Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100039
Name   oriT_pTB11 in_silico
Organism   uncultured bacterium pTB11
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   AJ744860 (55435..55534 [+], 100 nt)
oriT length   100 nt
IRs (inverted repeats)      13..31, 34..52  (GTGAAGAAGGAACACCCGC..GCGGGTGGGCCTACTTCAC)
Location of nic site      60..61nt
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   _

  oriT sequence  


Download         Length: 100 nt

>oriT_pTB11
GAATAAGGGACAGTGAAGAAGGAACACCCGCTCGCGGGTGGGCCTACTTCACCTATCCTGCCCGGCTGACGCCGTTGGATACACCAAGGAAAGTCTACAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Tennstedt T et al. (2005) Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements. Plasmid. 53(3):218-38. [PMID:15848226]


Relaxase

ID   37 GenBank   CAG30901
Name   TraI_pTB11 insolico UniProt ID   Q5ZHE0
Length   732 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 732 a.a.        Molecular weight: 81563.20 Da        Isoelectric Point: 10.5791

>CAG30901.1 DNA relaxase (plasmid) [uncultured bacterium]
MIAKHVPMRSIKKSDFAELVKYITDEQGKTERLGHVRVTNCEANTLPAVMAEVMATQHGNTRSEADKTYH
LLVSFRAGEKPDAETLRAIEDRICAGLGFAEHQRVSAVHHDTDNLHIHIAINKIHPTRNTIHEPYRAYRA
LADLCATLERDYGLERDNHETRQRVSENRANDMERHAGVESLVGWIKRECLPELQAAQSWEDLHRVLREN
GLKLRERGNGFIFEAGDGTTVKASTVSRDLSKPKLEARFGAFTPAEGGEAPRRREYRAKPLKTRIDTTEL
YARYQSERQEMGAVRKGELDTLRRRRDRLIEAAMRSNRLRRAAIKLLGEGRIAKRLMYAQAHKALRADLD
KINREYRQGRQAVQERTQRRAWADWLKAEAMKGDDKALAALRAREGRSDLKGNTIQGSGEAKPGHAAVTD
NITKKGTIIYRVGSSAVRDDGDRLQVSREATTDGLDAALRLAMERFGDRITVNGTAEFKERIAQAAAAGR
LAITFDDAALERRRQELLTKEQAHEQPERNDGRRDRGGDGGIRPAAARTTLNATGGDGDRRDARAVSAGG
TVALRKPNVGRIGRKPPPQSQNRLRALSQLGVVRIAGGAEMLLPRDVPGHVEQQGAEPAHALRRGVSGPG
RGLKPEQIAAAEKYVAEREQKRLNGFDIPKHARYTDYVGALSYAGTRNVEDQALALLRKENDEILVLPVD
KATVQRMKRLAIGDPVTVTPRGSLKTTRGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(417-507)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)


  Protein structure


Source ID Structure
AlphaFold DB Q5ZHE0

  Reference


[1] Tennstedt T et al. (2005) Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements. Plasmid. 53(3):218-38. [PMID:15848226]


Auxiliary protein

ID   57 GenBank   CAG30902
Name   TraH_pTB11 insolico UniProt ID   Q5ZHD9
Length   119 a.a. PDB ID   _
Note   involved in conjugative DNA transfer; relaxosome stabilisation

  Auxiliary protein sequence


Download         Length: 119 a.a.        Molecular weight: 12869.28 Da        Isoelectric Point: 4.1047

>CAG30902.1 TraH protein (plasmid) [uncultured bacterium]
MSNPNEMTDEEIAAAMEAFDLPQPEPPSTPQAATATDGTLAPSAPAEPSHSASPTLDALDESRRPKAKTV
CERCPNSVWFASPAELKCYCRVMFLVTWSSKEPNQLTHCDGEFLGQEEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q5ZHD9

  Reference


[1] Tennstedt T et al. (2005) Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements. Plasmid. 53(3):218-38. [PMID:15848226]

ID   58 GenBank   CAG30903
Name   TraJ_pTB11 insolico UniProt ID   Q5ZHD8
Length   123 a.a. PDB ID   _
Note   oriT-binding protein

  Auxiliary protein sequence


Download         Length: 123 a.a.        Molecular weight: 13463.65 Da        Isoelectric Point: 7.9867

>CAG30903.1 oriT-binding protein (plasmid) [uncultured bacterium]
MADETKPTRKGSPPIKVYCLPDERRAIEEKAAAAGMSLSAYLLAVGQGYKITGVVDYEHVRELARINGDL
GRLGGLLKLWLTDDPRTARFGDATILALLAKIEEKQDELGKVMMGVVRPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q5ZHD8

  Reference


[1] Tennstedt T et al. (2005) Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements. Plasmid. 53(3):218-38. [PMID:15848226]

ID   59 GenBank   CAG30904
Name   TraK_pTB11 insolico UniProt ID   Q5ZHD7
Length   134 a.a. PDB ID   _
Note   involved in conjugative DNA transfer

  Auxiliary protein sequence


Download         Length: 134 a.a.        Molecular weight: 14716.82 Da        Isoelectric Point: 10.5082

>CAG30904.1 oriT-binding protein TraK (plasmid) [uncultured bacterium]
MPKSYTDELAEWVESRAAKKRRRDEAAVAFLAVRADVEAALASGYALVTIWEHMRETGKVKFSYETFRSH
ARRHIKAKPADVPAPQAKAAEPAPAPKTPEPRRPKQGGKAEKPAPAAAPTGFTFNPTPDKKDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure


Source ID Structure
AlphaFold DB Q5ZHD7

  Reference


[1] Tennstedt T et al. (2005) Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements. Plasmid. 53(3):218-38. [PMID:15848226]


T4CP

ID   37 GenBank   CAG30900
Name   TraG_pTB11 insolico UniProt ID   Q5ZHE1
Length   635 a.a. PDB ID   _
Note   conjugal transfer coupling protein TraG; Provisional

  T4CP protein sequence


Download         Length: 635 a.a.        Molecular weight: 69857.88 Da        Isoelectric Point: 9.1256

>CAG30900.1 nucleotide binding protein (plasmid) [uncultured bacterium]
MKNRNNAVGPQIRAKKPKASKTVPILAGLSLGAGLQTATQYFAHSFQYQAGLGWNINHVYTPWSILQWAG
KWYGQYPDDFMRAASMGMVVSTVGLLGTAVTQMVKANTGKANDYLHGSARWADKKDIQAAGLLPRPRTVV
ELVSGKHPPTSSGVYVGGWQDKDGKFHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWAHSAVITDLKG
ELWALTAGWRKKHARNKVVRFEPASAQGSACWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLESHWQK
TSQALLVGVILHALYKAKNEGTPATLPSVDGMLADPNRDVGELWMEMTTYGHVDGQNHPAVGSAARDMMD
RPEEESGSVLSTAKSYLALYRDPVVARNVSKSDFRIKQLMHHDDPVSLFIVTQPNDKARLRPLVRVMVNM
IVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDINQLKSRETG
YGHDESITSNCHVQNAYPPNRVETAEHLSKLTGTTTIVKEQITTSGRRTSALLGNVSRTFQEVQRPLLTP
DECLRMPGPKKSADGSIEEAGDMVVYVAGYPAIYGKQPLYFKDPIFQARAAVPAPKVSDKLIQTATVEEG
EGITI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(120-621)

  Protein structure


Source ID Structure
AlphaFold DB Q5ZHE1

  Reference


[1] Tennstedt T et al. (2005) Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements. Plasmid. 53(3):218-38. [PMID:15848226]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15087..25514

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_8 10770..11390 + 621 CAG30854 invertase/recombinase-like protein -
Locus_9 11486..11965 + 480 CAG30855 hypothetical protein -
Locus_10 12121..12627 - 507 CAG30856 hypothetical protein -
Locus_11 12783..13931 - 1149 CAG30857 transcriptional repressor protein -
Locus_12 13980..14330 - 351 CAG30858 single-strand DNA-binding protein -
Locus_13 14505..14816 + 312 CAG30859 regulator protein TrbA -
Locus_14 15087..16046 + 960 CAG30860 ATPase virB11
Locus_15 16059..16496 + 438 CAG30861 prepilin virB2
Locus_16 16499..16810 + 312 CAG30862 putative ATPase virB3
Locus_17 16807..19365 + 2559 CAG30863 putative ATPase virb4
Locus_18 19362..20120 + 759 CAG30864 putative pilus protein virB8
Locus_19 20132..21025 + 894 CAG30865 TrbG protein virB9
Locus_20 21029..21511 + 483 CAG30866 TrbH protein -
Locus_21 21516..22907 + 1392 CAG30867 TrbI protein virB10
Locus_22 22924..23700 + 777 CAG30868 putative entry exclusion protein virB5
Locus_23 23712..23921 + 210 CAG30869 entry exclusion protein -
Locus_24 23928..25514 + 1587 CAG30870 TrbL protein virB6
Locus_25 25538..26137 + 600 CAG30871 TrbM protein -
Locus_26 26153..26857 + 705 CAG30872 transglycosidase -
Locus_27 26888..27151 + 264 CAG30873 TrbO protein -
Locus_28 27188..27922 + 735 CAG30874 TrbP protein -
Locus_29 27939..28358 + 420 CAG30875 Upf31.7 protein -
Locus_30 28373..29068 + 696 CAG30876 FiwA protein -
Locus_31 29104..29766 + 663 CAG30877 Upf32.8 protein -
Locus_32 29790..30449 - 660 CAG30878 site-specific recombinase/resolvase -

Host bacterium

ID   37 GenBank   AJ744860
Plasmid name   pTB11 Incompatibility group   IncP1
Plasmid size   68869 bp Coordinate of oriT [Strand]   55435..55534 [+]
Host baterium   uncultured bacterium pTB11

Cargo genes

Drug resistance gene   Resistance spectrum: ampicillin, cefaclor, cefuroxime, gentamicin, kanamycin, streptomycin, spectinomycin, tetracycline and tobramycin
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -