Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   109192
Name   oriT_pBYT5-3 in_silico
Organism   Pseudomonas sp. BYT-5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP097492 (10235..10333 [-], 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_pBYT5-3
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   6166 GenBank   WP_011117146
Name   Relaxase_M6G63_RS27845_pBYT5-3 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   6720 GenBank   WP_000694765
Name   t4cp2_M6G63_RS27850_pBYT5-3 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   6721 GenBank   WP_011114047
Name   t4cp2_M6G63_RS28025_pBYT5-3 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: 41003..51680

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
M6G63_RS27950 (M6G63_27950) 36219..36434 - 216 WP_021561443 antitoxin MazE family protein -
M6G63_RS27955 (M6G63_27955) 36723..37478 + 756 WP_232476757 recombinase family protein -
M6G63_RS27960 (M6G63_27960) 37480..38154 - 675 WP_011178411 DNA methylase -
M6G63_RS27965 (M6G63_27965) 38309..38740 - 432 WP_001665065 OmpA family protein -
M6G63_RS27970 (M6G63_27970) 38756..39454 - 699 WP_011114053 TraX family protein -
M6G63_RS27975 (M6G63_27975) 39454..39720 - 267 WP_010890140 hypothetical protein -
M6G63_RS27980 (M6G63_27980) 39749..40384 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
M6G63_RS27985 (M6G63_27985) 40398..40985 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
M6G63_RS27990 (M6G63_27990) 41003..42721 - 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
M6G63_RS27995 (M6G63_27995) 42732..42959 - 228 WP_000644148 entry exclusion lipoprotein TrbK -
M6G63_RS28000 (M6G63_28000) 42969..43733 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
M6G63_RS28005 (M6G63_28005) 43754..45175 - 1422 WP_011114050 TrbI/VirB10 family protein virB10
M6G63_RS28010 (M6G63_28010) 45180..45668 - 489 WP_006122479 conjugal transfer protein TrbH -
M6G63_RS28015 (M6G63_28015) 45671..46570 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
M6G63_RS28020 (M6G63_28020) 46588..47370 - 783 WP_006122481 conjugal transfer protein TrbF virB8
M6G63_RS28025 (M6G63_28025) 47367..49925 - 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
M6G63_RS28030 (M6G63_28030) 49922..50233 - 312 WP_001207961 conjugal transfer protein TrbD virB3
M6G63_RS28035 (M6G63_28035) 50237..50701 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
M6G63_RS28040 (M6G63_28040) 50718..51680 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
M6G63_RS28045 (M6G63_28045) 51990..52352 - 363 WP_010890126 transcriptional regulator -
M6G63_RS28050 (M6G63_28050) 52466..52807 + 342 WP_000019167 single-stranded DNA-binding protein -
M6G63_RS28055 (M6G63_28055) 52854..54074 + 1221 WP_011114072 plasmid replication initiator TrfA -
M6G63_RS28060 (M6G63_28060) 55397..55711 - 315 WP_011117139 type II toxin-antitoxin system RelE/ParE family toxin -
M6G63_RS28065 (M6G63_28065) 55708..55977 - 270 WP_001260984 type II toxin-antitoxin system ParD family antitoxin -

Host bacterium

ID   9627 GenBank   NZ_CP097492
Plasmid name   pBYT5-3 Incompatibility group   IncP1
Plasmid size   56145 bp Coordinate of oriT [Strand]   10235..10333 [-]
Host baterium   Pseudomonas sp. BYT-5

Cargo genes

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