ICEberg
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ICE family: ICEclc
ICEclc(B13) is a well studied ICE. We selected it as a reference and defined ICEclc family. We classified any ICE that encodes an integrase gene closely related to intB13;, defined as over 60% protein homology and that has significant sequence alignment and syntenic 'core' structure into the ICEclc family.

#IDICE nameStrainReplicon
148 in_silico ICEBxeLB400-1Burkholderia xenovorans LB400NC_007951
249 in_silico ICECmeCH34-1Cupriavidus metallidurans CH34NC_007973
350 in_silico ICEXcaVe85-1Xanthomonas campestris pv. vesicatoria str. 85-10NC_007508
451 in_silico ICEXcaCa8004-1Xanthomonas campestris pv. campestris str. 8004NC_007086
552 in_silico ICEPaeLESB58-1Pseudomonas aeruginosa LESB58NC_011770
653 in_silico ICEHaeULPAs1-1Herminiimonas arsenicoxydansNC_009138
754 in_silico ICETauDSM9187-1Tolumonas auensis DSM 9187NC_012691
855 in_silico ICEAciJS42-1Acidovorax sp. JS42NC_008782
956 experimental ICEclc(B13)Pseudomonas knackmussii B13-
1057 experimental ICEclc(JS705)Ralstonia sp. JS705-
11174 experimental PAGI-2Pseudomonas aeruginosa C-
12218 in_silico ICEAxyA8-1Achromobacter xylosoxidans A8NC_014640
13219 experimental ICE-GI1Bordetella petrii DSM 12804NC_010170
14220 experimental ICE-GI2Bordetella petrii DSM 12804NC_010170
15221 experimental ICE-GI3Bordetella petrii DSM 12804NC_010170
16222 experimental ICE-GI6Bordetella petrii DSM 12804NC_010170
17965 in_silico ICEclc(LB400)Burkholderia xenovorans LB400-
181010 experimental ICEPae690Pseudomonas aeruginosa-
191077 experimental ICEXTDAzoarcus sp. CIB
experimental Data derived from experimental literature
in_silico Putative ICEs predicted by bioinformatic methods
(1) Botelho J et al. (2018). Unravelling the genome of a Pseudomonas aeruginosa isolate belonging to the high-risk clone ST235 reveals an integrative conjugative element housing a blaGES-6 carbapenemase. J Antimicrob Chemother. 73(1):77-83. [PudMed:29029083]
(2) Zamarro MT et al. (2016). The ICEXTD of Azoarcus sp. CIB, an integrative and conjugative element with aerobic and anaerobic catabolic properties. Environ Microbiol. 18(12):5018-5031. [PudMed:27450529] experimental
(3) Martin-Moldes Z et al. (2015). Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features. Syst Appl Microbiol. 38(7):462-71. [PudMed:26259823] experimental in_silico
(4) Miyazaki R et al. (2015). Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environ Microbiol. 17(1):91-104. [PudMed:24803113] experimental in_silico
(5) Miyazaki R et al. (2012). Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element. PLoS Genet. 8(7):e1002818. [PudMed:22807690] experimental
(6) Miyazaki R et al. (2011). How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element. Mob Genet Elements. 1(1):82-84. [PudMed:22016851]
(7) Miyazaki R et al. (2011). A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13. Mol Microbiol. 79(3):743-58. [PudMed:21255116] experimental
(8) Gaillard M et al. (2010). Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13. BMC Microbiol. 0.522916667. [PudMed:20504315] experimental
(9) Lechner M et al. (2009). Genomic island excisions in Bordetella petrii. BMC Microbiol. 0.472916667. [PudMed:19615092] experimental
(10) Sentchilo V et al. (2009). Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13. Mol Microbiol. 72(5):1293-306. [PudMed:19432799] experimental
(11) Gaillard M et al. (2008). Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1. Proc Natl Acad Sci U S A. 105(19):7058-63. [PudMed:18448680] experimental
(12) Chain PS et al. (2006). Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A. 103(42):15280-7. [PudMed:17030797] in_silico
(13) Gaillard M et al. (2006). The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties. J Bacteriol. 188(5):1999-2013. [PudMed:16484212] experimental
(14) She Q et al. (2004). Archaeal integrases and mechanisms of gene capture. Biochem Soc Trans. 32(Pt 2):222-6. [PudMed:15046576]
(15) Sentchilo V et al. (2003). Characterization of two alternative promoters for integrase expression in the clc genomic island of Pseudomonas sp. strain B13. Mol Microbiol. 49(1):93-104. [PudMed:12823813] experimental
(16) Muller TA et al. (2003). Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia. Environ Microbiol. 5(3):163-73. [PudMed:12588296] experimental
(17) Larbig KD et al. (2002). Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. J Bacteriol. 184(23):6665-80. [PudMed:12426355] experimental
(18) Ravatn R et al. (1998). Int-B13, an unusual site-specific recombinase of the bacteriophage P4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of Pseudomonas sp. Strain B13. J Bacteriol. 180(21):5505-14. [PudMed:9791097] experimental
 
experimental experimental literature
in_silico in silico analysis literature