Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121005
Name   oriT_pKAM339_2 in_silico
Organism   Aeromonas caviae strain KAM339
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP024942 (21847..21945 [-], 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_pKAM339_2
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13254 GenBank   WP_011342947
Name   traI_LDN97_RS23340_pKAM339_2 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   15533 GenBank   WP_000694765
Name   t4cp2_LDN97_RS23345_pKAM339_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: 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   15534 GenBank   WP_011342945
Name   t4cp2_LDN97_RS23550_pKAM339_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: 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: 53306..63983

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDN97_RS23475 48817..48882 - 66 Protein_54 hypothetical protein -
LDN97_RS23480 (KAM339_045500) 48930..49781 + 852 WP_223955011 recombinase family protein -
LDN97_RS23485 (KAM339_045510) 49783..50457 - 675 WP_011178411 DNA methylase -
LDN97_RS23490 (KAM339_045520) 50612..51043 - 432 WP_001665065 OmpA family protein -
LDN97_RS23495 (KAM339_045530) 51059..51757 - 699 WP_011114053 TraX family protein -
LDN97_RS23500 (KAM339_045540) 51757..52023 - 267 WP_010890140 hypothetical protein -
LDN97_RS23505 (KAM339_045550) 52052..52687 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
LDN97_RS23510 (KAM339_045560) 52701..53288 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
LDN97_RS23515 (KAM339_045570) 53306..55024 - 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
LDN97_RS23520 (KAM339_045580) 55035..55262 - 228 WP_000644148 entry exclusion lipoprotein TrbK -
LDN97_RS23525 (KAM339_045590) 55272..56036 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
LDN97_RS23530 (KAM339_045600) 56057..57478 - 1422 WP_223955012 TrbI/VirB10 family protein virB10
LDN97_RS23535 (KAM339_045610) 57483..57971 - 489 WP_006122479 conjugal transfer protein TrbH -
LDN97_RS23540 (KAM339_045620) 57974..58873 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
LDN97_RS23545 (KAM339_045630) 58891..59673 - 783 WP_006122481 conjugal transfer protein TrbF virB8
LDN97_RS23550 (KAM339_045640) 59670..62228 - 2559 WP_011342945 VirB4 family type IV secretion/conjugal transfer ATPase virb4
LDN97_RS23555 (KAM339_045650) 62225..62536 - 312 WP_001207961 conjugal transfer protein TrbD virB3
LDN97_RS23560 (KAM339_045660) 62540..63004 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
LDN97_RS23565 (KAM339_045670) 63021..63983 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
LDN97_RS23570 (KAM339_045680) 64293..64655 - 363 WP_010890126 transcriptional regulator -
LDN97_RS23575 (KAM339_045690) 64769..65110 + 342 WP_000019167 single-stranded DNA-binding protein -

Host bacterium

ID   21434 GenBank   NZ_AP024942
Plasmid name   pKAM339_2 Incompatibility group   IncP1
Plasmid size   65156 bp Coordinate of oriT [Strand]   21847..21945 [-]
Host baterium   Aeromonas caviae strain KAM339

Cargo genes

Drug resistance gene   fosE, blaIMP-1, sul1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -