Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100027
Name   oriT_pB4 in_silico
Organism   Uncultured bacterium
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   AJ431260 (72051..72142 [+], 92 nt)
oriT length   92 nt
IRs (inverted repeats)      13..31, 34..52  (GCGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCGC)
Location of nic site      60..61
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   _

  oriT sequence  


Download         Length: 92 nt

>oriT_pB4
GAATAAGGGACAGCGAAGATAGATAACCGGCTTGCCGGTTAGCTAACTTCGCCTATCCTGCCCGCCTTACGACGTCTTTTACTCCAAGAATG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   26 GenBank   CAD24395
Name   TraI_pB4 insolico UniProt ID   Q8RSH1
Length   752 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 752 a.a.        Molecular weight: 83020.85 Da        Isoelectric Point: 10.7945

>CAD24395.1 TraI protein (plasmid) [uncultured bacterium]
MIVKHVPMRSLGKSDFAGLVNYVTDAQSKDHRLGQVQITNCDAMSVQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGFAEHQRVSAVHNDTDNLHIHIAINKIHPTRHTMHEPFGQHRT
LAELCVALERDYGLERDNHEPRQRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMHDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARLGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTATRGQALEQARRRKDRLVEAAKRSNRLRRATIKMVGENRTNKKLLYAQASKALRDE
IQAINKQYQQDRQALYDSHSRRTWADWLKKEATHGNAEALAALRAREAAQGLQGNTIQGRGDARPGHAPV
TDNITKKGTIIFRAGLSAVRDDGDKLQVSREATREGLQEALRLAMERYGSRITVNGTTQFKAQVIRAAVD
SQLPITFADPALESRRLALLKKENTHERPDRTERADQRPAEHRGRTGRGPGGPGQRAAAHDDAARPVAVA
RAGFGRPGAGRTDAAGVHAGAVHWKPDIGRIGRVPPPQSQHRLRTLSQLGVVRIAGGSEVLLPRDVPRHL
EQQGTQPDHQLRRGISRPGTGVAAAPPGLAAADKYIAEREAKRSKGFDIPKHARYTAGDGALAFQGVRNI
EGQALALLKRGDEVMVMPIDQATARRLSRIAVGDAVTVTPKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(420-507)


  Protein structure


Source ID Structure
AlphaFold DB Q8RSH1

  Reference


[1] Tauch A et al. (2003) The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family. Mol Genet Genomics. 268(5):570-84. [PMID:12589432]


Auxiliary protein

ID   38 GenBank   CAD24396
Name   TraH_pB4 insolico UniProt ID   Q8RSH0
Length   136 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 136 a.a.        Molecular weight: 14537.89 Da        Isoelectric Point: 3.6668

>CAD24396.1 TraH protein (plasmid) [uncultured bacterium]
MSDPTEPSEPTSDPQNIEDELDAALAALDSEPLPTTTLPDPSPSPEQASGDQVPGEPTPPAFTPEPSTGS
PTLDALDESRRPKASTVCERCPNSVWFASPAEVKCYCRVMFLVTWSSKEPSQITNCDGEFLGQEQG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q8RSH0

  Reference


[1] Tauch A et al. (2003) The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family. Mol Genet Genomics. 268(5):570-84. [PMID:12589432]

ID   39 GenBank   CAD24398
Name   TraJ_pB4 insolico UniProt ID   Q8RSG8
Length   123 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 123 a.a.        Molecular weight: 13936.01 Da        Isoelectric Point: 8.4443

>CAD24398.1 TraJ protein (plasmid) [uncultured bacterium]
MEADEQPTAKRRQHLRVPVFPEEKELIEANAKRAGVSVARYLRDVGQGYQIKGVMDYEYVRELVRVNGDL
GRLGGLLKLWLTDDPRTARFGDATILALLGRIEATQDEMSRLMKSVVQPRAEP

  Protein domains



No domain identified.



  Protein structure



No available structure.



  Reference


[1] Tauch A et al. (2003) The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family. Mol Genet Genomics. 268(5):570-84. [PMID:12589432]

ID   40 GenBank   CAD24399
Name   TraK_pB4 insolico UniProt ID   Q8RSG7
Length   137 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 137 a.a.        Molecular weight: 15067.19 Da        Isoelectric Point: 10.3031

>CAD24399.1 TraK protein (plasmid) [uncultured bacterium]
MAKSLSDRIAERMSARKPTGAGKNRAEFLAMRNDVKKAMDDGWPVKVIWETLRDEGKISFGYDAFIGYVN
RLIRNVDATAPAPVPPSTADQAKGQKPAQQEGGSKAKKPKPAEPKKTEPSGIASFNYNPKMEDKDLF

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(3-72)


  Protein structure


Source ID Structure
AlphaFold DB Q8RSG7

  Reference


[1] Tauch A et al. (2003) The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family. Mol Genet Genomics. 268(5):570-84. [PMID:12589432]


T4CP

ID   26 GenBank   CAD24394
Name   TraG_pB4 insolico UniProt ID   Q8RSH2
Length   634 a.a. PDB ID   _
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 634 a.a.        Molecular weight: 69671.68 Da        Isoelectric Point: 8.5000

>CAD24394.1 TraG protein (plasmid) [uncultured bacterium]
MKIKMNNSVGPQVRSAKPKTPKLLPILGGVSLVGGLQAATQFFAYTFQYHASLGANLGHVYAPWSILNWS
AKWYSQYPDEIMRAGSIGMVTATVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKDAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSSGGVCWNPLDEIRVGTEAEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKARNEGGTATLPSVDAMLADPNRDIGELWMEMTTYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKDLMHSDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLRSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNDKGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFQARASIPAPKATDRLRQVVEAGE
GITI

  Protein domains


Predicted by InterproScan.

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

(121-618)

  Protein structure


Source ID Structure
AlphaFold DB Q8RSH2

  Reference


[1] Tauch A et al. (2003) The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family. Mol Genet Genomics. 268(5):570-84. [PMID:12589432]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 41819..52420

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_41 39425..40648 - 1224 CAD24364 TrfA1 -
Locus_42 39425..40294 - 870 CAD24365 TrfA2 protein -
Locus_43 40697..41035 - 339 CAD24366 Ssb protein -
Locus_44 41145..41504 + 360 CAD24367 TrbA protein -
Locus_45 41819..42784 + 966 CAD24368 TrbB protein virB11
Locus_46 42798..43262 + 465 CAD24369 TrbC protein virB2
Locus_47 43266..43577 + 312 CAD24370 TrbD protein virB3
Locus_48 43574..46132 + 2559 CAD24371 TrbE protein virb4
Locus_49 46129..46917 + 789 CAD24372 TrbF protein virB8
Locus_50 46914..47828 + 915 CAD24373 TrbG protein virB9
Locus_51 47831..48292 + 462 CAD24374 TrbH protein -
Locus_52 48296..49678 + 1383 CAD24375 TrbI protein virB10
Locus_53 49695..50468 + 774 CAD24376 TrbJ protein virB5
Locus_54 50478..50696 + 219 CAD24377 TrbK protein -
Locus_55 50708..52420 + 1713 CAD24378 TrbL protein virB6
Locus_56 52438..53016 + 579 CAD24379 TrbM protein -
Locus_57 53018..53653 + 636 CAD24380 TrbN protein -
Locus_58 53683..53952 + 270 CAD24381 TrbO protein -
Locus_59 53964..54647 + 684 CAD24382 TrbP protein -
Locus_60 54663..55106 + 444 CAD24383 Upf30.5 protein -
Locus_61 55130..55411 + 282 CAD24384 UpfA protein -
Locus_62 55607..56281 + 675 CAD24385 Upf31.0 protein -
Locus_63 56337..56885 + 549 CAD24386 UpfB protein -
Locus_64 56854..57326 - 473 CAD24387 ParA protein -

Host bacterium

ID   26 GenBank   AJ431260
Plasmid name   pB4 Incompatibility group   IncP1
Plasmid size   79370 bp Coordinate of oriT [Strand]   72051..72142 [+]
Host baterium   Uncultured bacterium

Cargo genes

Drug resistance gene   resistance to streptomycin, erythromycin and amoxicillin

The plasmid contains the the beta-lactam antibiotic resistance gene blaNPS-1.
Virulence gene   _
Metal resistance gene   _
Degradation gene   _
Symbiosis gene   -
Anti-CRISPR   -