Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102258
Name   oriT_YKJ|unnamed in_silico
Organism   Pseudomonas oleovorans strain YKJ
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_PTLV01000205 (12485..12583 [+], 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_YKJ|unnamed
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1738 GenBank   WP_011342947
Name   Relaxase_C5L43_RS20885_YKJ|unnamed insolico UniProt ID   A0A077KSK4
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_011342947.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
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 A0A077KSK4


T4CP

ID   1321 GenBank   WP_000694765
Name   t4cp2_C5L43_RS20880_YKJ|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: 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   1322 GenBank   WP_011342945
Name   t4cp2_C5L43_RS21050_YKJ|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: 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 35842..46519

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C5L43_RS21015 (C5L43_21005) 30884..32440 + 1557 WP_104730185 IS91 family transposase -
C5L43_RS21020 (C5L43_21010) 33448..34668 - 1221 WP_011114072 plasmid replication initiator TrfA -
C5L43_RS21025 (C5L43_21015) 34715..35056 - 342 WP_000019167 single-stranded DNA-binding protein -
C5L43_RS21030 (C5L43_21020) 35170..35532 + 363 WP_010890126 transcriptional regulator -
C5L43_RS21035 (C5L43_21025) 35842..36804 + 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
C5L43_RS21040 (C5L43_21030) 36821..37285 + 465 WP_011114046 conjugal transfer system pilin TrbC virB2
C5L43_RS21045 (C5L43_21035) 37289..37600 + 312 WP_001207961 conjugal transfer protein TrbD virB3
C5L43_RS21050 (C5L43_21040) 37597..40155 + 2559 WP_011342945 VirB4 family type IV secretion/conjugal transfer ATPase virb4
C5L43_RS21055 (C5L43_21045) 40152..40934 + 783 WP_006122481 conjugal transfer protein TrbF virB8
C5L43_RS21060 (C5L43_21050) 40952..41851 + 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
C5L43_RS21065 (C5L43_21055) 41854..42342 + 489 WP_006122479 conjugal transfer protein TrbH -
C5L43_RS21070 (C5L43_21060) 42347..43768 + 1422 WP_011114050 TrbI/VirB10 family protein virB10
C5L43_RS21075 (C5L43_21065) 43789..44553 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
C5L43_RS21080 (C5L43_21070) 44563..44790 + 228 WP_000644148 entry exclusion lipoprotein TrbK -
C5L43_RS21085 (C5L43_21075) 44801..46519 + 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
C5L43_RS21090 (C5L43_21080) 46537..47124 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
C5L43_RS21095 (C5L43_21085) 47138..47773 + 636 WP_011114052 transglycosylase SLT domain-containing protein -
C5L43_RS21100 (C5L43_21090) 47802..48068 + 267 WP_010890140 hypothetical protein -
C5L43_RS21105 (C5L43_21095) 48068..48766 + 699 WP_011114053 TraX family protein -
C5L43_RS21110 (C5L43_21100) 48782..49213 + 432 WP_001665065 OmpA family protein -
C5L43_RS21115 (C5L43_21105) 49368..50042 + 675 WP_011178411 DNA methylase -
C5L43_RS21120 (C5L43_21110) 50044..50871 - 828 WP_012805980 recombinase family protein -

Host bacterium

ID   2702 GenBank   NZ_PTLV01000205
Plasmid name   YKJ|unnamed Incompatibility group   IncP1
Plasmid size   50932 bp Coordinate of oriT [Strand]   12485..12583 [+]
Host baterium   Pseudomonas oleovorans strain YKJ

Cargo genes

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