Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116785
Name   oriT_pADPe in_silico
Organism   Pseudomonas sp. ADPe
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP062123 (11853..11951 [-], 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_pADPe
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10709 GenBank   WP_011117146
Name   traI_IG194_RS32400_pADPe 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   12506 GenBank   WP_000694765
Name   t4cp2_IG194_RS32405_pADPe 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.



ID   12507 GenBank   WP_011114047
Name   t4cp2_IG194_RS32515_pADPe 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: 31066..41743

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IG194_RS32445 (IG194_32465) 26209..26658 + 450 WP_040435306 nucleoside deaminase -
IG194_RS32450 (IG194_32470) 26920..27300 + 381 WP_064987548 ring-opening amidohydrolase -
IG194_RS32455 (IG194_32475) 27408..28322 - 915 Protein_30 IS91-like element ISPps1 family transposase -
IG194_RS32460 (IG194_32480) 28323..29294 - 972 Protein_31 NAD(P)/FAD-dependent oxidoreductase -
IG194_RS32465 (IG194_32485) 29440..29769 + 330 Protein_32 DUF4158 domain-containing protein -
IG194_RS32470 (IG194_32490) 29812..30447 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
IG194_RS32475 (IG194_32495) 30461..31048 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
IG194_RS32480 (IG194_32500) 31066..32784 - 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
IG194_RS32485 (IG194_32505) 32795..33022 - 228 WP_011117181 entry exclusion lipoprotein TrbK -
IG194_RS32490 (IG194_32510) 33032..33796 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
IG194_RS32495 (IG194_32515) 33817..35238 - 1422 WP_011114050 TrbI/VirB10 family protein virB10
IG194_RS32500 (IG194_32520) 35243..35731 - 489 WP_006122479 conjugal transfer protein TrbH -
IG194_RS32505 (IG194_32525) 35734..36633 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
IG194_RS32510 (IG194_32530) 36651..37433 - 783 WP_011114048 conjugal transfer protein TrbF virB8
IG194_RS32515 (IG194_32535) 37430..39988 - 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
IG194_RS32520 (IG194_32540) 39985..40296 - 312 WP_001207961 conjugal transfer protein TrbD virB3
IG194_RS32525 (IG194_32545) 40300..40764 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
IG194_RS32530 (IG194_32550) 40781..41743 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
IG194_RS32535 (IG194_32555) 42053..42415 - 363 WP_011114045 transcriptional regulator -
IG194_RS32540 (IG194_32560) 42529..42870 + 342 WP_000019167 single-stranded DNA-binding protein -
IG194_RS32545 (IG194_32565) 42917..44137 + 1221 WP_011114072 plasmid replication initiator TrfA -
IG194_RS32550 (IG194_32570) 44533..45903 - 1371 WP_011117183 IS1182-like element ISPsp5 family transposase -

Host bacterium

ID   17218 GenBank   NZ_CP062123
Plasmid name   pADPe Incompatibility group   IncP1
Plasmid size   62583 bp Coordinate of oriT [Strand]   11853..11951 [-]
Host baterium   Pseudomonas sp. ADPe

Cargo genes

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