ICEberg
I. Information of ICE
ICEberg ID56
Name ICEclc(B13) This ICE is derived from experimental literature
ICEO ID ICEO_0000108
OrganismPseudomonas knackmussii B13
Size (bp)102766
GC content [Genome] (%)62.51
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 
Putative oriT region -
Putative relaxase coordinates: 50240..52087;   Family:  MOBH


II. ICE interaction with IME/CIME/

The interaction information of ICEclc(B13) is not available.



The graph information of ICEclc(B13) components from AJ617740
Complete gene list of ICEclc(B13) from AJ617740
#Gene Coordinates [+/-], size (bp) Product 
(GenBank annotation)		 *Reannotation 
1intB13262..2235 [+], 1974integraseIntegrase 
2-2848..4233 [-], 1386putative permease
3-4438..5157 [-], 720oxidoreductase
4-5512..5991 [-], 480putative ring dioxygenase beta
5-5994..7256 [-], 1263large subunit aromatic dioxygenase
6-8052..9035 [-], 984hypothetical protein
7clcE9151..10209 [-], 1059maleylacetate reductase
8clcD10206..10916 [-], 711dienelactone hydrolase
9-10938..11921 [-], 984hypothetical protein
10clcB11948..13060 [-], 1113chloromuconate cycloisomerase
11clcA13057..13839 [-], 783chlorocatechol 1,2-dioxygenase
12clcR14009..14893 [+], 885LysR family transcriptional regulator
13-15037..15387 [-], 351putative threonine efflux protein
14-15405..15647 [-], 243hypothetical protein
15-15675..16103 [-], 429chlorocatechol 1,2-dioxygenase
16-16054..16494 [-], 441putative outer membrane protein
17- (tciR)17162..17959 [-], 798transcriptional regulatorTciR; global regulator for ICEclc activation; [PMID: 24945944] 
18- (mfsR)18502..19188 [-], 687transcriptional regulatorMfsR; global regulator for ICEclc activation; [PMID: 24945944] 
19-19619..20563 [-], 945hypothetical protein
20-20709..21128 [-], 420hypothetical protein
21-21241..21900 [-], 660TetR-type transcriptional regulator
22-21922..22674 [-], 753hypothetical protein
23-22813..23430 [-], 618putative aminophenol repressor
24-23526..23939 [+], 414ferredoxin-like protein
25-23951..24865 [+], 915uncharacterized conserved protein
26-24910..25722 [+], 8132-aminophenol 1,6-dioxygenase alpha subunit
27-25781..27259 [+], 14792-aminomuconic semialdehyde dehydrogenase
28-27249..27701 [+], 4532-aminomuconate deaminase
29-27716..28525 [+], 810putative 2-keto-4-pentenoate hydratase
30-28522..29286 [+], 765putative 4-oxalocrotonate decarboxylase
31-29347..30288 [+], 942acetylating aldehyde dehydrogenase
32-30304..31341 [+], 1038putative 4-hydroxy-2-ketovalerate aldolase
33-31453..31953 [+], 501hypothetical protein
34-31950..32345 [+], 396hypothetical protein
35-32963..34498 [+], 1536putative outer membrane protein or channel-forming component
36-34495..36069 [+], 1575putative permease of the major facilitator superfamily
37-36077..37111 [+], 1035putative multidrug efflux pump
38-37143..37445 [+], 303hypothetical protein
39-37489..38133 [+], 645hypothetical protein
40-38184..39365 [+], 1182putative esterase of the alpha-beta hydrolase superfamily
41-39860..40894 [-], 1035hypothetical protein
42-40922..41917 [-], 996predicted amidohydrolase/nitrilase
43-41973..43385 [-], 1413putative acyl-CoA synthetase
44-43387..44967 [-], 1581putative acyl-CoA synthetase
45-45180..46136 [+], 957putative transcriptional regulator
46-46315..46698 [-], 384hypothetical protein
47-46777..46932 [-], 156transposase
48-47630..48811 [-], 1182putative transport protein
49-48922..49725 [+], 804putative transcriptional regulator
50-50240..52087 [-], 1848hypothetical proteinRelaxase, MOBH Family
51-52324..52710 [+], 387hypothetical protein
52-52710..53168 [+], 459hypothetical protein
53-53196..53573 [+], 378hypothetical protein
54-53587..55104 [-], 1518hypothetical proteinTfc19, T4SS component 
55-55120..55479 [-], 360hypothetical protein
56-55476..56873 [-], 1398hypothetical proteinTfc22, T4SS component 
57-56883..57830 [-], 948hypothetical proteinTfc23, T4SS component 
58-57827..58273 [-], 447hypothetical proteinTfc24, T4SS component 
59-58432..58926 [-], 495putative DNA repair protein
60-59110..59874 [-], 765putative protein-disulfide isomerase
61-59888..62755 [-], 2868conserved hypothetical protein with VirB4 domainTfc16, T4SS component 
62-62755..63195 [-], 441hypothetical proteinTfc15, T4SS component 
63-63176..64594 [-], 1419hypothetical proteinTfc14, T4SS component 
64-64584..65516 [-], 933hypothetical proteinTfc13, T4SS component 
65-65513..66205 [-], 693hypothetical proteinTfc12, T4SS component 
66-66202..66612 [-], 411hypothetical proteinTfc11, T4SS component 
67-66625..66984 [-], 360hypothetical proteinTfc10, T4SS component 
68-67001..67234 [-], 234hypothetical protein
69-67231..67614 [-], 384hypothetical proteinTfc9, T4SS component 
70-67800..68204 [+], 405hypothetical protein
71-68241..68990 [-], 750hypothetical proteinTfc8, T4SS component 
72-68987..71173 [-], 2187hypothetical proteinTfc6, T4SS component 
73-71178..71726 [-], 549hypothetical proteinTfc5, T4SS component 
74-71723..72313 [-], 591hypothetical proteinTfc4, T4SS component 
75-72295..73014 [-], 720hypothetical proteinTfc3, T4SS component 
76-73029..73679 [-], 651hypothetical proteinTfc2, T4SS component 
77-73676..74296 [-], 621hypothetical proteinTfc2, T4SS component 
78-74436..75305 [-], 870hypothetical protein
79-75419..77698 [-], 2280putative DNA/RNA helicase
80-77798..78907 [-], 1110hypothetical protein
81-78972..79622 [-], 651hypothetical protein
82-79699..79959 [-], 261hypothetical protein
83-79976..80383 [-], 408hypothetical protein
84-80480..80812 [-], 333plasmid protein
85-80908..81597 [-], 690hypothetical protein
86-81655..82572 [-], 918hypothetical protein
87-83350..84192 [-], 843phage-related protein
88-84338..84691 [-], 354hypothetical protein
89-84835..85647 [-], 813hypothetical protein
90-85934..86212 [-], 279hypothetical protein
91-86310..87047 [-], 738hypothetical protein
92-87127..87939 [-], 813hypothetical protein
93-87986..88378 [-], 393hypothetical protein
94-88400..88612 [-], 213hypothetical protein
95-89247..89501 [-], 255hypothetical protein
96-89746..91347 [-], 1602putative DNA methyltransferase
97-91884..93896 [-], 2013putative DNA topoisomerase III
98- (ssb)94175..94615 [-], 441putative single-stranded DNA binding proteinSsb; single-strand DNA binding protein; [PMID: 19943900] 
99inrR94689..95216 [-], 528probable transcriptional regulator
100-95213..95992 [-], 780hypothetical protein
101-96323..97567 [-], 1245hypothetical protein
102-97571..98131 [-], 561hypothetical protein
103- (parB)98147..99799 [-], 1653hypothetical proteinParB; bacterial partitioning protein; [PMID: 11522360] 
104- (shi)99792..100049 [-], 258hypothetical proteinShi; Impairment of cell division; [PMID: 23333318] 
105- (parA)100033..100908 [-], 876hypothetical proteinParA; bacterial partitioning protein; [PMID: 11522360] 
106- (alpA)100952..101164 [-], 213putative transcriptional regulatorAlpA; outer membrane (OM) protein; [PMID: 10200971] 
107-101284..102039 [-], 756hypothetical protein
 

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. [PubMed: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. [PubMed: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. [PubMed: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. 0.522916667. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed:9791097] experimental
 
experimental experimental literature

Genomics & Bioinformatics Group in MML, SJTU