Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105188
Name   oriT_pRHBSTW-00039_5 in_silico
Organism   Klebsiella grimontii strain RHBSTW-00039
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP058184 (28821..28869 [-], 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-00039_5
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3579 GenBank   WP_181334963
Name   traI_HV042_RS30915_pRHBSTW-00039_5 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190248.05 Da        Isoelectric Point: 6.2060

>WP_181334963.1 conjugative transfer relaxase/helicase TraI [Klebsiella grimontii]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMHHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRAETMPVAEGERLAVLGKIPDTRLKGGESVTVMKVEEGQLTVQRPGQKTTQTLVVGAGVFDGIK
ISHGWVESPGRSVSETATVFASLTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADIAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFAPAQEKAIEK
ALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSDGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVAGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPV
DRVKEVIGDVIRGLERDRPGPEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

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

(576-628)

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

(634-713)

AAA domain (AAA_30)

(970-1156)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




Auxiliary protein

ID   1599 GenBank   WP_032426796
Name   WP_032426796_pRHBSTW-00039_5 insolico UniProt ID   _
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 15036.10 Da        Isoelectric Point: 4.5326

>WP_032426796.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKEKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKVLGIECLSPHVKDDPRWQWKGMVQNIQEDVQEVMRTFFPDEQEEADE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   3542 GenBank   WP_020316650
Name   traD_HV042_RS30910_pRHBSTW-00039_5 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 85197.99 Da        Isoelectric Point: 4.8865

>WP_020316650.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRSLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPAEVTV
SPAPVKATQTTKMPAEEPSVRATEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTEQELAQQ
SAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 31290..56739

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV042_RS30715 (HV042_30720) 26469..26816 + 348 WP_022644944 hypothetical protein -
HV042_RS30720 (HV042_30725) 26909..27055 + 147 WP_022644943 hypothetical protein -
HV042_RS31385 27103..27339 + 237 Protein_39 SAM-dependent DNA methyltransferase -
HV042_RS30730 (HV042_30735) 27688..28230 + 543 WP_022644941 antirestriction protein -
HV042_RS30735 (HV042_30740) 28254..28676 - 423 WP_072205880 transglycosylase SLT domain-containing protein -
HV042_RS30740 (HV042_30745) 29182..29574 + 393 WP_032426796 conjugal transfer relaxosome DNA-binding protein TraM -
HV042_RS30745 (HV042_30750) 29812..30504 + 693 WP_032426795 conjugal transfer protein TrbJ -
HV042_RS30750 (HV042_30755) 30680..30844 + 165 WP_032426810 TraY domain-containing protein -
HV042_RS30755 (HV042_30760) 30908..31276 + 369 WP_032426794 type IV conjugative transfer system pilin TraA -
HV042_RS30760 (HV042_30765) 31290..31595 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HV042_RS30765 (HV042_30770) 31615..32181 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
HV042_RS30770 (HV042_30775) 32168..32908 + 741 WP_110222093 type-F conjugative transfer system secretin TraK traK
HV042_RS30775 (HV042_30780) 32908..34332 + 1425 WP_181334965 F-type conjugal transfer pilus assembly protein TraB traB
HV042_RS30780 (HV042_30785) 34325..34921 + 597 WP_103214945 conjugal transfer pilus-stabilizing protein TraP -
HV042_RS30785 (HV042_30790) 34944..35513 + 570 WP_023316399 type IV conjugative transfer system lipoprotein TraV traV
HV042_RS30790 (HV042_30795) 35645..36055 + 411 WP_032419923 hypothetical protein -
HV042_RS30795 (HV042_30800) 36060..36350 + 291 WP_048993668 hypothetical protein -
HV042_RS30800 (HV042_30805) 36374..36592 + 219 WP_023316402 hypothetical protein -
HV042_RS30805 (HV042_30810) 36593..36904 + 312 WP_023316403 hypothetical protein -
HV042_RS30810 (HV042_30815) 36971..37375 + 405 WP_023340941 hypothetical protein -
HV042_RS30815 (HV042_30820) 37372..37662 + 291 WP_023340940 hypothetical protein -
HV042_RS30820 (HV042_30825) 37670..38068 + 399 WP_074186017 hypothetical protein -
HV042_RS30825 (HV042_30830) 38140..40779 + 2640 WP_181334960 type IV secretion system protein TraC virb4
HV042_RS30830 (HV042_30835) 40779..41168 + 390 WP_020314627 type-F conjugative transfer system protein TrbI -
HV042_RS30835 (HV042_30840) 41168..41794 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
HV042_RS30840 (HV042_30845) 41838..42797 + 960 WP_239689303 conjugal transfer pilus assembly protein TraU traU
HV042_RS30845 (HV042_30850) 42810..43448 + 639 WP_032456788 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV042_RS30850 (HV042_30855) 43507..45462 + 1956 WP_181334961 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV042_RS30855 (HV042_30860) 45494..45748 + 255 WP_004195500 conjugal transfer protein TrbE -
HV042_RS30860 (HV042_30865) 45726..45974 + 249 WP_004152675 hypothetical protein -
HV042_RS30865 (HV042_30870) 45987..46313 + 327 WP_004194451 hypothetical protein -
HV042_RS30870 (HV042_30875) 46334..47086 + 753 WP_009309874 type-F conjugative transfer system pilin assembly protein TraF traF
HV042_RS30875 (HV042_30880) 47097..47336 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
HV042_RS30880 (HV042_30885) 47308..47880 + 573 WP_009309876 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV042_RS30885 (HV042_30890) 47873..48301 + 429 WP_004152689 hypothetical protein -
HV042_RS30890 (HV042_30895) 48288..49658 + 1371 WP_009309877 conjugal transfer pilus assembly protein TraH traH
HV042_RS30895 (HV042_30900) 49658..52480 + 2823 WP_181334962 conjugal transfer mating-pair stabilization protein TraG traG
HV042_RS30900 (HV042_30905) 52504..53106 + 603 WP_048263624 hypothetical protein -
HV042_RS30905 (HV042_30910) 53357..54088 + 732 WP_016831056 conjugal transfer complement resistance protein TraT -
HV042_RS30910 (HV042_30915) 54448..56739 + 2292 WP_020316650 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5626 GenBank   NZ_CP058184
Plasmid name   pRHBSTW-00039_5 Incompatibility group   -
Plasmid size   67313 bp Coordinate of oriT [Strand]   28821..28869 [-]
Host baterium   Klebsiella grimontii strain RHBSTW-00039

Cargo genes

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