Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103105
Name   oriT_U25P002 in_silico
Organism   Klebsiella pneumoniae strain U25
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT818627 (56959..57044 [-], 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_U25P002
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   987 GenBank   WP_001354030
Name   WP_001354030_U25P002 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

ID   988 GenBank   WP_000089263
Name   WP_000089263_U25P002 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


T4CP

ID   2053 GenBank   WP_087760849
Name   traD_HTG18_RS00030_U25P002 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   2054 GenBank   WP_172686297
Name   traC_HTG18_RS00415_U25P002 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: 99209.89 Da        Isoelectric Point: 6.1130

>WP_172686297.1 type IV secretion system protein TraC [Klebsiella pneumoniae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALEHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-764)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 56391..70030

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTG18_RS00300 (AU29_02680) 52363..52797 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTG18_RS00305 (AU29_02755) 52794..53513 + 720 WP_001276217 plasmid SOS inhibition protein A -
HTG18_RS01085 53735..53884 + 150 Protein_60 plasmid maintenance protein Mok -
HTG18_RS00310 (AU29_02975) 53826..53951 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTG18_RS01075 54270..54566 - 297 Protein_62 hypothetical protein -
HTG18_RS00325 (AU29_03045) 54866..55162 + 297 WP_001272251 hypothetical protein -
HTG18_RS00330 (AU29_03075) 55273..56094 + 822 WP_001234445 DUF932 domain-containing protein -
HTG18_RS00335 (AU29_03140) 56391..56993 - 603 WP_000243713 transglycosylase SLT domain-containing protein -
HTG18_RS00340 (AU29_03245) 57316..57699 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HTG18_RS00345 (AU29_03290) 57893..58564 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HTG18_RS00350 (AU29_03300) 58701..58928 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HTG18_RS00355 (AU29_03340) 58961..59320 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HTG18_RS00360 (AU29_03390) 59335..59646 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HTG18_RS00365 (AU29_03415) 59668..60234 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HTG18_RS00370 (AU29_03445) 60221..60949 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HTG18_RS00375 (AU29_03450) 60949..62400 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HTG18_RS00380 (AU29_03550) 62390..62956 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HTG18_RS00385 (AU29_03555) 62943..63263 + 321 WP_001057307 conjugal transfer protein TrbD -
HTG18_RS00390 (AU29_03575) 63260..63775 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HTG18_RS00395 (AU29_03600) 63910..64131 + 222 WP_001278683 conjugal transfer protein TraR -
HTG18_RS00400 (AU29_03635) 64124..64600 + 477 WP_000549587 hypothetical protein -
HTG18_RS00405 (AU29_03645) 64680..64898 + 219 WP_000556745 hypothetical protein -
HTG18_RS00410 (AU29_03670) 64926..65273 + 348 WP_000836682 hypothetical protein -
HTG18_RS00415 (AU29_03685) 65399..68029 + 2631 WP_172686297 type IV secretion system protein TraC virb4
HTG18_RS00420 (AU29_03690) 68026..68412 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTG18_RS00425 (AU29_03730) 68409..69041 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HTG18_RS00430 (AU29_03735) 69038..70030 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTG18_RS00435 (AU29_03760) 70218..70915 + 698 WP_223174630 IS1 family transposase -
HTG18_RS00440 (AU29_03790) 71000..71860 - 861 WP_000027057 broad-spectrum class A beta-lactamase TEM-1 -
HTG18_RS00445 (AU29_03820) 72043..72360 - 318 Protein_87 recombinase family protein -
HTG18_RS00450 72560..73384 - 825 WP_000722315 oxacillin-hydrolyzing class D beta-lactamase OXA-9 -
HTG18_RS00455 (AU29_03880) 73444..74232 - 789 WP_001206315 ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1 -
HTG18_RS00460 (AU29_03905) 74302..74856 - 555 WP_063840280 AAC(6')-Ib family aminoglycoside 6'-N-acetyltransferase -

Host bacterium

ID   3548 GenBank   NZ_KT818627
Plasmid name   U25P002 Incompatibility group   IncFII
Plasmid size   172679 bp Coordinate of oriT [Strand]   56959..57044 [-]
Host baterium   Klebsiella pneumoniae strain U25

Cargo genes

Drug resistance gene   erm(B), mph(A), blaTEM-1B, blaTEM-1A, blaOXA-9, ant(3'')-Ia, aac(6')-Ib, blaCTX-M-15, aac(3)-IId, blaSHV-187, cmlA1, qacE, sul1, aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -