Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103329
Name   oriT_pICP-4GES in_silico
Organism   Pseudomonas aeruginosa strain PA1280
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH053445 (20602..20700 [-], 99 nt)
oriT length   99 nt
IRs (inverted repeats)      24..31, 34..41  (TAACCGGC..GCCGGTTA)
Location of nic site      60..61
Conserved sequence flanking the
  nic site    		  TCCTGCCCGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 99 nt

>oriT_pICP-4GES
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2487 GenBank   WP_011342947
Name   Relaxase_HTR84_RS00140_pICP-4GES insolico UniProt ID   A0A077KSK4
Length   746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82038.71 Da        Isoelectric Point: 10.7900

>WP_011342947.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(422-508)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)


  Protein structure


Source ID Structure
AlphaFold DB A0A077KSK4


T4CP

ID   2271 GenBank   WP_019373230
Name   t4cp2_HTR84_RS00145_pICP-4GES insolico UniProt ID   _
Length   637 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 69925.10 Da        Isoelectric Point: 8.2999

>WP_019373230.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVARVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDDGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRAVAQAET
EGEGITI

  Protein domains


Predicted by InterproScan.

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

(121-620)

  Protein structure



No available structure.



ID   2272 GenBank   WP_011114047
Name   t4cp2_HTR84_RS00240_pICP-4GES insolico UniProt ID   _
Length   852 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 852 a.a.        Molecular weight: 93980.15 Da        Isoelectric Point: 6.3901

>WP_011114047.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Bacteria]
MIEAIAIAIAVLGAVLLLILFARIRAVDAELKLKKHRAKDAGLADLLNYAAVVDDGVIVGKNGSFMAAWL
YKGDDNASSTEEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPNYSERGVSSFPDSVSFAIDEERRRLF
EGLGAMFEGYFVLTVTWFPPVLAQRKFVELMFDDDAVAPDHTARTTGLIAQFKREITSLESRLSSAVKMT
RLRGQKVVSEEGREVTHDDFLSWLQFCVTGLHHPVMLPSNPMYLDAVIGGQELWGGVVPKIGRKFIQVVA
IEGFPLESTPGVLSALAELPSEYRWSSRFIFMDQHESLKHLDKFRKKWKQKIRGFFDQVFNTNTGSINQD
AAAMVGDAEAAIAEVNSGLVAAGYYTSVVVLMDEDRERLAASALLVEKAVNRLAFAARIETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSSIWTGSATAPCPMYPPLSPALMHCVTVGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMSMYPLAAGIRAATKGKSGLHFTVAADDDRLAFC
PLQFLETKGDRAWAMEWIDTILALNGVNTTPAQRNEIGNAIMSMHASGARTLSEFSVTIQDEAIREAIKQ
YTVDGSMGHLLDAEEDGLSLSDFTVFEIEELMNLGEKFALPVLLYLFRRIERALKGQPSVIILDEAWLML
GHPAFRAKIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMG
LNARQIEILATAIPKRQYYYVSENGRRLYDLALGPMALAFVGASDKESVATIKSLEAKFGHEWVHEWLAG
RGLNLNDYLEAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(626-754)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(218-431)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 39074..49751

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTR84_RS00175 34330..35193 + 864 WP_012658785 carbapenem-hydrolyzing class A beta-lactamase GES-5 -
HTR84_RS00180 35350..36213 + 864 WP_012658785 carbapenem-hydrolyzing class A beta-lactamase GES-5 -
HTR84_RS00185 36370..37233 + 864 WP_237043942 class A beta-lactamase -
HTR84_RS00190 37390..38253 + 864 WP_012658785 carbapenem-hydrolyzing class A beta-lactamase GES-5 -
HTR84_RS00195 38366..38455 - 90 Protein_38 muramidase -
HTR84_RS00200 38469..39056 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
HTR84_RS00205 39074..40792 - 1719 WP_027814021 P-type conjugative transfer protein TrbL virB6
HTR84_RS00210 40803..41030 - 228 WP_000644148 entry exclusion lipoprotein TrbK -
HTR84_RS00215 41040..41804 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
HTR84_RS00220 41825..43246 - 1422 WP_172693339 TrbI/VirB10 family protein virB10
HTR84_RS00225 43251..43739 - 489 WP_006122479 conjugal transfer protein TrbH -
HTR84_RS00230 43742..44641 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
HTR84_RS00235 44659..45441 - 783 WP_006122481 conjugal transfer protein TrbF virB8
HTR84_RS00240 45438..47996 - 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTR84_RS00245 47993..48304 - 312 WP_001207961 conjugal transfer protein TrbD virB3
HTR84_RS00250 48308..48772 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
HTR84_RS00255 48789..49751 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
HTR84_RS00260 50061..50423 - 363 WP_010890126 transcriptional regulator -
HTR84_RS00265 50537..50878 + 342 WP_000019167 single-stranded DNA-binding protein -

Host bacterium

ID   3772 GenBank   NZ_MH053445
Plasmid name   pICP-4GES Incompatibility group   IncP1
Plasmid size   50914 bp Coordinate of oriT [Strand]   20602..20700 [-]
Host baterium   Pseudomonas aeruginosa strain PA1280

Cargo genes

Drug resistance gene   blaPAU-1, blaGES-5
Virulence gene   -
Metal resistance gene   merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -