Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114426
Name   oriT_pDCB2 in_silico
Organism   Diaphorobacter sp. JS3051
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP065408 (25793..25891 [+], 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_pDCB2
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9246 GenBank   WP_011114057
Name   traI_I3K84_RS21370_pDCB2 insolico UniProt ID   A0A4P7LSA6
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_011114057.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Bacteria]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
LQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
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 A0A4P7LSA6


T4CP

ID   10713 GenBank   WP_011342945
Name   t4cp2_I3K84_RS21270_pDCB2 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: 93952.10 Da        Isoelectric Point: 6.3901

>WP_011342945.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Pseudomonadota]
MIEAIAIAIAVLGAVLLLILFARIRAVDAELKLKKHRAKDAGLADLLNYAAAVDDGVIVGKNGSFMAAWL
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.



ID   10714 GenBank   WP_000694765
Name   t4cp2_I3K84_RS21365_pDCB2 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: 69897.09 Da        Isoelectric Point: 8.2993

>WP_000694765.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Bacteria]
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1..8923

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
I3K84_RS21270 (I3K84_21265) 1..2559 + 2559 WP_011342945 VirB4 family type IV secretion/conjugal transfer ATPase virb4
I3K84_RS21275 (I3K84_21270) 2556..3338 + 783 WP_011114048 conjugal transfer protein TrbF virB8
I3K84_RS21280 (I3K84_21275) 3356..4255 + 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
I3K84_RS21285 (I3K84_21280) 4258..4746 + 489 WP_006122479 conjugal transfer protein TrbH -
I3K84_RS21290 (I3K84_21285) 4751..6172 + 1422 WP_011114050 TrbI/VirB10 family protein virB10
I3K84_RS21295 (I3K84_21290) 6193..6957 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
I3K84_RS21300 (I3K84_21295) 6967..7194 + 228 WP_000644148 entry exclusion lipoprotein TrbK -
I3K84_RS21305 (I3K84_21300) 7205..8923 + 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
I3K84_RS21310 (I3K84_21305) 8941..9528 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
I3K84_RS21315 (I3K84_21310) 9542..10177 + 636 WP_011114052 transglycosylase SLT domain-containing protein -
I3K84_RS21320 (I3K84_21315) 10206..10472 + 267 WP_010890140 hypothetical protein -
I3K84_RS21325 (I3K84_21320) 10472..11170 + 699 WP_011114053 TraX family protein -
I3K84_RS21330 (I3K84_21325) 11186..11617 + 432 WP_001665065 OmpA family protein -
I3K84_RS21335 (I3K84_21330) 11772..12446 + 675 WP_011178411 DNA methylase -
I3K84_RS21340 (I3K84_21335) 12448..13299 - 852 WP_011296189 recombinase family protein -

Host bacterium

ID   14861 GenBank   NZ_CP065408
Plasmid name   pDCB2 Incompatibility group   IncP1
Plasmid size   77623 bp Coordinate of oriT [Strand]   25793..25891 [+]
Host baterium   Diaphorobacter sp. JS3051

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF24