Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121494
Name   oriT_RA8|4 in_silico
Organism   Variovorax sp. RA8
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LR594665 (6794..6888 [-], 95 nt)
oriT length   95 nt
IRs (inverted repeats)      26..32, 37..43  (TAACCGG..CCGGTTA)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  TCCTGCCCGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 95 nt

>oriT_RA8|4
CGAATAAGGGGATAGTGAAGATAGATAACCGGCTTTCCGGTTAGCTAACTTCACCTATCCTGCCCGCCTTTCGGCGGTATGAACACCAAGGAAAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13550 GenBank   WP_015063533
Name   traI_E5P3_RS35355_RA8|4 insolico UniProt ID   K4IYE5
Length   730 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 730 a.a.        Molecular weight: 80015.48 Da        Isoelectric Point: 10.3609

>WP_015063533.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Burkholderiales]
MIAKHVSMKTVQKSDFAGLVKYITDEQAKNERVGYVAVTNCHTDRPEVAITEVLNTQAQNTRSGADKTYH
LIVSFRPGEQPDDATLKAIEARICEGLGFGEHQRVSAVHHDTDNLHIHIAINKIHPTRYTILEPFNAYHT
LGQLCEKLEREYGLERDNHQGNKLVSEGRAQDMERHAGVESLQGWVKRECAADMQAAQSWEALHQVMRDN
GLELRERGNGFVIQAADGLAVKASSIGREFSKAKLEERLGTFEPSAEHLERAAQKPRKQYDKKPVRSRVN
TVELHAKYKADQLTISGSRTAEWEKARAKKDRLIEAAKRSGRLKRSTIKLISGAGVGKKLMYSATSKTMK
SEIEKINKQYLKERQEIHEKYQRRAWADWLRAKAAEGDQEALGALRARDAAQGLKGNTVAGTGPLRPQAA
AAEQDSVTKKGTIIYRVGPTAVRDDGDRLKVSRGADQDGMQAALRMAMDRYGDRISVGGTPAFKEQIAQA
AAASKLPITFDDDALERRRQELLTQATTKENDHDRTDRGRAAGGGISGSGPAIAAIPGAARAGQPRAAAA
GRTTKPNVGRVGRKPPPQSQNRLRRLSQLGVVQLASGSEVLLPRHVPGDVEQQGAKPVDGLRRDIFGPGR
LSPQVAAAADKYIAEREGKRLKGFDIPKHSRYTDGQDGAATFAGIRQVEGQSLALLTRGEEVMVLPVDEP
TARRLKRLAVGDAITVTPQGSIKTTKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(424-512)

Relaxase/Mobilisation nuclease domain (Relaxase)

(13-250)


  Protein structure


Source ID Structure
AlphaFold DB K4IYE5


T4CP

ID   15839 GenBank   WP_015063532
Name   t4cp2_E5P3_RS35360_RA8|4 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: 69689.93 Da        Isoelectric Point: 9.0430

>WP_015063532.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Burkholderiales]
MTKDRFNNAVGPQVRAEKEGPGKVIPALAVLSLGGGLQAATQFFAHDFKYQAALGAHINHIYPPWGIVQW
AGKWYGQYPDAFMRAGSIGVTITGVGLISLVVAKMVLANSSKVNEYLHGSARWANVRDIQAAGLIPRARS
FWQTITGKDAAASSGVYVGAWIDKKGKQHYLRHNGPEHVLCYAPTRSGKGVGLVVPTLLSWGHSAVITDL
KGELWALTAGWRQKHAKNKVLRFEPATASGSVCWNPLDEIRLGTENEVGDVQNLATLIVDPDGKGLESHW
QKTSQALLVGVILHALYKAKAEGTPATLPGVDAMLADPNRDIGELWMEMTTYSHVDGQVHPVVGSAARDM
MDRPDEEAGSVLSTAKSYLALYRDPIVARNVSKSEFKIKDLMHHDNAVSLYIVTQPNDKARLRPLVRVMV
NMIVRLLADKMDFENGRPVAHYKHRMLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRE
TGYGHDESITSNCHVQNAYPPNRVETAEHLSKLTGQTTVAKEQITTSGRRTSALLGQVSRTIQEVQRPLL
TPDECLRMPGPVKTEGGDIAKAGDMVVYVAGYPAIYGKQPLYFQDPTFQARAAIPAPKNSDKLRNSFVAP
AGEGITI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(122-620)

  Protein structure



No available structure.



ID   15840 GenBank   WP_015063520
Name   t4cp2_E5P3_RS35475_RA8|4 insolico UniProt ID   _
Length   845 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 845 a.a.        Molecular weight: 93707.73 Da        Isoelectric Point: 6.3402

>WP_015063520.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Burkholderiales]
MIEAIAIGIAALGALLLLILFARIRAVDAELKLKKHRSKDAGLADLLNYAAMVDDGVIVGKNGSFIASWL
YKGDDNASSTDEQREMVSFRINQALAGLGNGWMLHVDAVRRPAPNYTETGLSHFPDPVSAAMDEERRRLF
EGLGTMYEGYFIVTMTYFPPLLAQSKFVELMFDDEAKTPGNKARTQGLIDYFKRECTSIESRLSSAVKLQ
RLRGNKVVNEDGSTVTHDDLLRWLQFCITGMDHPVLLPSNPMYLDAVIGGQELFGGVVPKIGRKFVQVVA
IEGFPLESTPGVLTALGELPVEYRWSSRFIFMDSHEAVKHLDKFRKKWKQKIRGFFDQVFNTNTGSVDQD
AMSMVNDAESAIAEVNSGLVAVGYYTSVVVLMDEDREKLETSARQVEKAINRLGFAARIETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSTIWTGLNKAPCPMYPPLSPALMHCVTHGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLALIAAQLRRYQGMSIYAFDKGMSMYPLAKATGGKHFTVAADDDKLAFCPLQFLES
KSDRAWAMEWIDTILALNNVETTPAQRNEIGNAIMSMHASGARTLSEFSVTIQDEAIREAIRQYTVDGNM
GHLLDAEEDGLSLTDFTVFEIEELMNLGEKYALPTLLYLFRRIERSLKGQPAVIILDEAWLMLGHPAFRA
KIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTAALYRRMGLNARQIE
ILATAIPKRQYYYVSENGRRLYDLALGPLALAFVGASDKESVAAIKSLEAKFGDAWVHEWLAGRNLKLSD
YGVAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(619-747)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(220-431)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 26130..36727

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
E5P3_RS36100 22212..22373 - 162 Protein_19 antitoxin VbhA family protein -
E5P3_RS35400 (G3W91_RS35395) 22340..22621 + 282 Protein_20 helix-turn-helix domain-containing protein -
E5P3_RS35405 (G3W91_RS35400) 22578..22985 - 408 WP_031944013 hypothetical protein -
E5P3_RS35410 (G3W91_RS35405) 22982..23467 - 486 WP_015063510 thermonuclease family protein -
E5P3_RS35415 (G3W91_RS35410) 23469..23894 - 426 WP_053057113 OmpA family protein -
E5P3_RS35420 (G3W91_RS35415) 23908..24606 - 699 WP_269474032 TraX family protein -
E5P3_RS35425 (G3W91_RS35420) 24609..24872 - 264 WP_162572153 conjugal transfer protein TrbO -
E5P3_RS35430 (G3W91_RS35425) 24898..25503 - 606 WP_162572154 transglycosylase SLT domain-containing protein -
E5P3_RS35435 (G3W91_RS35430) 25517..26110 - 594 WP_015063527 TrbM/KikA/MpfK family conjugal transfer protein -
E5P3_RS35440 (G3W91_RS35435) 26130..27863 - 1734 WP_174259956 P-type conjugative transfer protein TrbL virB6
E5P3_RS35445 (G3W91_RS35440) 27874..28113 - 240 WP_031944010 entry exclusion lipoprotein TrbK -
E5P3_RS35450 (G3W91_RS35445) 28124..28897 - 774 WP_031944011 P-type conjugative transfer protein TrbJ virB5
E5P3_RS35455 (G3W91_RS35450) 28916..30310 - 1395 WP_015063524 TrbI/VirB10 family protein virB10
E5P3_RS35460 (G3W91_RS35455) 30316..30783 - 468 WP_015063523 TrbH Mating pair formation protein -
E5P3_RS35465 (G3W91_RS35460) 30786..31691 - 906 WP_015063522 P-type conjugative transfer protein TrbG virB9
E5P3_RS35470 (G3W91_RS35465) 31704..32480 - 777 WP_015063521 conjugal transfer protein TrbF virB8
E5P3_RS35475 (G3W91_RS35470) 32477..35014 - 2538 WP_015063520 VirB4 family type IV secretion/conjugal transfer ATPase virb4
E5P3_RS35480 (G3W91_RS35475) 35011..35322 - 312 WP_011171720 conjugal transfer protein TrbD virB3
E5P3_RS35485 (G3W91_RS35480) 35325..35753 - 429 WP_011171719 IncP-type conjugal transfer pilin TrbC virB2
E5P3_RS35490 (G3W91_RS35485) 35765..36727 - 963 WP_011171718 P-type conjugative transfer ATPase TrbB virB11
E5P3_RS35495 (G3W91_RS35490) 36980..37357 - 378 WP_011171717 transcriptional regulator -
E5P3_RS35500 (G3W91_RS35495) 37678..38547 + 870 WP_015063508 plasmid replication initiator TrfA -
E5P3_RS35505 (G3W91_RS35500) 38916..40022 + 1107 WP_162572156 NotI family restriction endonuclease -
E5P3_RS35510 (G3W91_RS35505) 40122..41150 + 1029 WP_162572157 DNA adenine methylase -

Host bacterium

ID   21921 GenBank   NZ_LR594665
Plasmid name   RA8|4 Incompatibility group   -
Plasmid size   68393 bp Coordinate of oriT [Strand]   6794..6888 [-]
Host baterium   Variovorax sp. RA8

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA9, AcrIF24