Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103702
Name   oriT_pIncFIBk_3243 in_silico
Organism   Klebsiella pneumoniae strain NMI3243_13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MT439326 (168585..168634 [+], 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_pIncFIBk_3243
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2747 GenBank   WP_032441895
Name   traI_H5I88_RS00635_pIncFIBk_3243 insolico UniProt ID   A0A7D5G561
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190517.07 Da        Isoelectric Point: 6.0893

>WP_032441895.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVIGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKLSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNRESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   2582 GenBank   WP_032441894
Name   traD_H5I88_RS00640_pIncFIBk_3243 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: 85957.93 Da        Isoelectric Point: 5.0577

>WP_032441894.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEARESEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRVTEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 140087..169192

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H5I88_RS00640 140087..142396 - 2310 WP_032441894 type IV conjugative transfer system coupling protein TraD virb4
H5I88_RS00645 142523..143212 - 690 WP_074185211 hypothetical protein -
H5I88_RS00650 143404..144135 - 732 WP_032441892 conjugal transfer complement resistance protein TraT -
H5I88_RS00655 144386..144988 - 603 WP_013214035 conjugal transfer protein TraS -
H5I88_RS00660 145011..147833 - 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
H5I88_RS00665 147833..149212 - 1380 WP_074185210 conjugal transfer pilus assembly protein TraH traH
H5I88_RS00670 149190..149633 - 444 WP_032441890 F-type conjugal transfer protein TrbF -
H5I88_RS00675 149679..150236 - 558 WP_032441889 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
H5I88_RS00680 150208..150447 - 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
H5I88_RS00685 150458..151210 - 753 WP_032441888 type-F conjugative transfer system pilin assembly protein TraF traF
H5I88_RS00690 151231..151557 - 327 WP_023284640 hypothetical protein -
H5I88_RS00695 151570..151818 - 249 WP_004152675 hypothetical protein -
H5I88_RS00700 151796..152050 - 255 WP_004152674 conjugal transfer protein TrbE -
H5I88_RS00705 152082..154037 - 1956 WP_032441887 type-F conjugative transfer system mating-pair stabilization protein TraN traN
H5I88_RS00710 154096..154734 - 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
H5I88_RS00715 154747..155736 - 990 WP_032441886 conjugal transfer pilus assembly protein TraU traU
H5I88_RS00720 155733..156134 - 402 WP_004194979 hypothetical protein -
H5I88_RS00725 156169..156804 - 636 WP_032441885 type-F conjugative transfer system protein TraW traW
H5I88_RS00730 156804..157193 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
H5I88_RS00735 157190..159832 - 2643 WP_181727702 type IV secretion system protein TraC virb4
H5I88_RS00740 159904..160302 - 399 WP_023179972 hypothetical protein -
H5I88_RS00745 160680..161084 - 405 WP_004197817 hypothetical protein -
H5I88_RS00750 161151..161480 - 330 WP_032441883 hypothetical protein -
H5I88_RS00755 161481..161699 - 219 WP_004195235 hypothetical protein -
H5I88_RS00760 161805..162215 - 411 WP_004152499 hypothetical protein -
H5I88_RS00765 162347..162931 - 585 WP_032441881 type IV conjugative transfer system lipoprotein TraV traV
H5I88_RS00770 163045..164469 - 1425 WP_032441880 F-type conjugal transfer pilus assembly protein TraB traB
H5I88_RS00775 164469..165209 - 741 WP_015065528 type-F conjugative transfer system secretin TraK traK
H5I88_RS00780 165196..165762 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
H5I88_RS00785 165782..166087 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
H5I88_RS00790 166101..166469 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
H5I88_RS00795 166523..166894 - 372 WP_004208838 TraY domain-containing protein -
H5I88_RS00800 166978..167664 - 687 WP_071561590 transcriptional regulator TraJ family protein -
H5I88_RS00805 167880..168272 - 393 WP_032441878 conjugal transfer relaxosome DNA-binding protein TraM -
H5I88_RS00810 168707..169192 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
H5I88_RS00815 169225..169554 - 330 WP_011977736 DUF5983 family protein -
H5I88_RS00820 169587..170408 - 822 WP_004178064 DUF932 domain-containing protein -
H5I88_RS00825 171242..171655 - 414 WP_004152722 helix-turn-helix domain-containing protein -
H5I88_RS00830 171656..171934 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
H5I88_RS00835 171924..172244 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
H5I88_RS00840 172325..172549 - 225 WP_014343499 hypothetical protein -
H5I88_RS00845 172560..172772 - 213 WP_019706020 hypothetical protein -
H5I88_RS00850 172833..173189 - 357 WP_019706019 hypothetical protein -
H5I88_RS00855 173821..174171 - 351 WP_023287104 hypothetical protein -

Host bacterium

ID   4145 GenBank   NZ_MT439326
Plasmid name   pIncFIBk_3243 Incompatibility group   IncFIB
Plasmid size   199248 bp Coordinate of oriT [Strand]   168585..168634 [+]
Host baterium   Klebsiella pneumoniae strain NMI3243_13

Cargo genes

Drug resistance gene   mph(A), tet(A)
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, kdeA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9