Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100154
Name   oriT_pUO1 in_silico
Organism   Delftia acidovorans
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_005088 (56496..56868 [+], 373 nt)
oriT length   373 nt
IRs (inverted repeats)      IR1: 64..68, 72..76  (GCGCC..GGCGC)
  IR2: 89..107, 110..128  (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site      136..137
Conserved sequence flanking the
  nic site    		  CATCCTG|C
Note   _

  oriT sequence  


Download         Length: 373 nt

>oriT_pUO1
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Sota M et al. (2003) Structure of haloacetate-catabolic IncP-1beta plasmid pUO1 and genetic mobility of its residing haloacetate-catabolic transposon. J Bacteriol. 185(22):6741-5. [PMID:14594853]


Relaxase

ID   148 GenBank   NP_904299
Name   TraI_pUO1 insolico UniProt ID   Q76M03
Length   746 a.a. PDB ID   
Note   conjugal transfer relaxase TraI

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82068.74 Da        Isoelectric Point: 10.7900

>NP_904299.1 hypothetical protein pUO1_50 (plasmid) [Delftia acidovorans]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
LQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRITGGSEVLLPRDVPRHVEQQGTQ
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 Q76M03


Auxiliary protein

ID   214 GenBank   NP_904300
Name   TraH_pUO1 insolico UniProt ID   Q76M02
Length   130 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 13936.41 Da        Isoelectric Point: 3.9776

>NP_904300.1 hypothetical protein pUO1_51 (plasmid) [Delftia acidovorans]
MSEPKDQSIEDELDAALAALDSGPLPTSTLPEPQPSPEQATAGQPPAEATAPTPAFTPPPSTGSPTLDAL
EENRRPKASTVCEHCPNSVWFASPAEVKCYCRVMFLVTWSSKEPNQITHCDGEFLGQEQE

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q76M02

ID   215 GenBank   NP_904301
Name   TraJ_pUO1 insolico UniProt ID   Q76M01
Length   124 a.a. PDB ID   _
Note   conjugal transfer relaxosome component TraJ

  Auxiliary protein sequence


Download         Length: 124 a.a.        Molecular weight: 14206.27 Da        Isoelectric Point: 8.5329

>NP_904301.1 hypothetical protein pUO1_52 (plasmid) [Delftia acidovorans]
MENDEKEHGRRRRQHLRVPVFPEEKDEIEANAKRAGVSVARYLRDVGQGYQIKGVMDYQHVRELVRVNGD
LGRLGGLLKLWLTDDVRTLQFGEATILALLGRIEATQDEMSRIMKAVVQPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q76M01

ID   216 GenBank   NP_904302
Name   TraK_pUO1 insolico UniProt ID   Q76M00
Length   132 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 132 a.a.        Molecular weight: 14621.83 Da        Isoelectric Point: 9.9884

>NP_904302.1 hypothetical protein pUO1_53 (plasmid) [Delftia acidovorans]
MPKTYPEELAEWVKGREAKKPRQDKHVVAFLAVKSDVQAALDAGYAMKTIWEHMKETGRLRCRYETFTQH
VKRYIKAAPVASPPPPATPPDSQPKGAKPEPKAAPPASESKSEPPKIGGFTFDATPKKEDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure


Source ID Structure
AlphaFold DB Q76M00


T4CP

ID   148 GenBank   NP_904298
Name   TraG_pUO1 insolico UniProt ID   Q76M04
Length   637 a.a. PDB ID   _
Note   conjugal transfer coupling protein TraG

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 69897.09 Da        Isoelectric Point: 8.2993

>NP_904298.1 hypothetical protein pUO1_49 (plasmid) [Delftia acidovorans]
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


Source ID Structure
AlphaFold DB Q76M04


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 19324..30001

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXB85_RS00060 14849..15746 - 898 Protein_12 Tn3 family transposase -
HXB85_RS00065 15857..16138 - 282 WP_176451034 type II toxin-antitoxin system YafQ family toxin -
HXB85_RS00070 16125..16391 - 267 WP_013521177 type II toxin-antitoxin system RelB/DinJ family antitoxin -
HXB85_RS00075 (pUO1_10) 16930..18150 - 1221 WP_011114072 plasmid replication initiator TrfA -
HXB85_RS00080 (pUO1_11) 18197..18538 - 342 WP_000019167 single-stranded DNA-binding protein -
HXB85_RS00085 (pUO1_12) 18652..19014 + 363 WP_011137961 transcriptional regulator -
HXB85_RS00090 (pUO1_13) 19324..20286 + 963 WP_011137962 P-type conjugative transfer ATPase TrbB virB11
HXB85_RS00095 (pUO1_14) 20303..20767 + 465 WP_011114046 conjugal transfer system pilin TrbC virB2
HXB85_RS00100 (pUO1_15) 20771..21082 + 312 WP_001207961 conjugal transfer protein TrbD virB3
HXB85_RS00105 (pUO1_16) 21079..23637 + 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXB85_RS00110 (pUO1_17) 23634..24416 + 783 WP_006122481 conjugal transfer protein TrbF virB8
HXB85_RS00115 (pUO1_18) 24434..25333 + 900 WP_013521178 P-type conjugative transfer protein TrbG virB9
HXB85_RS00120 (pUO1_19) 25336..25824 + 489 WP_006122479 conjugal transfer protein TrbH -
HXB85_RS00125 (pUO1_20) 25829..27250 + 1422 WP_011114050 TrbI/VirB10 family protein virB10
HXB85_RS00130 (pUO1_21) 27271..28035 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
HXB85_RS00135 (pUO1_22) 28045..28272 + 228 WP_000644148 entry exclusion lipoprotein TrbK -
HXB85_RS00140 (pUO1_23) 28283..30001 + 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
HXB85_RS00145 (pUO1_24) 30019..30606 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
HXB85_RS00150 (pUO1_25) 30620..31255 + 636 WP_011114052 transglycosylase SLT domain-containing protein -
HXB85_RS00155 (pUO1_26) 31284..31550 + 267 WP_010890140 hypothetical protein -
HXB85_RS00160 (pUO1_27) 31550..32239 + 690 Protein_32 TraX family protein -
HXB85_RS00165 (pUO1_28) 32382..34064 + 1683 WP_011137965 DDE-type integrase/transposase/recombinase -
HXB85_RS00170 (pUO1_29) 34067..34975 + 909 WP_011137966 TniB family NTP-binding protein -

Host bacterium

ID   148 GenBank   NC_005088
Plasmid name   pUO1 Incompatibility group   IncP1
Plasmid size   67066 bp Coordinate of oriT [Strand]   56496..56868 [+]
Host baterium   Delftia acidovorans

Cargo genes

Drug resistance gene   _
Virulence gene   _
Metal resistance gene   merE, merD, merA, merF, merP, merT, merR2
Degradation gene   dehH2, dehH1
Symbiosis gene   -
Anti-CRISPR   -