Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102717
Name   oriT_pKPN-d90 in_silico
Organism   Klebsiella pneumoniae strain Kpn555
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP015132 (85681..85730 [+], 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_pKPN-d90
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1997 GenBank   WP_023307532
Name   traI_WM92_RS27475_pKPN-d90 insolico UniProt ID   A0A2R4ND60
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190476.66 Da        Isoelectric Point: 6.4600

>WP_023307532.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRAMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELACAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRHNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QTQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALITIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIE
KALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRTLNGMIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSDGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASERYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRIWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1433-1555)

AAA domain (AAA_30)

(971-1154)

TrwC relaxase (TrwC)

(10-284)

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

(635-714)

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

(577-629)


  Protein structure



No available structure.




T4CP

ID   1641 GenBank   WP_015065643
Name   traD_WM92_RS27480_pKPN-d90 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: 85851.84 Da        Isoelectric Point: 5.0577

>WP_015065643.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTSIVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEAREAEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRATEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
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: 58040..86288

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
WM92_RS27480 (WM92_27475) 58040..60349 - 2310 WP_015065643 type IV conjugative transfer system coupling protein TraD virb4
WM92_RS27485 (WM92_27480) 60711..61442 - 732 Protein_61 conjugal transfer complement resistance protein TraT -
WM92_RS27490 (WM92_27485) 61632..62159 - 528 WP_064154289 hypothetical protein -
WM92_RS27495 (WM92_27490) 62165..65014 - 2850 WP_015065640 conjugal transfer mating-pair stabilization protein TraG traG
WM92_RS27500 (WM92_27495) 65014..66393 - 1380 WP_011977731 conjugal transfer pilus assembly protein TraH traH
WM92_RS27505 (WM92_27500) 66371..66814 - 444 WP_015065638 F-type conjugal transfer protein TrbF -
WM92_RS27510 (WM92_27505) 66859..67416 - 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
WM92_RS27515 (WM92_27510) 67388..67627 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
WM92_RS27520 (WM92_27515) 67638..68390 - 753 WP_015065637 type-F conjugative transfer system pilin assembly protein TraF traF
WM92_RS27525 (WM92_27520) 68411..68737 - 327 WP_004152685 hypothetical protein -
WM92_RS32425 (WM92_27525) 68783..68968 - 186 WP_023307535 hypothetical protein -
WM92_RS27535 (WM92_27530) 68965..69201 - 237 WP_023307536 conjugal transfer protein TrbE -
WM92_RS27540 (WM92_27535) 69233..71188 - 1956 WP_015065636 type-F conjugative transfer system mating-pair stabilization protein TraN traN
WM92_RS27545 (WM92_27540) 71247..71885 - 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
WM92_RS27550 (WM92_27545) 71898..72857 - 960 WP_015065634 conjugal transfer pilus assembly protein TraU traU
WM92_RS27555 (WM92_27550) 72901..73527 - 627 WP_015065633 type-F conjugative transfer system protein TraW traW
WM92_RS27560 (WM92_27555) 73527..73916 - 390 WP_004152506 type-F conjugative transfer system protein TrbI -
WM92_RS27565 (WM92_27560) 73916..76555 - 2640 WP_016528865 type IV secretion system protein TraC virb4
WM92_RS27570 (WM92_27565) 76627..77025 - 399 WP_015065631 hypothetical protein -
WM92_RS27575 (WM92_27570) 77050..77454 - 405 WP_023320104 hypothetical protein -
WM92_RS27580 (WM92_27575) 77521..77838 - 318 WP_015065629 hypothetical protein -
WM92_RS27585 (WM92_27580) 77839..78057 - 219 WP_004171484 hypothetical protein -
WM92_RS27590 (WM92_27585) 78081..78371 - 291 WP_032426790 hypothetical protein -
WM92_RS32220 78400..78798 - 399 WP_223177007 hypothetical protein -
WM92_RS27595 (WM92_27590) 78954..79523 - 570 WP_015065628 type IV conjugative transfer system lipoprotein TraV traV
WM92_RS31875 79543..79698 - 156 WP_153587559 hypothetical protein -
WM92_RS27600 (WM92_27595) 79729..80148 - 420 Protein_86 conjugal transfer pilus-stabilizing protein TraP -
WM92_RS27605 (WM92_27600) 80141..81565 - 1425 WP_040228261 F-type conjugal transfer pilus assembly protein TraB traB
WM92_RS27610 (WM92_27605) 81565..82305 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
WM92_RS27615 (WM92_27610) 82292..82858 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
WM92_RS27620 (WM92_27615) 82878..83183 - 306 WP_015065625 type IV conjugative transfer system protein TraL traL
WM92_RS27625 (WM92_27620) 83197..83565 - 369 WP_004178060 type IV conjugative transfer system pilin TraA -
WM92_RS30135 83619..83990 - 372 WP_004208838 TraY domain-containing protein -
WM92_RS30140 84074..84769 - 696 WP_077268150 transcriptional regulator TraJ family protein -
WM92_RS27635 (WM92_27630) 84976..85368 - 393 WP_004206766 conjugal transfer relaxosome DNA-binding protein TraM -
WM92_RS27640 (WM92_27635) 85803..86288 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
WM92_RS31255 86321..86635 - 315 WP_001568110 DUF5983 family protein -
WM92_RS27645 (WM92_27640) 86683..87504 - 822 WP_015065622 DUF932 domain-containing protein -
WM92_RS27660 (WM92_27655) 88338..88751 - 414 WP_004182074 helix-turn-helix domain-containing protein -
WM92_RS27665 (WM92_27660) 88752..89030 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
WM92_RS27670 (WM92_27665) 89020..89340 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
WM92_RS27675 (WM92_27670) 89421..89645 - 225 WP_004152719 hypothetical protein -
WM92_RS27680 (WM92_27675) 89656..89868 - 213 WP_021313197 hypothetical protein -
WM92_RS27685 (WM92_27680) 89929..90285 - 357 WP_064184164 hypothetical protein -
WM92_RS27690 (WM92_27685) 90914..91264 - 351 WP_015065620 hypothetical protein -

Host bacterium

ID   3160 GenBank   NZ_CP015132
Plasmid name   pKPN-d90 Incompatibility group   IncFII
Plasmid size   224457 bp Coordinate of oriT [Strand]   85681..85730 [+]
Host baterium   Klebsiella pneumoniae strain Kpn555

Cargo genes

Drug resistance gene   blaSHV-1
Virulence gene   -
Metal resistance gene   fecD, fecE, 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