Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107664
Name   oriT_pPH1JI in_silico
Organism   Agrobacterium fabrum strain EHA105
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP067036 (44890..44988 [+], 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_pPH1JI
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5153 GenBank   WP_011342947
Name   Relaxase_EML540_RS26685_pPH1JI 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   5392 GenBank   WP_011342945
Name   t4cp2_EML540_RS26535_pPH1JI 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.



ID   5393 GenBank   WP_000694765
Name   t4cp2_EML540_RS26680_pPH1JI 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 8446..19123

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EML540_RS26500 (EML540_26500) 4291..5295 + 1005 WP_000427623 IS110-like element IS4321 family transposase -
EML540_RS26505 (EML540_26505) 6052..7272 - 1221 WP_011114072 plasmid replication initiator TrfA -
EML540_RS26510 (EML540_26510) 7319..7660 - 342 WP_000019167 single-stranded DNA-binding protein -
EML540_RS26515 (EML540_26515) 7774..8136 + 363 WP_010890126 transcriptional regulator -
EML540_RS26520 (EML540_26520) 8446..9408 + 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
EML540_RS26525 (EML540_26525) 9425..9889 + 465 WP_011114046 conjugal transfer system pilin TrbC virB2
EML540_RS26530 (EML540_26530) 9893..10204 + 312 WP_001207961 conjugal transfer protein TrbD virB3
EML540_RS26535 (EML540_26535) 10201..12759 + 2559 WP_011342945 VirB4 family type IV secretion/conjugal transfer ATPase virb4
EML540_RS26540 (EML540_26540) 12756..13538 + 783 WP_006122481 conjugal transfer protein TrbF virB8
EML540_RS26545 (EML540_26545) 13556..14455 + 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
EML540_RS26550 (EML540_26550) 14458..14946 + 489 WP_006122479 conjugal transfer protein TrbH -
EML540_RS26555 (EML540_26555) 14951..16372 + 1422 WP_011114050 TrbI/VirB10 family protein virB10
EML540_RS26560 (EML540_26560) 16393..17157 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
EML540_RS26565 (EML540_26565) 17167..17394 + 228 WP_000644148 entry exclusion lipoprotein TrbK -
EML540_RS26570 (EML540_26570) 17405..19123 + 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
EML540_RS26575 (EML540_26575) 19141..19728 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
EML540_RS26580 (EML540_26580) 19742..20377 + 636 WP_011114052 transglycosylase SLT domain-containing protein -
EML540_RS26585 (EML540_26585) 20406..20672 + 267 WP_010890140 hypothetical protein -
EML540_RS26590 (EML540_26590) 20672..21370 + 699 WP_011114053 TraX family protein -
EML540_RS26595 (EML540_26595) 21386..21817 + 432 WP_001665065 OmpA family protein -
EML540_RS26600 (EML540_26600) 21972..22496 + 525 WP_010890143 hypothetical protein -
EML540_RS26605 (EML540_26605) 22743..23756 - 1014 WP_000845054 class 1 integron integrase IntI1 -

Host bacterium

ID   8099 GenBank   NZ_CP067036
Plasmid name   pPH1JI Incompatibility group   IncP1
Plasmid size   55971 bp Coordinate of oriT [Strand]   44890..44988 [+]
Host baterium   Agrobacterium fabrum strain EHA105

Cargo genes

Drug resistance gene   aac(3)-Ia, aadA2, cmlA1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -