Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102926
Name   oriT_ZLB004|p3 in_silico
Organism   Levilactobacillus brevis strain ZLB004
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021459 (40538..40741 [+], 204 nt)
oriT length   204 nt
IRs (inverted repeats)      125..130, 143..148  (AAATCC..GGATTT)
 66..72, 83..89  (ACCCCCC..GGGGGGT)
Location of nic site      135..136
Conserved sequence flanking the
  nic site    		  TTTGGTTACA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 204 nt

>oriT_ZLB004|p3
AAGCGGAAGTCGCAGGTGTGGACTGATCTTGCTGGCTGGTGTGGCAATAGCCACGCCAGCACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATACGCCTTTTTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2196 GenBank   WP_000398284
Name   Rep_trans_CCS05_RS12675_ZLB004|p3 insolico UniProt ID   A0A3P3PY43
Length   401 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 401 a.a.        Molecular weight: 47398.10 Da        Isoelectric Point: 6.5091

>WP_000398284.1 MULTISPECIES: MobT family relaxase [Bacteria]
MEGFLLNEQTWLQHLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLWEALERFNPDAP
LEMLFDYVRIRFPTTDVQQVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDVLVAGGVMKRLDLAINDKTGILNIPVLTEKCQQEECISVFRSFKSYRS
GELVRKEEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKK

  Protein domains


Predicted by InterproScan.

Helix-turn-helix (HTH_3)

(15-53)

Replication initiation factor (Rep_trans)

(169-373)

Rolling Circle replication initiation protein N-terminal domain (Rol_Rep_N)

(73-161)


  Protein structure


Source ID Structure
AlphaFold DB A0A3P3PY43


T4CP

ID   1873 GenBank   WP_000813488
Name   tcpA_CCS05_RS12665_ZLB004|p3 insolico UniProt ID   _
Length   461 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 461 a.a.        Molecular weight: 53370.27 Da        Isoelectric Point: 9.0687

>WP_000813488.1 MULTISPECIES: FtsK/SpoIIIE domain-containing protein [Bacteria]
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKEKITYFPKMYYRLKN
GLIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVEAKDGKLRL
MKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLL
SCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSV
ISEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD

  Protein domains


Predicted by InterproScan.

FtsK/SpoIIIE family (FtsK_SpoIIIE)

(217-301)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 30993..49843

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CCS05_RS12590 (CCS05_12595) 26498..27496 - 999 WP_012490951 IS30 family transposase -
CCS05_RS12595 (CCS05_12600) 27720..28889 + 1170 WP_110140126 metallophosphoesterase -
CCS05_RS12600 (CCS05_12605) 28901..29257 + 357 Protein_33 asparagine synthetase B -
CCS05_RS12610 (CCS05_12615) 29432..30670 - 1239 WP_110140127 ISL3 family transposase -
CCS05_RS12615 (CCS05_12620) 30993..31922 + 930 WP_110140128 ABC transporter ATP-binding protein virb4
CCS05_RS12620 (CCS05_12625) 31924..33444 + 1521 WP_110140129 ABC transporter permease/substrate-binding protein -
CCS05_RS12625 (CCS05_12630) 33847..34776 - 930 WP_110140130 IS30-like element ISLpl1 family transposase -
CCS05_RS12635 (CCS05_12635) 35437..36018 + 582 WP_014216283 recombinase family protein -
CCS05_RS12640 (CCS05_12640) 36416..37048 + 633 WP_110140131 recombinase family protein -
CCS05_RS12645 (CCS05_12645) 37151..38002 + 852 WP_225426374 Fic family protein -
CCS05_RS12655 (CCS05_12655) 38433..38747 + 315 WP_000420682 YdcP family protein orf23
CCS05_RS12660 (CCS05_12660) 38763..39149 + 387 WP_000985015 YdcP family protein orf23
CCS05_RS12665 (CCS05_12665) 39178..40563 + 1386 WP_000813488 FtsK/SpoIIIE domain-containing protein virb4
CCS05_RS12670 (CCS05_12670) 40566..40718 + 153 WP_000879507 hypothetical protein -
CCS05_RS12675 (CCS05_12675) 40741..41946 + 1206 WP_000398284 MobT family relaxase -
CCS05_RS12680 (CCS05_12680) 41989..42210 + 222 WP_001009056 hypothetical protein orf19
CCS05_RS12685 (CCS05_12685) 42327..42824 + 498 WP_000342539 antirestriction protein ArdA -
CCS05_RS12690 (CCS05_12690) 42913..43305 + 393 WP_240005880 conjugal transfer protein orf17a
CCS05_RS12695 (CCS05_12695) 43289..45736 + 2448 WP_000331160 ATP-binding protein virb4
CCS05_RS12700 (CCS05_12700) 45739..47916 + 2178 WP_000804748 membrane protein orf15
CCS05_RS12705 (CCS05_12705) 47913..48914 + 1002 WP_000769868 bifunctional lysozyme/C40 family peptidase orf14
CCS05_RS12710 (CCS05_12710) 48911..49843 + 933 WP_001224319 conjugal transfer protein orf13
CCS05_RS13510 (CCS05_12715) 50088..50204 + 117 WP_001791010 tetracycline resistance determinant leader peptide -
CCS05_RS12720 (CCS05_12720) 50220..52139 + 1920 WP_110140133 tetracycline resistance ribosomal protection protein Tet(M) -

Host bacterium

ID   3369 GenBank   NZ_CP021459
Plasmid name   ZLB004|p3 Incompatibility group   -
Plasmid size   52778 bp Coordinate of oriT [Strand]   40538..40741 [+]
Host baterium   Levilactobacillus brevis strain ZLB004

Cargo genes

Drug resistance gene   tet(M)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -