ICEberg
ICEberg ID56
NameICEclc(B13)
FamilyICEclc
OrganismPseudomonas knackmussii B13
Size (bp)102766
GC content [Genome] (%)62.5
Insertion sitetRNA-Gly
Function3-chlorobenzoic acid degradation
Species that ICE can be transferred toPseudomonas putida; Pseudomonas aeruginosa; Cupriavidus necator
Nucleotide SequenceAJ617740 (complete ICE sequence in this GenBank file)
Replicon-
Coordinates60..102843
Link to view genome context of this ICE in the genome browser
experimental This is a ICE derived from experimental literature.
Complete gene list of ICEclc(B13) form AJ617740
#GeneCoordinates [+/-], size (bp)Protein GI Product *
1intB13262..2235 [+], 197440019127  [UniProt] integrase
2-2848..4233 [-], 138640019128  [UniProt] putative permease
3-4438..5157 [-], 72040019129  [UniProt] oxidoreductase
4-5512..5991 [-], 48040019130  [UniProt] putative ring dioxygenase beta
5-5994..7256 [-], 126340019131  [UniProt] large subunit aromatic dioxygenase
6-8052..9035 [-], 98440019132  [UniProt] hypothetical protein
7clcE9151..10209 [-], 105940019133  [UniProt] maleylacetate reductase
8clcD10206..10916 [-], 71140019134  [UniProt] dienelactone hydrolase
9-10938..11921 [-], 98440019135  [UniProt] hypothetical protein
10clcB11948..13060 [-], 111340019136  [UniProt] chloromuconate cycloisomerase
11clcA13057..13839 [-], 78340019137  [UniProt] chlorocatechol 1,2-dioxygenase
12clcR14009..14893 [+], 88540019138  [UniProt] LysR family transcriptional regulator
13-15037..15387 [-], 35140019139  [UniProt] putative threonine efflux protein
14-15405..15647 [-], 24340019140  [UniProt] hypothetical protein
15-15675..16103 [-], 42940019141  [UniProt] chlorocatechol 1,2-dioxygenase
16-16054..16494 [-], 44140019142  [UniProt] putative outer membrane protein
17-17162..17959 [-], 79840019143  [UniProt] transcriptional regulator
18-18502..19188 [-], 68740019144  [UniProt] transcriptional regulator
19-19619..20563 [-], 94540019145  [UniProt] hypothetical protein
20-20709..21128 [-], 42040019146  [UniProt] hypothetical protein
21-21241..21900 [-], 66040019147  [UniProt] TetR-type transcriptional regulator
22-21922..22674 [-], 75340019148  [UniProt] hypothetical protein
23-22813..23430 [-], 61840019149  [UniProt] putative aminophenol repressor
24-23526..23939 [+], 41440019150  [UniProt] ferredoxin-like protein
25-23951..24865 [+], 91540019151  [UniProt] uncharacterized conserved protein
26-24910..25722 [+], 81340019152  [UniProt] 2-aminophenol 1,6-dioxygenase alpha subunit
27-25781..27259 [+], 147940019153  [UniProt] 2-aminomuconic semialdehyde dehydrogenase
28-27249..27701 [+], 45340019154  [UniProt] 2-aminomuconate deaminase
29-27716..28525 [+], 81040019155  [UniProt] putative 2-keto-4-pentenoate hydratase
30-28522..29286 [+], 76540019156  [UniProt] putative 4-oxalocrotonate decarboxylase
31-29347..30288 [+], 94240019157  [UniProt] acetylating aldehyde dehydrogenase
32-30304..31341 [+], 103840019158  [UniProt] putative 4-hydroxy-2-ketovalerate aldolase
33-31453..31953 [+], 50140019159  [UniProt] hypothetical protein
34-31950..32345 [+], 39640019160  [UniProt] hypothetical protein
35-32963..34498 [+], 153640019161  [UniProt] putative outer membrane protein or channel-forming component
36-34495..36069 [+], 157540019162  [UniProt] putative permease of the major facilitator superfamily
37-36077..37111 [+], 103540019163  [UniProt] putative multidrug efflux pump
38-37143..37445 [+], 30340019164  [UniProt] hypothetical protein
39-37489..38133 [+], 64540019165  [UniProt] hypothetical protein
40-38184..39365 [+], 118240019166  [UniProt] putative esterase of the alpha-beta hydrolase superfamily
41-39860..40894 [-], 103540019167  [UniProt] hypothetical protein
42-40922..41917 [-], 99640019168  [UniProt] predicted amidohydrolase/nitrilase
43-41973..43385 [-], 141340019169  [UniProt] putative acyl-CoA synthetase
44-43387..44967 [-], 158140019170  [UniProt] putative acyl-CoA synthetase
45-45180..46136 [+], 95740019171  [UniProt] putative transcriptional regulator
46-46315..46698 [-], 38440019172  [UniProt] hypothetical protein
47-46777..46932 [-], 15640019173 transposase
48-47630..48811 [-], 118240019174  [UniProt] putative transport protein
49-48922..49725 [+], 80440019175  [UniProt] putative transcriptional regulator
50-50240..52087 [-], 184840019176  [UniProt] hypothetical protein
51-52324..52710 [+], 38740019177  [UniProt] hypothetical proteinTA
52-52710..53168 [+], 45940019178  [UniProt] hypothetical proteinTA
53-53196..53573 [+], 37840019179  [UniProt] hypothetical protein
54-53587..55104 [-], 151840019180  [UniProt] hypothetical protein
55-55120..55479 [-], 36040019181  [UniProt] hypothetical protein
56-55476..56873 [-], 139840019182  [UniProt] hypothetical protein
57-56883..57830 [-], 94840019183  [UniProt] hypothetical protein
58-57827..58273 [-], 44740019184  [UniProt] hypothetical protein
59-58432..58926 [-], 49540019185  [UniProt] putative DNA repair proteinVF
60-59110..59874 [-], 76540019186  [UniProt] putative protein-disulfide isomerase
61-59888..62755 [-], 286840019187  [UniProt] conserved hypothetical protein with VirB4 domain
62-62755..63195 [-], 44140019188  [UniProt] hypothetical protein
63-63176..64594 [-], 141940019189  [UniProt] hypothetical protein
64-64584..65516 [-], 93340019190  [UniProt] hypothetical protein
65-65513..66205 [-], 69340019191  [UniProt] hypothetical protein
66-66202..66612 [-], 41140019192  [UniProt] hypothetical protein
67-66625..66984 [-], 36040019193  [UniProt] hypothetical protein
68-67001..67234 [-], 23440019194  [UniProt] hypothetical protein
69-67231..67614 [-], 38440019195  [UniProt] hypothetical protein
70-67800..68204 [+], 40540019196  [UniProt] hypothetical protein
71-68241..68990 [-], 75040019197  [UniProt] hypothetical protein
72-68987..71173 [-], 218740019198  [UniProt] hypothetical protein
73-71178..71726 [-], 54940019199  [UniProt] hypothetical protein
74-71723..72313 [-], 59140019200  [UniProt] hypothetical protein
75-72295..73014 [-], 72040019201  [UniProt] hypothetical protein
76-73029..73679 [-], 65140019202  [UniProt] hypothetical protein
77-73676..74296 [-], 62140019203  [UniProt] hypothetical proteinVF
78-74436..75305 [-], 87040019204  [UniProt] hypothetical protein
79-75419..77698 [-], 228040019205  [UniProt] putative DNA/RNA helicase
80-77798..78907 [-], 111040019206  [UniProt] hypothetical protein
81-78972..79622 [-], 65140019207  [UniProt] hypothetical protein
82-79699..79959 [-], 26140019208  [UniProt] hypothetical protein
83-79976..80383 [-], 40840019209  [UniProt] hypothetical protein
84-80480..80812 [-], 33340019210  [UniProt] plasmid protein
85-80908..81597 [-], 69040019211  [UniProt] hypothetical protein
86-81655..82572 [-], 91840019212  [UniProt] hypothetical protein
87-83350..84192 [-], 84340019213  [UniProt] phage-related protein
88-84338..84691 [-], 35440019214  [UniProt] hypothetical protein
89-84835..85647 [-], 81340019215  [UniProt] hypothetical protein
90-85934..86212 [-], 27940019216  [UniProt] hypothetical protein
91-86310..87047 [-], 73840019217  [UniProt] hypothetical protein
92-87127..87939 [-], 81340019218  [UniProt] hypothetical protein
93-87986..88378 [-], 39340019219  [UniProt] hypothetical protein
94-88400..88612 [-], 21340019220  [UniProt] hypothetical protein
95-89247..89501 [-], 25540019221  [UniProt] hypothetical protein
96-89746..91347 [-], 160240019222  [UniProt] putative DNA methyltransferase
97-91884..93896 [-], 201340019223  [UniProt] putative DNA topoisomerase III
98-94175..94615 [-], 44140019224  [UniProt] putative single-stranded DNA binding protein
99inrR94689..95216 [-], 52840019225  [UniProt] probable transcriptional regulator
100-95213..95992 [-], 78040019226  [UniProt] hypothetical protein
101-96323..97567 [-], 124540019227  [UniProt] hypothetical protein
102-97571..98131 [-], 56140019228  [UniProt] hypothetical protein
103-98147..99799 [-], 165340019229  [UniProt] hypothetical protein
104-99792..100049 [-], 25840019230  [UniProt] hypothetical protein
105-100033..100908 [-], 87640019231  [UniProt] hypothetical protein
106-100952..101164 [-], 21340019232  [UniProt] putative transcriptional regulatorVF
107-101284..102039 [-], 75640019233  [UniProt] hypothetical protein
 
integrase Gene may contribute to site-specific recombination
conjugation Gene may play role in conjugative transfer
regulation Gene may play role in regulation of transfer

ElementNo. of sequencesDownload
Nucleotide sequences1Fasta
Proteins107Fasta
(1) Miyazaki R; Minoia M; Pradervand N; Sulser S; Reinhard F; van der Meer JR (2012). Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element. PLoS Genet. 8(7):e1002818. [PudMed:22807690] experimental
(2) Miyazaki R; van der Meer JR (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]
(3) Miyazaki R; van der Meer JR (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
(4) Gaillard M; Pradervand N; Minoia M; Sentchilo V; Johnson DR; van der Meer JR (2010). Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13. BMC Microbiol. 10:153. [PudMed:20504315] experimental
(5) Sentchilo V; Czechowska K; Pradervand N; Minoia M; Miyazaki R; van der Meer JR (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
(6) Gaillard M; Pernet N; Vogne C; Hagenbuchle O; van der Meer JR (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
(7) Gaillard M; Vallaeys T; Vorholter FJ; Minoia M; Werlen C; Sentchilo V; Puhler A; van der Meer JR (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
(8) She Q; Shen B; Chen L (2004). Archaeal integrases and mechanisms of gene capture. Biochem Soc Trans. 32(Pt 2):222-6. [PudMed:15046576]
(9) Sentchilo V; Zehnder AJ; van der Meer JR (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
(10) Ravatn R; Studer S; Zehnder AJ; van der Meer JR (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