Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105481
Name   oriT_p652-2 in_silico
Organism   Klebsiella pneumoniae strain 15-652
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP097192 (164520..164569 [+], 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_p652-2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3735 GenBank   WP_022631527
Name   traI_M4I39_RS27600_p652-2 insolico UniProt ID   U5N3A2
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190332.06 Da        Isoelectric Point: 6.2397

>WP_022631527.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMSREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQLELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGGGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




T4CP

ID   3728 GenBank   WP_015065541
Name   traD_M4I39_RS27605_p652-2 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: 136095..165127

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
M4I39_RS27605 (M4I39_27575) 136095..138407 - 2313 WP_015065541 type IV conjugative transfer system coupling protein TraD virb4
M4I39_RS27610 (M4I39_27580) 138536..139225 - 690 WP_015065540 hypothetical protein -
M4I39_RS27615 (M4I39_27585) 139417..140148 - 732 WP_032329926 conjugal transfer complement resistance protein TraT -
M4I39_RS27620 (M4I39_27590) 140457..140981 - 525 WP_015065538 hypothetical protein -
M4I39_RS27625 (M4I39_27595) 140992..143835 - 2844 WP_032420975 conjugal transfer mating-pair stabilization protein TraG traG
M4I39_RS27630 (M4I39_27600) 143835..145205 - 1371 WP_117259850 conjugal transfer pilus assembly protein TraH traH
M4I39_RS27635 (M4I39_27605) 145192..145620 - 429 WP_015065560 hypothetical protein -
M4I39_RS27640 (M4I39_27610) 145613..146185 - 573 WP_023292147 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
M4I39_RS27645 (M4I39_27615) 146157..146396 - 240 WP_004152687 type-F conjugative transfer system pilin chaperone TraQ -
M4I39_RS27650 (M4I39_27620) 146407..147159 - 753 WP_020803149 type-F conjugative transfer system pilin assembly protein TraF traF
M4I39_RS27655 (M4I39_27625) 147180..147506 - 327 WP_004144402 hypothetical protein -
M4I39_RS27660 (M4I39_27630) 147519..147767 - 249 WP_004152675 hypothetical protein -
M4I39_RS27665 (M4I39_27635) 147745..147999 - 255 WP_004152674 conjugal transfer protein TrbE -
M4I39_RS27670 (M4I39_27640) 148031..149986 - 1956 WP_030003482 type-F conjugative transfer system mating-pair stabilization protein TraN traN
M4I39_RS27675 (M4I39_27645) 150045..150683 - 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
M4I39_RS27680 (M4I39_27650) 150696..151685 - 990 WP_011977785 conjugal transfer pilus assembly protein TraU traU
M4I39_RS27685 (M4I39_27655) 151682..152071 - 390 WP_015065532 hypothetical protein -
M4I39_RS27690 (M4I39_27660) 152113..152739 - 627 WP_009309871 type-F conjugative transfer system protein TraW traW
M4I39_RS27695 (M4I39_27665) 152739..153128 - 390 WP_110917693 type-F conjugative transfer system protein TrbI -
M4I39_RS27700 (M4I39_27670) 153128..155767 - 2640 WP_064162928 type IV secretion system protein TraC virb4
M4I39_RS27705 (M4I39_27675) 155839..156237 - 399 WP_023179972 hypothetical protein -
M4I39_RS27710 (M4I39_27680) 156615..157019 - 405 WP_004197817 hypothetical protein -
M4I39_RS27715 (M4I39_27685) 157086..157415 - 330 WP_032441883 hypothetical protein -
M4I39_RS27720 (M4I39_27690) 157416..157634 - 219 WP_004195235 hypothetical protein -
M4I39_RS27725 (M4I39_27695) 157740..158150 - 411 WP_004152499 hypothetical protein -
M4I39_RS27730 (M4I39_27700) 158282..158866 - 585 WP_032441881 type IV conjugative transfer system lipoprotein TraV traV
M4I39_RS27735 (M4I39_27705) 158980..160404 - 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
M4I39_RS27740 (M4I39_27710) 160404..161144 - 741 WP_015065528 type-F conjugative transfer system secretin TraK traK
M4I39_RS27745 (M4I39_27715) 161131..161697 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
M4I39_RS27750 (M4I39_27720) 161717..162022 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
M4I39_RS27755 (M4I39_27725) 162036..162404 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
M4I39_RS27760 (M4I39_27730) 162458..162829 - 372 WP_004208838 TraY domain-containing protein -
M4I39_RS27765 (M4I39_27735) 162913..163599 - 687 WP_071561590 transcriptional regulator TraJ family protein -
M4I39_RS27770 (M4I39_27740) 163815..164207 - 393 WP_032441878 conjugal transfer relaxosome DNA-binding protein TraM -
M4I39_RS27775 (M4I39_27745) 164642..165127 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
M4I39_RS27780 (M4I39_27750) 165160..165489 - 330 WP_011977736 DUF5983 family protein -
M4I39_RS27785 (M4I39_27755) 165522..166343 - 822 WP_004178064 DUF932 domain-containing protein -
M4I39_RS27790 (M4I39_27760) 167177..167590 - 414 WP_004152722 helix-turn-helix domain-containing protein -
M4I39_RS27795 (M4I39_27765) 167591..167869 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
M4I39_RS27800 (M4I39_27770) 167859..168179 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
M4I39_RS27805 (M4I39_27775) 168260..168484 - 225 WP_014343499 hypothetical protein -
M4I39_RS27810 (M4I39_27780) 168495..168707 - 213 WP_019706020 hypothetical protein -
M4I39_RS27815 (M4I39_27785) 168768..169124 - 357 WP_019706019 hypothetical protein -

Host bacterium

ID   5919 GenBank   NZ_CP097192
Plasmid name   p652-2 Incompatibility group   IncFIB
Plasmid size   192753 bp Coordinate of oriT [Strand]   164520..164569 [+]
Host baterium   Klebsiella pneumoniae strain 15-652

Cargo genes

Drug resistance gene   aadA2, qacE, sul1, mph(A), blaTEM-1B
Virulence gene   mrkJ, mrkF, mrkD, mrkC, mrkB, mrkA
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