Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105030
Name   oriT_p47733_NDM_5 in_silico
Organism   Klebsiella pneumoniae strain 47733
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050367 (7625..7710 [+], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_p47733_NDM_5
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   1567 GenBank   WP_000089263
Name   WP_000089263_p47733_NDM_5 insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9

ID   1568 GenBank   WP_001354030
Name   WP_001354030_p47733_NDM_5 insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3


T4CP

ID   3482 GenBank   WP_087760849
Name   traD_HB636_RS29445_p47733_NDM_5 insolico UniProt ID   _
Length   759 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 759 a.a.        Molecular weight: 86374.22 Da        Isoelectric Point: 5.1644

>WP_087760849.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEM
EQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   3483 GenBank   WP_000069777
Name   traC_HB636_RS29540_p47733_NDM_5 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 894..8278

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HB636_RS28945 (HB636_28960) 69..545 - 477 WP_000549587 hypothetical protein -
HB636_RS28950 (HB636_28965) 538..759 - 222 WP_001278683 conjugal transfer protein TraR -
HB636_RS28955 (HB636_28970) 894..1409 - 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HB636_RS28960 (HB636_28975) 1406..1726 - 321 WP_001057307 conjugal transfer protein TrbD -
HB636_RS28965 (HB636_28980) 1713..2279 - 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HB636_RS28970 (HB636_28985) 2269..3720 - 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HB636_RS28975 (HB636_28990) 3720..4448 - 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HB636_RS28980 (HB636_28995) 4435..5001 - 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HB636_RS28985 (HB636_29000) 5023..5334 - 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HB636_RS28990 (HB636_29005) 5349..5708 - 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HB636_RS28995 (HB636_29010) 5741..5968 - 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HB636_RS29000 (HB636_29015) 6105..6776 - 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HB636_RS29005 (HB636_29020) 6970..7353 - 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HB636_RS29010 (HB636_29025) 7688..8278 + 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
HB636_RS29015 (HB636_29030) 8575..9396 - 822 WP_001234445 DUF932 domain-containing protein -
HB636_RS29020 (HB636_29035) 9507..9803 - 297 WP_001272251 hypothetical protein -
HB636_RS29025 (HB636_29040) 9873..10577 + 705 WP_155367594 IS6-like element IS26 family transposase -
HB636_RS29030 (HB636_29045) 10632..11498 - 867 Protein_17 class 1 integron integrase IntI1 -
HB636_RS29035 (HB636_29050) 11643..12140 + 498 WP_001083725 trimethoprim-resistant dihydrofolate reductase DfrA12 -
HB636_RS29040 (HB636_29055) 12346..13050 - 705 WP_155367594 IS6-like element IS26 family transposase -

Region 2: 83202..102355

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HB636_RS29445 (HB636_29460) 83202..85481 - 2280 WP_087760849 type IV conjugative transfer system coupling protein TraD prgC
HB636_RS29450 (HB636_29465) 85532..86269 - 738 WP_000199905 hypothetical protein -
HB636_RS29455 (HB636_29470) 86472..87203 - 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HB636_RS29460 (HB636_29475) 87252..87737 - 486 WP_000605870 hypothetical protein -
HB636_RS29465 (HB636_29480) 87753..90575 - 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HB636_RS29470 (HB636_29485) 90572..91954 - 1383 WP_001309243 conjugal transfer pilus assembly protein TraH traH
HB636_RS29475 (HB636_29490) 91932..92324 - 393 WP_000660699 F-type conjugal transfer protein TrbF -
HB636_RS29480 (HB636_29495) 92305..92652 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HB636_RS29485 (HB636_29500) 92582..93127 - 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HB636_RS29490 (HB636_29505) 93114..93398 - 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HB636_RS29495 (HB636_29510) 93517..93861 - 345 WP_000556796 conjugal transfer protein TrbA -
HB636_RS29500 (HB636_29515) 93875..94624 - 750 WP_001336806 type-F conjugative transfer system pilin assembly protein TraF traF
HB636_RS29505 (HB636_29520) 94611..94868 - 258 WP_000864353 conjugal transfer protein TrbE -
HB636_RS29510 (HB636_29525) 94895..96745 - 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HB636_RS29515 (HB636_29530) 96742..97380 - 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HB636_RS29520 (HB636_29535) 97389..97694 - 306 WP_000224416 hypothetical protein -
HB636_RS29525 (HB636_29540) 97724..98716 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HB636_RS29530 (HB636_29545) 98713..99345 - 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HB636_RS29535 (HB636_29550) 99342..99728 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HB636_RS29540 (HB636_29555) 99725..102355 - 2631 WP_000069777 type IV secretion system protein TraC virb4
HB636_RS29545 (HB636_29560) 102481..102828 - 348 WP_000836682 hypothetical protein -
HB636_RS29550 (HB636_29565) 102856..103074 - 219 WP_000556745 hypothetical protein -

Host bacterium

ID   5468 GenBank   NZ_CP050367
Plasmid name   p47733_NDM_5 Incompatibility group   IncFII
Plasmid size   103085 bp Coordinate of oriT [Strand]   7625..7710 [+]
Host baterium   Klebsiella pneumoniae strain 47733

Cargo genes

Drug resistance gene   dfrA12, aadA2, qacE, sul1, blaNDM-5, rmtB, blaTEM-1B, mph(A), erm(B)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11