Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101883
Name   oriT_pIncFII_IncR in_silico
Organism   Klebsiella pneumoniae strain CM15_K_mino
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKKDF010000014 (60746..60794 [-], 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_pIncFII_IncR
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1545 GenBank   WP_208396774
Name   traI_L3495_RS24710_pIncFII_IncR 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: 190332.17 Da        Isoelectric Point: 6.2882

>WP_208396774.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDLPVMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNSVIRDSLRNEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHHALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIQK
ALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSDGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSSDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPV
DRVKEVIGDVIRGLERDRPGPEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

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

(634-713)

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

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   463 GenBank   WP_020805752
Name   WP_020805752_pIncFII_IncR insolico UniProt ID   A0A377TIM3
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14772.81 Da        Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   1216 GenBank   WP_064392679
Name   traD_L3495_RS24705_pIncFII_IncR 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: 85646.68 Da        Isoelectric Point: 5.0577

>WP_064392679.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPDDAGSHAGERPELASQPA
PAEVTVSPAPVKAPATTTMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNKDGVIEDMQAYDAWLADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 63173..89969

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L3495_RS24515 (L3495_24495) 59626..60156 + 531 WP_208396761 antirestriction protein -
L3495_RS24520 (L3495_24500) 60194..60601 - 408 WP_277460314 transglycosylase SLT domain-containing protein -
L3495_RS24525 (L3495_24505) 61105..61497 + 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
L3495_RS24530 (L3495_24510) 61735..62436 + 702 WP_023316396 hypothetical protein -
L3495_RS24535 (L3495_24515) 62522..62722 + 201 WP_048289787 TraY domain-containing protein -
L3495_RS24540 (L3495_24520) 62791..63159 + 369 WP_020316649 type IV conjugative transfer system pilin TraA -
L3495_RS24545 (L3495_24525) 63173..63478 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
L3495_RS24550 (L3495_24530) 63498..64064 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
L3495_RS24555 (L3495_24535) 64051..64791 + 741 WP_208396763 type-F conjugative transfer system secretin TraK traK
L3495_RS24560 (L3495_24540) 64791..66215 + 1425 WP_208396764 F-type conjugal transfer pilus assembly protein TraB traB
L3495_RS24565 (L3495_24545) 66208..66804 + 597 WP_208396765 conjugal transfer pilus-stabilizing protein TraP -
L3495_RS24570 (L3495_24550) 66827..67411 + 585 WP_208396766 type IV conjugative transfer system lipoprotein TraV traV
L3495_RS24575 (L3495_24555) 67543..67953 + 411 WP_032419923 hypothetical protein -
L3495_RS24580 (L3495_24560) 67958..68242 + 285 WP_023316401 hypothetical protein -
L3495_RS24585 (L3495_24565) 68266..68490 + 225 WP_208396767 hypothetical protein -
L3495_RS24590 (L3495_24570) 68483..68794 + 312 WP_208396768 hypothetical protein -
L3495_RS24595 (L3495_24575) 68861..69265 + 405 WP_208396769 hypothetical protein -
L3495_RS24600 (L3495_24580) 69262..69552 + 291 WP_039698507 hypothetical protein -
L3495_RS24605 (L3495_24585) 69560..69958 + 399 WP_072156904 hypothetical protein -
L3495_RS24610 (L3495_24590) 70030..72669 + 2640 WP_039698506 type IV secretion system protein TraC virb4
L3495_RS24615 (L3495_24595) 72669..73058 + 390 WP_042939105 type-F conjugative transfer system protein TrbI -
L3495_RS24620 (L3495_24600) 73058..73693 + 636 WP_208396770 type-F conjugative transfer system protein TraW traW
L3495_RS24625 (L3495_24605) 73728..74129 + 402 WP_208396771 hypothetical protein -
L3495_RS24630 (L3495_24610) 74126..75118 + 993 WP_208396772 conjugal transfer pilus assembly protein TraU traU
L3495_RS24635 (L3495_24615) 75394..76041 + 648 WP_127807661 type-F conjugative transfer system pilin assembly protein TrbC trbC
L3495_RS24640 (L3495_24620) 76100..78055 + 1956 WP_208396773 type-F conjugative transfer system mating-pair stabilization protein TraN traN
L3495_RS24645 (L3495_24625) 78088..78369 + 282 WP_032419932 hypothetical protein -
L3495_RS24650 (L3495_24630) 78359..78586 + 228 WP_012540032 conjugal transfer protein TrbE -
L3495_RS24655 (L3495_24635) 78597..78923 + 327 WP_020323521 hypothetical protein -
L3495_RS24660 (L3495_24640) 78944..79696 + 753 WP_020316647 type-F conjugative transfer system pilin assembly protein TraF traF
L3495_RS24665 (L3495_24645) 79707..79946 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
L3495_RS24670 (L3495_24650) 79918..80475 + 558 WP_020804677 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
L3495_RS24675 (L3495_24655) 80521..80964 + 444 WP_020316643 F-type conjugal transfer protein TrbF -
L3495_RS24680 (L3495_24660) 80942..82321 + 1380 WP_072198238 conjugal transfer pilus assembly protein TraH traH
L3495_RS24685 (L3495_24665) 82321..85170 + 2850 WP_064392671 conjugal transfer mating-pair stabilization protein TraG traG
L3495_RS24690 (L3495_24670) 85183..85731 + 549 WP_049164063 conjugal transfer entry exclusion protein TraS -
L3495_RS24695 (L3495_24675) 85915..86646 + 732 WP_064392678 conjugal transfer complement resistance protein TraT -
L3495_RS24700 (L3495_24680) 86839..87528 + 690 WP_074186016 hypothetical protein -
L3495_RS24705 (L3495_24685) 87657..89969 + 2313 WP_064392679 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2327 GenBank   NZ_JAKKDF010000014
Plasmid name   pIncFII_IncR Incompatibility group   IncR
Plasmid size   100614 bp Coordinate of oriT [Strand]   60746..60794 [-]
Host baterium   Klebsiella pneumoniae strain CM15_K_mino

Cargo genes

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