Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115360
Name   oriT_p_kv_NDM1 in_silico
Organism   Klebsiella variicola strain BD_DM_115
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP095680 (80543..80591 [-], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_p_kv_NDM1
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9825 GenBank   WP_040120371
Name   traI_DY002_RS00710_p_kv_NDM1 insolico UniProt ID   A0A6G9HHF7
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190710.48 Da        Isoelectric Point: 6.0005

>WP_040120371.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGI
KVGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTDLTAGQRAATR
MILESTDQFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVSSGDTDQLPPIASGQPFRLTQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRLWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(577-629)

DNA helicase TraI (TraI_C)

(1433-1555)

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

(635-714)

TrwC relaxase (TrwC)

(10-284)

AAA domain (AAA_30)

(971-1157)


  Protein structure



No available structure.




T4CP

ID   11448 GenBank   WP_040120372
Name   traD_DY002_RS00705_p_kv_NDM1 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: 85972.07 Da        Isoelectric Point: 5.1806

>WP_040120372.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDTPEPGPADTNSHAGEQPEPVSPPA
PAVMTVTPAPVKSPPTTKRPAAEPSVRATEPPVLRGTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 79985..108454

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DY002_RS00500 (DY002_000505) 76037..76417 + 381 WP_020802391 hypothetical protein -
DY002_RS00505 (DY002_000510) 76484..76831 + 348 WP_032445771 hypothetical protein -
DY002_RS00510 (DY002_000515) 76926..77072 + 147 WP_004152750 hypothetical protein -
DY002_RS00515 (DY002_000520) 77123..77956 + 834 WP_032445769 N-6 DNA methylase -
DY002_RS00520 (DY002_000525) 78291..78482 + 192 WP_309353568 hypothetical protein -
DY002_RS00525 (DY002_000530) 78769..79590 + 822 WP_004152492 DUF932 domain-containing protein -
DY002_RS00530 (DY002_000535) 79623..79952 + 330 WP_011977736 DUF5983 family protein -
DY002_RS00535 (DY002_000540) 79985..80470 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
DY002_RS00540 (DY002_000545) 80902..81294 + 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
DY002_RS00545 (DY002_000550) 81524..82225 + 702 WP_040120380 hypothetical protein -
DY002_RS00550 (DY002_000555) 82311..82511 + 201 WP_046664192 TraY domain-containing protein -
DY002_RS00555 (DY002_000560) 82579..82947 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
DY002_RS00560 (DY002_000565) 82961..83266 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
DY002_RS00565 (DY002_000570) 83286..83852 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
DY002_RS00570 (DY002_000575) 83839..84579 + 741 WP_040120379 type-F conjugative transfer system secretin TraK traK
DY002_RS00575 (DY002_000580) 84579..86003 + 1425 WP_040120378 F-type conjugal transfer pilus assembly protein TraB traB
DY002_RS00580 (DY002_000585) 86075..86659 + 585 WP_040120377 type IV conjugative transfer system lipoprotein TraV traV
DY002_RS00585 (DY002_000590) 86982..87200 + 219 WP_004195468 hypothetical protein -
DY002_RS00590 (DY002_000595) 87201..87512 + 312 WP_029497417 hypothetical protein -
DY002_RS00595 (DY002_000600) 87579..87983 + 405 WP_004197817 hypothetical protein -
DY002_RS00600 (DY002_000605) 88026..88178 + 153 WP_224518895 hypothetical protein -
DY002_RS00605 (DY002_000610) 88360..88758 + 399 WP_023179972 hypothetical protein -
DY002_RS00610 (DY002_000615) 88830..91469 + 2640 WP_013214024 type IV secretion system protein TraC virb4
DY002_RS00615 (DY002_000620) 91469..91858 + 390 WP_004167468 type-F conjugative transfer system protein TrbI -
DY002_RS00620 (DY002_000625) 91858..92493 + 636 WP_029497419 type-F conjugative transfer system protein TraW traW
DY002_RS00625 (DY002_000630) 92528..92929 + 402 WP_040120376 hypothetical protein -
DY002_RS00630 (DY002_000635) 92926..93915 + 990 WP_029497420 conjugal transfer pilus assembly protein TraU traU
DY002_RS00635 (DY002_000640) 93928..94566 + 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
DY002_RS00640 (DY002_000645) 94625..96580 + 1956 WP_040120375 type-F conjugative transfer system mating-pair stabilization protein TraN traN
DY002_RS00645 (DY002_000650) 96612..96866 + 255 WP_004152674 conjugal transfer protein TrbE -
DY002_RS00650 (DY002_000655) 96844..97092 + 249 WP_004152675 hypothetical protein -
DY002_RS00655 (DY002_000660) 97105..97431 + 327 WP_004144402 hypothetical protein -
DY002_RS00660 (DY002_000665) 97452..98204 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
DY002_RS00665 (DY002_000670) 98215..98454 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
DY002_RS00670 (DY002_000675) 98426..98983 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
DY002_RS00675 (DY002_000680) 99029..99472 + 444 WP_014343488 F-type conjugal transfer protein TrbF -
DY002_RS00680 (DY002_000685) 99450..100829 + 1380 WP_072198320 conjugal transfer pilus assembly protein TraH traH
DY002_RS00685 (DY002_000690) 100829..103678 + 2850 WP_040120373 conjugal transfer mating-pair stabilization protein TraG traG
DY002_RS00690 (DY002_000695) 103684..104211 + 528 WP_040120388 conjugal transfer protein TraS -
DY002_RS00695 (DY002_000700) 104400..105131 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
DY002_RS00700 (DY002_000705) 105324..106013 + 690 WP_072198322 hypothetical protein -
DY002_RS00705 (DY002_000710) 106142..108454 + 2313 WP_040120372 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   15793 GenBank   NZ_CP095680
Plasmid name   p_kv_NDM1 Incompatibility group   IncFIB
Plasmid size   119162 bp Coordinate of oriT [Strand]   80543..80591 [-]
Host baterium   Klebsiella variicola strain BD_DM_115

Cargo genes

Drug resistance gene   blaNDM-1, aph(3')-VI, qnrS1, blaCTX-M-15, aac(6')-Ib, ant(3'')-Ia, blaOXA-9, blaTEM-1B
Virulence gene   -
Metal resistance gene   merE, merD, merA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9