Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114490
Name   oriT_AT13|p3 in_silico
Organism   Agrobacterium leguminum strain AT13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP119975 (93691..93789 [-], 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_AT13|p3
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9282 GenBank   WP_011117146
Name   traI_PX860_RS27835_AT13|p3 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   10769 GenBank   WP_000694765
Name   t4cp2_PX860_RS27840_AT13|p3 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   10770 GenBank   WP_011114047
Name   t4cp2_PX860_RS28125_AT13|p3 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: 50330..61007

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PX860_RS28060 (PX860_28060) 45972..46481 - 510 Protein_45 DUF1116 domain-containing protein -
PX860_RS28065 (PX860_28065) 46672..47586 - 915 Protein_46 IS91-like element ISPps1 family transposase -
PX860_RS28070 (PX860_28070) 47587..48558 - 972 Protein_47 NAD(P)/FAD-dependent oxidoreductase -
PX860_RS28075 (PX860_28075) 48704..49033 + 330 Protein_48 DUF4158 domain-containing protein -
PX860_RS28080 (PX860_28080) 49076..49711 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
PX860_RS28085 (PX860_28085) 49725..50312 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
PX860_RS28090 (PX860_28090) 50330..52048 - 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
PX860_RS28095 (PX860_28095) 52059..52286 - 228 WP_011117181 entry exclusion lipoprotein TrbK -
PX860_RS28100 (PX860_28100) 52296..53060 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
PX860_RS28105 (PX860_28105) 53081..54502 - 1422 WP_011114050 TrbI/VirB10 family protein virB10
PX860_RS28110 (PX860_28110) 54507..54995 - 489 WP_006122479 conjugal transfer protein TrbH -
PX860_RS28115 (PX860_28115) 54998..55897 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
PX860_RS28120 (PX860_28120) 55915..56697 - 783 WP_006122481 conjugal transfer protein TrbF virB8
PX860_RS28125 (PX860_28125) 56694..59252 - 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
PX860_RS28130 (PX860_28130) 59249..59560 - 312 WP_001207961 conjugal transfer protein TrbD virB3
PX860_RS28135 (PX860_28135) 59564..60028 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
PX860_RS28140 (PX860_28140) 60045..61007 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
PX860_RS28145 (PX860_28145) 61317..61679 - 363 WP_010890126 transcriptional regulator -
PX860_RS28150 (PX860_28150) 61793..62134 + 342 WP_000019167 single-stranded DNA-binding protein -
PX860_RS28155 (PX860_28155) 62181..63401 + 1221 WP_011114072 plasmid replication initiator TrfA -
PX860_RS28160 (PX860_28160) 63797..65167 - 1371 WP_304984421 IS1182-like element ISPsp5 family transposase -

Host bacterium

ID   14925 GenBank   NZ_CP119975
Plasmid name   AT13|p3 Incompatibility group   IncP1
Plasmid size   96511 bp Coordinate of oriT [Strand]   93691..93789 [-]
Host baterium   Agrobacterium leguminum strain AT13

Cargo genes

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