Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104797
Name   oriT_IncFIB IncFII in_silico
Organism   Klebsiella pneumoniae strain 1_GR_13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP027044 (35645..35694 [+], 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_IncFIB IncFII
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3404 GenBank   WP_004153029
Name   traI_A6D67_RS26850_IncFIB IncFII insolico UniProt ID   A0A422WEA5
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190808.90 Da        Isoelectric Point: 6.2081

>WP_004153029.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANRHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRLVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKKAEQTAREMAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1433-1555)

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

(577-629)

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

(635-714)

AAA domain (AAA_30)

(971-1157)

TrwC relaxase (TrwC)

(10-284)


  Protein structure



No available structure.




T4CP

ID   3340 GenBank   WP_060577930
Name   traD_A6D67_RS26855_IncFIB IncFII 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: 85931.98 Da        Isoelectric Point: 5.0612

>WP_060577930.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENHNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIPRRLDTRVDARLSALLEEREAEGSLARALFTPDAPASGPADTDSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAAEPSVRATEPPVLRVTTVPLIKPKAAAAAAAASTASSAGIPAAAAGGTE
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: 7825..36252

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
A6D67_RS26855 (A6D67_027035) 7825..10134 - 2310 WP_060577930 type IV conjugative transfer system coupling protein TraD virb4
A6D67_RS26860 (A6D67_027040) 10494..11225 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
A6D67_RS26865 (A6D67_027045) 11415..11942 - 528 WP_004153030 hypothetical protein -
A6D67_RS26870 (A6D67_027050) 11948..14797 - 2850 WP_004178054 conjugal transfer mating-pair stabilization protein TraG traG
A6D67_RS26875 (A6D67_027055) 14797..16167 - 1371 WP_004178055 conjugal transfer pilus assembly protein TraH traH
A6D67_RS26880 (A6D67_027060) 16154..16582 - 429 WP_004152689 hypothetical protein -
A6D67_RS26885 (A6D67_027065) 16575..17147 - 573 WP_004152688 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
A6D67_RS26890 (A6D67_027070) 17119..17358 - 240 WP_004152687 type-F conjugative transfer system pilin chaperone TraQ -
A6D67_RS26895 (A6D67_027075) 17369..18121 - 753 WP_004152686 type-F conjugative transfer system pilin assembly protein TraF traF
A6D67_RS26900 (A6D67_027080) 18142..18468 - 327 WP_004152685 hypothetical protein -
A6D67_RS30320 (A6D67_027085) 18514..18699 - 186 WP_004152684 hypothetical protein -
A6D67_RS26910 (A6D67_027090) 18696..18932 - 237 WP_004152683 conjugal transfer protein TrbE -
A6D67_RS26915 (A6D67_027095) 18964..20919 - 1956 WP_060577929 type-F conjugative transfer system mating-pair stabilization protein TraN traN
A6D67_RS26920 (A6D67_027100) 20978..21616 - 639 WP_020316653 type-F conjugative transfer system pilin assembly protein TrbC trbC
A6D67_RS26925 (A6D67_027105) 21629..22588 - 960 WP_202386622 conjugal transfer pilus assembly protein TraU traU
A6D67_RS26930 (A6D67_027110) 22632..23258 - 627 WP_020314628 type-F conjugative transfer system protein TraW traW
A6D67_RS26935 (A6D67_027115) 23258..23647 - 390 WP_020316628 type-F conjugative transfer system protein TrbI -
A6D67_RS26940 (A6D67_027120) 23647..26286 - 2640 WP_020316635 type IV secretion system protein TraC virb4
A6D67_RS26945 (A6D67_027125) 26358..26755 - 398 Protein_23 hypothetical protein -
A6D67_RS26950 (A6D67_027130) 26763..27053 - 291 WP_032419928 hypothetical protein -
A6D67_RS26955 (A6D67_027135) 27050..27454 - 405 WP_060577928 hypothetical protein -
A6D67_RS26960 (A6D67_027140) 27521..27838 - 318 WP_004152595 hypothetical protein -
A6D67_RS26965 (A6D67_027145) 27839..28057 - 219 WP_004171484 hypothetical protein -
A6D67_RS26970 (A6D67_027150) 28081..28371 - 291 WP_004152596 hypothetical protein -
A6D67_RS26975 (A6D67_027155) 28376..28786 - 411 WP_004152597 lipase chaperone -
A6D67_RS26980 (A6D67_027160) 28918..29487 - 570 WP_004152598 type IV conjugative transfer system lipoprotein TraV traV
A6D67_RS26985 (A6D67_027165) 29510..30106 - 597 WP_004152599 conjugal transfer pilus-stabilizing protein TraP -
A6D67_RS26990 (A6D67_027170) 30099..31523 - 1425 WP_004152600 F-type conjugal transfer pilus assembly protein TraB traB
A6D67_RS26995 (A6D67_027175) 31523..32263 - 741 WP_004152601 type-F conjugative transfer system secretin TraK traK
A6D67_RS27000 (A6D67_027180) 32250..32816 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
A6D67_RS27005 (A6D67_027185) 32836..33141 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
A6D67_RS27010 (A6D67_027190) 33155..33523 - 369 WP_004178060 type IV conjugative transfer system pilin TraA -
A6D67_RS27015 (A6D67_027195) 33577..33948 - 372 WP_004208838 TraY domain-containing protein -
A6D67_RS27020 (A6D67_027200) 34032..34727 - 696 WP_004178061 transcriptional regulator TraJ family protein -
A6D67_RS27025 (A6D67_027205) 34941..35333 - 393 WP_004178062 conjugal transfer relaxosome DNA-binding protein TraM -
A6D67_RS27030 (A6D67_027210) 35767..36252 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
A6D67_RS27035 (A6D67_027215) 36285..36614 - 330 WP_072196951 DUF5983 family protein -
A6D67_RS27040 (A6D67_027220) 36647..37468 - 822 WP_004178064 DUF932 domain-containing protein -
A6D67_RS27055 (A6D67_027235) 38302..38499 - 198 Protein_43 helix-turn-helix domain-containing protein -

Host bacterium

ID   5236 GenBank   NZ_CP027044
Plasmid name   IncFIB IncFII Incompatibility group   IncFII
Plasmid size   168873 bp Coordinate of oriT [Strand]   35645..35694 [+]
Host baterium   Klebsiella pneumoniae strain 1_GR_13

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib, dfrA14, aph(3')-Ia, dfrA1
Virulence gene   -
Metal resistance gene   fecE, fecD, merR, merT, merP, merC, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9