Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105263
Name   oriT_pRHB39-C24_3 in_silico
Organism   Klebsiella pneumoniae strain RHB39-C24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP057036 (47571..47619 [-], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pRHB39-C24_3
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3608 GenBank   WP_075874369
Name   traI_HVZ90_RS26985_pRHB39-C24_3 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: 190669.51 Da        Isoelectric Point: 6.0127

>WP_075874369.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRADALPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTDLTAGQRAATR
MILESTDQFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVSSGDTDQLPPIASGQPFRLTQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRLWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1433-1555)

TrwC relaxase (TrwC)

(10-284)

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)


  Protein structure



No available structure.




T4CP

ID   3571 GenBank   WP_077272500
Name   traD_HVZ90_RS26980_pRHB39-C24_3 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 85949.93 Da        Isoelectric Point: 5.0156

>WP_077272500.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTTKRPAAEPSVRATEPSVLRGTTVPLIKPKAAAAAAAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 47019..75608

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HVZ90_RS26765 (HVZ90_26770) 42113..42433 + 321 WP_181578661 type II toxin-antitoxin system RelE/ParE family toxin -
HVZ90_RS26770 (HVZ90_26775) 42423..42701 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
HVZ90_RS26775 (HVZ90_26780) 42702..43115 + 414 WP_004182074 helix-turn-helix domain-containing protein -
HVZ90_RS26780 (HVZ90_26785) 43833..44213 + 381 WP_044265040 hypothetical protein -
HVZ90_RS26785 (HVZ90_26790) 44279..44626 + 348 WP_044265036 hypothetical protein -
HVZ90_RS26790 (HVZ90_26795) 44715..44945 + 231 WP_044265034 hypothetical protein -
HVZ90_RS26795 (HVZ90_26800) 44992..45825 + 834 WP_044265032 N-6 DNA methylase -
HVZ90_RS26800 (HVZ90_26805) 46029..46259 - 231 WP_044265030 hypothetical protein -
HVZ90_RS26805 (HVZ90_26810) 46451..46981 + 531 WP_075874364 antirestriction protein -
HVZ90_RS26810 (HVZ90_26815) 47019..47426 - 408 WP_225378279 transglycosylase SLT domain-containing protein virB1
HVZ90_RS26815 (HVZ90_26820) 47930..48322 + 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
HVZ90_RS26820 (HVZ90_26825) 48552..49253 + 702 WP_040120380 hypothetical protein -
HVZ90_RS26825 (HVZ90_26830) 49339..49539 + 201 WP_046664192 TraY domain-containing protein -
HVZ90_RS26830 (HVZ90_26835) 49607..49975 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HVZ90_RS26835 (HVZ90_26840) 49989..50294 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HVZ90_RS26840 (HVZ90_26845) 50314..50880 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
HVZ90_RS26845 (HVZ90_26850) 50867..51607 + 741 WP_040120379 type-F conjugative transfer system secretin TraK traK
HVZ90_RS26850 (HVZ90_26855) 51607..53031 + 1425 WP_181578653 F-type conjugal transfer pilus assembly protein TraB traB
HVZ90_RS26855 (HVZ90_26860) 53104..53688 + 585 WP_040120377 type IV conjugative transfer system lipoprotein TraV traV
HVZ90_RS26860 (HVZ90_26865) 54011..54229 + 219 WP_004195468 hypothetical protein -
HVZ90_RS26865 (HVZ90_26870) 54230..54541 + 312 WP_029497417 hypothetical protein -
HVZ90_RS26870 (HVZ90_26875) 54608..55012 + 405 WP_004197817 hypothetical protein -
HVZ90_RS27310 55055..55207 + 153 WP_224518895 hypothetical protein -
HVZ90_RS26880 (HVZ90_26885) 55389..55787 + 399 WP_023179972 hypothetical protein -
HVZ90_RS26885 (HVZ90_26890) 55859..58498 + 2640 WP_013214024 type IV secretion system protein TraC virb4
HVZ90_RS26890 (HVZ90_26895) 58498..58887 + 390 WP_004167468 type-F conjugative transfer system protein TrbI -
HVZ90_RS26895 (HVZ90_26900) 58887..59522 + 636 WP_029497419 type-F conjugative transfer system protein TraW traW
HVZ90_RS26900 (HVZ90_26905) 59557..59958 + 402 WP_004194979 hypothetical protein -
HVZ90_RS26905 (HVZ90_26910) 59955..60944 + 990 WP_029497420 conjugal transfer pilus assembly protein TraU traU
HVZ90_RS26910 (HVZ90_26915) 60957..61595 + 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
HVZ90_RS26915 (HVZ90_26920) 61654..63609 + 1956 WP_181578654 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HVZ90_RS26920 (HVZ90_26925) 63641..63895 + 255 WP_044265005 conjugal transfer protein TrbE -
HVZ90_RS26925 (HVZ90_26930) 63873..64121 + 249 WP_004152675 hypothetical protein -
HVZ90_RS26930 (HVZ90_26935) 64134..64460 + 327 WP_004144402 hypothetical protein -
HVZ90_RS26935 (HVZ90_26940) 64481..65233 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
HVZ90_RS26940 (HVZ90_26945) 65244..65483 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
HVZ90_RS26945 (HVZ90_26950) 65455..66012 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HVZ90_RS26950 (HVZ90_26955) 66058..66501 + 444 WP_014343488 F-type conjugal transfer protein TrbF -
HVZ90_RS26955 (HVZ90_26960) 66479..67858 + 1380 WP_072198320 conjugal transfer pilus assembly protein TraH traH
HVZ90_RS26960 (HVZ90_26965) 67858..70680 + 2823 WP_075874360 conjugal transfer mating-pair stabilization protein TraG traG
HVZ90_RS26965 (HVZ90_26970) 70703..71305 + 603 WP_013214035 conjugal transfer protein TraS -
HVZ90_RS26970 (HVZ90_26975) 71556..72287 + 732 WP_016831056 conjugal transfer complement resistance protein TraT -
HVZ90_RS26975 (HVZ90_26980) 72480..73169 + 690 WP_014343485 hypothetical protein -
HVZ90_RS26980 (HVZ90_26985) 73296..75608 + 2313 WP_077272500 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5701 GenBank   NZ_CP057036
Plasmid name   pRHB39-C24_3 Incompatibility group   IncFII
Plasmid size   86316 bp Coordinate of oriT [Strand]   47571..47619 [-]
Host baterium   Klebsiella pneumoniae strain RHB39-C24

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9