Abstract:
Background:Insight into the function of carbohydrate-active enzymes is required to understand their biological role and industrial potential. There is a need for better use of the ample genomic data in order to enable selection of the most interesting proteins for further studies. The basis for elaborating a new approach to sequence analysis is the hypothesis that when using conserved peptide patterns to determine the similarities between proteins, the exact spacing between conserved adjacent amino acids in the proteins plays a prominent functional role. Thus, the objective of developing the method of conserved unique peptide patterns (CUPP) is to construct a peptide-based grouping and validate the method to provide evidence that CUPP captures function-related features of the individual carbohydrate-active enzymes (as defined by CAZy families). This approach facilitates grouping of enzymes at a level lower than protein families and/or subfamilies. A standardized, efficient, and robust approach to functional annotation of carbohydrate-active enzymes would support improved molecular insight into enzyme-substrate interaction. Results:A new nonalignment-based clustering and functional annotation tool was developed that uses conserved unique peptides patterns to perform automated clustering of proteins and formation of protein groups. A peptide-based model was constructed for each of these protein CUPP groups to be used to automatically annotate protein family, subfamily, and EC function of carbohydrate-active enzymes. CUPP prediction can annotate proteins (from any CAZy family) with high F-score to existing family (0.966), subfamily (0.961), and EC-function (0.843). The speed of the CUPP program was estimated and exemplified by prediction of the 504,017 nonredundant proteins of CAZy in less than four CPU hours. Conclusion:It was possible to construct an automated system for clustering proteins within families and use the resulting CUPP groups to directly build peptide-based models for genome annotation. The CUPP runtime, F-score, sensitivity, and precisions of family and subfamily annotations match or represent an improvement compared to state-of-the-art tools. The speed of the CUPP annotation is similar to the rapid DIAMOND annotation tool. CUPP facilitates automated annotation of full genome assemblies to any CAZy family.
journal_name
Biotechnol Biofuelsjournal_title
Biotechnology for biofuelsauthors
Barrett K,Lange Ldoi
10.1186/s13068-019-1436-5subject
Has Abstractpub_date
2019-04-30 00:00:00pages
102issn
1754-6834pii
1436journal_volume
12pub_type
杂志文章abstract:BACKGROUND:The production of value-added chemicals alongside biofuels from lignocellulosic hydrolysates is critical for developing economically viable biorefineries. Here, the production of propionic acid (PA), a potential building block for C3-based chemicals, from corn stover hydrolysate is investigated using the nat...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-017-0884-z
更新日期:2017-08-17 00:00:00
abstract:Background:Plant seed oil is an important bioresource for human food and animal feed, as well as industrial bioproducts. Therefore, increasing oil content in seeds has been one of the primary targets in the breeding programs of oilseed crops. Thraustochytrium is a marine protist that can produce a high level of very lo...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1514-8
更新日期:2019-06-29 00:00:00
abstract:BACKGROUND:Starch is the second most abundant plant-derived biomass and a major feedstock in non-food industrial applications and first generation biofuel production. In contrast to lignocellulose, detailed insight into fungal degradation of starch is currently lacking. This study explores the secretomes of Aspergillus...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-016-0604-0
更新日期:2016-09-01 00:00:00
abstract:BACKGROUND:Consolidated bioprocessing (CBP) of lignocellulosic biomass to hydrogen offers great potential for lower cost and higher efficiency compared to processes featuring dedicated cellulase production. Current studies on CBP-based hydrogen production mainly focus on using the thermophilic cellulolytic bacterium Cl...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-7-82
更新日期:2014-06-03 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-016-0488-z
更新日期:2016-03-29 00:00:00
abstract::Biorefineries, designed for the production of lignocellulose-based chemicals and fuels, are receiving increasing attention from the public, governments, and industries. A major obstacle for biorefineries to advance to commercial scale is the high cost of the enzymes required to derive the fermentable sugars from the f...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章,评审
doi:10.1186/s13068-019-1571-z
更新日期:2019-10-08 00:00:00
abstract::[This retracts the article DOI: 10.1186/s13068-017-0920-z.]. ...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章,撤回出版物
doi:10.1186/s13068-018-1086-z
更新日期:2018-04-06 00:00:00
abstract:BACKGROUND:Low- and high-affinity glucose transport system is a conserved strategy of microorganism to cope with environmental glucose fluctuation for their growth and competitiveness. In Neurospora crassa, the dual-affinity glucose transport system consists of a low-affinity glucose transporter GLT-1 and two high-affi...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-021-01877-2
更新日期:2021-01-28 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-020-1648-8
更新日期:2020-01-17 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-6-28
更新日期:2013-02-20 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-020-01734-8
更新日期:2020-05-29 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-017-0702-7
更新日期:2017-01-19 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1378-y
更新日期:2019-02-27 00:00:00
abstract:BACKGROUND:Microalgae accumulate a considerable amount of lipids and carbohydrate under nutrient-deficient conditions, which makes them one of the promising sustainable resources for biofuel production. In the present study, to obtain the biomass with higher lipid and carbohydrate contents, we implemented a short-term ...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-017-0747-7
更新日期:2017-03-09 00:00:00
abstract:Background:l-Fucose is a rare sugar with potential uses in the pharmaceutical, cosmetic, and food industries. The enzymatic approach using l-fucose isomerase, which interconverts l-fucose and l-fuculose, can be an efficient way of producing l-fucose for industrial applications. Here, we performed biochemical and struct...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1619-0
更新日期:2019-12-05 00:00:00
abstract:BACKGROUND:In this study, the dilute maleic acid pretreatment of wheat straw is optimized, using pretreatment time, temperature and maleic acid concentration as design variables. A central composite design was applied to the experimental set up. The response factors used in this study are: (1) glucose benefits from imp...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-2-31
更新日期:2009-12-21 00:00:00
abstract:BACKGROUND:Switchgrass (Panicum virgatum L.) is a warm-season C4 grass that is a target lignocellulosic biofuel species. In many regions, drought stress is one of the major limiting factors for switchgrass growth. The objective of this study was to evaluate the drought tolerance of 49 switchgrass genotypes. The relativ...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-015-0342-8
更新日期:2015-09-22 00:00:00
abstract:Background:Camelina (Camelina sativa L.) is a promising oilseed crop that may provide sustainable feedstock for biofuel production. One of the major drawbacks of Camelina is its smaller seeds compared to other major oil crops such as canola, which limit oil yield and may also pose challenges in successful seedling esta...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-018-1334-2
更新日期:2018-12-18 00:00:00
abstract:Background:Saccharification is the most crucial and cost-intensive process in second generation biofuel production. The deficiency of β-glucosidase in commercial enzyme leads to incomplete biomass hydrolysis. The decomposition of biomass at high temperature environments leads us to isolate thermotolerant microbes with ...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-017-0932-8
更新日期:2017-10-30 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-016-0652-5
更新日期:2016-11-09 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1643-0
更新日期:2020-01-11 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-018-1280-z
更新日期:2018-10-11 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-019-1540-6
更新日期:2019-08-20 00:00:00
abstract:BACKGROUND:The recent development of improved enzymes and pentose-using yeast for cellulosic ethanol processes calls for new attention to the lignocellulose pretreatment step. This study assessed the influence of pretreatment pH, temperature, and time, and their interactions on the enzymatic glucose and xylose yields f...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-4-11
更新日期:2011-05-13 00:00:00
abstract:BACKGROUND:Lignocellulosic materials are abundant and among the most important potential sources for bioethanol production. Although the pretreatment of lignocellulose is necessary for efficient saccharification and fermentation, numerous by-products, including furan derivatives, weak acids, and phenolic compounds, are...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-1-3
更新日期:2008-04-15 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-018-1111-2
更新日期:2018-04-23 00:00:00
abstract:BACKGROUND:Saccharomyces cerevisiae, a key organism used for the manufacture of renewable fuels and chemicals, has been engineered to utilize non-native sugars derived from plant cell walls, such as cellobiose and xylose. However, the rates and efficiencies of these non-native sugar fermentations pale in comparison wit...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-014-0126-6
更新日期:2014-08-27 00:00:00
abstract:BACKGROUND:D-2,3-butanediol has many industrial applications such as chiral reagents, solvents, anti-freeze agents, and low freezing point fuels. Traditional D-2,3-butanediol producing microorganisms, such as Klebsiella pneumonia and K. xoytoca, are pathogenic and not capable of producing D-2,3-butanediol at high optic...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/1754-6834-7-16
更新日期:2014-01-29 00:00:00
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journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-016-0566-2
更新日期:2016-07-19 00:00:00
abstract:Background:Cyanobacteria are potential sources for third generation biofuels. Their capacity for biofuel production has been widely improved using metabolically engineered strains. In this study, we employed metabolic engineering design with target genes involved in selected processes including the fatty acid synthesis...
journal_title:Biotechnology for biofuels
pub_type: 杂志文章
doi:10.1186/s13068-018-1349-8
更新日期:2019-01-04 00:00:00