Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104977
Name   oriT_PPO 9019|unnamed in_silico
Organism   Dickeya solani strain PPO 9019
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM003649 (29995..30093 [-], 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_PPO 9019|unnamed
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3496 GenBank   WP_011117146
Name   Relaxase_RS73_RS00210_PPO 9019|unnamed insolico UniProt ID   Q937B9
Length   746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82120.82 Da        Isoelectric Point: 10.8213

>WP_011117146.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWVKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQNLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHRRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(422-508)


  Protein structure


Source ID Structure
AlphaFold DB Q937B9


T4CP

ID   3446 GenBank   WP_011114047
Name   t4cp2_RS73_RS00080_PPO 9019|unnamed 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   3447 GenBank   WP_011655356
Name   t4cp2_RS73_RS00215_PPO 9019|unnamed 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: 69870.06 Da        Isoelectric Point: 8.2993

>WP_011655356.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKASEYLHGSARWAEKKDIQAAGLLPRERNV
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: 4618..15295

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RS73_RS00010 806..1186 - 381 WP_011655359 hypothetical protein -
RS73_RS00015 1272..1769 - 498 WP_011655360 SAM-dependent methyltransferase -
RS73_RS00020 1924..2355 - 432 WP_001665065 OmpA family protein -
RS73_RS00025 2371..3069 - 699 WP_011114053 TraX family protein -
RS73_RS00030 3069..3335 - 267 WP_010890140 hypothetical protein -
RS73_RS00035 3364..3999 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
RS73_RS00040 4013..4600 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
RS73_RS00045 4618..6336 - 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
RS73_RS00050 6347..6574 - 228 WP_000644148 entry exclusion lipoprotein TrbK -
RS73_RS00055 6584..7348 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
RS73_RS00060 7369..8790 - 1422 WP_011114050 TrbI/VirB10 family protein virB10
RS73_RS00065 8795..9283 - 489 WP_006122479 conjugal transfer protein TrbH -
RS73_RS00070 9286..10185 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
RS73_RS00075 10203..10985 - 783 WP_006122481 conjugal transfer protein TrbF virB8
RS73_RS00080 10982..13540 - 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
RS73_RS00085 13537..13848 - 312 WP_001207961 conjugal transfer protein TrbD virB3
RS73_RS00090 13852..14316 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
RS73_RS00095 14333..15295 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
RS73_RS00100 15605..15967 - 363 WP_010890126 transcriptional regulator -
RS73_RS00105 16081..16422 + 342 WP_000019167 single-stranded DNA-binding protein -
RS73_RS00110 16469..17689 + 1221 WP_011114072 plasmid replication initiator TrfA -
RS73_RS00115 19012..19326 - 315 WP_011117139 type II toxin-antitoxin system RelE/ParE family toxin -
RS73_RS00120 19323..19592 - 270 WP_001260984 type II toxin-antitoxin system ParD family antitoxin -
RS73_RS00125 19761..20189 + 429 WP_001095942 antirestriction protein -

Host bacterium

ID   5415 GenBank   NZ_CM003649
Plasmid name   PPO 9019|unnamed Incompatibility group   IncP1
Plasmid size   43581 bp Coordinate of oriT [Strand]   29995..30093 [-]
Host baterium   Dickeya solani strain PPO 9019

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -