Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118908
Name   oriT_pJNQH473-2 in_silico
Organism   Klebsiella quasipneumoniae strain JNQH473
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP075888 (44436..44484 [+], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pJNQH473-2
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11983 GenBank   WP_214632884
Name   traI_KLH66_RS29160_pJNQH473-2 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: 190493.30 Da        Isoelectric Point: 6.1558

>WP_214632884.1 conjugative transfer relaxase/helicase TraI [Klebsiella quasipneumoniae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMSREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHLALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGGGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
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)

(970-1154)


  Protein structure



No available structure.




Auxiliary protein

ID   6850 GenBank   WP_022644939
Name   WP_022644939_pJNQH473-2 insolico UniProt ID   W8QGP1
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 15048.16 Da        Isoelectric Point: 4.5248

>WP_022644939.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEVAEKINAIVEKRRVEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNKAL
LEYVVKTQFSVNKVLGIECLSPHVKDDPRWQWKGMVQNIQEDVQEVMLRFFPDEDNEVEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB W8QGP1


T4CP

ID   14033 GenBank   WP_013214038
Name   traD_KLH66_RS29165_pJNQH473-2 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 86010.07 Da        Isoelectric Point: 5.1787

>WP_013214038.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 14692..45042

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KLH66_RS29165 (KLH66_29165) 14692..17004 - 2313 WP_013214038 type IV conjugative transfer system coupling protein TraD virb4
KLH66_RS29170 (KLH66_29170) 17131..17820 - 690 WP_013023831 hypothetical protein -
KLH66_RS29175 (KLH66_29175) 18013..18744 - 732 WP_004152622 conjugal transfer complement resistance protein TraT -
KLH66_RS29180 (KLH66_29180) 18928..19476 - 549 WP_004152623 conjugal transfer entry exclusion protein TraS -
KLH66_RS29185 (KLH66_29185) 19489..22338 - 2850 WP_004152624 conjugal transfer mating-pair stabilization protein TraG traG
KLH66_RS29190 (KLH66_29190) 22338..23717 - 1380 WP_004165169 conjugal transfer pilus assembly protein TraH traH
KLH66_RS29195 (KLH66_29195) 23695..24138 - 444 WP_004152679 F-type conjugal transfer protein TrbF -
KLH66_RS29200 (KLH66_29200) 24184..24741 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KLH66_RS29205 (KLH66_29205) 24713..24952 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
KLH66_RS29210 (KLH66_29210) 24963..25715 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
KLH66_RS29215 (KLH66_29215) 25736..26062 - 327 WP_004144402 hypothetical protein -
KLH66_RS29220 (KLH66_29220) 26075..26323 - 249 WP_004152675 hypothetical protein -
KLH66_RS29225 (KLH66_29225) 26301..26555 - 255 WP_004152674 conjugal transfer protein TrbE -
KLH66_RS29230 (KLH66_29230) 26587..28542 - 1956 WP_214632885 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KLH66_RS29235 (KLH66_29235) 28601..29248 - 648 WP_214632886 type-F conjugative transfer system pilin assembly protein TrbC trbC
KLH66_RS29240 (KLH66_29240) 29393..29995 - 603 WP_022631520 hypothetical protein -
KLH66_RS29245 (KLH66_29245) 30052..30741 + 690 WP_032427592 hypothetical protein -
KLH66_RS29250 (KLH66_29250) 30716..31264 - 549 WP_022631518 hypothetical protein -
KLH66_RS29255 (KLH66_29255) 31279..32238 - 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
KLH66_RS29260 (KLH66_29260) 32282..32908 - 627 WP_070612662 type-F conjugative transfer system protein TraW traW
KLH66_RS29265 (KLH66_29265) 32908..33297 - 390 WP_004197815 type-F conjugative transfer system protein TrbI -
KLH66_RS29270 (KLH66_29270) 33297..35936 - 2640 WP_004197813 type IV secretion system protein TraC virb4
KLH66_RS29275 (KLH66_29275) 36008..36406 - 399 WP_015065631 hypothetical protein -
KLH66_RS29280 (KLH66_29280) 36431..36835 - 405 WP_023320104 hypothetical protein -
KLH66_RS29285 (KLH66_29285) 36902..37219 - 318 WP_015065629 hypothetical protein -
KLH66_RS29290 (KLH66_29290) 37220..37438 - 219 WP_004171484 hypothetical protein -
KLH66_RS29295 (KLH66_29295) 37462..37752 - 291 WP_032426790 hypothetical protein -
KLH66_RS29830 37781..38179 - 399 WP_223294961 hypothetical protein -
KLH66_RS29305 (KLH66_29305) 38334..38903 - 570 WP_032426791 type IV conjugative transfer system lipoprotein TraV traV
KLH66_RS29310 (KLH66_29310) 39017..40441 - 1425 WP_032426793 F-type conjugal transfer pilus assembly protein TraB traB
KLH66_RS29315 (KLH66_29315) 40441..41181 - 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
KLH66_RS29320 (KLH66_29320) 41168..41734 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
KLH66_RS29325 (KLH66_29325) 41754..42059 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
KLH66_RS29330 (KLH66_29330) 42073..42441 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
KLH66_RS29340 (KLH66_29340) 42795..43496 - 702 WP_022644938 hypothetical protein -
KLH66_RS29345 (KLH66_29345) 43731..44123 - 393 WP_022644939 conjugal transfer relaxosome DNA-binding protein TraM -
KLH66_RS29350 (KLH66_29350) 44557..45042 + 486 WP_022631514 transglycosylase SLT domain-containing protein virB1
KLH66_RS29355 (KLH66_29355) 45075..45404 - 330 WP_011977736 DUF5983 family protein -
KLH66_RS29360 (KLH66_29360) 45437..46258 - 822 WP_064161333 DUF932 domain-containing protein -
KLH66_RS29365 (KLH66_29365) 47078..47911 - 834 WP_211669400 N-6 DNA methylase -
KLH66_RS29370 (KLH66_29370) 47958..48188 - 231 WP_020314756 hypothetical protein -
KLH66_RS29375 (KLH66_29375) 48278..48625 - 348 WP_032426798 hypothetical protein -
KLH66_RS29380 (KLH66_29380) 48680..49018 - 339 WP_032426799 hypothetical protein -

Host bacterium

ID   19340 GenBank   NZ_CP075888
Plasmid name   pJNQH473-2 Incompatibility group   -
Plasmid size   70940 bp Coordinate of oriT [Strand]   44436..44484 [+]
Host baterium   Klebsiella quasipneumoniae strain JNQH473

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -