Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111152
Name   oriT_EGD-AKN5|unnamed in_silico
Organism   Pseudomonas sp. EGD-AKN5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KP289281 (11959..12057 [-], 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_EGD-AKN5|unnamed
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7300 GenBank   WP_011117146
Name   traI_HTG53_RS00100_EGD-AKN5|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   8320 GenBank   WP_000694765
Name   t4cp2_HTG53_RS00105_EGD-AKN5|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   8321 GenBank   WP_011114047
Name   t4cp2_HTG53_RS00425_EGD-AKN5|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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 77534..88211

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTG53_RS00365 72897..74444 - 1548 WP_008328818 IS91-like element ISPps1 family transposase -
HTG53_RS00370 74553..75762 - 1210 Protein_75 NAD(P)/FAD-dependent oxidoreductase -
HTG53_RS00375 75908..76237 + 330 Protein_76 DUF4158 domain-containing protein -
HTG53_RS00380 76280..76915 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
HTG53_RS00385 76929..77516 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
HTG53_RS00390 77534..79252 - 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
HTG53_RS00395 79263..79490 - 228 WP_011117181 entry exclusion lipoprotein TrbK -
HTG53_RS00400 79500..80264 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
HTG53_RS00405 80285..81706 - 1422 WP_011114050 TrbI/VirB10 family protein virB10
HTG53_RS00410 81711..82199 - 489 WP_006122479 conjugal transfer protein TrbH -
HTG53_RS00415 82202..83101 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
HTG53_RS00420 83119..83901 - 783 WP_011114048 conjugal transfer protein TrbF virB8
HTG53_RS00425 83898..86456 - 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTG53_RS00430 86453..86764 - 312 WP_001207961 conjugal transfer protein TrbD virB3
HTG53_RS00435 86768..87232 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
HTG53_RS00440 87249..88211 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
HTG53_RS00445 88521..88883 - 363 WP_011114045 transcriptional regulator -
HTG53_RS00450 88997..89338 + 342 WP_000019167 single-stranded DNA-binding protein -
HTG53_RS00455 89497..90399 + 903 WP_256675734 plasmid replication initiator TrfA -
HTG53_RS00460 90795..92165 - 1371 WP_011117183 IS1182-like element ISPsp5 family transposase -

Host bacterium

ID   11587 GenBank   NZ_KP289281
Plasmid name   EGD-AKN5|unnamed Incompatibility group   IncP1
Plasmid size   108845 bp Coordinate of oriT [Strand]   11959..12057 [-]
Host baterium   Pseudomonas sp. EGD-AKN5

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   merE, merD, merA, merF, merP, merT, merR2
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -