ICEberg
I. Information of ICE
ICEberg ID3
Name CTnDOT This ICE is derived from experimental literature
FamilyCTnDOT/ERL
OrganismBacteroides thetaiotaomicron
Size (bp)~65 kb
GC content [Genome] (%)-
Insertion siteTTTGCNNNNN
FunctionTetracycline resistance and erythromycin resistance
Species that ICE can be transferred toBacteroides thetaiotaomicron; Bacteroides spp.; Escherichia coli
Nucleotide SequenceAJ431573; AF289050; AJ319661; AJ311171 (partial ICE sequence)
Putative oriT region -
Putative relaxase coordinates: 7955..8866; Locus tag: -;  Family:  MOBP


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 
1CTnDOT ermF region  [IME] experimentalin trans Bacteroides thetaiotaomicron Bacteroides thetaiotaomicron 11472924
2CTnDOT NBU1  [IME] experimentalin trans Bacteroides uniformis Bacteroides thetaiotaomicron 5482 8407835
3CTnDOT NBU2  [IME] experimentalin trans Bacteroides thetaiotaomicron; Bacteroides uniformis Bacteroides thetaiotaomicron 5482 8407835
4CTnDOT Tn4399 [IME] experimentalin trans Bacteroides Bacteroides 8397185

experimental This is an interactioin derived from experimental literature



The graph information of CTnDOT components from AF289050
Incomplete gene list of CTnDOT from AF289050
#Gene Coordinates [+/-], size (bp) Product 
(GenBank annotation)
*Reannotation 
1-1..702 [-], 702unknown
2-733..1980 [-], 1248unknown
3traA3069..3824 [+], 756TraApart of transfer region; [PMID: 11319931
4traB3830..4279 [+], 450TraBpart of transfer region; [PMID: 11319931
5traC4300..4659 [+], 360TraCpart of transfer region; [PMID: 11319931
6traD4656..5396 [+], 741TraDpart of transfer region; [PMID: 11319931
7traE5597..5914 [+], 318TraEpart of transfer region; [PMID: 11319931
8traF5926..6258 [+], 333TraFpart of transfer region; [PMID: 11319931
9traG6255..8771 [+], 2517TraGpart of transfer region; [PMID: 11319931
10traH8611..9186 [+], 576TraHpart of transfer region; [PMID: 11319931
11traI9211..9840 [+], 630TraIpart of transfer region; [PMID: 11319931
12traJ9845..10849 [+], 1005TraJpart of transfer region; [PMID: 11319931
13traK10882..11505 [+], 624TraKpart of transfer region; [PMID: 11319931
14traL11512..11832 [+], 321TraLpart of transfer region; [PMID: 11319931
15traM11813..13171 [+], 1359TraMpart of transfer region; [PMID: 11319931
16traN13209..14198 [+], 990TraNpart of transfer region; [PMID: 11319931
17traO14201..14776 [+], 576TraOpart of transfer region; [PMID: 11319931
18traP14803..15669 [+], 867TraPpart of transfer region; [PMID: 11319931
19traQ15683..16180 [+], 498TraQpart of transfer region; [PMID: 11319931


The graph information of CTnDOT components from AJ431573
Incomplete gene list of CTnDOT from AJ431573
#Gene Coordinates [+/-], size (bp) Product 
(GenBank annotation)
*Reannotation 
1-370..672 [-], 303hypothetical protein
2-704..1480 [-], 777hypothetical protein
3xis2c1284..1640 [+], 357excisionase of CTnDOTXis2c; resembles other Recombination Directionality Factors (RDFs); [PMID: 26104696
4xis2d1643..1993 [+], 351excisionase of CTnDOTXis2d; resembles other Recombination Directionality Factors (RDFs); [PMID: 26104696
5-2014..3582 [+], 1569hypothetical protein
6exc3644..5731 [+], 2088Exc proteina topoisomerases-related protein required for excision; [PMID: 11532130; 12453211
7-4397..5593 [-], 1197hypothetical protein
8rteR5562..5759 [+], 198RteR protein
9-5759..6346 [+], 588hypothetical protein


The graph information of CTnDOT components from AJ319661
Incomplete gene list of CTnDOT from AJ319661
#Gene Coordinates [+/-], size (bp) Product 
(GenBank annotation)
*Reannotation 
1-1..1569 [+], 1569hypothetical protein
2exc1631..3718 [+], 2088Exc proteina topoisomerases-related protein required for excision; [PMID: 11532130; 12453211


The graph information of CTnDOT components from AJ311171
Incomplete gene list of CTnDOT from AJ311171
#Gene Coordinates [+/-], size (bp) Product 
(GenBank annotation)
*Reannotation 
1intDOT847..2082 [+], 1236integrase proteinIntegrase 
2-2095..2457 [+], 363hypothetical protein
3intF2672..4006 [+], 1335putative integrase
4-4011..4196 [+], 186hypothetical protein
5-5172..5471 [+], 300hypothetical protein
6-5649..6518 [+], 870hypothetical protein
7prmF6589..7542 [+], 954hypothetical protein
8mobB7612..7974 [+], 363MobB proteinfunctional mobilization gene; [PMID: 11472924
9mobA7955..8866 [+], 912MobA proteinRelaxase, MOBP Family
10-8871..9464 [+], 594hypothetical protein
11aadS9763..10599 [-], 837aminoglycoside 6-adenylyltransferasea streptomycin resistance determinant; [PMID: 11472924
12tetX210775..11941 [-], 1167TetX2 proteinAR 
13tetX112110..13189 [-], 1080TetX1 protein
14ermF13555..14355 [+], 801rRNA adenine-N6 methyltransferaseAR 
15tpnF14593..15432 [+], 840TpnF protein
16-15901..16218 [-], 318hypothetical protein
17-16249..16734 [-], 486hypothetical protein
 
integrase Gene may contribute to site-specific recombination
conjugation Gene may play role in conjugative transfer
virulence  Gene may be involved in adaptative function

ElementNo. of sequencesDownload
Nucleotide sequences0Fasta
Proteins0Fasta
(1) Park J; Salyers AA (2011). Characterization of the Bacteroides CTnDOT regulatory protein RteC. J Bacteriol. 193(1):91-7. [PudMed:21037014] experimental
(2) Wood MM; Dichiara JM; Yoneji S; Gardner JF (2010). CTnDOT integrase interactions with attachment site DNA and control of directionality of the recombination reaction. J Bacteriol. 192(15):3934-43. [PudMed:20511494] experimental
(3) Laprise J; Yoneji S; Gardner JF (2010). Homology-dependent interactions determine the order of strand exchange by IntDOT recombinase. Nucleic Acids Res. 38(3):958-69. [PudMed:19952068] experimental
(4) Jeters RT; Wang GR; Moon K; Shoemaker NB; Salyers AA (2009). Tetracycline-associated transcriptional regulation of transfer genes of the Bacteroides conjugative transposon CTnDOT. J Bacteriol. 191(20):6374-82. [PudMed:19700528] experimental
(5) Malanowska K; Yoneji S; Salyers AA; Gardner JF (2007). CTnDOT integrase performs ordered homology-dependent and homology-independent strand exchanges. Nucleic Acids Res. 35(17):5861-73. [PudMed:17720706] experimental
(6) Moon K; Sonnenburg J; Salyers AA (2007). Unexpected effect of a Bacteroides conjugative transposon, CTnDOT, on chromosomal gene expression in its bacterial host. Mol Microbiol. 64(6):1562-71. [PudMed:17555438] experimental
(7) Dichiara JM; Mattis AN; Gardner JF (2007). IntDOT interactions with core- and arm-type sites of the conjugative transposon CTnDOT. J Bacteriol. 189(7):2692-701. [PudMed:17277054] experimental
(8) Malanowska K; Salyers AA; Gardner JF (2006). Characterization of a conjugative transposon integrase, IntDOT. Mol Microbiol. 60(5):1228-40. [PudMed:16689798] experimental
(9) Moon K; Shoemaker NB; Gardner JF; Salyers AA (2005). Regulation of excision genes of the Bacteroides conjugative transposon CTnDOT. J Bacteriol. 187(16):5732-41. [PudMed:16077120] experimental
(10) DiChiara JM; Salyers AA; Gardner JF (2005). In vitro analysis of sequence requirements for the excision reaction of the Bacteroides conjugative transposon, CTnDOT. Mol Microbiol. 56(4):1035-48. [PudMed:15853888] experimental
(11) Wang Y; Rotman ER; Shoemaker NB; Salyers AA (2005). Translational control of tetracycline resistance and conjugation in the Bacteroides conjugative transposon CTnDOT. J Bacteriol. 187(8):2673-80. [PudMed:15805513] experimental
(12) Sutanto Y; DiChiara JM; Shoemaker NB; Gardner JF; Salyers AA (2004). Factors required in vitro for excision of the Bacteroides conjugative transposon, CTnDOT. Plasmid. 52(2):119-30. [PudMed:15336489] experimental
(13) Wang Y; Shoemaker NB; Salyers AA (2004). Regulation of a Bacteroides operon that controls excision and transfer of the conjugative transposon CTnDOT. J Bacteriol. 186(9):2548-57. [PudMed:15090494] experimental
(14) Whittle G; Shoemaker NB; Salyers AA (2002). The role of Bacteroides conjugative transposons in the dissemination of antibiotic resistance genes. Cell Mol Life Sci. 59(12):2044-54. [PudMed:12568330]
(15) Sutanto Y; Shoemaker NB; Gardner JF; Salyers AA (2002). Characterization of Exc, a novel protein required for the excision of Bacteroides conjugative transposon. Mol Microbiol. 46(5):1239-46. [PudMed:12453211] experimental
(16) Cheng Q; Wesslund N; Shoemaker NB; Salyers AA; Gardner JF (2002). Development of an in vitro integration assay for the Bacteroides conjugative transposon CTnDOT. J Bacteriol. 184(17):4829-37. [PudMed:12169608] experimental
(17) Whittle G; Shoemaker NB; Salyers AA (2002). Characterization of genes involved in modulation of conjugal transfer of the Bacteroides conjugative transposon CTnDOT. J Bacteriol. 184(14):3839-47. [PudMed:12081954] experimental
(18) Cheng Q; Sutanto Y; Shoemaker NB; Gardner JF; Salyers AA (2001). Identification of genes required for excision of CTnDOT, a Bacteroides conjugative transposon. Mol Microbiol. 41(3):625-32. [PudMed:11532130] experimental
(19) Whittle G; Hund BD; Shoemaker NB; Salyers AA (2001). Characterization of the 13-kilobase ermF region of the Bacteroides conjugative transposon CTnDOT. Appl Environ Microbiol. 67(8):3488-95. [PudMed:11472924] experimental
(20) Cheng Q; Paszkiet BJ; Shoemaker NB; Gardner JF; Salyers AA (2000). Integration and excision of a Bacteroides conjugative transposon, CTnDOT. J Bacteriol. 182(14):4035-43. [PudMed:10869083] experimental
(21) Li LY; Shoemaker NB; Salyers AA (1995). Location and characteristics of the transfer region of a Bacteroides conjugative transposon and regulation of transfer genes. J Bacteriol. 177(17):4992-9. [PudMed:7665476] experimental
(22) Valentine PJ; Shoemaker NB; Salyers AA (1988). Mobilization of Bacteroides plasmids by Bacteroides conjugal elements. J Bacteriol. 170(3):1319-24. [PudMed:3343220] experimental
(23) Bedzyk LA; Shoemaker NB; Young KE; Salyers AA (1992). Insertion and excision of Bacteroides conjugative chromosomal elements. J Bacteriol. 174(1):166-72. [PudMed:1309516] experimental
 
experimental experimental literature