Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200029
Name   oriT_ICESpn9409 in_silico
Organism   Streptococcus pneumoniae Tn916-type integrative and
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   FR671418 (2106..2320 [+], 215 nt)
oriT length   215 nt
IRs (inverted repeats)      61..76, 80..95  (ACTTAACCCCCCGTAT..ACAGGGGGGTACAAAT)
  123..134, 139..150  (GAAAATCCTTTG..CAAGGGATTTAC)
Location of nic site      135..136
Conserved sequence flanking the
  nic site    		  TGG|T
Note   blastn alignment with the oriT_Tn916

  oriT sequence  


Download         Length: 215 nt

>oriT_ICESpn9409
AAGCGGAAGTCGCAGGTGTGGACTGATCTTGCTGGCTGGTGTGGCAATAGCCACGCCAGCACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTAAAATGGGCTTTAAAAGTTGACATACGCCTTTTTGATTGGAGGGATTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   243 GenBank   CBW39427
Name   Orf20_ICESpn9409 insolico UniProt ID   E8ZEI5
Length   420 a.a. PDB ID   
Note   _

  Relaxase protein sequence


Download         Length: 420 a.a.        Molecular weight: 49663.70 Da        Isoelectric Point: 7.3929

>CBW39427.1 putative conjugative transposon replication initiation factor [Streptococcus pneumoniae]
MEGFLLNEQTWLQHLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLWEALERFNPDAP
LEMLFDYVRIRFPTTDVQQVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDVLVAGGVMKRLDLAINDKTGILNIPVLTEKCQQEECISVFRSFKSYRS
GELVRKEEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKKGYLSTIPVDRYPKKRYNGR

  Protein domains


Predicted by InterproScan.

Replication initiation factor (Rep_trans)

(169-373)

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

(73-161)

Helix-turn-helix (HTH_3)

(15-53)


  Protein structure


Source ID Structure
AlphaFold DB E8ZEI5


T4CP

ID   243 GenBank   CBW39426
Name   Orf21_ICESpn9409 insolico UniProt ID   B7UTY5
Length   461 a.a. PDB ID   _
Note   conjugative transposon FtsK/SpoIIIE-family protein

  T4CP protein sequence


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

>CBW39426.1 conjugative transposon FtsK/SpoIIIE-family protein [Streptococcus pneumoniae]
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKEKITYFPKMYYRLKN
GLIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVEAKDGKLRL
MKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLL
SCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSV
ISEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD

  Protein domains


Predicted by InterproScan.

FtsK/SpoIIIE family (FtsK_SpoIIIE)

(217-301)

  Protein structure


Source ID Structure
AlphaFold DB B7UTY5


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1..16654

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_0 1..315 + 315 CBW39424 conjugative transposon protein orf23
Locus_1 334..717 + 384 CBW39425 conjugative transposon protein orf23
Locus_2 746..2131 + 1386 CBW39426 conjugative transposon FtsK/SpoIIIE-family protein virb4
Locus_3 2309..3571 + 1263 CBW39427 putative conjugative transposon replication initiation factor -
Locus_4 3561..3815 + 255 CBW39428 Omega transcriptional repressor protein -
Locus_5 3908..4702 + 795 CBW39429 Aminoglycoside phosphotransferase -
Locus_6 5186..5551 + 366 CBW39430 Conserved hypothetical protein -
Locus_7 5575..5724 + 150 CBW39431 Conserved hypothetical protein -
Locus_8 5880..6149 + 270 CBW39432 Omega transcriptional repressor protein -
Locus_9 6379..7116 + 738 CBW39433 rRNA methylase -
Locus_10 7373..8620 - 1248 CBW39434 Transposase -
Locus_11 8800..9021 + 222 CBW39435 conjugative transposon protein orf19
Locus_12 9138..9635 + 498 CBW39436 conjugative transposon protein -
Locus_13 9886..10116 + 231 CBW39437 putative conjugative transposon membrane protein orf17a
Locus_14 10100..12547 + 2448 CBW39438 conjugative transposon ATP/GTP-binding protein virb4
Locus_15 12550..14727 + 2178 CBW39439 conjugative transposon membrane protein orf15
Locus_16 14724..15725 + 1002 CBW39440 putative cell wall hydrolase orf14
Locus_17 15740..16654 + 915 CBW39441 putative conjugative transposon exported protein orf13
Locus_18 17031..18950 + 1920 CBW39442 conjugative transposon tetracycline resistance protein -
Locus_19 19296..19649 - 354 CBW39443 putative conjugative transposon regulatory protein -
Locus_20 19779..19925 + 147 CBW39444 putative uncharacterized protein -
Locus_21 20154..20576 + 423 CBW39445 putative conjugative transposon regulatory protein -
Locus_22 21264..21467 + 204 CBW39446 excisionase -

Host bacterium

ID   34 Element type   Transposon
Element name   ICESpn9409 GenBank   FR671418
Element size   22765 bp Coordinate of oriT [Strand]   2106..2320 [+]
Host bacterium   Streptococcus pneumoniae Tn916-type integrative and

Cargo genes

Drug resistance gene   aph(3')-III, erm(B), tet(M)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -