Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100159
Name   oriT_pKJK5 in_silico
Organism   Uncultured bacterium IncP-1
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   AM261282 (44857..44952 [+], 96 nt)
oriT length   96 nt
IRs (inverted repeats)      7..25, 28..46  (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site      54..55
Conserved sequence flanking the
  nic site    		  CATCCTG|C
Note   _

  oriT sequence  


Download         Length: 96 nt

>oriT_pKJK5
GGGACAGTGAAGATAGATAACCGGCTTGCCGGTTAGCTAACTTCACCCATCCTGCCCGCCTTACGGCGACGTTAACGCCAAGAATGAAATCAGATT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]
[2] Bahl MI et al. (2007) The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta sub-groups. Plasmid. 58(1):31-43. [PMID:17306874]


Relaxase

ID   153 GenBank   CAK02686
Name   TraI_pKJK5 insolico UniProt ID   H2EQ20
Length   740 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 740 a.a.        Molecular weight: 81453.36 Da        Isoelectric Point: 10.7289

>CAK02686.1 TraI protein (plasmid) [uncultured bacterium]
MIAKHVPMRSLGKSDFAGLVQYITDAQSKTERLGLVTLTNCQAGTVQAATDEVLATQHMNTRATGDKTFH
LLVSFRAGEKPDADTLKAIEERICAGLGYGEHQRISAVHHDTDNLHIHIAINKIHPTRNTMHEPFQSYRT
LGELCEVLERDYGLEKDNHTPARSIAEGRAADMERHAGVESLVGWIKRECLEEIKAAQSWTELHQALQAN
GLELRAKGNGFVIEAGDGTQVKASTVARELSKPKLEARFGPFEASPERQAQTKAKRQYQKKPVRLRVNTT
ELYARYKADQQTLAAAQRAALDKARQSKTRKVEDAKRSSRLRRAAIKLMGGKAATKKLLYAQASKALRDE
IQAINKEHQRERQGCYDEHKRRTWADWLKKEALQGNAEALAALRAREAAQGLKGNTVEGQGQAKPGHAPV
VDNITKKGTIIFRAGKTAVRDDGDKLQVSREATREGLQQALRLAMERYGSRITVNGTTEFKAQIIRAAVD
SQLPITFADPALESRRQALLKKENTHDRPQQDRGRTGRGTGRPGSRPAADNDAARSSVNADRGGRDPAGR
VHATGQHRKPDIGRIGRVPPPQSKNRLRALSKLGVVRIASGSEVLLPRDVPGHMEQQGTQPDNALRRGVS
RPGGRLEAGPQYKPEQVKAMDKYIAEREGKRLKGFDIPKHSRYTAGDGALSFAGMRNVEGQTLALVKRGD
DVLVMPIDQATANRLKRIAVGDAVSITPKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(421-508)


  Protein structure


Source ID Structure
AlphaFold DB H2EQ20

  Reference


[1] Bahl MI et al. (2007) The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta sub-groups. Plasmid. 58(1):31-43. [PMID:17306874]


Auxiliary protein

ID   221 GenBank   CAK02687
Name   TraH_pKJK5 insolico UniProt ID   H2EPP9
Length   120 a.a. PDB ID   _
Note   involved in conjugative DNA-transfer

  Auxiliary protein sequence


Download         Length: 120 a.a.        Molecular weight: 13064.46 Da        Isoelectric Point: 3.9959

>CAK02687.1 TraH protein (plasmid) [uncultured bacterium]
MTDPNKIEDELDAALAALDQDPLPTTTLPDPASTPTEAAAIQQEGFTPPDSTGSPTLDALEESRRPKART
VCEHCPNSVWFASPAEVKCYCRVMFLVTWSSKEPNQITHCDGEFLGQEEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB H2EPP9

  Reference


[1] Bahl MI et al. (2007) The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta sub-groups. Plasmid. 58(1):31-43. [PMID:17306874]

ID   222 GenBank   CAK02688
Name   TraJ_pKJK5 insolico UniProt ID   H2EQ19
Length   124 a.a. PDB ID   _
Note   conjugal transfer relaxosome component TraJ; oriT binding protein

  Auxiliary protein sequence


Download         Length: 124 a.a.        Molecular weight: 14196.30 Da        Isoelectric Point: 10.1233

>CAK02688.1 oriT binding protein (plasmid) [uncultured bacterium]
MEKDEKQTGRKRRHHLRVPVFPDEKEEIERQARQAGLSVARYLREVGQGYEIKGITDYERVRELARINGD
LGRLGGLLKLWLTDDARTAKFGEATILALLGRIEATQDEMGRVMKAVVRPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB H2EQ19

  Reference


[1] Bahl MI et al. (2007) The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta sub-groups. Plasmid. 58(1):31-43. [PMID:17306874]

ID   223 GenBank   CAK02689
Name   TraK_pKJK5 insolico UniProt ID   H2EPP6
Length   129 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14231.17 Da        Isoelectric Point: 10.3151

>CAK02689.1 TraK protein (plasmid) [uncultured bacterium]
MAKSLSERIAQRVSAKQPSRTGKNRASFLAVRDDVRKALDDGWPVKVIWDTLRDEGKIEFGYDAFIGYVN
RLIRNAETSPAKPPADQVKADKPAPKAKAKTDAPQEPKAEAPSIGGFNFNPKPNKEDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(3-72)


  Protein structure


Source ID Structure
AlphaFold DB H2EPP6

  Reference


[1] Bahl MI et al. (2007) The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta sub-groups. Plasmid. 58(1):31-43. [PMID:17306874]


T4CP

ID   153 GenBank   CAK02685
Name   TraG_pKJK5 insolico UniProt ID   H2EQ83
Length   634 a.a. PDB ID   _
Note   conjugal transfer coupling protein TraG; Provisional

  T4CP protein sequence


Download         Length: 634 a.a.        Molecular weight: 69544.72 Da        Isoelectric Point: 8.2324

>CAK02685.1 TraG protein (plasmid) [uncultured bacterium]
MKIKMNNAVGPQVRSAKPKAGKLLPTLGVLSLAGGLQAATQYFAHTFDYQASLGGHIGHIYAPWSILQWA
SKWYSHYPNEIMSAGSVGMLVSTVGLLGVAIAKVVASNTSKANQFLHGSARWAEKKDIQAAGLLPRPRTV
LEVVTGKEEPTATGVYVGGWEDKDGSFYYLRHSGPEHVLCYAPTRSGKGVGLVVPTMLSWPASAVITDLK
GELWALTAGWRKKHAKNKVLRFEPASSNGGICWNPLDEIRLGTEFEVGDVQNLAQLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAQADGTYATLPSVDAMLADPNRDVGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLSLYRDPVVARSVSKSEFRIKDLMHQDDPASLYIVTQPNDKARLRPLVRIMVN
MIVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDINQLKSRET
GYGHDETITSNCHVQNAYPPNRVETAEHLSRLTGQTTIVKEQITTSGRRTAAMLGQVSRTFQEVQRPLLT
PDECLRMPGPRKSATGEIEEAGDMVVYVAGYPAIYGKQPLYFKDPVFQARAAIPAPKVSDKTIHVQDAGQ
GITI

  Protein domains


Predicted by InterproScan.

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

(121-621)

  Protein structure


Source ID Structure
AlphaFold DB H2EQ83

  Reference


[1] Bahl MI et al. (2007) The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta sub-groups. Plasmid. 58(1):31-43. [PMID:17306874]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3707..14675

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
pKJK5_1 1315..2538 - 1224 CAK02642 replication initiation protein -
pKJK5_2 2590..2931 - 342 CAK02643 single strand DNA binding protein -
pKJK5_3 3043..3417 + 375 CAK02644 transcriptional regulator protein -
pKJK5_4 3707..4669 + 963 CAK02645 TrbB protein virB11
pKJK5_5 4683..5147 + 465 CAK02646 putative prepilin virB2
pKJK5_6 5151..5462 + 312 CAK02647 TrbD protein virB3
pKJK5_7 5459..8017 + 2559 CAK02648 TrbE protien virb4
pKJK5_8 8014..8787 + 774 CAK02649 TrbF protein virB8
pKJK5_9 8805..9698 + 894 CAK02650 TrbG protein virB9
pKJK5_10 9701..10156 + 456 CAK02651 TrbH protein -
pKJK5_11 10160..11563 + 1404 CAK02652 TrbI protein virB10
pKJK5_12 11582..12352 + 771 CAK02653 TrbJ protein virB5
pKJK5_13 12362..12535 + 174 CAK02654 TrbK protein -
pKJK5_14 12520..12747 + 228 CAK02655 hypothetical protein predicted by Glimmer/Critica -
pKJK5_15 12759..14675 + 1917 CAK02656 TrbL protein virB6
pKJK5_16 14711..15298 + 588 CAK02657 TrbM protein -
pKJK5_17 15315..15944 + 630 CAK02658 TrbN protein -
pKJK5_18 15973..16242 + 270 CAK02659 TrbO protein -
pKJK5_19 16239..16937 + 699 CAK02660 TrbP protein -
pKJK5_20 16952..17383 + 432 CAK02661 putative outer membrane protein -
pKJK5_21 17426..17839 + 414 CAK02662 putative major outer membrane lipoprotein -
pKJK5_22 17865..18833 + 969 CAK02663 hypothetical protein -
pKJK5_23 18816..19421 - 606 CAK02664 plasmid stablization protein ParA, resolvase -

Host bacterium

ID   153 GenBank   AM261282
Plasmid name   pKJK5 Incompatibility group   IncP1
Plasmid size   54383 bp Coordinate of oriT [Strand]   44857..44952 [+]
Host baterium   Uncultured bacterium IncP-1

Cargo genes

Drug resistance gene   resistance to spectinomycin, tetracycline and trimethoprim
Virulence gene   _
Metal resistance gene   _
Degradation gene   _
Symbiosis gene   -
Anti-CRISPR   -