 327 WP_015065534 hypothetical protein -
LGM27_RS25670 (LGM27_25670) 188514..188762 - 249 WP_004152675 hypothetical protein -
LGM27_RS25675 (LGM27_25675) 188740..188994 - 255 WP_015065558 conjugal transfer protein TrbE -
LGM27_RS25680 (LGM27_25680) 189026..190981 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LGM27_RS25685 (LGM27_25685) 191040..191687 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
LGM27_RS25690 (LGM27_25690) 191766..191942 - 177 WP_162866177 hypothetical protein -
LGM27_RS25695 (LGM27_25695) 191963..192952 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
LGM27_RS25700 (LGM27_25700) 192949..193350 - 402 WP_023158005 hypothetical protein -
LGM27_RS25705 (LGM27_25705) 193385..194020 - 636 WP_023158006 type-F conjugative transfer system protein TraW traW
LGM27_RS25710 (LGM27_25710) 194020..194409 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
LGM27_RS25715 (LGM27_25715) 194409..197048 - 2640 WP_023158007 type IV secretion system protein TraC virb4
LGM27_RS25720 (LGM27_25720) 197120..197518 - 399 WP_023158008 hypothetical protein -
LGM27_RS25725 (LGM27_25725) 197526..197915 - 390 WP_023158009 hypothetical protein -
LGM27_RS25730 (LGM27_25730) 197958..198362 - 405 WP_016831042 hypothetical protein -
LGM27_RS25735 (LGM27_25735) 198429..198740 - 312 WP_014386200 hypothetical protein -
LGM27_RS25740 (LGM27_25740) 198741..198959 - 219 WP_014386199 hypothetical protein -
LGM27_RS25745 (LGM27_25745) 198983..199272 - 290 Protein_215 hypothetical protein -
LGM27_RS25750 (LGM27_25750) 199277..199687 - 411 WP_016831039 hypothetical protein -
LGM27_RS25755 (LGM27_25755) 199819..200403 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
LGM27_RS25760 (LGM27_25760) 200426..201022 - 597 Protein_218 conjugal transfer pilus-stabilizing protein TraP -
LGM27_RS25765 (LGM27_25765) 201015..202439 - 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
LGM27_RS25770 (LGM27_25770) 202439..203179 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
LGM27_RS25775 (LGM27_25775) 203166..203732 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
LGM27_RS25780 (LGM27_25780) 203752..204057 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
LGM27_RS25785 (LGM27_25785) 204071..204439 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LGM27_RS25790 (LGM27_25790) 204504..204707 - 204 WP_171486139 TraY domain-containing protein -
LGM27_RS25795 (LGM27_25795) 204840..205559 - 720 WP_226680531 conjugal transfer protein TrbJ -
LGM27_RS25800 (LGM27_25800) 205759..206175 - 417 WP_168429831 conjugal transfer relaxosome DNA-binding protein TraM -
LGM27_RS25805 (LGM27_25805) 206566..207051 + 486 WP_022631514 transglycosylase SLT domain-containing protein virB1
LGM27_RS25810 (LGM27_25810) 207084..207413 - 330 WP_011977736 DUF5983 family protein -
LGM27_RS25815 (LGM27_25815) 207446..208267 - 822 WP_004152492 DUF932 domain-containing protein -
LGM27_RS25820 (LGM27_25820) 209100..209513 - 414 WP_004182074 type II toxin-antitoxin system HigA family antitoxin -
LGM27_RS25825 (LGM27_25825) 209514..209792 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
LGM27_RS25830 (LGM27_25830) 209782..210102 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
LGM27_RS25835 (LGM27_25835) 210183..210407 - 225 WP_020325128 hypothetical protein -
LGM27_RS25840 (LGM27_25840) 210418..210630 - 213 WP_004182070 hypothetical protein -
LGM27_RS25845 (LGM27_25845) 210691..211047 - 357 WP_004152717 hypothetical protein -
LGM27_RS25850 (LGM27_25850) 211683..212033 - 351 WP_004182068 hypothetical protein -

Host bacterium

ID   20443 GenBank   NZ_CP084780
Plasmid name   pKqs_12A476_1 Incompatibility group   IncFIB
Plasmid size   239503 bp Coordinate of oriT [Strand]   206444..206493 [+]
Host baterium   Klebsiella quasipneumoniae subsp. similipneumoniae strain 12A476

Cargo genes

Drug resistance gene   aadA2, qacE, sul1
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsH, arsC, arsB, arsA, arsD, arsR, fecD, fecE, merR2, merT, merP, merF, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9