Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104445
Name   oriT_pBY221-2 in_silico
Organism   Klebsiella pneumoniae strain BY221
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP090220 (164279..164328 [+], 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_pBY221-2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3226 GenBank   WP_032441895
Name   traI_LVJ43_RS27180_pBY221-2 insolico UniProt ID   A0A7D5G561
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190517.07 Da        Isoelectric Point: 6.0893

>WP_032441895.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVIGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKLSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNRESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

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   3139 GenBank   WP_032441894
Name   traD_LVJ43_RS27185_pBY221-2 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: 85957.93 Da        Isoelectric Point: 5.0577

>WP_032441894.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEARESEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRVTEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
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: 135781..164886

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LVJ43_RS27185 (LVJ43_27160) 135781..138090 - 2310 WP_032441894 type IV conjugative transfer system coupling protein TraD virb4
LVJ43_RS27190 (LVJ43_27165) 138217..138906 - 690 WP_074185211 hypothetical protein -
LVJ43_RS27195 (LVJ43_27170) 139098..139829 - 732 WP_032441892 conjugal transfer complement resistance protein TraT -
LVJ43_RS27200 (LVJ43_27175) 140080..140682 - 603 WP_013214035 conjugal transfer protein TraS -
LVJ43_RS27205 (LVJ43_27180) 140705..143527 - 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
LVJ43_RS27210 (LVJ43_27185) 143527..144906 - 1380 WP_074185210 conjugal transfer pilus assembly protein TraH traH
LVJ43_RS27215 (LVJ43_27190) 144884..145327 - 444 WP_032441890 F-type conjugal transfer protein TrbF -
LVJ43_RS27220 (LVJ43_27195) 145373..145930 - 558 WP_032441889 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LVJ43_RS27225 (LVJ43_27200) 145902..146141 - 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
LVJ43_RS27230 (LVJ43_27205) 146152..146904 - 753 WP_032441888 type-F conjugative transfer system pilin assembly protein TraF traF
LVJ43_RS27235 (LVJ43_27210) 146925..147251 - 327 WP_023284640 hypothetical protein -
LVJ43_RS27240 (LVJ43_27215) 147264..147512 - 249 WP_004152675 hypothetical protein -
LVJ43_RS27245 (LVJ43_27220) 147490..147744 - 255 WP_004152674 conjugal transfer protein TrbE -
LVJ43_RS27250 (LVJ43_27225) 147776..149731 - 1956 WP_032441887 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LVJ43_RS27255 (LVJ43_27230) 149790..150428 - 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
LVJ43_RS27260 (LVJ43_27235) 150441..151430 - 990 WP_032441886 conjugal transfer pilus assembly protein TraU traU
LVJ43_RS27265 (LVJ43_27240) 151427..151828 - 402 WP_004194979 hypothetical protein -
LVJ43_RS27270 (LVJ43_27245) 151863..152498 - 636 WP_032441885 type-F conjugative transfer system protein TraW traW
LVJ43_RS27275 (LVJ43_27250) 152498..152887 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
LVJ43_RS27280 (LVJ43_27255) 152884..155526 - 2643 WP_032441884 type IV secretion system protein TraC virb4
LVJ43_RS27285 (LVJ43_27260) 155598..155996 - 399 WP_023179972 hypothetical protein -
LVJ43_RS27290 (LVJ43_27265) 156374..156778 - 405 WP_004197817 hypothetical protein -
LVJ43_RS27295 (LVJ43_27270) 156845..157174 - 330 WP_032441883 hypothetical protein -
LVJ43_RS27300 (LVJ43_27275) 157175..157393 - 219 WP_004195235 hypothetical protein -
LVJ43_RS27305 (LVJ43_27280) 157499..157909 - 411 WP_004152499 hypothetical protein -
LVJ43_RS27310 (LVJ43_27285) 158041..158625 - 585 WP_032441881 type IV conjugative transfer system lipoprotein TraV traV
LVJ43_RS27315 (LVJ43_27290) 158739..160163 - 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
LVJ43_RS27320 (LVJ43_27295) 160163..160903 - 741 WP_015065528 type-F conjugative transfer system secretin TraK traK
LVJ43_RS27325 (LVJ43_27300) 160890..161456 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
LVJ43_RS27330 (LVJ43_27305) 161476..161781 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
LVJ43_RS27335 (LVJ43_27310) 161795..162163 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LVJ43_RS27340 (LVJ43_27315) 162217..162588 - 372 WP_004208838 TraY domain-containing protein -
LVJ43_RS27345 (LVJ43_27320) 162672..163367 - 696 WP_072271345 transcriptional regulator TraJ family protein -
LVJ43_RS27350 (LVJ43_27325) 163574..163966 - 393 WP_032441878 conjugal transfer relaxosome DNA-binding protein TraM -
LVJ43_RS27355 (LVJ43_27330) 164401..164886 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
LVJ43_RS27360 (LVJ43_27335) 164919..165248 - 330 WP_011977736 DUF5983 family protein -
LVJ43_RS27365 (LVJ43_27340) 165281..166102 - 822 WP_004178064 DUF932 domain-containing protein -
LVJ43_RS27370 (LVJ43_27345) 166936..167349 - 414 WP_004152722 helix-turn-helix domain-containing protein -
LVJ43_RS27375 (LVJ43_27350) 167350..167628 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
LVJ43_RS27380 (LVJ43_27355) 167618..167938 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
LVJ43_RS27385 (LVJ43_27360) 168019..168243 - 225 WP_014343499 hypothetical protein -
LVJ43_RS27390 (LVJ43_27365) 168254..168466 - 213 WP_019706020 hypothetical protein -
LVJ43_RS27395 (LVJ43_27370) 168527..168883 - 357 WP_019706019 hypothetical protein -
LVJ43_RS27400 (LVJ43_27375) 169515..169865 - 351 WP_023287104 hypothetical protein -

Host bacterium

ID   4884 GenBank   NZ_CP090220
Plasmid name   pBY221-2 Incompatibility group   IncFIB
Plasmid size   193044 bp Coordinate of oriT [Strand]   164279..164328 [+]
Host baterium   Klebsiella pneumoniae strain BY221

Cargo genes

Drug resistance gene   aac(3)-IId, aph(3')-Ia
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
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9