Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105175
Name   oriT_pRHBSTW-00636_3 in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00636
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056374 (119423..119472 [+], 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-00636_3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3570 GenBank   WP_042922338
Name   traI_HV253_RS27590_pRHBSTW-00636_3 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   3534 GenBank   WP_013214038
Name   traD_HV253_RS27595_pRHBSTW-00636_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: 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: 91111..120030

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV253_RS27595 (HV253_27600) 91111..93423 - 2313 WP_013214038 type IV conjugative transfer system coupling protein TraD virb4
HV253_RS27600 (HV253_27605) 93550..94239 - 690 WP_013023831 hypothetical protein -
HV253_RS27605 (HV253_27610) 94432..95161 - 730 Protein_94 conjugal transfer complement resistance protein TraT -
HV253_RS27615 (HV253_27620) 95350..95880 - 531 WP_074187241 conjugal transfer protein TraS -
HV253_RS27620 (HV253_27625) 95883..98732 - 2850 WP_042922342 conjugal transfer mating-pair stabilization protein TraG traG
HV253_RS27625 (HV253_27630) 98732..100111 - 1380 WP_074187239 conjugal transfer pilus assembly protein TraH traH
HV253_RS27630 (HV253_27635) 100089..100532 - 444 WP_181486932 F-type conjugal transfer protein TrbF -
HV253_RS27635 (HV253_27640) 100578..101135 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV253_RS27640 (HV253_27645) 101107..101346 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
HV253_RS27645 (HV253_27650) 101357..102109 - 753 WP_048288586 type-F conjugative transfer system pilin assembly protein TraF traF
HV253_RS27650 (HV253_27655) 102130..102456 - 327 WP_016529362 hypothetical protein -
HV253_RS29215 102502..102687 - 186 WP_042922350 hypothetical protein -
HV253_RS27655 (HV253_27660) 102684..102920 - 237 WP_042922352 conjugal transfer protein TrbE -
HV253_RS27660 (HV253_27665) 102952..104907 - 1956 WP_015065636 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV253_RS27665 (HV253_27670) 104966..105604 - 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV253_RS27670 (HV253_27675) 105617..106606 - 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
HV253_RS27675 (HV253_27680) 106603..106992 - 390 WP_042922355 hypothetical protein -
HV253_RS27680 (HV253_27685) 107034..107660 - 627 WP_009309871 type-F conjugative transfer system protein TraW traW
HV253_RS27685 (HV253_27690) 107660..108049 - 390 WP_004152591 type-F conjugative transfer system protein TrbI -
HV253_RS27690 (HV253_27695) 108049..110688 - 2640 WP_042922359 type IV secretion system protein TraC virb4
HV253_RS27695 (HV253_27700) 110760..111158 - 399 WP_023179972 hypothetical protein -
HV253_RS27700 (HV253_27705) 111536..111940 - 405 WP_004197817 hypothetical protein -
HV253_RS27705 (HV253_27710) 112007..112318 - 312 WP_004195465 hypothetical protein -
HV253_RS27710 (HV253_27715) 112319..112537 - 219 WP_004195468 hypothetical protein -
HV253_RS27715 (HV253_27720) 112643..113053 - 411 WP_009309869 hypothetical protein -
HV253_RS27720 (HV253_27725) 113185..113769 - 585 WP_009309868 type IV conjugative transfer system lipoprotein TraV traV
HV253_RS27725 (HV253_27730) 113883..115307 - 1425 WP_042922367 F-type conjugal transfer pilus assembly protein TraB traB
HV253_RS27730 (HV253_27735) 115307..116047 - 741 WP_015065528 type-F conjugative transfer system secretin TraK traK
HV253_RS27735 (HV253_27740) 116034..116600 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
HV253_RS27740 (HV253_27745) 116620..116925 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HV253_RS27745 (HV253_27750) 116939..117307 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HV253_RS27750 (HV253_27755) 117361..117732 - 372 WP_004208838 TraY domain-containing protein -
HV253_RS27755 (HV253_27760) 117816..118502 - 687 WP_071561590 transcriptional regulator TraJ family protein -
HV253_RS27760 (HV253_27765) 118718..119110 - 393 WP_032441878 conjugal transfer relaxosome DNA-binding protein TraM -
HV253_RS27765 (HV253_27770) 119545..120030 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
HV253_RS27770 (HV253_27775) 120063..120392 - 330 WP_011977736 DUF5983 family protein -
HV253_RS27775 (HV253_27780) 120425..121246 - 822 WP_023316395 DUF932 domain-containing protein -
HV253_RS27780 (HV253_27785) 122074..122487 - 414 WP_021312979 helix-turn-helix domain-containing protein -
HV253_RS27785 (HV253_27790) 122488..122766 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
HV253_RS27790 (HV253_27795) 122756..123076 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
HV253_RS27795 (HV253_27800) 123157..123381 - 225 WP_014343499 hypothetical protein -
HV253_RS27800 (HV253_27805) 123392..123604 - 213 WP_019706020 hypothetical protein -
HV253_RS27805 (HV253_27810) 123665..124021 - 357 WP_019706019 hypothetical protein -

Host bacterium

ID   5613 GenBank   NZ_CP056374
Plasmid name   pRHBSTW-00636_3 Incompatibility group   IncFII
Plasmid size   171701 bp Coordinate of oriT [Strand]   119423..119472 [+]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00636

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   ncrA, ncrB, ncrC, ncrY
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9