Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107305
Name   oriT_pYS1 in_silico
Organism   Burkholderia cepacia
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_019369 (29988..30084 [+], 97 nt)
oriT length   97 nt
IRs (inverted repeats)      71..76, 80..85  (GGCGTT..AACGCC)
 24..31, 34..41  (TAACCGGC..GCCGGTTA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 97 nt

>oriT_pYS1
GAATAAGGGGGAGCGAAGATAGATAACCGGCTTGCCGGTTAGCTAACTTCGCCCATCTTGCCCGCCTTACGGCGTTGATAACGCCAAGGAAAGTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4859 GenBank   WP_015063387
Name   Relaxase_HTB02_RS00140_pYS1 insolico UniProt ID   J9R8K8
Length   747 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 747 a.a.        Molecular weight: 82577.51 Da        Isoelectric Point: 10.8056

>WP_015063387.1 TraI/MobA(P) family conjugative relaxase [Burkholderia cepacia]
MILKHVPMRSLGKSDFAGLVNYVTDSQSKEHRLGVVQITNCEAGSVRDAITEVLATQHTNTRAIGDKTYH
LLIGFPPGENPSADTLKQIEERVCAALGYGEHQRVSAVHNDTDHLHIHLAINKIHPTRHTMHEPFQAYRT
MAEIAAKLEEEYGLQRVNHESRRSLAEGRAGDMEQHSGIESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARLGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTATRAQALEQARRRKDRLVEAAKRSNRLRRATIKVVGENRTNKKLLYAQASKALRDE
IQAINKQYQKDRQALYDSHSRRTWADWLKKEATHGNAEALTALRAREAAQGLQGNTIQGRGEARPGRAPV
TDNITKKGTIIFRAGLSAVRDDGDKLQVSREATREGLQEALRLAMERYGSRITVNGTTQFKAQVIRAAVD
SQLPITFADPALESRRLALLKKENTHERPDRTERADQRPAEHRGRAGRGPGGPGQRAAAHDDAARPVAVA
RAGFGRTDAAGVHAGAVHRKPDIGRIGRVPPPQSQHRLRTLSQLGVVRIAGGSEVLLPRDVPRHLEQQGT
QPDHQLRRGISRPGTGVAAAPPGLAAADKYIAEREAKRSKGFDIPKHARYTAGDGALAFQGVRNIEGQAL
ALLKRGDEVMVMPIDQATARRLSRIAVGDAVTITPKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(420-507)


  Protein structure


Source ID Structure
AlphaFold DB J9R8K8


T4CP

ID   5042 GenBank   WP_015063366
Name   t4cp2_HTB02_RS00035_pYS1 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: 94175.10 Da        Isoelectric Point: 6.3996

>WP_015063366.1 VirB4 family type IV secretion/conjugal transfer ATPase [Burkholderia cepacia]
MIEAIAIGIAVLGAVLLLILFSRIRQVDAELKLKKHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWL
YKGDDNASSTDEQREMVSFRINQALAGLGSGWMVHVDAVRRPAPNYSERGVSTFTDPVSAAIDEERRRLF
ESLGTMYEGHFVFTVTWFPPVLAQRKFVELMFDDDAVAPDHTARTVGLIEQFKREIRSLESRLSSAVKLT
RLQGHKMATEEGREVTHDDFLSWLQFCVTGNYHPVQLPSNPMYLDAVIGGQELWGGVVPKVGRKFIQVVS
IEGFPLESTPGLLSALAELPSEYRWSSRFIFMDQHESLKHLDKFRKKWKQKIRGFFDQVFNTNTGSVNQD
AATMVADAEAAIAEVNSGLVAAGYFTSVVVLMDEDRERLAASALSVEKAINRLAFAARIETINTMDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSSIWTGSATAPCPMYPPLAPALMHCVTVGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMSMYPLAAAINAGSKGKTGLHFTVAADDDRLAFC
PLQFLETKGDRAWAMEWIDTILALNGVDTTPAQRNEIGHAIMSMHASGARTLSEFSVTIQDEAIREAIKQ
YTVDGSMGHLLDAEEDGLSLSDFTVFEIEELMNLGEKFALPVLLYLFRRIERGLKGQPAVIILDEAWLML
GHPAFRAKIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTAALYRRMG
LNKRQIEILATAVPKRQYYYVSENGRRLYDLALGPLALAFVGASDKESVAAIKSLQAKFGHEWVDHWLAG
RNLNLNDYLEAA

  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)

(220-431)

  Protein structure



No available structure.



ID   5043 GenBank   WP_015063386
Name   t4cp2_HTB02_RS00135_pYS1 insolico UniProt ID   _
Length   634 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 634 a.a.        Molecular weight: 69541.54 Da        Isoelectric Point: 8.5000

>WP_015063386.1 type IV secretory system conjugative DNA transfer family protein [Burkholderia cepacia]
MKIKMNNAVGPQVRSAKAKTPKLLPILGGVSLVGGLQAATQFFAYTFQYHASLGANLGHVYAPWSILNWS
AKWYSQYPDEIMRAGSIGMVTATVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKDAPAATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSSGGVCWNPLDEIRVGTEAEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKARNEGGTATLPSVDAMLADPNRDIGELWMEMTTYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKDLMHSDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLRSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNDKGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFQARAAIPAPKASDRLRQAVEAGE
GITI

  Protein domains


Predicted by InterproScan.

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

(121-617)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2390..13036

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTB02_RS00005 (pYS10001) 1..1224 - 1224 WP_015063361 plasmid replication initiator TrfA -
HTB02_RS00010 (pYS10002) 1272..1610 - 339 WP_011304114 single-stranded DNA-binding protein -
HTB02_RS00015 (pYS10003) 1719..2078 + 360 WP_015063362 transcriptional regulator -
HTB02_RS00020 (pYS10004) 2390..3355 + 966 WP_015063363 P-type conjugative transfer ATPase TrbB virB11
HTB02_RS00025 (pYS10005) 3377..3841 + 465 WP_015063364 conjugal transfer system pilin TrbC virB2
HTB02_RS00030 (pYS10006) 3845..4156 + 312 WP_015063365 conjugal transfer protein TrbD virB3
HTB02_RS00035 (pYS10007) 4153..6711 + 2559 WP_015063366 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTB02_RS00040 (pYS10008) 6708..7496 + 789 WP_015063367 conjugal transfer protein TrbF virB8
HTB02_RS00045 (pYS10009) 7514..8407 + 894 WP_015063368 P-type conjugative transfer protein TrbG virB9
HTB02_RS00050 (pYS10010) 8410..8871 + 462 WP_015063369 lipoprotein -
HTB02_RS00055 (pYS10011) 8876..10267 + 1392 WP_015063370 TrbI/VirB10 family protein virB10
HTB02_RS00060 (pYS10012) 10284..11057 + 774 WP_015063371 P-type conjugative transfer protein TrbJ virB5
HTB02_RS00065 (pYS10013) 11067..11288 + 222 WP_011304125 entry exclusion lipoprotein TrbK -
HTB02_RS00070 (pYS10014) 11300..13036 + 1737 WP_015063373 P-type conjugative transfer protein TrbL virB6
HTB02_RS00075 (pYS10015) 13054..13632 + 579 WP_015063374 TrbM/KikA/MpfK family conjugal transfer protein -
HTB02_RS00080 (pYS10016) 13634..14269 + 636 WP_015063375 transglycosylase SLT domain-containing protein -
HTB02_RS00085 (pYS10017) 14299..14568 + 270 WP_015063376 hypothetical protein -
HTB02_RS00090 (pYS10018) 14565..15263 + 699 WP_015063377 TraX family protein -
HTB02_RS00095 (pYS10019) 15279..15722 + 444 WP_015063378 OmpA family protein -
HTB02_RS00100 (pYS10020) 15914..16588 + 675 WP_015063379 class I SAM-dependent methyltransferase -
HTB02_RS00105 (pYS10022) 16679..17188 + 510 WP_181411585 hypothetical protein -
HTB02_RS00110 (pYS10021) 17145..17813 - 669 WP_015063381 recombinase family protein -

Host bacterium

ID   7741 GenBank   NC_019369
Plasmid name   pYS1 Incompatibility group   -
Plasmid size   82988 bp Coordinate of oriT [Strand]   29988..30084 [+]
Host baterium   Burkholderia cepacia

Cargo genes

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