Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116401
Name   oriT_pAV3334-2 in_silico
Organism   Acidovorax sp. SUPP3334
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP025674 (14906..15000 [-], 95 nt)
oriT length   95 nt
IRs (inverted repeats)      26..33, 36..43  (TAACCGGC..GCCGGTTA)
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_pAV3334-2
CGAATAAGGGGGAGGTGAAGATAGATAACCGGCTTGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTTCGGCGGTATGAACACCAAGGAAAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10480 GenBank   WP_317623890
Name   traI_AVHM3334_RS00410_pAV3334-2 insolico UniProt ID   _
Length   857 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 857 a.a.        Molecular weight: 93176.79 Da        Isoelectric Point: 10.3380

>WP_317623890.1 TraI/MobA(P) family conjugative relaxase [Acidovorax sp. SUPP3334]
MIAKHVSMKTVQKSDFAGLVKYITDEQGKNERVGYVAVTNCQTGRPEVAITEVLNTQAQNTRSAADKTYH
LIVSFRAGEQPDQATLQAIEKRICEGLGFGEHQRVSAVHHDTDNLHIHIAINKIHPTRYTTHEPYYPHKE
LAKLCEKLEIEFGLERDNHRAAKVASENRAQDMERHAGVESLLGWVKRECAADMQAAQSWEALHQVMRDN
GLELRERGNGFVIQAADGLAVKASSIGREFSKAKLEERLGTFEPSAEHLERAAQKPRKQYDKKPVWSRVN
TVELHAKYKADQLNISGSRTAEWEKARAKKDRLIEAAKRSGRLKRSTIKLISGAGVGKKLMYSATSKTMK
SEIEKINKQYLKERQEIYEKYQRRAWADWLRAKAAEGDQEALGALRARDAAQGLKGNTVAGTGPLRPQAA
AAEQDSVTKKGTIIYRVGPTAVRDDGDRLKVSRGADQDGMQAALRMAMDRYGDRISVGGTPAFKEQIAQA
AAASKLPITFDDDALERRRQELLTQATTKENDHDRTDHDRTDRGRTDRGRTDGGGISSSGPATAAIPGVA
AAGRTSKPNVGRVGRKPPPQSQNRLRRLSELGVVQLAITFDDDALECRRQELLTQATTKENDHDRTDHDR
TDRGRTDGGGISGSGPATAAIPGAARAGQPHAAAAAAAAAAAAAAAAAAAAAAAAAAGRTSKPNVGRVGR
KPPPQSQNRLRRLSQLGVVQLASGSEVLLPRHVPGDVEQQGAKPVDGLRRDIFGSGRLSPQVATAADKYI
AEREGKRLNGFDIPKHSRYTDGQDGAATFAGIRQIEGQSLALLKRGEEVMVLPVDEPTARRLKRLAVGDS
ITVTPQGSIRTTKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(13-250)

Large polyvalent protein-associated domain 7 (LPD7)

(424-512)


  Protein structure



No available structure.




T4CP

ID   12232 GenBank   WP_317623891
Name   t4cp2_AVHM3334_RS00415_pAV3334-2 insolico UniProt ID   _
Length   661 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 661 a.a.        Molecular weight: 73058.73 Da        Isoelectric Point: 9.5063

>WP_317623891.1 type IV secretory system conjugative DNA transfer family protein [Acidovorax sp. SUPP3334]
MTKDRFNNAVGPQVRAKKGGAGKVMPALAVLSLGGGLQVATQFFAHDFKYQAALGTHINHIYPPWGVIQW
AGKWSSQYPDAFMRAGSIGVVTAGIGLLGLAVTQMVLANSSKVNEYLHGSARWANQKDIREAGLMPRKLT
FWQKLRGKEPEGSSGVYVGAWLDKSGNVQYLRHNGPEHVLTYAPTRSGKGVGLVVTTLLSWPHSAVVTDL
KGELWAMTAGWRQKYAKNKVIRFEPATLNGSAAWNPLDELRVGTEHEVGDVQNIATLIVDPDGKGLESHW
QKTSQALLVGVILHALYKAKNEGGTASLPSVDAMLADPNRDIAELWMEMTTYSHVNGQVHPVVGSAARDM
MDRPEEEAGSVLSTAKSYLSLYRDPVVARNVSKSEFRIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMM
NMIVRLLADKMEFERVIAEMPWWRRVLARFGFTDAAHSYVRSKKSYKHRLLGMIDEFPSLGKLEIMQESL
AFVAGYGIKFYLICQDLNQLKSRETGYGPDETITSNCHVQNAYPPNRLETAEHLSKLTGTTTVIKEQITT
SGRRTAALLGQVSRTTQEVQRPLLTPDECLRMPGPKKDADGQITEAGDMVVYVAGFPAIYGRQPLYFHDA
TFTARAAVPEPAVSDRLRQIHEVKAGEGITI

  Protein domains


Predicted by InterproScan.

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

(464-646)

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

(122-434)

  Protein structure



No available structure.



ID   12233 GenBank   WP_317623865
Name   t4cp2_AVHM3334_RS00535_pAV3334-2 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: 94341.61 Da        Isoelectric Point: 6.5551

>WP_317623865.1 VirB4 family type IV secretion/conjugal transfer ATPase [Acidovorax sp. SUPP3334]
MIEAIAIGIAALGALLLLILFARIRAVDAELKLKKHRSKDAGLADLLNYAAMVDDGVIVGKNGSFIASWL
YKGDDNASSTDEQREMVSFRINQALAGLGNGWMLHVDAVRRPAPNYTEIGLSHFPDAVSSAIDEERRRLF
EGLGTMYEGYFIVTMTYFPPLLAQRKFVELMFDDEAKPLGNKARTQGLIDYFKRECTSIESRLSSAIKLQ
RLRGNKVVKEDGATVTHDDLLRWLQFCITGMDHPVLLPSNPMYLDAVIGGQELFGGVVPKIGRKFVQVVA
IEGFPLESTPGILTALGELPVEYRWSSRFIFMDAHEAVKHLDKFRKKWKQKIRGFFDQVFNTNTGSVDQD
AMSMVNDAESAIAEVNSGLVAVGYYTSVVVLMDEDRDKLETSARQVEKSINRLGFAARIETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSTIWTGLNKAPCPMYPPLSPALMHCVTHGATPFRLNLHVRDLGH
TFMFGPPGAGKSTHLALIAAQLRRYQGMSIYAFDKGMSMYPLAAGIRAATKGHSGLHFTVAADDDRLAFC
PLQFLETKGDRAWAMEWIDTTLALNGLNTTPAQRNEIGNAIMSMHASGARTLSEFSVTIQDESIREAIRQ
YTVDGNMGHLLDAEEDGLSLSDFTVFEIEALMNLGEKYALPTLLYLFRRIELSLKGQPAVIILDEAWLML
GHTAFRAKIREWLKVLRKANCLLLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTAALYRRMG
LNTRQIEILATAIAKQQYYYVSENGRRLYDLALGPMALAFVGASDKESLAAIKGLETKFGDAWIHEWLAG
RNLKLSDYGVAA

  Protein domains


Predicted by InterproScan.

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

(220-431)

TraG P-loop domain (P-loop_TraG)

(625-754)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 33604..44249

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AVHM3334_RS00455 (AVHM3334_23420) 29106..29768 + 663 WP_317623897 recombinase family protein -
AVHM3334_RS00460 (AVHM3334_23425) 29725..30144 - 420 WP_317623850 hypothetical protein -
AVHM3334_RS00465 (AVHM3334_23430) 30129..30614 - 486 WP_317623851 thermonuclease family protein -
AVHM3334_RS00470 (AVHM3334_23435) 30616..31041 - 426 WP_317623852 OmpA family protein -
AVHM3334_RS00475 (AVHM3334_23440) 31056..31754 - 699 WP_317623853 TraX family protein -
AVHM3334_RS00480 (AVHM3334_23445) 31757..32020 - 264 WP_317623854 conjugal transfer protein TrbO -
AVHM3334_RS00485 (AVHM3334_23450) 32041..32286 - 246 WP_317623855 hypothetical protein -
AVHM3334_RS00490 (AVHM3334_23455) 32370..32975 - 606 WP_317623856 transglycosylase SLT domain-containing protein -
AVHM3334_RS00495 (AVHM3334_23460) 32989..33582 - 594 WP_317623857 TrbM/KikA/MpfK family conjugal transfer protein -
AVHM3334_RS00500 (AVHM3334_23465) 33604..35367 - 1764 WP_317623858 P-type conjugative transfer protein TrbL virB6
AVHM3334_RS00505 (AVHM3334_23470) 35378..35614 - 237 WP_317623859 entry exclusion lipoprotein TrbK -
AVHM3334_RS00510 (AVHM3334_23475) 35625..36398 - 774 WP_317623860 P-type conjugative transfer protein TrbJ virB5
AVHM3334_RS00515 (AVHM3334_23480) 36417..37811 - 1395 WP_317623861 TrbI/VirB10 family protein virB10
AVHM3334_RS00520 (AVHM3334_23485) 37817..38284 - 468 WP_317623862 conjugal transfer protein TrbH -
AVHM3334_RS00525 (AVHM3334_23490) 38287..39192 - 906 WP_317623863 P-type conjugative transfer protein TrbG virB9
AVHM3334_RS00530 (AVHM3334_23495) 39205..39981 - 777 WP_317623864 conjugal transfer protein TrbF virB8
AVHM3334_RS00535 (AVHM3334_23500) 39978..42536 - 2559 WP_317623865 VirB4 family type IV secretion/conjugal transfer ATPase virb4
AVHM3334_RS00540 (AVHM3334_23505) 42533..42844 - 312 WP_317623866 conjugal transfer protein TrbD virB3
AVHM3334_RS00545 (AVHM3334_23510) 42847..43275 - 429 WP_317623867 IncP-type conjugal transfer pilin TrbC virB2
AVHM3334_RS00550 (AVHM3334_23515) 43287..44249 - 963 WP_317623868 P-type conjugative transfer ATPase TrbB virB11
AVHM3334_RS00555 (AVHM3334_23520) 44518..44895 - 378 WP_317623869 transcriptional regulator -

Host bacterium

ID   16834 GenBank   NZ_AP025674
Plasmid name   pAV3334-2 Incompatibility group   -
Plasmid size   45215 bp Coordinate of oriT [Strand]   14906..15000 [-]
Host baterium   Acidovorax sp. SUPP3334

Cargo genes

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