Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105308
Name   oriT_pRHBSTW-00409_4 in_silico
Organism   Klebsiella michiganensis strain RHBSTW-00409
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055328 (82269..82317 [-], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pRHBSTW-00409_4
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3628 GenBank   WP_064359958
Name   traI_HV187_RS31860_pRHBSTW-00409_4 insolico UniProt ID   A0A7D6JMG2
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 189724.34 Da        Isoelectric Point: 5.9228

>WP_064359958.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MLSFSQVKSAGSAGNYYTEKDNYYVTGSMEERWQGKGAETLELEGKVDKQVFTALLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALEQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKETIDPAEKMVEWMNT
LKETGFDIRGYREAADARAKELASAPAAPVKTDGPDIGDVVTNAIAGLSDRKVQFTYADLLARTVGQLEA
KPGVFERARGGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVTVTPDATVVRLAPF
SDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQNGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGRQTTADIISEPDKGARYNRLAQEFAVSVREGQESVAQISGTREQGVLNGIIRDTLKNEGALGTKEM
AITALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVANGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQALSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDATRTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIATQKAGLHTPAEQVIHLSIPLLESEALTFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGQGNDLLISRQTWDAEKSILTKVLEGKDAVPPLMDSVPGSLMADLTSGQRAATRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQAPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPAQEKAIQK
ALSEGEILPAGQPATLYEALVKDYADRTPEAQLQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKAVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAITA
HGAQGASEPYAIALEGVTGGRKQMASFESAYVGLSRMKLHVQVYTDSREGWVNAIQASPSKATAHDILAP
RNERAVKTADLLFGRAQPLNETAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKNAGIW
LSPLTDKDGRLEAIGGDGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMGRQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4CP

ID   3597 GenBank   WP_080848157
Name   traD_HV187_RS31855_pRHBSTW-00409_4 insolico UniProt ID   _
Length   764 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 764 a.a.        Molecular weight: 85403.54 Da        Isoelectric Point: 4.9713

>WP_080848157.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTISYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTVCVVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIQRRLDARVDGRLSALLEAREAEGSLARALFTPDEPVSESAEEKAGVQPEQTKPAEDS
VLPVPVKTSSKAAEGAGKTPDVPLSGAPVTRVKTVPLIRPEPAASVTGTAAAASTAAVIATAGGTAQELA
QQPVEADQNMLPAGMNEDGVIEDMQAYDEWLAGEQTQRDMQRREEVNINHSRSEQDDIEIGGNF

  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: 81702..109019

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV187_RS31660 (HV187_31670) 76812..77159 + 348 WP_064182675 hypothetical protein -
HV187_RS31665 (HV187_31675) 77248..77478 + 231 WP_060415465 hypothetical protein -
HV187_RS31670 (HV187_31680) 77525..78358 + 834 WP_060415466 N-6 DNA methylase -
HV187_RS31675 (HV187_31685) 78598..79593 + 996 WP_077254794 IS5 family transposase -
HV187_RS31680 (HV187_31690) 79595..80563 + 969 WP_074185243 IS5 family transposase -
HV187_RS31685 (HV187_31695) 80774..81142 - 369 WP_080848162 hypothetical protein -
HV187_RS31690 (HV187_31700) 81137..81679 + 543 WP_060415467 antirestriction protein -
HV187_RS31695 (HV187_31705) 81702..82124 - 423 WP_073972322 transglycosylase SLT domain-containing protein virB1
HV187_RS31700 (HV187_31710) 82628..83026 + 399 WP_228728719 conjugal transfer relaxosome DNA-binding protein TraM -
HV187_RS31710 (HV187_31720) 83691..84017 + 327 WP_181248431 type IV conjugative transfer system pilin TraA -
HV187_RS31715 (HV187_31725) 84031..84336 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
HV187_RS31720 (HV187_31730) 84352..84918 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
HV187_RS31725 (HV187_31735) 84905..85639 + 735 WP_099743468 type-F conjugative transfer system secretin TraK traK
HV187_RS31730 (HV187_31740) 85639..87060 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
HV187_RS31735 (HV187_31745) 87053..87487 + 435 WP_020322358 conjugal transfer protein TraP -
HV187_RS31740 (HV187_31750) 87521..88105 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
HV187_RS31745 (HV187_31755) 88718..88906 + 189 WP_053390286 hypothetical protein -
HV187_RS32265 88990..89391 + 402 WP_064343532 hypothetical protein -
HV187_RS31755 (HV187_31765) 89388..89687 + 300 WP_053390308 hypothetical protein -
HV187_RS31760 (HV187_31770) 89775..90158 + 384 WP_042946290 hypothetical protein -
HV187_RS31765 (HV187_31775) 90251..92890 + 2640 WP_064343533 type IV secretion system protein TraC virb4
HV187_RS31770 (HV187_31780) 92890..93282 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
HV187_RS31775 (HV187_31785) 93279..93905 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
HV187_RS31780 (HV187_31790) 93949..94908 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
HV187_RS31785 (HV187_31795) 94921..95568 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV187_RS31790 (HV187_31800) 95565..95948 + 384 WP_053390297 hypothetical protein -
HV187_RS31795 (HV187_31805) 95945..97900 + 1956 WP_080848160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV187_RS31800 (HV187_31810) 97932..98192 + 261 WP_053390216 hypothetical protein -
HV187_RS31805 (HV187_31815) 98185..98796 + 612 WP_053390217 hypothetical protein -
HV187_RS31810 (HV187_31820) 98786..99028 + 243 WP_053390218 conjugal transfer protein TrbE -
HV187_RS31815 (HV187_31825) 99074..99400 + 327 WP_053390219 hypothetical protein -
HV187_RS31820 (HV187_31830) 99421..100173 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
HV187_RS31825 (HV187_31835) 100184..100420 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
HV187_RS31830 (HV187_31840) 100395..100955 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV187_RS31835 (HV187_31845) 100942..102312 + 1371 WP_080848158 conjugal transfer pilus assembly protein TraH traH
HV187_RS31840 (HV187_31850) 102312..105155 + 2844 WP_049078361 conjugal transfer mating-pair stabilization protein TraG traG
HV187_RS31845 (HV187_31855) 105161..105676 + 516 WP_049078360 conjugal transfer protein TraS -
HV187_RS31850 (HV187_31860) 105739..106485 + 747 WP_049078359 hypothetical protein -
HV187_RS31855 (HV187_31865) 106725..109019 + 2295 WP_080848157 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5746 GenBank   NZ_CP055328
Plasmid name   pRHBSTW-00409_4 Incompatibility group   IncFII
Plasmid size   120646 bp Coordinate of oriT [Strand]   82269..82317 [-]
Host baterium   Klebsiella michiganensis strain RHBSTW-00409

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -