Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113707
Name   oriT_pKGB1a in_silico
Organism   Klebsiella variicola strain KGB_1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP071736 (92290..92339 [+], 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_pKGB1a
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8777 GenBank   WP_253616159
Name   traI_KGB1_RS27715_pKGB1a insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190911.01 Da        Isoelectric Point: 5.9865

>WP_253616159.1 conjugative transfer relaxase/helicase TraI [Klebsiella variicola]
MMSIGSVKSAVSAGNYYTDKDNYYVIGSMDERWQGKGTEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSEMVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREVFKPLVE
TLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVECMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTGSSNMLTLKDREGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKNTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLHTPAEQAIHLSIPLLESQDLTFTRPQLLATALETGGDKVPMWSIEMTI
KKQIKSGQLLNVGVSPGHGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPHVIGLGPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGEGRAVLSGDTDQLQSISPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIDRDIDRALATIEQVTPERVPRKEGAWVPGSSVVEFTPTQEEEIR
KALSKGESLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNNDRRALNGLIHEARRENGETGREEVTL
PVLVTSNIRDGELRKLSTWTAHKGAVALVDNVYHRIDNVDKDNQLITLTDSEGKERYISPREASAEGVTL
YRQEEITVSQGDRMRFSKSDPERGYVANSVWEVQSISGDSVTLSDGKTTRTLTPKADEAQQHIDLAYAIT
AHGAQGASEPYAIALEGMVGARKLMASFKSAYVGLSRMKQHVQVYTDRREGWIKAIQHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDWDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAITGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAWEVAGEARKAGEP
VDRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRDRLQAVERDMVRDLNREKTL
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)

AAA domain (AAA_30)

(971-1158)

TrwC relaxase (TrwC)

(13-280)

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

(635-714)


  Protein structure



No available structure.




T4CP

ID   10169 GenBank   WP_253616162
Name   traD_KGB1_RS27720_pKGB1a insolico UniProt ID   _
Length   767 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 767 a.a.        Molecular weight: 85767.73 Da        Isoelectric Point: 4.9685

>WP_253616162.1 type IV conjugative transfer system coupling protein TraD [Klebsiella variicola]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKL
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGSKEDPFWQG
SGRTIFAEGAFLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAVGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAERFIPRTLDARVDARLSALLEAREAEGSLARALFTPDSPGSEPADTDSHAGEQPEPVSQPA
PAEVTVSPAPVKAPPTTKSPAVEPSVRATEPPVLRVTTVPLIKPKAAAAAAAASTASSAGTPAAGGTEQE
LAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSRRHDEQDDVEIGGNF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 62917..92891

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KGB1_RS27720 (KGB1_27700) 62917..65220 - 2304 WP_253616162 type IV conjugative transfer system coupling protein TraD virb4
KGB1_RS27725 (KGB1_27705) 65349..66038 - 690 WP_253616165 hypothetical protein -
KGB1_RS27730 (KGB1_27710) 66231..66962 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
KGB1_RS27735 (KGB1_27715) 67152..67679 - 528 WP_253616196 conjugal transfer protein TraS -
KGB1_RS27740 (KGB1_27720) 67685..70534 - 2850 WP_253616167 conjugal transfer mating-pair stabilization protein TraG traG
KGB1_RS27745 (KGB1_27725) 70534..71913 - 1380 WP_253616170 conjugal transfer pilus assembly protein TraH traH
KGB1_RS27750 (KGB1_27730) 71891..72334 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
KGB1_RS27755 (KGB1_27735) 72380..72937 - 558 WP_253616172 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KGB1_RS27760 (KGB1_27740) 72909..73148 - 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
KGB1_RS27765 (KGB1_27745) 73159..73911 - 753 WP_253616175 type-F conjugative transfer system pilin assembly protein TraF traF
KGB1_RS27770 (KGB1_27750) 73932..74258 - 327 WP_064144773 hypothetical protein -
KGB1_RS27775 (KGB1_27755) 74269..74496 - 228 WP_110244276 conjugal transfer protein TrbE -
KGB1_RS27780 (KGB1_27760) 74528..76483 - 1956 WP_253616177 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KGB1_RS27785 (KGB1_27765) 76542..77189 - 648 WP_253616180 type-F conjugative transfer system pilin assembly protein TrbC trbC
KGB1_RS27790 (KGB1_27770) 77381..77620 + 240 WP_253616182 hypothetical protein -
KGB1_RS27795 (KGB1_27775) 77617..77796 - 180 WP_253616185 hypothetical protein -
KGB1_RS27800 (KGB1_27780) 77817..78800 - 984 WP_223172941 conjugal transfer pilus assembly protein TraU traU
KGB1_RS27805 (KGB1_27785) 78820..79446 - 627 WP_253616187 type-F conjugative transfer system protein TraW traW
KGB1_RS27810 (KGB1_27790) 79446..79835 - 390 WP_004152591 type-F conjugative transfer system protein TrbI -
KGB1_RS27815 (KGB1_27795) 79835..82474 - 2640 WP_253616190 type IV secretion system protein TraC virb4
KGB1_RS27820 (KGB1_27800) 82546..82944 - 399 WP_072158599 hypothetical protein -
KGB1_RS27825 (KGB1_27805) 82952..83266 - 315 WP_253616121 hypothetical protein -
KGB1_RS27830 (KGB1_27810) 83371..83661 - 291 WP_253616123 hypothetical protein -
KGB1_RS27835 (KGB1_27815) 83658..84062 - 405 WP_253616126 hypothetical protein -
KGB1_RS27840 (KGB1_27820) 84129..84446 - 318 WP_253616128 hypothetical protein -
KGB1_RS27845 (KGB1_27825) 84447..84665 - 219 WP_004171484 hypothetical protein -
KGB1_RS27850 (KGB1_27830) 84689..84979 - 291 WP_253616131 hypothetical protein -
KGB1_RS27855 85008..85406 - 399 WP_223170083 hypothetical protein -
KGB1_RS27860 (KGB1_27840) 85562..86131 - 570 WP_046622829 type IV conjugative transfer system lipoprotein TraV traV
KGB1_RS27865 (KGB1_27845) 86151..86306 - 156 WP_153587559 hypothetical protein -
KGB1_RS27870 (KGB1_27850) 86344..86757 - 414 Protein_96 conjugal transfer pilus-stabilizing protein TraP -
KGB1_RS27875 (KGB1_27855) 86750..88174 - 1425 WP_253616134 F-type conjugal transfer pilus assembly protein TraB traB
KGB1_RS27880 (KGB1_27860) 88174..88914 - 741 WP_049155519 type-F conjugative transfer system secretin TraK traK
KGB1_RS27885 (KGB1_27865) 88901..89467 - 567 WP_020316627 type IV conjugative transfer system protein TraE traE
KGB1_RS27890 (KGB1_27870) 89487..89792 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
KGB1_RS27895 (KGB1_27875) 89806..90174 - 369 WP_047665762 type IV conjugative transfer system pilin TraA -
KGB1_RS27900 (KGB1_27880) 90228..90599 - 372 WP_004208838 TraY domain-containing protein -
KGB1_RS27905 (KGB1_27885) 90683..91378 - 696 WP_225372886 transcriptional regulator TraJ family protein -
KGB1_RS27910 (KGB1_27890) 91585..91977 - 393 WP_253616136 conjugal transfer relaxosome DNA-binding protein TraM -
KGB1_RS27915 (KGB1_27895) 92484..92891 + 408 WP_253616198 transglycosylase SLT domain-containing protein virB1
KGB1_RS27920 (KGB1_27900) 92928..93458 - 531 WP_087846439 antirestriction protein -
KGB1_RS27925 (KGB1_27905) 94083..94916 - 834 WP_253616138 N-6 DNA methylase -
KGB1_RS27930 (KGB1_27910) 94962..95192 - 231 WP_047722596 hypothetical protein -
KGB1_RS27935 (KGB1_27915) 95279..95626 - 348 WP_114501446 hypothetical protein -
KGB1_RS27940 (KGB1_27920) 95692..96072 - 381 WP_240289755 hypothetical protein -
KGB1_RS27945 (KGB1_27925) 96900..97316 - 417 WP_049010942 type II toxin-antitoxin system HigA family antitoxin -
KGB1_RS27950 (KGB1_27930) 97313..97624 - 312 WP_023292165 type II toxin-antitoxin system HigB family toxin -

Host bacterium

ID   14142 GenBank   NZ_CP071736
Plasmid name   pKGB1a Incompatibility group   IncFIB
Plasmid size   160574 bp Coordinate of oriT [Strand]   92290..92339 [+]
Host baterium   Klebsiella variicola strain KGB_1

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   fecD, fecE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -