Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120072
Name   oriT_pKqs_SB610_3 in_silico
Organism   Klebsiella quasipneumoniae subsp. similipneumoniae strain SB610
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084773 (115936..115984 [+], 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_pKqs_SB610_3
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12640 GenBank   WP_063160318
Name   traI_LGM29_RS27715_pKqs_SB610_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: 190491.29 Da        Isoelectric Point: 6.2578

>WP_063160318.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQIFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIAFGKIYQNTLRADVES
LGYRTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTSDASVVRQAPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHKTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VAHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADIAIMKEIVRQVPELRPAVYSLIERDVHHALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPTQEKAIQK
ALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKKAEQTAREMAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

TrwC relaxase (TrwC)

(11-283)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




Auxiliary protein

ID   7134 GenBank   WP_004197733
Name   WP_004197733_pKqs_SB610_3 insolico UniProt ID   A0A0E3KB00
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14835.90 Da        Isoelectric Point: 4.6012

>WP_004197733.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKILGIECLSPHVKDDPRWQWKSMVLNIQEDVQEAMRNFFPDEDAEGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure


Source ID Structure
AlphaFold DB A0A0E3KB00


T4CP

ID   14841 GenBank   WP_009309880
Name   traD_LGM29_RS27720_pKqs_SB610_3 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85571.58 Da        Isoelectric Point: 5.1733

>WP_009309880.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPDDAGSHAGEQPEPVSQPA
PAVMTVTPAPVKSPPTTKRPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAGTAATASSAGTPAAAAGGTE
QVLAQQSAEQGQAMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDLEIGGNF

  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: 86399..116542

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LGM29_RS27720 (LGM29_27720) 86399..88708 - 2310 WP_009309880 type IV conjugative transfer system coupling protein TraD virb4
LGM29_RS27725 (LGM29_27725) 88834..89526 - 693 WP_009309879 hypothetical protein -
LGM29_RS27730 (LGM29_27730) 90261..93134 - 2874 WP_009309878 conjugal transfer mating-pair stabilization protein TraG traG
LGM29_RS27735 (LGM29_27735) 93134..94504 - 1371 WP_009309877 conjugal transfer pilus assembly protein TraH traH
LGM29_RS27740 (LGM29_27740) 94491..94919 - 429 WP_004152689 hypothetical protein -
LGM29_RS27745 (LGM29_27745) 94912..95484 - 573 WP_063160290 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LGM29_RS27750 (LGM29_27750) 95456..95695 - 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
LGM29_RS27755 (LGM29_27755) 95706..96458 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
LGM29_RS27760 (LGM29_27760) 96479..96805 - 327 WP_004194451 hypothetical protein -
LGM29_RS27765 (LGM29_27765) 96818..97066 - 249 WP_004152675 hypothetical protein -
LGM29_RS27770 (LGM29_27770) 97044..97298 - 255 WP_004195500 conjugal transfer protein TrbE -
LGM29_RS27775 (LGM29_27775) 97330..99285 - 1956 WP_148866277 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LGM29_RS27780 (LGM29_27780) 99344..99991 - 648 WP_039698503 type-F conjugative transfer system pilin assembly protein TrbC trbC
LGM29_RS27785 (LGM29_27785) 100135..100737 - 603 WP_022631520 hypothetical protein -
LGM29_RS27790 (LGM29_27790) 101458..102006 - 549 WP_022631518 hypothetical protein -
LGM29_RS27795 (LGM29_27795) 102021..103004 - 984 WP_223176982 conjugal transfer pilus assembly protein TraU traU
LGM29_RS27800 (LGM29_27800) 103024..103650 - 627 WP_020314628 type-F conjugative transfer system protein TraW traW
LGM29_RS27805 (LGM29_27805) 103650..104042 - 393 WP_080816432 type-F conjugative transfer system protein TrbI -
LGM29_RS27810 (LGM29_27810) 104039..106678 - 2640 WP_042946320 type IV secretion system protein TraC virb4
LGM29_RS27815 (LGM29_27815) 106750..107148 - 399 WP_074186017 hypothetical protein -
LGM29_RS27820 (LGM29_27820) 107156..107446 - 291 WP_023340940 hypothetical protein -
LGM29_RS27825 (LGM29_27825) 107443..107847 - 405 WP_042939116 hypothetical protein -
LGM29_RS27830 (LGM29_27830) 107914..108225 - 312 WP_023316403 hypothetical protein -
LGM29_RS27835 (LGM29_27835) 108226..108444 - 219 WP_023316402 hypothetical protein -
LGM29_RS27840 (LGM29_27840) 108468..108752 - 285 WP_023316401 hypothetical protein -
LGM29_RS27845 (LGM29_27845) 108757..109167 - 411 WP_020805613 hypothetical protein -
LGM29_RS27850 (LGM29_27850) 109299..109868 - 570 WP_023340942 type IV conjugative transfer system lipoprotein TraV traV
LGM29_RS27855 (LGM29_27855) 109891..110487 - 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
LGM29_RS27860 (LGM29_27860) 110480..111904 - 1425 WP_042946342 F-type conjugal transfer pilus assembly protein TraB traB
LGM29_RS27865 (LGM29_27865) 111904..112644 - 741 WP_032738531 type-F conjugative transfer system secretin TraK traK
LGM29_RS27870 (LGM29_27870) 112631..113197 - 567 WP_020316627 type IV conjugative transfer system protein TraE traE
LGM29_RS27875 (LGM29_27875) 113217..113522 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
LGM29_RS27880 (LGM29_27880) 113536..113904 - 369 WP_063267011 type IV conjugative transfer system pilin TraA -
LGM29_RS27885 (LGM29_27885) 113966..114130 - 165 WP_032444506 TraY domain-containing protein -
LGM29_RS27890 (LGM29_27890) 114322..114996 - 675 WP_004197737 hypothetical protein -
LGM29_RS27895 (LGM29_27895) 115235..115624 - 390 WP_004197733 conjugal transfer relaxosome DNA-binding protein TraM -
LGM29_RS27900 (LGM29_27900) 116057..116542 + 486 WP_022631514 transglycosylase SLT domain-containing protein virB1
LGM29_RS27905 (LGM29_27905) 116575..116904 - 330 WP_011977736 DUF5983 family protein -
LGM29_RS27910 (LGM29_27910) 116937..117758 - 822 WP_004152492 DUF932 domain-containing protein -
LGM29_RS27915 (LGM29_27915) 118578..119411 - 834 WP_004152751 N-6 DNA methylase -
LGM29_RS27920 (LGM29_27920) 119462..119608 - 147 WP_004152750 hypothetical protein -
LGM29_RS27925 (LGM29_27925) 119703..120050 - 348 WP_004152749 hypothetical protein -
LGM29_RS27930 (LGM29_27930) 120107..120460 - 354 WP_004152748 hypothetical protein -
LGM29_RS27935 (LGM29_27935) 121090..121440 - 351 WP_004153414 hypothetical protein -

Host bacterium

ID   20502 GenBank   NZ_CP084773
Plasmid name   pKqs_SB610_3 Incompatibility group   IncFIB
Plasmid size   150964 bp Coordinate of oriT [Strand]   115936..115984 [+]
Host baterium   Klebsiella quasipneumoniae subsp. similipneumoniae strain SB610

Cargo genes

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