Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200048
Name   oriT_ICESpnTCH8341-1 in_silico
Organism   Streptococcus pneumoniae TCH8431/19A
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   CP001993 (2007439..2007653 [+], 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_ICESpnTCH8341-1
AAGCGGAAGTCGCAGGTGTGGACTGATCTTGCTGGCTGGTGTGGCAATAGCCACGCCAGCACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATACGCCTTTTTGATTGGAGGGATTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   262 GenBank   ADI70423
Name   Relaxase_ICESpnTCH8341-1 insolico UniProt ID   D6ZP77
Length   420 a.a. PDB ID   
Note   DNA-binding helix-turn-helix protein

  Relaxase protein sequence


Download         Length: 420 a.a.        Molecular weight: 49596.61 Da        Isoelectric Point: 7.3929

>ADI70423.1 DNA-binding helix-turn-helix protein [Streptococcus pneumoniae TCH8431/19A]
MEGFLLNEQTWLQQLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLFEALERFNPDAP
LEMLFDYVRIRFPTTDVQHVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDALVAGGVMKRLDLAINDKTGILNIPVLTEKCQQEECISVFRSFKSYRS
GELVRKEEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKKGYLSTIPVDRYPKKRYNGR

  Protein domains


Predicted by InterproScan.

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

(73-161)

Replication initiation factor (Rep_trans)

(169-373)

Helix-turn-helix (HTH_3)

(15-61)


  Protein structure


Source ID Structure
AlphaFold DB D6ZP77


T4CP

ID   262 GenBank   ADI70421
Name   T4CP_ICESpnTCH8341-1 insolico UniProt ID   D6ZP75
Length   461 a.a. PDB ID   _
Note   FtsK/SpoIIIE family protein

  T4CP protein sequence


Download         Length: 461 a.a.        Molecular weight: 53369.29 Da        Isoelectric Point: 9.1761

>ADI70421.1 FtsK/SpoIIIE family protein [Streptococcus pneumoniae TCH8431/19A]
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKEKITYFPKMYYRLKN
GLIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVQAKDGKLRL
MKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLL
SCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSV
ISEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD

  Protein domains


Predicted by InterproScan.

FtsK/SpoIIIE family (FtsK_SpoIIIE)

(217-300)

  Protein structure


Source ID Structure
AlphaFold DB D6ZP75


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2005334..2019593

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HMPREF0837_12185 2000721..2001737 - 1017 ADI70413 cell envelope-like function transcriptional attenuator common domain protein -
HMPREF0837_12186 2001745..2002263 - 519 ADI70414 acetyltransferase, GNAT family -
HMPREF0837_12187 2002253..2002696 - 444 ADI70415 hydrolase, P-loop family -
HMPREF0837_12188 2002782..2003402 - 621 ADI70416 hypothetical protein -
HMPREF0837_12189 2003708..2004571 - 864 ADI70417 DNA-binding helix-turn-helix protein -
HMPREF0837_12190 2004762..2004932 + 171 ADI70418 hypothetical protein -
HMPREF0837_12191 2005334..2005648 + 315 ADI70419 hypothetical protein orf23
HMPREF0837_12192 2005664..2006050 + 387 ADI70420 hypothetical protein orf23
HMPREF0837_12193 2006079..2007464 + 1386 ADI70421 FtsK/SpoIIIE family protein virb4
HMPREF0837_12194 2007467..2007619 + 153 ADI70422 hypothetical protein -
HMPREF0837_12195 2007642..2008904 + 1263 ADI70423 DNA-binding helix-turn-helix protein -
HMPREF0837_12196 2008894..2009061 + 168 ADI70424 omega transcriptional repressor -
HMPREF0837_12197 2009318..2010055 + 738 ADI70425 ribosomal RNA adenine dimethylase family protein -
HMPREF0837_12198 2010060..2010191 + 132 ADI70426 hypothetical protein -
HMPREF0837_12199 2010312..2011559 - 1248 ADI70427 transposase -
HMPREF0837_12200 2011739..2011960 + 222 ADI70428 hypothetical protein orf19
HMPREF0837_12201 2012077..2012574 + 498 ADI70429 antirestriction protein ArdA -
HMPREF0837_12202 2012549..2013055 + 507 ADI70430 hypothetical protein orf17a
HMPREF0837_12203 2013039..2015486 + 2448 ADI70431 hypothetical protein virb4
HMPREF0837_12204 2015489..2017666 + 2178 ADI70432 hypothetical protein orf15
HMPREF0837_12205 2017663..2018664 + 1002 ADI70433 NlpC/P60 family protein orf14
HMPREF0837_12206 2018661..2019593 + 933 ADI70434 hypothetical protein orf13
HMPREF0837_12207 2019955..2021889 + 1935 ADI70435 putative translation elongation factor G -
HMPREF0837_12208 2022068..2022256 + 189 ADI70436 hypothetical protein -
HMPREF0837_12209 2022253..2022498 + 246 ADI70437 hypothetical protein -
HMPREF0837_12210 2022495..2022830 + 336 ADI70438 hypothetical protein -
HMPREF0837_12211 2022843..2023211 + 369 ADI70439 YolD-like protein -
HMPREF0837_12212 2023198..2023497 + 300 ADI70440 hypothetical protein -

Host bacterium

ID   53 Element type   Transposon
Element name   ICESpnTCH8341-1 GenBank   CP001993
Element size   2088772 bp Coordinate of oriT [Strand]   2007439..2007653 [+]
Host bacterium   Streptococcus pneumoniae TCH8431/19A Coordinate of element   2004999..2031388

Cargo genes

Drug resistance gene   erm(B), tet(M), msr(D), mef(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -