Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120772
Name   oriT_pKA04-3 in_silico
Organism   Klebsiella aerogenes strain KA04
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP139030 (200516..200565 [+], 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_pKA04-3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13100 GenBank   WP_032448280
Name   traI_SH589_RS27535_pKA04-3 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: 190581.22 Da        Isoelectric Point: 5.9995

>WP_032448280.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWLTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
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)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   15378 GenBank   WP_013214038
Name   traD_SH589_RS27540_pKA04-3 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: 86010.07 Da        Isoelectric Point: 5.1787

>WP_013214038.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 171144..201123

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SH589_RS27540 (SH589_27545) 171144..173456 - 2313 WP_013214038 type IV conjugative transfer system coupling protein TraD virb4
SH589_RS27545 (SH589_27550) 173583..174272 - 690 WP_014343485 hypothetical protein -
SH589_RS27550 (SH589_27555) 174465..175196 - 732 WP_013214036 conjugal transfer complement resistance protein TraT -
SH589_RS27555 (SH589_27560) 175448..176050 - 603 WP_013214035 conjugal transfer protein TraS -
SH589_RS27560 (SH589_27565) 176073..178895 - 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
SH589_RS27565 (SH589_27570) 178895..180274 - 1380 WP_074160414 conjugal transfer pilus assembly protein TraH traH
SH589_RS27570 (SH589_27575) 180252..180695 - 444 WP_013214032 F-type conjugal transfer protein TrbF -
SH589_RS27575 (SH589_27580) 180741..181298 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SH589_RS27580 (SH589_27585) 181270..181509 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
SH589_RS27585 (SH589_27590) 181520..182272 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
SH589_RS27590 (SH589_27595) 182293..182619 - 327 WP_013214030 hypothetical protein -
SH589_RS27595 (SH589_27600) 182632..182880 - 249 WP_013214029 hypothetical protein -
SH589_RS27600 (SH589_27605) 182858..183112 - 255 WP_004152674 conjugal transfer protein TrbE -
SH589_RS27605 (SH589_27610) 183144..185099 - 1956 WP_032448279 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SH589_RS27610 (SH589_27615) 185158..185805 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
SH589_RS27615 (SH589_27620) 186081..187070 - 990 WP_032439620 conjugal transfer pilus assembly protein TraU traU
SH589_RS27620 (SH589_27625) 187067..187468 - 402 WP_016831047 hypothetical protein -
SH589_RS27625 (SH589_27630) 187503..188138 - 636 WP_020325113 type-F conjugative transfer system protein TraW traW
SH589_RS27630 (SH589_27635) 188138..188527 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
SH589_RS27635 (SH589_27640) 188527..191166 - 2640 WP_032448278 type IV secretion system protein TraC virb4
SH589_RS27640 (SH589_27645) 191238..191636 - 399 WP_023158008 hypothetical protein -
SH589_RS27645 (SH589_27650) 191644..192033 - 390 WP_065799586 hypothetical protein -
SH589_RS27650 (SH589_27655) 192076..192480 - 405 WP_016831042 hypothetical protein -
SH589_RS27655 (SH589_27660) 192547..192859 - 313 Protein_196 hypothetical protein -
SH589_RS27660 (SH589_27665) 192860..193078 - 219 WP_014386199 hypothetical protein -
SH589_RS27665 (SH589_27670) 193038..193352 - 315 WP_032448277 hypothetical protein -
SH589_RS27670 (SH589_27675) 193357..193767 - 411 WP_014386197 hypothetical protein -
SH589_RS27675 (SH589_27680) 193898..194482 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
SH589_RS27680 (SH589_27685) 194529..195101 - 573 WP_014386195 conjugal transfer pilus-stabilizing protein TraP -
SH589_RS27685 (SH589_27690) 195094..196518 - 1425 WP_014386194 F-type conjugal transfer pilus assembly protein TraB traB
SH589_RS27690 (SH589_27695) 196518..197258 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
SH589_RS27695 (SH589_27700) 197245..197811 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
SH589_RS27700 (SH589_27705) 197831..198136 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
SH589_RS27705 (SH589_27710) 198150..198518 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
SH589_RS27710 (SH589_27715) 198580..198786 - 207 WP_171773970 TraY domain-containing protein -
SH589_RS27715 (SH589_27720) 198919..199638 - 720 WP_014386192 conjugal transfer protein -
SH589_RS27720 (SH589_27725) 199831..200247 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
SH589_RS27725 (SH589_27730) 200638..201123 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
SH589_RS27730 (SH589_27735) 201156..201485 - 330 WP_014386191 DUF5983 family protein -
SH589_RS27735 (SH589_27740) 201518..202339 - 822 WP_004182076 DUF932 domain-containing protein -
SH589_RS27740 (SH589_27745) 203172..203585 - 414 WP_013023817 type II toxin-antitoxin system HigA family antitoxin -
SH589_RS27745 (SH589_27750) 203586..203864 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
SH589_RS27750 (SH589_27755) 203854..204174 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
SH589_RS27755 (SH589_27760) 204255..204479 - 225 WP_014386189 hypothetical protein -
SH589_RS27760 (SH589_27765) 204490..204702 - 213 WP_014386188 hypothetical protein -
SH589_RS27765 (SH589_27770) 204764..205090 - 327 WP_014386187 hypothetical protein -

Host bacterium

ID   21201 GenBank   NZ_CP139030
Plasmid name   pKA04-3 Incompatibility group   IncFIB
Plasmid size   215871 bp Coordinate of oriT [Strand]   200516..200565 [+]
Host baterium   Klebsiella aerogenes strain KA04

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR
Virulence gene   iutA, iucD, iucC, iucB, iucA
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsR, arsD, arsA, arsB, arsC, fecD, fecE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -