Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200298
Name   oriT_ICE_Cdi630_guaA in_silico
Organism   Clostridioides difficile 630
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_009089 (_)
oriT length   126 nt
IRs (inverted repeats)      101..107, 120..126  (TGTCAAC..GTTGACA)
 61..66, 78..83  (AATCCC..GGGATT)
 2..8, 19..25  (ACCCCTC..GAGGGGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 126 nt

>oriT_ICE_Cdi630_guaA
AACCCCTCGTATCTAACAGAGGGGTACAAATCGACAGGTAACAACCAAACAACAGGGCAGAATCCCACGGTACACAAGGGATTTTCCCATATCCGGCGTGTGTCAACAAGGCTCTGAAAGTTGACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14335 GenBank   WP_032506928
Name   mobT_CD630_RS17765_ICE_Cdi630_guaA insolico UniProt ID   _
Length   403 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 403 a.a.        Molecular weight: 47872.61 Da        Isoelectric Point: 6.2843

>WP_032506928.1 MULTISPECIES: MobT family relaxase [Clostridia]
MRFFRQEGFSLNEETWVRDIKEKREIYGISQQKLALAAGITRPYLSDIETGKAHPSEALQEAITEALERF
NPDAPLEMLFDYVRIRFPTTDVKHIVEDVLRLKLSYFIHEDYGFYSYTEHYYLGDIFVLVSPELEKGVLL
ELKGRGCRQFESYLLAQERSWYEFFMDVLMEDGVMKRLDLAINDKTGILNIPHLTEKCRNEECISVFRSF
KSYRSGELVRREEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKHDIPIADAEVKNRFEIRLKNERAFYA
IRDLLEHDNPERTAFQIINRYVRFVDRDDTKPRSDWRISEEWEWFIGEHRGSLKLTTKPEPYSFERTLHW
LSHQVAPTLKLALRLDKMNHTQIVHDIITHARLTEKHEKILKQQAAAAKEVVL

  Protein domains


Predicted by InterproScan.

Helix-turn-helix (HTH_3)

(20-67)

Replication initiation factor (Rep_trans)

(174-378)

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

(78-166)


  Protein structure



No available structure.




T4CP

ID   16827 GenBank   WP_011861922
Name   tcpA_CD630_RS17770_ICE_Cdi630_guaA insolico UniProt ID   _
Length   465 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 465 a.a.        Molecular weight: 53978.86 Da        Isoelectric Point: 7.3405

>WP_011861922.1 MULTISPECIES: FtsK/SpoIIIE domain-containing protein [Clostridia]
MKQLFPRGKRIRPTDKDLMFHTALAALFPVFLLVVLLFHIRQIAGTNWQEVSLSQITQDVNIPYLLFSIG
MAGMVCLIAVLLFWRYRRDEVKQLIHRQKLARMVLENKWYESEQRKEDAFFKDLSSSRSKETITYFPKIY
YRMKQGLLHIRVEITLGKYQEQLLNLERKLESGLYCELTDKELKDSYVEYTLLYDTIANRISIEDVQAKD
GRLRLMENVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLRTNAVLFVLDPKNADLADLQAVMPDVYYK
KEDMLACIDRFYEEMMKRSEDMKLMENYRTGENYAYLGLPANFLIFDEYVAFMEMLGTKENAAVLNKLKQ
IVMLGRQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGETTKDFFLKQIKGRGYVDV
GTSVISEFYTPLVPKGHDFLKEIKKLTDSRQGVQAACEAEAAETD

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(227-350)

  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   -