Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105199
Name   oriT_pRHBSTW-00113_2 in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00113
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056855 (130139..130188 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pRHBSTW-00113_2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3583 GenBank   WP_042922338
Name   traI_HV075_RS25560_pRHBSTW-00113_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: 190652.47 Da        Isoelectric Point: 6.0664

>WP_042922338.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHLALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRIWAEPAPVAPVPQTGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1432-1554)

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

(576-628)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1154)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   3544 GenBank   WP_013214038
Name   traD_HV075_RS25565_pRHBSTW-00113_2 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: 86010.07 Da        Isoelectric Point: 5.1787

>WP_013214038.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
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: 123901..130746

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV075_RS25615 (HV075_25620) 120178..121146 - 969 WP_077257689 IS5-like element IS903B family transposase -
HV075_RS25620 (HV075_25625) 121180..121404 - 225 Protein_127 TraC family protein -
HV075_RS25625 (HV075_25630) 121476..121874 - 399 WP_023179972 hypothetical protein -
HV075_RS25630 (HV075_25635) 122252..122656 - 405 WP_004197817 hypothetical protein -
HV075_RS25635 (HV075_25640) 122723..123034 - 312 WP_004195240 hypothetical protein -
HV075_RS25640 (HV075_25645) 123035..123253 - 219 WP_004195235 hypothetical protein -
HV075_RS25645 (HV075_25650) 123359..123769 - 411 WP_004152499 hypothetical protein -
HV075_RS25650 (HV075_25655) 123901..124485 - 585 WP_032441881 type IV conjugative transfer system lipoprotein TraV traV
HV075_RS25655 (HV075_25660) 124599..126023 - 1425 WP_042922367 F-type conjugal transfer pilus assembly protein TraB traB
HV075_RS25660 (HV075_25665) 126023..126763 - 741 WP_015065528 type-F conjugative transfer system secretin TraK traK
HV075_RS25665 (HV075_25670) 126750..127316 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
HV075_RS25670 (HV075_25675) 127336..127641 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HV075_RS25675 (HV075_25680) 127655..128023 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HV075_RS25680 (HV075_25685) 128077..128448 - 372 WP_004208838 TraY domain-containing protein -
HV075_RS25685 (HV075_25690) 128532..129218 - 687 WP_071561590 transcriptional regulator TraJ family protein -
HV075_RS25690 (HV075_25695) 129434..129826 - 393 WP_032441878 conjugal transfer relaxosome DNA-binding protein TraM -
HV075_RS25695 (HV075_25700) 130261..130746 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
HV075_RS25700 (HV075_25705) 130779..131108 - 330 WP_011977736 DUF5983 family protein -
HV075_RS25705 (HV075_25710) 131141..131962 - 822 WP_023316395 DUF932 domain-containing protein -
HV075_RS25710 (HV075_25715) 132790..133203 - 414 WP_021312979 helix-turn-helix domain-containing protein -
HV075_RS25715 (HV075_25720) 133204..133482 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
HV075_RS25720 (HV075_25725) 133472..133792 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
HV075_RS25725 (HV075_25730) 133873..134097 - 225 WP_014343499 hypothetical protein -
HV075_RS25730 (HV075_25735) 134108..134320 - 213 WP_019706020 hypothetical protein -
HV075_RS25735 (HV075_25740) 134381..134737 - 357 WP_019706019 hypothetical protein -

Host bacterium

ID   5637 GenBank   NZ_CP056855
Plasmid name   pRHBSTW-00113_2 Incompatibility group   IncFIB
Plasmid size   188591 bp Coordinate of oriT [Strand]   130139..130188 [+]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00113

Cargo genes

Drug resistance gene   -
Virulence gene   mrkA, mrkB, mrkC, mrkD, mrkF, mrkJ
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, fecD, fecE, ncrA, ncrB, ncrC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9