Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118399
Name   oriT_2,4-D|p24D-65 in_silico
Organism   Pseudomonas sp. 24-D
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAUHUI010000035 (40627..40725 [+], 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_2,4-D|p24D-65
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11687 GenBank   WP_011114057
Name   Relaxase_QYE47_RS20970_2,4-D|p24D-65 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   13684 GenBank   WP_011114047
Name   t4cp2_QYE47_RS20870_2,4-D|p24D-65 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.



ID   13685 GenBank   WP_000694765
Name   t4cp2_QYE47_RS20965_2,4-D|p24D-65 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: 13080..23757

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QYE47_RS20825 (QYE47_20825) 9429..9704 - 276 WP_003131987 mercury resistance system periplasmic binding protein MerP -
QYE47_RS20830 (QYE47_20830) 9717..10067 - 351 WP_003131974 mercuric ion transporter MerT -
QYE47_RS20835 (QYE47_20835) 10139..10573 + 435 WP_003131969 mercury resistance transcriptional regulator MerR -
QYE47_RS20840 (QYE47_20840) 10686..11906 - 1221 WP_011114072 plasmid replication initiator TrfA -
QYE47_RS20845 (QYE47_20845) 11953..12294 - 342 WP_000019167 single-stranded DNA-binding protein -
QYE47_RS20850 (QYE47_20850) 12408..12770 + 363 WP_011114045 transcriptional regulator -
QYE47_RS20855 (QYE47_20855) 13080..14042 + 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
QYE47_RS20860 (QYE47_20860) 14059..14523 + 465 WP_011114046 conjugal transfer system pilin TrbC virB2
QYE47_RS20865 (QYE47_20865) 14527..14838 + 312 WP_001207961 conjugal transfer protein TrbD virB3
QYE47_RS20870 (QYE47_20870) 14835..17393 + 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
QYE47_RS20875 (QYE47_20875) 17390..18172 + 783 WP_011114048 conjugal transfer protein TrbF virB8
QYE47_RS20880 (QYE47_20880) 18190..19089 + 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
QYE47_RS20885 (QYE47_20885) 19092..19580 + 489 WP_006122479 conjugal transfer protein TrbH -
QYE47_RS20890 (QYE47_20890) 19585..21006 + 1422 WP_011114050 TrbI/VirB10 family protein virB10
QYE47_RS20895 (QYE47_20895) 21027..21791 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
QYE47_RS20900 (QYE47_20900) 21801..22028 + 228 WP_000644148 entry exclusion lipoprotein TrbK -
QYE47_RS20905 (QYE47_20905) 22039..23757 + 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
QYE47_RS20910 (QYE47_20910) 23775..24362 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
QYE47_RS20915 (QYE47_20915) 24376..25011 + 636 WP_011114052 transglycosylase SLT domain-containing protein -
QYE47_RS20920 (QYE47_20920) 25040..25306 + 267 WP_010890140 hypothetical protein -
QYE47_RS20925 (QYE47_20925) 25306..26004 + 699 WP_011114053 TraX family protein -
QYE47_RS20930 (QYE47_20930) 26020..26451 + 432 WP_001665065 OmpA family protein -
QYE47_RS20935 (QYE47_20935) 26606..27280 + 675 WP_011178411 DNA methylase -
QYE47_RS20940 (QYE47_20940) 27282..28133 - 852 WP_011296189 recombinase family protein -

Host bacterium

ID   18832 GenBank   NZ_JAUHUI010000035
Plasmid name   2,4-D|p24D-65 Incompatibility group   IncP1
Plasmid size   65919 bp Coordinate of oriT [Strand]   40627..40725 [+]
Host baterium   Pseudomonas sp. 24-D

Cargo genes

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