Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121215
Name   oriT_pLM159.2 in_silico
Organism   Xanthomonas vesicatoria strain LM159
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP018471 (45117..45215 [-], 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_pLM159.2
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13398 GenBank   WP_058664035
Name   traI_BI313_RS23735_pLM159.2 insolico UniProt ID   _
Length   746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 81930.51 Da        Isoelectric Point: 10.7900

>WP_058664035.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGQVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTTLERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARGQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRTNKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGSADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRAGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAASVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVSRHVEQQGTQ
PDHALRRGISRPGAGVGPTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALSFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(422-508)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)


  Protein structure



No available structure.




T4CP

ID   15701 GenBank   WP_074052969
Name   t4cp2_BI313_RS23445_pLM159.2 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: 93902.02 Da        Isoelectric Point: 6.3901

>WP_074052969.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Gammaproteobacteria]
MIEAIAIAIAVLGAVLLLILFARIRAVDAELKLKKHRAKDAGLADLLNYAAVVDDGVIVGKNGSFMAAWL
YKGDDNASSTEEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPNYSERGVSSFPDSVSSAIDEERRRLF
EGLGAMFEGYFVLTVTWFPPVLAQRKFVELMFDDDAVAPDHTARTTGLIAQFKREITSLESRLSSAVKLT
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   15702 GenBank   WP_074052986
Name   t4cp2_BI313_RS23740_pLM159.2 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: 69925.14 Da        Isoelectric Point: 8.2993

>WP_074052986.1 type IV secretory system conjugative DNA transfer family protein [Xanthomonas vesicatoria]
MKIKMNNAVGPQVRSAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDEGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRVVAQAET
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: 4024..13731

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BI313_RS23420 (BI313_23320) 30..2915 - 2886 WP_001138082 Tn3 family transposase -
BI313_RS23425 (BI313_23325) 3041..3142 + 102 Protein_1 recombinase family protein -
BI313_RS23430 (BI313_23330) 3197..3961 - 765 WP_001389365 IS6-like element IS6100 family transposase -
BI313_RS23435 (BI313_23335) 4024..4488 + 465 WP_074052968 conjugal transfer system pilin TrbC virB2
BI313_RS23440 (BI313_23340) 4492..4803 + 312 WP_001207961 conjugal transfer protein TrbD virB3
BI313_RS23445 (BI313_23345) 4800..7358 + 2559 WP_074052969 VirB4 family type IV secretion/conjugal transfer ATPase virb4
BI313_RS23450 (BI313_23350) 7355..8137 + 783 WP_011798705 conjugal transfer protein TrbF virB8
BI313_RS23455 (BI313_23355) 8155..9054 + 900 WP_000753228 P-type conjugative transfer protein TrbG virB9
BI313_RS23460 (BI313_23360) 9057..9545 + 489 WP_074052970 conjugal transfer protein TrbH -
BI313_RS23465 (BI313_23365) 9550..10968 + 1419 WP_011798703 TrbI/VirB10 family protein virB10
BI313_RS23470 (BI313_23370) 10986..11750 + 765 WP_011798702 P-type conjugative transfer protein TrbJ virB5
BI313_RS23475 (BI313_23375) 11760..11987 + 228 WP_011798701 entry exclusion lipoprotein TrbK -
BI313_RS23480 (BI313_23380) 11998..13731 + 1734 WP_011798700 P-type conjugative transfer protein TrbL virB6
BI313_RS23485 (BI313_23385) 13748..14332 + 585 WP_011798699 TrbM/KikA/MpfK family conjugal transfer protein -
BI313_RS23490 (BI313_23390) 14346..14990 + 645 WP_031942725 transglycosylase SLT domain-containing protein -
BI313_RS23495 (BI313_23395) 14987..15253 + 267 WP_074052971 hypothetical protein -
BI313_RS23500 (BI313_23400) 15330..15965 + 636 WP_229006823 TraX family protein -
BI313_RS23505 (BI313_23405) 15981..16412 + 432 WP_074052990 OmpA family protein -
BI313_RS23510 (BI313_23410) 16569..17243 + 675 WP_074052972 SAM-dependent methyltransferase -
BI313_RS23515 (BI313_23415) 17245..18096 - 852 WP_231117434 recombinase family protein -

Host bacterium

ID   21643 GenBank   NZ_CP018471
Plasmid name   pLM159.2 Incompatibility group   IncP1
Plasmid size   62784 bp Coordinate of oriT [Strand]   45117..45215 [-]
Host baterium   Xanthomonas vesicatoria strain LM159

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -