Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118609
Name   oriT_p15WZ-82_res in_silico
Organism   Klebsiella variicola strain 15WZ-82
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032357 (134334..134382 [+], 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_p15WZ-82_res
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11799 GenBank   WP_128206235
Name   traI_D4N21_RS29920_p15WZ-82_res 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: 190331.98 Da        Isoelectric Point: 6.0114

>WP_128206235.1 conjugative transfer relaxase/helicase TraI [Klebsiella variicola]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKARSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIETTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
MQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQIPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRTLNGMIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVEHDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1432-1554)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)

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

(576-628)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   6784 GenBank   WP_020805752
Name   WP_020805752_p15WZ-82_res insolico UniProt ID   A0A377TIM3
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14772.81 Da        Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   13824 GenBank   WP_128206236
Name   traD_D4N21_RS29925_p15WZ-82_res 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: 85865.77 Da        Isoelectric Point: 4.9615

>WP_128206236.1 type IV conjugative transfer system coupling protein TraD [Klebsiella variicola]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQSIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRSLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRATEPPVLRVTTVPLIKPKATAAATAASTASSAGAPAAAAGGTE
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: 106147..131955

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
D4N21_RS29925 (D4N21_30070) 106147..108456 - 2310 WP_128206236 type IV conjugative transfer system coupling protein TraD virb4
D4N21_RS29930 (D4N21_30075) 108818..109549 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
D4N21_RS29935 (D4N21_30080) 109739..110269 - 531 WP_128206265 conjugal transfer protein TraS -
D4N21_RS29940 (D4N21_30085) 110272..113121 - 2850 WP_128206237 conjugal transfer mating-pair stabilization protein TraG traG
D4N21_RS29945 (D4N21_30090) 113121..114500 - 1380 WP_164875722 conjugal transfer pilus assembly protein TraH traH
D4N21_RS29950 (D4N21_30095) 114478..114921 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
D4N21_RS29955 (D4N21_30100) 114967..115524 - 558 WP_032441889 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
D4N21_RS29960 (D4N21_30105) 115496..115735 - 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
D4N21_RS29965 (D4N21_30110) 115746..116498 - 753 WP_114435907 type-F conjugative transfer system pilin assembly protein TraF traF
D4N21_RS29970 (D4N21_30115) 116519..116845 - 327 WP_016529362 hypothetical protein -
D4N21_RS31970 (D4N21_30120) 116891..117076 - 186 WP_042922350 hypothetical protein -
D4N21_RS29980 (D4N21_30125) 117073..117309 - 237 WP_042922352 conjugal transfer protein TrbE -
D4N21_RS29985 (D4N21_30130) 117341..119296 - 1956 WP_114435906 type-F conjugative transfer system mating-pair stabilization protein TraN traN
D4N21_RS29990 (D4N21_30135) 119355..119993 - 639 WP_046622838 type-F conjugative transfer system pilin assembly protein TrbC trbC
D4N21_RS29995 (D4N21_30140) 120006..120995 - 990 WP_128206238 conjugal transfer pilus assembly protein TraU traU
D4N21_RS30000 (D4N21_30145) 120992..121381 - 390 WP_128206239 hypothetical protein -
D4N21_RS30005 (D4N21_30150) 121423..122049 - 627 WP_032445234 type-F conjugative transfer system protein TraW traW
D4N21_RS30010 (D4N21_30155) 122049..122438 - 390 WP_004152591 type-F conjugative transfer system protein TrbI -
D4N21_RS30015 (D4N21_30160) 122438..125077 - 2640 WP_128206240 type IV secretion system protein TraC virb4
D4N21_RS30020 (D4N21_30165) 125149..125547 - 399 WP_164875723 hypothetical protein -
D4N21_RS30025 (D4N21_30170) 125555..125869 - 315 WP_228258590 hypothetical protein -
D4N21_RS30030 (D4N21_30175) 125973..126263 - 291 WP_128206242 hypothetical protein -
D4N21_RS30035 (D4N21_30180) 126260..126664 - 405 WP_128206243 hypothetical protein -
D4N21_RS30040 (D4N21_30185) 126731..127048 - 318 WP_023320103 hypothetical protein -
D4N21_RS30045 (D4N21_30190) 127049..127267 - 219 WP_004171484 hypothetical protein -
D4N21_RS30050 (D4N21_30195) 127291..127581 - 291 WP_048993668 hypothetical protein -
D4N21_RS30055 (D4N21_30200) 127586..127996 - 411 WP_128206244 hypothetical protein -
D4N21_RS30060 (D4N21_30205) 128128..128712 - 585 WP_114502744 type IV conjugative transfer system lipoprotein TraV traV
D4N21_RS30065 (D4N21_30210) 128731..128916 - 186 WP_038990989 hypothetical protein -
D4N21_RS30070 (D4N21_30215) 128913..130337 - 1425 WP_128206245 F-type conjugal transfer pilus assembly protein TraB traB
D4N21_RS30075 (D4N21_30220) 130337..131077 - 741 WP_128206246 type-F conjugative transfer system secretin TraK traK
D4N21_RS30080 (D4N21_30225) 131064..131630 - 567 WP_020316627 type IV conjugative transfer system protein TraE traE
D4N21_RS30085 (D4N21_30230) 131650..131955 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
D4N21_RS30090 (D4N21_30235) 131969..132337 - 369 WP_020316649 type IV conjugative transfer system pilin TraA -
D4N21_RS30095 (D4N21_30240) 132406..132606 - 201 WP_048289787 TraY domain-containing protein -
D4N21_RS31805 132692..133393 - 702 WP_228258591 hypothetical protein -
D4N21_RS30105 (D4N21_30250) 133631..134023 - 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
D4N21_RS30110 (D4N21_30255) 134527..134934 + 408 WP_223170089 transglycosylase SLT domain-containing protein -
D4N21_RS30115 (D4N21_30260) 134972..135502 - 531 WP_128206247 antirestriction protein -

Host bacterium

ID   19042 GenBank   NZ_CP032357
Plasmid name   p15WZ-82_res Incompatibility group   IncFIB
Plasmid size   185478 bp Coordinate of oriT [Strand]   134334..134382 [+]
Host baterium   Klebsiella variicola strain 15WZ-82

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsH, arsC, arsB, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9