Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101748
Name   oriT_pRHBSTW-00065_2 in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00065
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABXRS010000002 (147621..147670 [+], 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_pRHBSTW-00065_2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1477 GenBank   WP_181575849
Name   traI_HV050_RS25520_pRHBSTW-00065_2 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: 190454.16 Da        Isoelectric Point: 6.1897

>WP_181575849.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGINAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALAPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGRLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRASTRM
ILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPHVIGLGPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSISPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSQIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVTSERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1144)


  Protein structure



No available structure.




T4CP

ID   1154 GenBank   WP_228725417
Name   traD_HV050_RS25525_pRHBSTW-00065_2 insolico UniProt ID   _
Length   760 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 760 a.a.        Molecular weight: 84917.00 Da        Isoelectric Point: 5.1110

>WP_228725417.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSPPA
PAEMTVSPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYDAWLADDQTQRDMQRREEVNINHSHRHDKQDDVEIGGNI

  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: 119651..148228

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV050_RS25525 (HV050_25525) 119651..121933 - 2283 WP_228725417 type IV conjugative transfer system coupling protein TraD virb4
HV050_RS25530 (HV050_25530) 122060..122749 - 690 WP_181575850 hypothetical protein -
HV050_RS25535 (HV050_25535) 122942..123673 - 732 WP_181575851 conjugal transfer complement resistance protein TraT -
HV050_RS25540 (HV050_25540) 123924..124526 - 603 WP_181575852 hypothetical protein -
HV050_RS25545 (HV050_25545) 124549..127371 - 2823 WP_101455613 conjugal transfer mating-pair stabilization protein TraG traG
HV050_RS25550 (HV050_25550) 127371..128750 - 1380 WP_181575853 conjugal transfer pilus assembly protein TraH traH
HV050_RS25555 (HV050_25555) 128728..129171 - 444 WP_014343488 F-type conjugal transfer protein TrbF -
HV050_RS25560 (HV050_25560) 129217..129774 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV050_RS25565 (HV050_25565) 129746..129985 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
HV050_RS25570 (HV050_25570) 129996..130748 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
HV050_RS25575 (HV050_25575) 130769..131095 - 327 WP_004152676 hypothetical protein -
HV050_RS25580 (HV050_25580) 131108..131356 - 249 WP_004152675 hypothetical protein -
HV050_RS25585 (HV050_25585) 131334..131588 - 255 WP_004152674 conjugal transfer protein TrbE -
HV050_RS25590 (HV050_25590) 131620..133575 - 1956 WP_181575854 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV050_RS25595 (HV050_25595) 133634..134272 - 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV050_RS25600 (HV050_25600) 134285..135274 - 990 WP_032408909 conjugal transfer pilus assembly protein TraU traU
HV050_RS25605 (HV050_25605) 135271..135672 - 402 WP_004194979 hypothetical protein -
HV050_RS25610 (HV050_25610) 135707..136342 - 636 WP_181575855 type-F conjugative transfer system protein TraW traW
HV050_RS25615 (HV050_25615) 136342..136731 - 390 WP_117046014 type-F conjugative transfer system protein TrbI -
HV050_RS25620 (HV050_25620) 136731..139370 - 2640 WP_032431388 type IV secretion system protein TraC virb4
HV050_RS25625 (HV050_25625) 139442..139840 - 399 WP_074188112 hypothetical protein -
HV050_RS25630 (HV050_25630) 139848..140093 - 246 WP_228725418 hypothetical protein -
HV050_RS25635 (HV050_25635) 140218..140622 - 405 WP_181575856 hypothetical protein -
HV050_RS25640 (HV050_25640) 140689..141000 - 312 WP_181575857 hypothetical protein -
HV050_RS25645 (HV050_25645) 141001..141219 - 219 WP_004195468 hypothetical protein -
HV050_RS25650 (HV050_25650) 141542..142126 - 585 WP_032440547 type IV conjugative transfer system lipoprotein TraV traV
HV050_RS25655 (HV050_25655) 142199..143623 - 1425 WP_004233801 F-type conjugal transfer pilus assembly protein TraB traB
HV050_RS25660 (HV050_25660) 143623..144363 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
HV050_RS25665 (HV050_25665) 144350..144916 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
HV050_RS25670 (HV050_25670) 144936..145241 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HV050_RS25675 (HV050_25675) 145255..145623 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HV050_RS25680 (HV050_25680) 145685..145891 - 207 WP_171773970 TraY domain-containing protein -
HV050_RS25685 (HV050_25685) 146024..146743 - 720 WP_014386192 conjugal transfer protein -
HV050_RS25690 (HV050_25690) 146936..147352 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
HV050_RS25695 (HV050_25695) 147743..148228 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
HV050_RS25700 (HV050_25700) 148261..148590 - 330 WP_014386191 DUF5983 family protein -
HV050_RS25705 (HV050_25705) 148623..149444 - 822 WP_004182076 DUF932 domain-containing protein -
HV050_RS25710 (HV050_25710) 150277..150690 - 414 WP_013023817 helix-turn-helix domain-containing protein -
HV050_RS25715 (HV050_25715) 150691..150969 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
HV050_RS25720 (HV050_25720) 150959..151278 - 320 Protein_163 type II toxin-antitoxin system RelE/ParE family toxin -
HV050_RS25725 (HV050_25725) 151359..151583 - 225 WP_014386189 hypothetical protein -
HV050_RS25730 (HV050_25730) 151594..151806 - 213 WP_014386188 hypothetical protein -
HV050_RS25735 (HV050_25735) 151868..152194 - 327 WP_014386187 hypothetical protein -
HV050_RS25740 (HV050_25740) 152831..153181 - 351 WP_014386186 hypothetical protein -

Host bacterium

ID   2192 GenBank   NZ_JABXRS010000002
Plasmid name   pRHBSTW-00065_2 Incompatibility group   IncFIB
Plasmid size   199484 bp Coordinate of oriT [Strand]   147621..147670 [+]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00065

Cargo genes

Drug resistance gene   tet(D), blaSHV-1
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsH, arsC, arsB, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9