Abstract：
BACKGROUND:The highly conserved bHLH (basic Helix-Loop-Helix) domain, found in many transcription factors, has been well characterized separately in Plants, Animals, and Fungi. While conserved, even functionally constrained sites have varied since the Eukarya split. Our research identifies those slightly variable sites that were highly characteristic of Plants, Animals, or Fungi. RESULTS:Through discriminant analysis, we identified five highly discerning DNA-binding amino acid sites. Additionally, by incorporating Kingdom specific HMMs, we were able to construct a tool to quickly and accurately identify and classify bHLH sequences using these sites. CONCLUSIONS:We conclude that highly discerning sites identified through our analysis were likely under functional constraints specific to each Kingdom. We also demonstrated the utility of our tool by identifying and classifying previously unknown bHLH domains in both characterized genomes and from sequences in a large environmental sample.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Sailsbery JK,Dean RAdoi
10.1186/1471-2148-12-154subject
Has Abstractpub_date
2012-08-24 00:00:00pages
154issn
1471-2148pii
1471-2148-12-154journal_volume
12pub_type
杂志文章abstract：BACKGROUND:Publication of the first diatom genome, that of Thalassiosira pseudonana, established it as a model species for experimental and genomic studies of diatoms. Virtually every ensuing study has treated T. pseudonana as a marine diatom, with genomic and experimental data valued for their insights into the ecolog...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-11-125
更新日期：2011-05-14 00:00:00
abstract：BACKGROUND:Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important characteristics, vertebrates obtained a well developed brain, anterior sensory structures, a closed...
journal_title：BMC evolutionary biology
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更新日期：2011-08-09 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-14-16
更新日期：2014-01-24 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-1-13
更新日期：2001-01-01 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-9-42
更新日期：2009-02-19 00:00:00
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journal_title：BMC evolutionary biology
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更新日期：2013-07-15 00:00:00
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更新日期：2010-11-02 00:00:00
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更新日期：2008-07-07 00:00:00
abstract：BACKGROUND:The Neotropical ovenbird-woodcreeper family (Furnariidae) is an avian group characterized by exceptionally diverse ecomorphological adaptations. For instance, members of the family are known to construct nests of a remarkable variety. This offers a unique opportunity to examine whether changes in nest design...
journal_title：BMC evolutionary biology
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更新日期：2009-11-21 00:00:00
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更新日期：2015-12-21 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2014-02-18 00:00:00
abstract：BACKGROUND:Hybridization between incipient species is expected to become progressively limited as their genetic divergence increases and reproductive isolation proceeds. Amphibian radiations and their secondary contact zones are useful models to infer the timeframes of speciation, but empirical data from natural system...
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pub_type： 杂志文章
doi：10.1186/s12862-015-0385-2
更新日期：2015-08-08 00:00:00
abstract：BACKGROUND:Computer-assisted analyses have shown that all bacterial genomes contain a small percentage of open reading frames with a frameshift or in-frame stop codon We report here a comparative analysis of these interrupted coding sequences (ICDSs) in six isolates of M. tuberculosis, two of M. bovis and one of M. afr...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2008-03-06 00:00:00
abstract：BACKGROUND:The Amazon molly (Poecilia formosa) is a small unisexual fish that has been suspected of being threatened by extinction from the stochastic accumulation of slightly deleterious mutations that is caused by Muller's ratchet in non-recombining populations. However, no detailed quantification of the extent of th...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-8-88
更新日期：2008-03-19 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-13-9
更新日期：2013-01-12 00:00:00
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pub_type： 杂志文章
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更新日期：2006-02-23 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2013-06-10 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-016-0685-1
更新日期：2016-05-20 00:00:00
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更新日期：2015-04-19 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2014-01-13 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-7-S1-S12
更新日期：2007-02-08 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-014-0261-5
更新日期：2014-12-19 00:00:00
abstract：BACKGROUND:Marine threespine sticklebacks colonized and adapted to brackish and freshwater environments since the last Pleistocene glacial. Throughout the Holarctic, three lateral plate morphs are observed; the low, partial and completely plated morph. We test if the three plate morphs in the brackish water Lake Engerv...
journal_title：BMC evolutionary biology
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更新日期：2018-02-05 00:00:00
abstract：BACKGROUND:Symbioses between invertebrates and prokaryotes are biological systems of particular interest in order to study the evolution of mutualism. The symbioses between the entomopathogenic nematodes Steinernema and their bacterial symbiont Xenorhabdus are very tractable model systems. Previous studies demonstrated...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-6-68
更新日期：2006-09-05 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-017-0905-3
更新日期：2017-02-20 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2011-04-19 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2019-01-14 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2010-05-06 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2007-08-16 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-019-1384-5
更新日期：2019-02-26 00:00:00
