Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120729
Name   oriT_pKqq_U41_2 in_silico
Organism   Klebsiella quasipneumoniae subsp. quasipneumoniae strain U41
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084791 (106120..106168 [-], 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_pKqq_U41_2
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13069 GenBank   WP_050888024
Name   traI_LGM24_RS28625_pKqq_U41_2 insolico UniProt ID   A0A2N5ANH3
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190263.91 Da        Isoelectric Point: 6.2218

>WP_050888024.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINTTQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARAGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPAQEKAIQK
ALSEGETLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIRHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
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)

AAA domain (AAA_30)

(970-1156)

TrwC relaxase (TrwC)

(10-283)

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

(634-713)


  Protein structure



No available structure.




Auxiliary protein

ID   7294 GenBank   WP_004197733
Name   WP_004197733_pKqq_U41_2 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   15338 GenBank   WP_136071121
Name   traD_LGM24_RS28620_pKqq_U41_2 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: 85652.75 Da        Isoelectric Point: 5.2499

>WP_136071121.1 type IV conjugative transfer system coupling protein TraD [Klebsiella quasipneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGTADTNSHAGEQPEPVSQPA
PAEVTVSPAPVKAPATTKMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNKDGVIEDMQAYDAWADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 108582..135197

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LGM24_RS28435 (LGM24_28435) 105000..105530 + 531 WP_015632491 antirestriction protein -
LGM24_RS28440 (LGM24_28440) 105568..105975 - 408 WP_020805750 transglycosylase SLT domain-containing protein -
LGM24_RS28445 (LGM24_28445) 106480..106869 + 390 WP_004197733 conjugal transfer relaxosome DNA-binding protein TraM -
LGM24_RS28450 (LGM24_28450) 107108..107782 + 675 WP_004197737 hypothetical protein -
LGM24_RS28455 (LGM24_28455) 107974..108138 + 165 WP_032444506 TraY domain-containing protein -
LGM24_RS28460 (LGM24_28460) 108200..108568 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LGM24_RS28465 (LGM24_28465) 108582..108887 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
LGM24_RS28470 (LGM24_28470) 108907..109473 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
LGM24_RS28475 (LGM24_28475) 109460..110200 + 741 WP_064182676 type-F conjugative transfer system secretin TraK traK
LGM24_RS28480 (LGM24_28480) 110200..111624 + 1425 WP_136071128 F-type conjugal transfer pilus assembly protein TraB traB
LGM24_RS28485 (LGM24_28485) 111617..112213 + 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
LGM24_RS28490 (LGM24_28490) 112236..112805 + 570 WP_023316399 type IV conjugative transfer system lipoprotein TraV traV
LGM24_RS28495 (LGM24_28495) 112937..113347 + 411 WP_023316400 hypothetical protein -
LGM24_RS28500 (LGM24_28500) 113352..113636 + 285 WP_023316401 hypothetical protein -
LGM24_RS28505 (LGM24_28505) 113660..113878 + 219 WP_023316402 hypothetical protein -
LGM24_RS28510 (LGM24_28510) 113879..114190 + 312 WP_023316403 hypothetical protein -
LGM24_RS28515 (LGM24_28515) 114257..114661 + 405 WP_023316404 hypothetical protein -
LGM24_RS28520 (LGM24_28520) 114658..114948 + 291 WP_020323516 hypothetical protein -
LGM24_RS28525 (LGM24_28525) 114956..115354 + 399 WP_168377456 hypothetical protein -
LGM24_RS28530 (LGM24_28530) 115426..118065 + 2640 WP_226650017 type IV secretion system protein TraC virb4
LGM24_RS28535 (LGM24_28535) 118065..118454 + 390 WP_020314627 type-F conjugative transfer system protein TrbI -
LGM24_RS28540 (LGM24_28540) 118454..119080 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
LGM24_RS28545 (LGM24_28545) 119124..120083 + 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
LGM24_RS28550 (LGM24_28550) 120096..120734 + 639 WP_020321224 type-F conjugative transfer system pilin assembly protein TrbC trbC
LGM24_RS28555 (LGM24_28555) 120793..122748 + 1956 WP_020803160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LGM24_RS28560 (LGM24_28560) 122781..123062 + 282 WP_022644736 hypothetical protein -
LGM24_RS28565 (LGM24_28565) 123052..123279 + 228 WP_136071132 conjugal transfer protein TrbE -
LGM24_RS28570 (LGM24_28570) 123290..123616 + 327 WP_020323521 hypothetical protein -
LGM24_RS28575 (LGM24_28575) 123637..124389 + 753 WP_023316406 type-F conjugative transfer system pilin assembly protein TraF traF
LGM24_RS28580 (LGM24_28580) 124844..125083 + 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
LGM24_RS28585 (LGM24_28585) 125055..125612 + 558 WP_020804677 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LGM24_RS28590 (LGM24_28590) 125658..126101 + 444 WP_020804675 F-type conjugal transfer protein TrbF -
LGM24_RS28595 (LGM24_28595) 126079..127458 + 1380 WP_072198238 conjugal transfer pilus assembly protein TraH traH
LGM24_RS28600 (LGM24_28600) 127458..130301 + 2844 WP_136071122 conjugal transfer mating-pair stabilization protein TraG traG
LGM24_RS28605 (LGM24_28605) 130312..130836 + 525 WP_023316410 hypothetical protein -
LGM24_RS28610 (LGM24_28610) 131146..131877 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
LGM24_RS28615 (LGM24_28615) 132070..132759 + 690 WP_023316411 hypothetical protein -
LGM24_RS28620 (LGM24_28620) 132888..135197 + 2310 WP_136071121 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21158 GenBank   NZ_CP084791
Plasmid name   pKqq_U41_2 Incompatibility group   IncFIA
Plasmid size   145852 bp Coordinate of oriT [Strand]   106120..106168 [-]
Host baterium   Klebsiella quasipneumoniae subsp. quasipneumoniae strain U41

Cargo genes

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