Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105945
Name   oriT_pECC33-49 in_silico
Organism   Enterobacter hormaechei subsp. hormaechei strain ECC33
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP098487 (12235..12333 [+], 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_pECC33-49
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4008 GenBank   WP_011342947
Name   Relaxase_NDJ97_RS22580_pECC33-49 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   4014 GenBank   WP_019373230
Name   t4cp2_NDJ97_RS22575_pECC33-49 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: 69925.10 Da        Isoelectric Point: 8.2999

>WP_019373230.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVARVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
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   4015 GenBank   WP_011114047
Name   t4cp2_NDJ97_RS22745_pECC33-49 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: 30910..41587

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NDJ97_RS22700 (NDJ97_22695) 27286..27651 + 366 WP_185812492 mercury resistance co-regulator MerD -
NDJ97_RS22705 (NDJ97_22700) 27648..27884 + 237 WP_003132004 broad-spectrum mercury transporter MerE -
NDJ97_RS22710 (NDJ97_22705) 27881..28009 + 129 Protein_31 EAL domain-containing protein -
NDJ97_RS22715 (NDJ97_22710) 28516..29736 - 1221 WP_011114072 plasmid replication initiator TrfA -
NDJ97_RS22720 (NDJ97_22715) 29783..30124 - 342 WP_000019167 single-stranded DNA-binding protein -
NDJ97_RS22725 (NDJ97_22720) 30238..30600 + 363 WP_010890126 transcriptional regulator -
NDJ97_RS22730 (NDJ97_22725) 30910..31872 + 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
NDJ97_RS22735 (NDJ97_22730) 31889..32353 + 465 WP_011114046 conjugal transfer system pilin TrbC virB2
NDJ97_RS22740 (NDJ97_22735) 32357..32668 + 312 WP_001207961 conjugal transfer protein TrbD virB3
NDJ97_RS22745 (NDJ97_22740) 32665..35223 + 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
NDJ97_RS22750 (NDJ97_22745) 35220..36002 + 783 WP_006122481 conjugal transfer protein TrbF virB8
NDJ97_RS22755 (NDJ97_22750) 36020..36919 + 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
NDJ97_RS22760 (NDJ97_22755) 36922..37410 + 489 WP_006122479 conjugal transfer protein TrbH -
NDJ97_RS22765 (NDJ97_22760) 37415..38836 + 1422 WP_172693339 TrbI/VirB10 family protein virB10
NDJ97_RS22770 (NDJ97_22765) 38857..39621 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
NDJ97_RS22775 (NDJ97_22770) 39631..39858 + 228 WP_000644148 entry exclusion lipoprotein TrbK -
NDJ97_RS22780 (NDJ97_22775) 39869..41587 + 1719 WP_027814021 P-type conjugative transfer protein TrbL virB6
NDJ97_RS22785 (NDJ97_22780) 41605..42192 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
NDJ97_RS22790 (NDJ97_22785) 42206..42841 + 636 WP_011114052 transglycosylase SLT domain-containing protein -
NDJ97_RS22795 (NDJ97_22790) 42870..43136 + 267 WP_010890140 hypothetical protein -
NDJ97_RS22800 (NDJ97_22795) 43136..43834 + 699 WP_011114053 TraX family protein -
NDJ97_RS22805 (NDJ97_22800) 43850..44281 + 432 WP_001665065 OmpA family protein -
NDJ97_RS22810 (NDJ97_22805) 44436..45110 + 675 WP_011178411 DNA methylase -
NDJ97_RS22815 (NDJ97_22810) 45112..45963 - 852 WP_011296189 recombinase family protein -
NDJ97_RS22820 (NDJ97_22815) 46006..46077 + 72 Protein_53 EAL domain-containing protein -
NDJ97_RS22825 (NDJ97_22820) 46152..46580 + 429 Protein_54 helix-turn-helix domain-containing protein -

Host bacterium

ID   6382 GenBank   NZ_CP098487
Plasmid name   pECC33-49 Incompatibility group   IncP1
Plasmid size   49381 bp Coordinate of oriT [Strand]   12235..12333 [+]
Host baterium   Enterobacter hormaechei subsp. hormaechei strain ECC33

Cargo genes

Drug resistance gene   blaIMP-1
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -