Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121565
Name   oriT_pKOX58_2 in_silico
Organism   Klebsiella michiganensis strain Kox58
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP089397 (4326..4375 [-], 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_pKOX58_2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13597 GenBank   WP_232421757
Name   traI_LUW95_RS29650_pKOX58_2 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: 190442.76 Da        Isoelectric Point: 5.5084

>WP_232421757.1 conjugative transfer relaxase/helicase TraI [Klebsiella michiganensis]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTNNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADTRAKELASAPAAPVKTDVPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLEA
KPGVFEQTRTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDTAVVRQSPF
SDAVSVLAQDRPTMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSREFLSADARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKMSLKETLSMLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGKQATADIISEPEKGARYSRLAQEFAASVREGQESVAQISGSREQGILNGLIRETLKSEGVLGEKDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRQHDRFVIDRVTASSNMLTLRDKEGERLDMKVSAVD
SQWTLFRADKLTVAEGERLAVLGKIPDTRLKGGESVTVLKAEEGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQGTARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIALQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
SQIQAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDNVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQVTPEQVPRKDGAWVPENSVVEFTPAQEEAIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKSTRTLNPKADQAQQHIDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESAYVGLSRMKQHVQVYTDNREGWIKAINNSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMERQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1432-1552)

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

(577-628)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1157)

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

(634-713)


  Protein structure



No available structure.




Auxiliary protein

ID   7485 GenBank   WP_053390193
Name   WP_053390193_pKOX58_2 insolico UniProt ID   A0A8G2A327
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14883.89 Da        Isoelectric Point: 4.3779

>WP_053390193.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEVADKINAIVEKRRVEGAKDKDISFSSISTMLLELGLRVYEAQMERKESGFNQMAFNKAL
LESVIKTQFTVNKVLGIECLSPHVSGNPRWEWPGLIENIRDDVQEVMLRFFPDEESEDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   15890 GenBank   WP_064386203
Name   traD_LUW95_RS29645_pKOX58_2 insolico UniProt ID   _
Length   772 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 772 a.a.        Molecular weight: 86585.38 Da        Isoelectric Point: 5.0283

>WP_064386203.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGKSLEYNSEQILADKYTIWCGEQLWTSFVFAAIVSLTVCIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKHSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDIWRECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFSEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLKNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLGMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDVQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRNLDTRVDARLNALLEAREAEGSLARTLFTPDAPAPELAEKDEKVGNPPEQSQPAE
SSGTSATVKVPSTAKTPEADESGQSPEVSNPAALLTKVVTVPLTRPRPAAATGTAAVASATDVPATPAGG
TEQALETQPAEQGQDMLPPGVNEYGEIDDMHAWDEWQSGEQTQRDMQRREEVNINHSHRRDEQDDIEIGG
NF

  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: 6787..33627

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LUW95_RS29460 (LUW95_29460) 3194..3736 + 543 WP_053390246 antirestriction protein -
LUW95_RS29465 (LUW95_29465) 3759..4181 - 423 WP_077268549 transglycosylase SLT domain-containing protein -
LUW95_RS29470 (LUW95_29470) 4687..5079 + 393 WP_053390193 conjugal transfer relaxosome DNA-binding protein TraM -
LUW95_RS29475 (LUW95_29475) 5317..6018 + 702 WP_094898581 hypothetical protein -
LUW95_RS29480 (LUW95_29480) 6179..6340 + 162 WP_172686697 TraY domain-containing protein -
LUW95_RS29485 (LUW95_29485) 6405..6773 + 369 WP_064386081 type IV conjugative transfer system pilin TraA -
LUW95_RS29490 (LUW95_29490) 6787..7092 + 306 WP_032744112 type IV conjugative transfer system protein TraL traL
LUW95_RS29495 (LUW95_29495) 7111..7677 + 567 WP_064386078 type IV conjugative transfer system protein TraE traE
LUW95_RS29500 (LUW95_29500) 7664..8398 + 735 WP_064386077 type-F conjugative transfer system secretin TraK traK
LUW95_RS29505 (LUW95_29505) 8398..9822 + 1425 WP_064386076 F-type conjugal transfer pilus assembly protein TraB traB
LUW95_RS29510 (LUW95_29510) 9885..10454 + 570 WP_074182910 type IV conjugative transfer system lipoprotein TraV traV
LUW95_RS29515 (LUW95_29515) 10478..10846 + 369 WP_224253886 hypothetical protein -
LUW95_RS29520 (LUW95_29520) 10853..11095 + 243 WP_064386074 hypothetical protein -
LUW95_RS29525 (LUW95_29525) 11092..11496 + 405 WP_064386072 hypothetical protein -
LUW95_RS29530 (LUW95_29530) 11493..11840 + 348 WP_064386070 hypothetical protein -
LUW95_RS29535 (LUW95_29535) 11837..12235 + 399 WP_224253887 hypothetical protein -
LUW95_RS29540 (LUW95_29540) 12319..14958 + 2640 WP_064386067 type IV secretion system protein TraC virb4
LUW95_RS29545 (LUW95_29545) 14958..15350 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
LUW95_RS29550 (LUW95_29550) 15347..15973 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
LUW95_RS29555 (LUW95_29555) 16017..16976 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
LUW95_RS29560 (LUW95_29560) 16989..17636 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
LUW95_RS29565 (LUW95_29565) 17633..18016 + 384 WP_053390297 hypothetical protein -
LUW95_RS29570 (LUW95_29570) 18013..19968 + 1956 WP_080848160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LUW95_RS29575 (LUW95_29575) 20000..20260 + 261 WP_053390216 hypothetical protein -
LUW95_RS29580 (LUW95_29580) 20253..20864 + 612 WP_053390217 hypothetical protein -
LUW95_RS29585 (LUW95_29585) 20854..21096 + 243 WP_053390218 conjugal transfer protein TrbE -
LUW95_RS29590 (LUW95_29590) 21142..21468 + 327 WP_053390219 hypothetical protein -
LUW95_RS29595 (LUW95_29595) 21489..22241 + 753 WP_064386181 type-F conjugative transfer system pilin assembly protein TraF traF
LUW95_RS29600 (LUW95_29600) 22655..23014 - 360 WP_064386183 hypothetical protein -
LUW95_RS29605 (LUW95_29605) 23103..23339 + 237 WP_064386186 type-F conjugative transfer system pilin chaperone TraQ -
LUW95_RS29610 (LUW95_29610) 23314..23880 + 567 WP_100663597 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LUW95_RS29615 (LUW95_29615) 23873..24301 + 429 WP_100663598 conjugal transfer protein TrbF -
LUW95_RS29620 (LUW95_29620) 24288..25658 + 1371 WP_064386191 conjugal transfer pilus assembly protein TraH traH
LUW95_RS29625 (LUW95_29625) 25658..28537 + 2880 WP_064386194 conjugal transfer mating-pair stabilization protein TraG traG
LUW95_RS29630 (LUW95_29630) 28554..29222 + 669 WP_128317877 hypothetical protein -
LUW95_RS29635 (LUW95_29635) 29575..30306 + 732 WP_064386198 conjugal transfer complement resistance protein TraT -
LUW95_RS29640 (LUW95_29640) 30498..31190 + 693 WP_202395549 hypothetical protein -
LUW95_RS29645 (LUW95_29645) 31309..33627 + 2319 WP_064386203 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21992 GenBank   NZ_CP089397
Plasmid name   pKOX58_2 Incompatibility group   IncFII
Plasmid size   117431 bp Coordinate of oriT [Strand]   4326..4375 [-]
Host baterium   Klebsiella michiganensis strain Kox58

Cargo genes

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