Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200297
Name   oriT_ICE_Cdi630_fic in_silico
Organism   Clostridioides difficile 630
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_009089 (2494..2626 [+], 133 nt)
oriT length   133 nt
IRs (inverted repeats)      65..70, 83..88  (AAATCC..GGATTT)
 6..12, 23..29  (ACCCCCC..GGGGGGT)
Location of nic site      75..76
Conserved sequence flanking the
  nic site    		  TTTGGTTACA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 133 nt

>oriT_ICE_Cdi630_fic
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGGCAAAAAAATAGTAGAAAATCCTTTGGTTACAAGGGATTTAGAAAATTTCGGTGTATGTCAAATGAGCTTTAAAAGTTGACATAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14334 GenBank   WP_025186485
Name   mobT_CD630_RS03050_ICE_Cdi630_fic insolico UniProt ID   A0A5N0YRV8
Length   401 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 401 a.a.        Molecular weight: 47190.89 Da        Isoelectric Point: 6.9549

>WP_025186485.1 MULTISPECIES: MobT family relaxase [Bacillota]
MGGISLNEQTWVQHLKEKRLSYGLSQNRLAIATGITRQYLSDIETGKVKPSDELQLALLETLERFNPDAP
LEMLFDYVRIRFPTTDVQHVVEDVLRLKLSYMLHEDYGFYSYTEHYALGNIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDALVASGVMKRLDLAINDKTGILNIPILTEKCRQEECISVFRSFKSYRS
GELVRKDEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
AYDNPEHTAFKIINRYIRFVDKDDSKARSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAITLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITNKK

  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)

(15-62)


  Protein structure


Source ID Structure
AlphaFold DB A0A5N0YRV8


T4CP

ID   16826 GenBank   WP_002324557
Name   tcpA_CD630_RS03040_ICE_Cdi630_fic 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: 53440.27 Da        Isoelectric Point: 8.2601

>WP_002324557.1 MULTISPECIES: FtsK/SpoIIIE domain-containing protein [Bacillota]
MKQRGKRIRPSDKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDLDLLQVDKIDIPYLVISFSVAIL
VCLLGAFIFRRYKYDMFKQLQHRQKLAKMILENKWYESEQVKTDGFFKDSTSRTKEKITYFPKMYYRLKD
GLISIRVEIMLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIANRLSIDEVQAKDGKLRL
MTNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTNSKLTILDPKNADLADLGSVMGNVYYRKDDML
SCIDRFYDEMMKRSEVMKKMENYKTGENYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVLNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKQIKGRGYVDVGTSV
ISEFYTPLVPKGHDFLEEIKRLSHSKQDTQATCEAEVAGVD

  Protein domains


Predicted by InterproScan.

FtsK/SpoIIIE family (FtsK_SpoIIIE)

(217-299)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 585695..599749

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CD630_RS03005 (CD630_04910) 581646..582062 + 417 WP_003434797 PTS sugar transporter subunit IIA -
CD630_RS03010 (CD630_04920) 582091..582564 + 474 WP_003426364 PTS sugar transporter subunit IIB -
CD630_RS03015 (CD630_04930) 582611..583369 + 759 WP_003434801 PTS sugar transporter subunit IIC -
CD630_RS03020 (CD630_04940) 583393..584232 + 840 WP_011860838 PTS system mannose/fructose/sorbose family transporter subunit IID -
CD630_RS03025 584769..585425 + 657 WP_022621482 Fic family protein -
CD630_RS03030 (CD630_04960) 585695..586009 + 315 WP_002324559 YdcP family protein orf23
CD630_RS03035 (CD630_04970) 586031..586417 + 387 WP_002324558 YdcP family protein orf23
CD630_RS03040 (CD630_04980) 586451..587836 + 1386 WP_002324557 FtsK/SpoIIIE domain-containing protein virb4
CD630_RS03045 (CD630_04981) 587839..587991 + 153 WP_011860839 hypothetical protein -
CD630_RS03050 (CD630_04990) 588013..589218 + 1206 WP_025186485 MobT family relaxase -
CD630_RS03055 (CD630_04991) 589261..589482 + 222 WP_001009056 hypothetical protein orf19
CD630_RS03060 (CD630_05000) 589599..590096 + 498 WP_002324555 antirestriction protein ArdA -
CD630_RS03065 (CD630_05010) 590184..590576 + 393 WP_002324554 conjugal transfer protein orf17a
CD630_RS03070 (CD630_05020) 590560..593007 + 2448 WP_002324553 ATP-binding protein virb4
CD630_RS03075 (CD630_05030) 593064..595175 + 2112 WP_231300444 YtxH domain-containing protein orf15
CD630_RS03080 (CD630_05040) 595172..596116 + 945 WP_022621483 bifunctional lysozyme/C40 family peptidase orf14
CD630_RS03085 (CD630_05060) 596830..598659 + 1830 WP_002335621 group II intron reverse transcriptase/maturase -
CD630_RS03095 (CD630_05070) 598817..599749 + 933 WP_002324550 conjugal transfer protein orf13
CD630_RS03105 (CD630_05080) 600034..601953 + 1920 WP_011860841 tetracycline resistance ribosomal protection protein Tet(M) -
CD630_RS03110 (CD630_05081) 602076..602243 + 168 WP_002319681 cysteine-rich KTR domain-containing protein -
CD630_RS03115 (CD630_05090) 602302..602655 - 354 WP_002324548 helix-turn-helix domain-containing protein -
CD630_RS03120 (CD630_05100) 603157..603582 + 426 WP_002324547 sigma-70 family RNA polymerase sigma factor -
CD630_RS03125 (CD630_05101) 603579..603809 + 231 WP_002334012 helix-turn-helix domain-containing protein -
CD630_RS19655 (CD630_05103) 604190..604330 + 141 WP_002324545 hypothetical protein -

Region 2: 3897502..3910292

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CD630_RS17675 (CD630_33280) 3892914..3893153 - 240 WP_009009556 helix-turn-helix domain-containing protein -
CD630_RS17680 (CD630_33290) 3893150..3893569 - 420 WP_020994407 sigma factor-like helix-turn-helix DNA-binding protein -
CD630_RS17685 (CD630_33300) 3894170..3894526 + 357 WP_009009558 helix-turn-helix domain-containing protein -
CD630_RS17690 (CD630_33310) 3894559..3895254 - 696 WP_011861910 transposase -
CD630_RS17695 (CD630_33320) 3895434..3896003 + 570 WP_011861911 TetR/AcrR family transcriptional regulator -
CD630_RS17700 (CD630_33330) 3896000..3896260 + 261 WP_094030748 competence protein TfoX -
CD630_RS17705 (CD630_33331) 3896491..3896733 + 243 WP_011861913 DUF3781 domain-containing protein -
CD630_RS17710 (CD630_33340) 3896730..3897200 + 471 WP_011861914 GyrI-like domain-containing protein -
CD630_RS17715 (CD630_33350) 3897502..3898410 - 909 WP_011861915 conjugal transfer protein orf13
CD630_RS17720 (CD630_33360) 3898427..3899431 - 1005 WP_011861916 bifunctional lysozyme/C40 family peptidase orf14
CD630_RS20415 (CD630_33370) 3899428..3901809 - 2382 WP_011861917 membrane protein orf15
CD630_RS17730 (CD630_33380) 3901806..3904259 - 2454 WP_011861918 ATP-binding protein virb4
CD630_RS17735 (CD630_33390) 3904243..3904635 - 393 WP_005427021 conjugal transfer protein orf17a
CD630_RS17740 (CD630_33400) 3904725..3905222 - 498 WP_011861919 antirestriction protein ArdA -
CD630_RS20085 3905239..3905511 - 273 WP_231300324 antirestriction protein ArdA -
CD630_RS17750 3905666..3905809 + 144 WP_022621533 hypothetical protein -
CD630_RS17755 (CD630_33420) 3905806..3906312 - 507 WP_011861920 superinfection exclusion B family protein -
CD630_RS17760 (CD630_33421) 3906498..3906719 - 222 WP_002570387 hypothetical protein orf19
CD630_RS17765 (CD630_33430) 3906771..3907982 - 1212 WP_032506928 MobT family relaxase -
CD630_RS17770 (CD630_33440) 3908146..3909543 - 1398 WP_011861922 FtsK/SpoIIIE domain-containing protein virb4
CD630_RS17775 (CD630_33450) 3909579..3909956 - 378 WP_011861923 YdcP family protein orf23
CD630_RS17780 (CD630_33460) 3909978..3910292 - 315 WP_002578441 YdcP family protein orf23
CD630_RS17785 (CD630_33470) 3910549..3911223 + 675 WP_011861924 hypothetical protein -
CD630_RS17790 (CD630_33480) 3911224..3912117 + 894 WP_011861925 MBL fold metallo-hydrolase -
CD630_RS17795 (CD630_33490) 3912316..3914301 - 1986 WP_011861926 collagen-like exosporium glycoprotein BclA3 -

Host bacterium

ID   268 Element type   ICE (Integrative and conjugative element)
Element name   ICE_Cdi630_fic GenBank   NC_009089
Element size   4290252 bp Coordinate of oriT [Strand]   2494..2626 [+]
Host bacterium   Clostridioides difficile 630 Coordinate of element   585378..606047

Cargo genes

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