Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121088
Name   oriT_pYD-K10_1 in_silico
Organism   Klebsiella aerogenes strain YD-K10
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP142847 (6103..6151 [+], 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_pYD-K10_1
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   7379 GenBank   WP_087858762
Name   WP_087858762_pYD-K10_1 insolico UniProt ID   _
Length   128 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 128 a.a.        Molecular weight: 14785.81 Da        Isoelectric Point: 4.6438

>WP_087858762.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Klebsiella]
MARVQAYPSDEVVEKINAIVEKRRTEGAKEKDISFSSVATMLLELGLRVYEAQMERKESGFNQAEFNKVL
LENVMKTQFTISKVLAMDSLSPHIKGDDRFDFKSMVMNIRDDAREVVERFFPSQDEEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   15604 GenBank   WP_329503067
Name   traD_U7121_RS24745_pYD-K10_1 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 82656.49 Da        Isoelectric Point: 5.7523

>WP_329503067.1 type IV conjugative transfer system coupling protein TraD [Klebsiella aerogenes]
MSFNAKDMTQGGQIASMRFRMFGQIANIILYVLFLFFWVLCGLILMYRLSWQTFVNGAVYWWCTTLGPMR
DIIRSQPVYTINYYGQQLQYTSEQILKDKYTIWCGEQLWTGFVFAGTVSLIICIVAFFVASWVLGHQGKQ
QSEDEVTGGRQLSEKPKEVARKMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSIDKILNPLDSRCAAWDLWKECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRSVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKGIA
EFAAGEIGEKELKKASENYSYGADPVRDGVSTGKEQKRETIVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRHFNQAIDDKLAAVLAAREAEGQSARILFMPDPVETVPVEKTDEKPASPVAAVPTP
QEEKAKVPPVTASNTFHKPASAAAAAASASVTPAGGVEQELHGKPEEQLPLPPGVNEDGEIEDMNAWDEW
QSSSDVLRDMHRREEVNINHSHHVDRDDIDLGSNF

  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: 1..6710

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U7121_RS24120 1..237 - 237 WP_329503081 hypothetical protein virb4
U7121_RS24125 209..1642 - 1434 WP_329503082 F-type conjugal transfer pilus assembly protein TraB traB
U7121_RS24130 1642..2382 - 741 WP_206352972 type-F conjugative transfer system secretin TraK traK
U7121_RS24135 2369..2935 - 567 WP_001568102 type IV conjugative transfer system protein TraE traE
U7121_RS24140 2954..3259 - 306 WP_024191986 type IV conjugative transfer system protein TraL traL
U7121_RS24145 3273..3641 - 369 WP_046883992 type IV conjugative transfer system pilin TraA -
U7121_RS24150 3721..4089 - 369 WP_058344120 type IV conjugative transfer system pilin TraA -
U7121_RS24155 4168..4332 - 165 WP_071594636 TraY domain-containing protein -
U7121_RS24160 4507..5196 - 690 WP_063862887 helix-turn-helix domain-containing protein -
U7121_RS24165 5416..5802 - 387 WP_087858762 conjugal transfer relaxosome DNA-binding protein TraM -
U7121_RS24170 6225..6710 + 486 WP_047047662 transglycosylase SLT domain-containing protein virB1
U7121_RS24175 6743..7051 - 309 WP_329503083 DUF5983 family protein -
U7121_RS24180 7117..7938 - 822 WP_315713307 DUF932 domain-containing protein -
U7121_RS24185 8335..8466 + 132 WP_255344245 hypothetical protein -
U7121_RS24190 8728..8853 - 126 WP_223274121 type I toxin-antitoxin system Hok family toxin -
U7121_RS24195 8798..8947 - 150 Protein_15 DUF5431 family protein -
U7121_RS24200 9485..9808 - 324 WP_329503084 theronine dehydrogenase -
U7121_RS24205 9811..10533 - 723 WP_058344126 plasmid SOS inhibition protein A -
U7121_RS24210 10530..10961 - 432 WP_047063361 conjugation system SOS inhibitor PsiB -

Region 2: 115067..134397

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U7121_RS24745 115067..117274 - 2208 WP_329503067 type IV conjugative transfer system coupling protein TraD virb4
U7121_RS24750 117459..118190 - 732 WP_329503068 conjugal transfer complement resistance protein TraT -
U7121_RS24755 118325..118915 - 591 WP_329503069 hypothetical protein -
U7121_RS24760 118931..121753 - 2823 WP_329503070 conjugal transfer mating-pair stabilization protein TraG traG
U7121_RS24765 121753..123123 - 1371 WP_023332869 conjugal transfer pilus assembly protein TraH traH
U7121_RS24770 123110..123646 - 537 WP_329503126 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
U7121_RS24775 123666..123899 - 234 WP_001568081 type-F conjugative transfer system pilin chaperone TraQ -
U7121_RS24780 123910..124659 - 750 WP_279925703 type-F conjugative transfer system pilin assembly protein TraF traF
U7121_RS24785 124675..125007 - 333 WP_329503071 hypothetical protein -
U7121_RS24790 125004..125264 - 261 WP_329503072 conjugal transfer protein TrbE -
U7121_RS24795 125278..127152 - 1875 WP_329503073 type-F conjugative transfer system mating-pair stabilization protein TraN traN
U7121_RS24800 127149..127775 - 627 WP_329503074 type-F conjugative transfer system pilin assembly protein TrbC trbC
U7121_RS24805 127788..128771 - 984 WP_162270604 conjugal transfer pilus assembly protein TraU traU
U7121_RS24810 128791..129420 - 630 WP_329503075 type-F conjugative transfer system protein TraW traW
U7121_RS24815 129417..129794 - 378 WP_329503076 type-F conjugative transfer system protein TrbI -
U7121_RS24820 129794..132433 - 2640 WP_329503077 type IV secretion system protein TraC virb4
U7121_RS24825 132510..132896 - 387 WP_329503078 hypothetical protein -
U7121_RS24830 132898..133296 - 399 WP_329503079 hypothetical protein -
U7121_RS24835 133301..133714 - 414 WP_329503080 hypothetical protein -
U7121_RS24840 133828..134397 - 570 WP_058344116 type IV conjugative transfer system lipoprotein TraV traV

Host bacterium

ID   21516 GenBank   NZ_CP142847
Plasmid name   pYD-K10_1 Incompatibility group   IncFIB
Plasmid size   134415 bp Coordinate of oriT [Strand]   6103..6151 [+]
Host baterium   Klebsiella aerogenes strain YD-K10

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsC, arsB, arsR, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -