Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103701
Name   oriT_pIncFIBk_6713 in_silico
Organism   Klebsiella pneumoniae strain NMI6713_12
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MT439327 (122443..122492 [-], 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_6713
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2746 GenBank   WP_032441895
Name   traI_H5J12_RS00800_pIncFIBk_6713 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   2581 GenBank   WP_032441894
Name   traD_H5J12_RS00795_pIncFIBk_6713 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: 121885..150990

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H5J12_RS00580 116906..117256 + 351 WP_023287104 hypothetical protein -
H5J12_RS00585 117888..118244 + 357 WP_019706019 hypothetical protein -
H5J12_RS00590 118305..118517 + 213 WP_019706020 hypothetical protein -
H5J12_RS00595 118537..118752 + 216 WP_142381705 hypothetical protein -
H5J12_RS00600 118833..119153 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
H5J12_RS00605 119143..119421 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
H5J12_RS00610 119422..119835 + 414 WP_004152722 helix-turn-helix domain-containing protein -
H5J12_RS00615 120669..121490 + 822 WP_004178064 DUF932 domain-containing protein -
H5J12_RS00620 121523..121852 + 330 WP_011977736 DUF5983 family protein -
H5J12_RS00625 121885..122370 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
H5J12_RS00630 122805..123197 + 393 WP_032441878 conjugal transfer relaxosome DNA-binding protein TraM -
H5J12_RS00635 123413..124099 + 687 WP_071561590 transcriptional regulator TraJ family protein -
H5J12_RS00640 124183..124554 + 372 WP_004208838 TraY domain-containing protein -
H5J12_RS00645 124608..124976 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
H5J12_RS00650 124990..125295 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
H5J12_RS00655 125315..125881 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
H5J12_RS00660 125868..126608 + 741 WP_015065528 type-F conjugative transfer system secretin TraK traK
H5J12_RS00665 126608..128032 + 1425 WP_032441880 F-type conjugal transfer pilus assembly protein TraB traB
H5J12_RS00670 128146..128730 + 585 WP_032441881 type IV conjugative transfer system lipoprotein TraV traV
H5J12_RS00675 128862..129272 + 411 WP_004152499 hypothetical protein -
H5J12_RS00680 129378..129596 + 219 WP_004195235 hypothetical protein -
H5J12_RS00685 129597..129926 + 330 WP_032441883 hypothetical protein -
H5J12_RS00690 129993..130397 + 405 WP_004197817 hypothetical protein -
H5J12_RS00695 130775..131173 + 399 WP_023179972 hypothetical protein -
H5J12_RS00700 131245..133887 + 2643 WP_032441884 type IV secretion system protein TraC virb4
H5J12_RS00705 133884..134273 + 390 WP_004167468 type-F conjugative transfer system protein TrbI -
H5J12_RS00710 134273..134908 + 636 WP_032441885 type-F conjugative transfer system protein TraW traW
H5J12_RS00715 134943..135344 + 402 WP_004194979 hypothetical protein -
H5J12_RS00720 135341..136330 + 990 WP_032441886 conjugal transfer pilus assembly protein TraU traU
H5J12_RS00725 136343..136981 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
H5J12_RS00730 137040..138995 + 1956 WP_032441887 type-F conjugative transfer system mating-pair stabilization protein TraN traN
H5J12_RS00735 139027..139281 + 255 WP_004152674 conjugal transfer protein TrbE -
H5J12_RS00740 139259..139507 + 249 WP_004152675 hypothetical protein -
H5J12_RS00745 139520..139846 + 327 WP_023284640 hypothetical protein -
H5J12_RS00750 139867..140619 + 753 WP_032441888 type-F conjugative transfer system pilin assembly protein TraF traF
H5J12_RS00755 140630..140869 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
H5J12_RS00760 140841..141398 + 558 WP_032441889 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
H5J12_RS00765 141444..141887 + 444 WP_032441890 F-type conjugal transfer protein TrbF -
H5J12_RS00770 141865..143244 + 1380 WP_074185210 conjugal transfer pilus assembly protein TraH traH
H5J12_RS00775 143244..146066 + 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
H5J12_RS00780 146089..146691 + 603 WP_013214035 conjugal transfer protein TraS -
H5J12_RS00785 146942..147673 + 732 WP_032441892 conjugal transfer complement resistance protein TraT -
H5J12_RS00790 147865..148554 + 690 WP_074185211 hypothetical protein -
H5J12_RS00795 148681..150990 + 2310 WP_032441894 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4144 GenBank   NZ_MT439327
Plasmid name   pIncFIBk_6713 Incompatibility group   IncFII
Plasmid size   189780 bp Coordinate of oriT [Strand]   122443..122492 [-]
Host baterium   Klebsiella pneumoniae strain NMI6713_12

Cargo genes

Drug resistance gene   tet(A), mph(A)
Virulence gene   -
Metal resistance gene   arsR, arsD, arsA, arsB, arsC, arsH, pcoE, pcoS, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9