Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114250
Name   oriT_p1-LC-1303-2020-KPC3 in_silico
Organism   Klebsiella grimontii strain LC-1303-2020
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP091753 (168056..168105 [+], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_p1-LC-1303-2020-KPC3
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9147 GenBank   WP_015065542
Name   traI_L6506_RS27410_p1-LC-1303-2020-KPC3 insolico UniProt ID   K7R3U7
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190318.03 Da        Isoelectric Point: 6.2890

>WP_015065542.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMSREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALAVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGGGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
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)

TrwC relaxase (TrwC)

(11-283)

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

(634-713)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




T4CP

ID   10597 GenBank   WP_015065541
Name   traD_L6506_RS27415_p1-LC-1303-2020-KPC3 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: 86025.00 Da        Isoelectric Point: 5.0577

>WP_015065541.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 139573..168663

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L6506_RS27415 (L6506_27415) 139573..141885 - 2313 WP_015065541 type IV conjugative transfer system coupling protein TraD virb4
L6506_RS27420 (L6506_27420) 142014..142703 - 690 WP_015065540 hypothetical protein -
L6506_RS27425 (L6506_27425) 142895..143626 - 732 WP_032329926 conjugal transfer complement resistance protein TraT -
L6506_RS27430 (L6506_27430) 143935..144459 - 525 WP_015065538 hypothetical protein -
L6506_RS27435 (L6506_27435) 144470..147313 - 2844 WP_023157999 conjugal transfer mating-pair stabilization protein TraG traG
L6506_RS27440 (L6506_27440) 147313..148692 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
L6506_RS27445 (L6506_27445) 148670..149113 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
L6506_RS27450 (L6506_27450) 149159..149716 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
L6506_RS27455 (L6506_27455) 149688..149927 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
L6506_RS27460 (L6506_27460) 149938..150690 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
L6506_RS27465 (L6506_27465) 150711..151037 - 327 WP_015065534 hypothetical protein -
L6506_RS27470 (L6506_27470) 151050..151298 - 249 WP_004152675 hypothetical protein -
L6506_RS27475 (L6506_27475) 151276..151530 - 255 WP_015065558 conjugal transfer protein TrbE -
L6506_RS27480 (L6506_27480) 151562..153517 - 1956 WP_132359030 type-F conjugative transfer system mating-pair stabilization protein TraN traN
L6506_RS27485 (L6506_27485) 153576..154214 - 639 WP_004152672 type-F conjugative transfer system pilin assembly protein TrbC trbC
L6506_RS27490 (L6506_27490) 154227..155216 - 990 WP_011977785 conjugal transfer pilus assembly protein TraU traU
L6506_RS27495 (L6506_27495) 155213..155602 - 390 WP_004152508 hypothetical protein -
L6506_RS27500 (L6506_27500) 155644..156270 - 627 WP_004152507 type-F conjugative transfer system protein TraW traW
L6506_RS27505 (L6506_27505) 156270..156659 - 390 WP_004152506 type-F conjugative transfer system protein TrbI -
L6506_RS27510 (L6506_27510) 156659..159298 - 2640 WP_064162928 type IV secretion system protein TraC virb4
L6506_RS27515 (L6506_27515) 159370..159768 - 399 WP_163593981 hypothetical protein -
L6506_RS27520 (L6506_27520) 159776..160165 - 390 WP_004153076 hypothetical protein -
L6506_RS27525 (L6506_27525) 160208..160612 - 405 WP_004152503 hypothetical protein -
L6506_RS27530 (L6506_27530) 160679..160990 - 312 WP_004152502 hypothetical protein -
L6506_RS27535 (L6506_27535) 160991..161209 - 219 WP_004152501 hypothetical protein -
L6506_RS27540 (L6506_27540) 161315..161725 - 411 WP_004152499 hypothetical protein -
L6506_RS27545 (L6506_27545) 161857..162441 - 585 WP_004161368 type IV conjugative transfer system lipoprotein TraV traV
L6506_RS27550 (L6506_27550) 162555..163979 - 1425 WP_004155033 F-type conjugal transfer pilus assembly protein TraB traB
L6506_RS27555 (L6506_27555) 163979..164719 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
L6506_RS27560 (L6506_27560) 164706..165272 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
L6506_RS27565 (L6506_27565) 165292..165597 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
L6506_RS27570 (L6506_27570) 165611..165979 - 369 WP_004152496 type IV conjugative transfer system pilin TraA -
L6506_RS27575 (L6506_27575) 166033..166419 - 387 WP_004152495 TraY domain-containing protein -
L6506_RS27580 (L6506_27580) 166498..167184 - 687 WP_004152494 transcriptional regulator TraJ family protein -
L6506_RS27585 (L6506_27585) 167358..167756 - 399 WP_004152493 conjugal transfer relaxosome DNA-binding protein TraM -
L6506_RS27590 (L6506_27590) 168178..168663 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
L6506_RS27595 (L6506_27595) 168696..169025 - 330 WP_011977736 DUF5983 family protein -
L6506_RS27600 (L6506_27600) 169058..169879 - 822 WP_004152492 DUF932 domain-containing protein -
L6506_RS27605 (L6506_27605) 170699..171532 - 834 WP_004152751 N-6 DNA methylase -
L6506_RS27610 (L6506_27610) 171583..171729 - 147 WP_004152750 hypothetical protein -
L6506_RS27615 (L6506_27615) 171824..172171 - 348 WP_004152749 hypothetical protein -
L6506_RS27620 (L6506_27620) 172228..172581 - 354 WP_004152748 hypothetical protein -
L6506_RS27625 (L6506_27625) 173211..173561 - 351 WP_004153414 hypothetical protein -

Host bacterium

ID   14685 GenBank   NZ_CP091753
Plasmid name   p1-LC-1303-2020-KPC3 Incompatibility group   IncFIB
Plasmid size   252919 bp Coordinate of oriT [Strand]   168056..168105 [+]
Host baterium   Klebsiella grimontii strain LC-1303-2020

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, blaCTX-M-15, aac(3)-IIa, aac(6')-Ib-cr, tet(A), qnrB1, dfrA14, blaKPC-3
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