Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118944
Name   oriT_DY2415|p1 in_silico
Organism   Raoultella sp. DY2415
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP111116 (54641..54690 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..13, 18..24  (GCAAAAT..ATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_DY2415|p1
AAATCTGCAAAATATTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12004 GenBank   WP_110522042
Name   traI_OQV00_RS26750_DY2415|p1 insolico UniProt ID   _
Length   1750 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1750 a.a.        Molecular weight: 189911.63 Da        Isoelectric Point: 6.3072

>WP_110522042.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MMSIGSVKSAGSASNYYTDKDNYYVIGSMDERWQGKGAEALGLDGKVDKQVFTDLLKGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSVMAMIGGDKRLIDAHNQAVTEAVKQVETLAATRVMTDGKSKTVLTGNLI
VAKFNHDTNRNQEPQLHTHAVVINATQNGGKWQSLGTDTVGKTGFIENVYANQIAFGKLYREVLKPLVEK
LGYETEVTGKHGMWEMKDVPVEPFSTRSQEVREAAGPDASLKSRDVATLDTRKSKETLDPAEKMVEWVNT
LKESGFDIHSYREDADKRAAEINRAPVSPAKTDGPDISDVVTKAIAGLSDRKVQFTYADMLARTVSQLEA
KPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVVRHAPF
SDAVSVLAQDRPAMGIVYGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLVGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETLSLLDGAMRHNVQVLLSDSGKRSGTGSAVTVLKESGVNTYR
WQGGNQTTADIISEPDKNVRYSRLAQEFAVSVREGQESVAQISGTREQNALNNVIRDTLKNEGVLGAKEI
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFLIDRVTASSNMLTLRDKEGERLDLKVSAVG
SQWTLFRADKLLVADGERLSVLGKIPETRLKGGESVTVLKAEAGQLTVQRPGQKTTQILAVGAGPFDGIK
VGHGWVESPGRSVSETATVFASLTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKARAGETELDAAIASQKARLHTPAEQAIHLSIPLLESDNLTFTRPQLLATAMESGGGKVPMADIDRSIQ
AQIKAGSLLNVPVAPGQGNDLLISRQTWDAEKSILTRVLEGKEAVAPLMDSVPGSLLSDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAINLLPEETRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLTDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDINTALATIEKVTPEQVPRKDGAWVPENSVVEFTPAQEEAIQK
SLNKGESVPAGQPDTLYGALVKDYTGRTPEAQSQTLIITHLNDDRRALNSLIHNARRENGETGREEVTLP
VLVTSNIRDGELRRLSTWTAHRGAVALVDNVYHRIGSVDKENQLITLTDSEGKERLISPREASAEGVTLY
REEAITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKTTRTMNPKADEAQRHIDLAYAITA
HGAQGASEPYAIALEGVAGGRERMASFESAYVGLSRMKQHVQVYTDSREGWIKAINHSPEKATAHDILAP
RNDRAVKTAELLFGRAKPLDETAAGRAALQQSGLARGSSPGKFISPGKKYPKPHVALPAFDKNGKDAGIW
LSPLTDKDGCLEAIGGEGRVMGNEAARFVGLQNSRNGESLLAGNMSEGVRMARDNPDSGVVVRLAGDDRP
WNPGAITGGRVWADPVPVFPQTGADVPLPPEVLAQRAAEEVQRQQMEKQAEQTAREVAGDGRKNGEPDDR
IKEVIGDVIRGLERDKPGGGKTVLPDDPQTHRQEMAVQQVVSESLQRERLQQMERDMVRDLSREKTLGGD

  Protein domains


Predicted by InterproScan.

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

(576-628)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(970-1156)

DNA helicase TraI (TraI_C)

(1432-1554)

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

(634-712)


  Protein structure



No available structure.




T4CP

ID   14057 GenBank   WP_266280848
Name   traD_OQV00_RS26745_DY2415|p1 insolico UniProt ID   _
Length   764 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 764 a.a.        Molecular weight: 85399.59 Da        Isoelectric Point: 4.9674

>WP_266280848.1 type IV conjugative transfer system coupling protein TraD [Raoultella sp. DY2415]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPML
DIIRSQPVYTISYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTICVVTFFVASWVLGRQGKL
QSEDENTGGRQLSDKPKDVARQMKRDGAASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMRGDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYNPRPKIAEGFIQRRLDTRIDERLSAQLEAREAEGSLVRALFTPDEPVSEPAEEKAGVQPEQTKPAKDS
VLPVPVKTSSMAAEGAGKTPDVPLSGAPVTRVKTVPLIRPKPAASVTGTAAAASTAAVSATAGGTEQELA
QQPVEADQDMLPAGMNEDGVIEDMQAYDAWLEGEQIQRDMQRREEVNINHSRSEQDDIEIGGNF

  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: 54082..82011

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OQV00_RS26545 50084..50515 + 432 WP_154949013 conjugation system SOS inhibitor PsiB -
OQV00_RS26550 50512..51243 + 732 WP_266280977 plasmid SOS inhibition protein A -
OQV00_RS26555 51240..51467 + 228 WP_154949017 hypothetical protein -
OQV00_RS26560 51467..51706 + 240 WP_154949019 hypothetical protein -
OQV00_RS26565 51882..52034 + 153 WP_224222653 DUF5431 family protein -
OQV00_RS26570 51979..52098 + 120 WP_223156217 type I toxin-antitoxin system Hok family toxin -
OQV00_RS26575 52866..53687 + 822 WP_266280980 DUF932 domain-containing protein -
OQV00_RS26580 53720..54049 + 330 WP_266280983 DUF5983 family protein -
OQV00_RS26585 54082..54567 - 486 WP_266281003 transglycosylase SLT domain-containing protein virB1
OQV00_RS26590 54998..55390 + 393 WP_032736874 conjugal transfer relaxosome DNA-binding protein TraM -
OQV00_RS26595 55628..56323 + 696 WP_154925432 sigma factor-like helix-turn-helix DNA-binding protein -
OQV00_RS26600 56414..56611 + 198 WP_154925430 TraY domain-containing protein -
OQV00_RS26605 56676..57041 + 366 WP_154925428 type IV conjugative transfer system pilin TraA -
OQV00_RS26610 57055..57360 + 306 WP_154925426 type IV conjugative transfer system protein TraL traL
OQV00_RS26615 57380..57946 + 567 WP_154925424 type IV conjugative transfer system protein TraE traE
OQV00_RS26620 57933..58667 + 735 WP_154925422 type-F conjugative transfer system secretin TraK traK
OQV00_RS26625 58667..60088 + 1422 WP_266280988 F-type conjugal transfer pilus assembly protein TraB traB
OQV00_RS26630 60081..60464 + 384 WP_154925419 conjugal transfer protein TraP -
OQV00_RS26635 60445..60669 + 225 WP_154925417 hypothetical protein -
OQV00_RS26640 60692..61261 + 570 WP_154925415 type IV conjugative transfer system lipoprotein TraV traV
OQV00_RS26645 61375..61707 + 333 WP_154925413 hypothetical protein -
OQV00_RS27105 61707..62112 + 406 Protein_66 hypothetical protein -
OQV00_RS26650 62109..62459 + 351 WP_154925411 hypothetical protein -
OQV00_RS26655 62607..65246 + 2640 WP_154925409 type IV secretion system protein TraC virb4
OQV00_RS26660 65246..65638 + 393 WP_154925407 type-F conjugative transfer system protein TrbI -
OQV00_RS26665 65635..66285 + 651 WP_154925405 type-F conjugative transfer system protein TraW traW
OQV00_RS26670 66307..67299 + 993 WP_154925403 conjugal transfer pilus assembly protein TraU traU
OQV00_RS26675 67312..67938 + 627 WP_154925401 type-F conjugative transfer system pilin assembly protein TrbC trbC
OQV00_RS26680 67935..69917 + 1983 WP_154949027 type-F conjugative transfer system mating-pair stabilization protein TraN traN
OQV00_RS26685 69910..70521 + 612 WP_154925397 hypothetical protein -
OQV00_RS26690 70511..70747 + 237 WP_154925395 conjugal transfer protein TrbE -
OQV00_RS26695 70966..71292 + 327 WP_154925393 hypothetical protein -
OQV00_RS26700 71315..72067 + 753 WP_154925391 type-F conjugative transfer system pilin assembly protein TraF traF
OQV00_RS26705 72078..72518 + 441 WP_154925389 hypothetical protein -
OQV00_RS26710 72481..72840 - 360 WP_177951992 hypothetical protein -
OQV00_RS26715 72929..73165 + 237 WP_154925387 type-F conjugative transfer system pilin chaperone TraQ -
OQV00_RS26720 73140..73715 + 576 WP_250210061 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
OQV00_RS26725 73702..75072 + 1371 WP_154925382 conjugal transfer pilus assembly protein TraH traH
OQV00_RS26730 75072..77966 + 2895 WP_154925380 conjugal transfer mating-pair stabilization protein TraG traG
OQV00_RS26735 77963..78478 + 516 WP_154925378 conjugal transfer protein TraS -
OQV00_RS26740 78790..79521 + 732 WP_154925376 conjugal transfer complement resistance protein TraT -
OQV00_RS26745 79717..82011 + 2295 WP_266280848 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   19376 GenBank   NZ_CP111116
Plasmid name   DY2415|p1 Incompatibility group   IncFIB
Plasmid size   152330 bp Coordinate of oriT [Strand]   54641..54690 [-]
Host baterium   Raoultella sp. DY2415

Cargo genes

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