ICEberg
I. Information of ICE
ICEberg ID103
Name Tn5397 This ICE is derived from experimental literature
ICEO ID ICEO_0000256
OrganismClostridium difficile 630
Size (bp)20657
GC content [Genome] (%)38.32[29.06]
Insertion siteAT rich regions
FunctionTetracycline resistance
Species that ICE can be transferred toBacillus subtilis; Clostridium difficile
Nucleotide SequenceAM180355 (complete ICE sequence in this genome)
Replicon chromosome (4290252 bp, BioProject:78) [NC_009089]
Genome coordinates585384..606040 
Putative oriT region -
Putative relaxase coordinates: 588010..589218; Locus tag: CD630_04990;  Family:  MOBT


II. ICE interaction with IME/CIME/

The Interaction Network among ICE/IME/CIME


Detailed Informatioin of the Interaction Network
# ICE  Inter_Ele [Type] Methods Donors Recipients Exper_Ref 
1Tn5397 Tn5398 [CIME] insolicoin cis - - -

insolico This is a putative interactioin



The graph information of Tn5397 components from AM180355
Complete gene list of Tn5397 from AM180355
#Gene Coordinates [+/-], size (bp) Product 
(GenBank annotation)		 *Reannotation 
1CD630_04900580547..581599 [+], 1053putative sugar-phosphate dehydrogenase
2CD630_04910581655..582062 [+], 408PTS system, mannose/fructose/sorbose IIA component
3CD630_04920582091..582564 [+], 474PTS system, mannose/fructose/sorbose IIB component
4CD630_04930582611..583369 [+], 759PTS system, mannose/fructose/sorbose IIC component
5CD630_04940583393..584232 [+], 840PTS system, mannose/fructose/sorbose IID component
6CD630_04950584769..606563 [+], 21795Fragment of putative regulatory protein
7CD630_04960585695..586009 [+], 315putative conjugative transposon protein DUF961 family Tn5397, CTn3-Orf23
8CD630_04970586031..586417 [+], 387putative conjugative transposon protein DUF961 family Tn5397, CTn3-Orf22
9CD630_04980586451..587836 [+], 1386putative cell-division FtsK/SpoIIIE-family protein Tn5397, CTn3-Orf21Orf21_Tn, T4SS component 
10CD630_04981587839..587991 [+], 153putative conjugative transposon protein Tn5397,CTn3-Orf20.1
11CD630_04990588010..589218 [+], 1209putative replication initiation factor Tn5397,CTn3-Orf20Relaxase, MOBT Family
12CD630_04991589261..589482 [+], 222putative conjugative transposon protein Tn5397,CTn3-Orf19Orf19_Tn, T4SS component 
13CD630_05000589599..590096 [+], 498putative antirestriction protein Tn5397,CTn3-Orf18
14CD630_05010590184..590576 [+], 393putative conjugative transposon protein Tn5397,CTn3-Orf17Orf17_Tn, T4SS component 
15CD630_05020590560..593007 [+], 2448putative ATPase Tn5397, CTn3-Orf16Orf16_Tn, T4SS component 
16CD630_05030593007..595175 [+], 2169putative membrane protein Tn5397, CTn3-Orf15Orf15_Tn, T4SS component 
17CD630_05040595172..598820 [+], 3649Fragment of putative conjugative transposon protein Tn5397, CTn3-Orf14
18CD630_05060596830..598659 [+], 1830Reverse transcriptase/maturase/endonuclease,Group II intron
19CD630_05070598817..599749 [+], 933putative conjugative transposon protein Tn5397,CTn3-Orf13Orf13_Tn, T4SS component 
20CD630_05071599965..600018 [+], 54Fragment of Tet(M) leader peptide Tn5397,CTn3-orf12 (C-terminal region)
21tetM600034..601953 [+], 1920Tetracycline resistance protein Tn5397AR 
22CD630_05081602049..602243 [+], 195putative conjugative transposon protein Tn5397,CTn3-Orf6
23CD630_05090602302..602655 [-], 354Transcriptional regulator, HTH-type Tn5397,CTn3-Orf9
24CD630_05091602866..602931 [+], 66putative conjugative transposon protein Tn5397,CTn3-Orf10
25CD630_05100603157..603582 [+], 426putative RNA polymerase sigma factor Tn5397,CTn3-Orf7
26CD630_05101603579..603809 [+], 231putative conjugative transposon protein Tn5397,CTn3-Orf8
27CD630_05102603931..604068 [-], 138Fragment of putative conjugative transposon protein Tn5397, CTn3-Orf5 (C-terminal region)
28CD630_05103604190..604330 [+], 141putative conjugative transposon protein Tn5397,CTn3-Orf4
29tndX604427..606028 [+], 1602Recombinase site-specific resolvase family Tn5397, CTn3-Orf3Integrase 
30CD630_04950584769..606563 [+], 21795Fragment of putative regulatory protein
31CD630_05130606589..606777 [+], 189conserved hypothetical protein
 
flank Flanking regions

ElementNo. of sequencesDownload
Nucleotide sequences1Fasta
Proteins20Fasta
(1) Jasni AS; Mullany P; Hussain H; Roberts AP (2010). Demonstration of conjugative transposon (Tn5397)-mediated horizontal gene transfer between Clostridium difficile and Enterococcus faecalis. Antimicrob Agents Chemother. 54(11):4924-6. [PubMed:20713671] experimental
(2) Sebaihia M; Wren BW; Mullany P; Fairweather NF; Minton N; Stabler R; Thomson NR; Roberts AP; Cerdeno-Tarraga AM; Wang H; Holden MT; Wright A; Churcher C; Quail MA; Baker S; Bason N; Brooks K; Chillingworth T; Cronin A; Davis P; Dowd L; Fraser A; Feltwell T; Hance Z; Holroyd S; Jagels K; Moule S; Mungall K; Price C; Rabbinowitsch E; Sharp S; Simmonds M; Stevens K; Unwin L; Whithead S; Dupuy B; Dougan G; Barrell B; Parkhill J (2006). The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet. 38(7):779-86. [PubMed:16804543]
(3) Wang H; Smith MC; Mullany P (2006). The conjugative transposon Tn5397 has a strong preference for integration into its Clostridium difficile target site. J Bacteriol. 188(13):4871-8. [PubMed:16788196] experimental
(4) Roberts AP; Johanesen PA; Lyras D; Mullany P; Rood JI (2001). Comparison of Tn5397 from Clostridium difficile, Tn916 from Enterococcus faecalis and the CW459tet(M) element from Clostridium perfringens shows that they have similar conjugation regions but different insertion and excision modules. Microbiology. 147(Pt 5):1243-51. [PubMed:11320127] experimental
(5) Wang H; Mullany P (2000). The large resolvase TndX is required and sufficient for integration and excision of derivatives of the novel conjugative transposon Tn5397. J Bacteriol. 182(23):6577-83. [PubMed:11073898] experimental
(6) Wang H; Roberts AP; Lyras D; Rood JI; Wilks M; Mullany P (2000). Characterization of the ends and target sites of the novel conjugative transposon Tn5397 from Clostridium difficile: excision and circularization is mediated by the large resolvase, TndX. J Bacteriol. 182(13):3775-83. [PubMed:10850994] experimental
(7) Roberts AP; Pratten J; Wilson M; Mullany P (1999). Transfer of a conjugative transposon, Tn5397 in a model oral biofilm. FEMS Microbiol Lett. 177(1):63-6. [PubMed:10436923] experimental
(8) Mullany P; Pallen M; Wilks M; Stephen JR; Tabaqchali S (1996). A group II intron in a conjugative transposon from the gram-positive bacterium, Clostridium difficile. Gene. 174(1):145-50. [PubMed:8863741] experimental
(9) Mullany P; Wilks M; Tabaqchali S (1995). Transfer of macrolide-lincosamide-streptogramin B (MLS) resistance in Clostridium difficile is linked to a gene homologous with toxin A and is mediated by a conjugative transposon, Tn5398. J Antimicrob Chemother. 35(2):305-15. [PubMed:7759394] experimental
 
experimental experimental literature

Genomics & Bioinformatics Group in MML, SJTU