Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106301
Name   oriT_pKPHRJ in_silico
Organism   Klebsiella pneumoniae strain KPHRJ
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP120848 (29800..29849 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pKPHRJ
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4212 GenBank   WP_014386206
Name   traI_P5D18_RS26410_pKPHRJ insolico UniProt ID   G7RVC9
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190526.05 Da        Isoelectric Point: 5.9990

>WP_014386206.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
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)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4CP

ID   4235 GenBank   WP_014386205
Name   traD_P5D18_RS26415_pKPHRJ 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: 85924.97 Da        Isoelectric Point: 5.1787

>WP_014386205.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAVAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 726..30407

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
P5D18_RS26415 (P5D18_26415) 726..3035 - 2310 WP_014386205 type IV conjugative transfer system coupling protein TraD virb4
P5D18_RS26420 (P5D18_26420) 3162..3851 - 690 WP_013023831 hypothetical protein -
P5D18_RS26425 (P5D18_26425) 4044..4775 - 732 WP_013214036 conjugal transfer complement resistance protein TraT -
P5D18_RS26430 (P5D18_26430) 5026..5628 - 603 WP_013214035 conjugal transfer protein TraS -
P5D18_RS26435 (P5D18_26435) 5651..8473 - 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
P5D18_RS26440 (P5D18_26440) 8473..9852 - 1380 WP_072157884 conjugal transfer pilus assembly protein TraH traH
P5D18_RS26445 (P5D18_26445) 9830..10273 - 444 WP_013214032 F-type conjugal transfer protein TrbF -
P5D18_RS26450 (P5D18_26450) 10319..10876 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
P5D18_RS26455 (P5D18_26455) 10848..11087 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
P5D18_RS26460 (P5D18_26460) 11098..11850 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
P5D18_RS26465 (P5D18_26465) 11871..12197 - 327 WP_004152676 hypothetical protein -
P5D18_RS26470 (P5D18_26470) 12210..12458 - 249 WP_004152675 hypothetical protein -
P5D18_RS26475 (P5D18_26475) 12436..12690 - 255 WP_004152674 conjugal transfer protein TrbE -
P5D18_RS26480 (P5D18_26480) 12722..14677 - 1956 WP_030003482 type-F conjugative transfer system mating-pair stabilization protein TraN traN
P5D18_RS26485 (P5D18_26485) 14736..15374 - 639 WP_069985712 type-F conjugative transfer system pilin assembly protein TrbC trbC
P5D18_RS26490 (P5D18_26490) 15387..16376 - 990 WP_029497420 conjugal transfer pilus assembly protein TraU traU
P5D18_RS26495 (P5D18_26495) 16373..16774 - 402 WP_004194979 hypothetical protein -
P5D18_RS26500 (P5D18_26500) 16809..17444 - 636 WP_029497419 type-F conjugative transfer system protein TraW traW
P5D18_RS26505 (P5D18_26505) 17444..17833 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
P5D18_RS26510 (P5D18_26510) 17833..20472 - 2640 WP_013214024 type IV secretion system protein TraC virb4
P5D18_RS26515 (P5D18_26515) 20544..20942 - 399 WP_023179972 hypothetical protein -
P5D18_RS26520 (P5D18_26520) 21321..21725 - 405 WP_004197817 hypothetical protein -
P5D18_RS26525 (P5D18_26525) 21792..22103 - 312 WP_029497417 hypothetical protein -
P5D18_RS26530 (P5D18_26530) 22104..22322 - 219 WP_004195468 hypothetical protein -
P5D18_RS26535 (P5D18_26535) 22346..22636 - 291 WP_014386198 hypothetical protein -
P5D18_RS26540 (P5D18_26540) 22641..23051 - 411 WP_014386197 hypothetical protein -
P5D18_RS26545 (P5D18_26545) 23182..23766 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
P5D18_RS26550 (P5D18_26550) 23813..24385 - 573 WP_014386195 conjugal transfer pilus-stabilizing protein TraP -
P5D18_RS26555 (P5D18_26555) 24378..25802 - 1425 WP_014386194 F-type conjugal transfer pilus assembly protein TraB traB
P5D18_RS26560 (P5D18_26560) 25802..26542 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
P5D18_RS26565 (P5D18_26565) 26529..27095 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
P5D18_RS26570 (P5D18_26570) 27115..27420 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
P5D18_RS26575 (P5D18_26575) 27434..27802 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
P5D18_RS26580 (P5D18_26580) 27864..28070 - 207 WP_171773970 TraY domain-containing protein -
P5D18_RS26585 (P5D18_26585) 28203..28922 - 720 WP_014386192 conjugal transfer protein -
P5D18_RS26590 (P5D18_26590) 29115..29531 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
P5D18_RS26595 (P5D18_26595) 29922..30407 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
P5D18_RS26600 (P5D18_26600) 30440..30769 - 330 WP_014386191 DUF5983 family protein -
P5D18_RS26605 (P5D18_26605) 30802..31623 - 822 WP_004182076 DUF932 domain-containing protein -
P5D18_RS26610 (P5D18_26610) 32456..32869 - 414 WP_013023817 helix-turn-helix domain-containing protein -
P5D18_RS26615 (P5D18_26615) 32870..33148 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
P5D18_RS26620 (P5D18_26620) 33138..33458 - 321 WP_014386190 type II toxin-antitoxin system RelE/ParE family toxin -
P5D18_RS26625 (P5D18_26625) 33539..33763 - 225 WP_014386189 hypothetical protein -
P5D18_RS26630 (P5D18_26630) 33774..33986 - 213 WP_014386188 hypothetical protein -
P5D18_RS26635 (P5D18_26635) 34048..34374 - 327 WP_014386187 hypothetical protein -
P5D18_RS26640 (P5D18_26640) 35011..35361 - 351 WP_014386186 hypothetical protein -

Host bacterium

ID   6738 GenBank   NZ_CP120848
Plasmid name   pKPHRJ Incompatibility group   -
Plasmid size   133718 bp Coordinate of oriT [Strand]   29800..29849 [+]
Host baterium   Klebsiella pneumoniae strain KPHRJ

Cargo genes

Drug resistance gene   blaKPC-33, tet(A)
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9