Evolution of secondary structure in the family of 7SL-like RNAs

1994 ◽  
Vol 39 (5) ◽  
Author(s):  
Damian Labuda ◽  
Ewa Zitkiewicz
Keyword(s):  
Secondary Structure ◽  
The Family

In silico, Physico-chemical characterization and analysis of Sandalwood proteins

2018 ◽  
Vol 3 (02) ◽  
pp. 150-157
Author(s):  
Asad Amir ◽  
Neelesh Kapoor ◽  
Hirdesh Kumar ◽  
Mohd. Tariq ◽  
Mohd. Asif Siddiqui
Keyword(s):  
Secondary Structure ◽  
In Silico ◽  
Chemical Characterization ◽  
In Silico Analysis ◽  
Chemical Parameters ◽  
Physico Chemical ◽  
In Silico Studies ◽  
The Family ◽  
Silico Analysis

Sandalwood is a commercially and culturally important plant species belonging to the family Santalaceae and the genus Santalum. In Indian sandalwood is renowned for its oil, which is highly rated for its sweet, fragrant, persistent aroma and the fixative property which is highly demanded by the perfume industry. For better production and varieties, requires to understanding the functions of proteins, their analysis and characterization of proteins sequences and their structures, their localizations in cell and their interaction with other functional partner. Due to limited number of in silico studies on sandalwood, in the present study we have performed in silico analysis by characterization of sandalwood proteins. Total 23 proteins were obtained and characterization using UniProtKB, identifying their physico-chemical parameters using ProtParam tool and prediction of their secondary structure elements using GOR of all 23 proteins.

scholarly journals Comprehensive Secondary Structure Elucidation of Four Genera of the Family Pospiviroidae

PLoS ONE ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. e98655 ◽  
Author(s):  
Tamara Giguère ◽  
Charith Raj Adkar-Purushothama ◽  
Jean-Pierre Perreault
Keyword(s):  
Secondary Structure ◽  
Structure Elucidation ◽  
The Family

scholarly journals Uncovering of Cytochrome P450 Anatomy by SecStrAnnotator

2020 ◽  
Author(s):  
Adam Midlik ◽  
Veronika Navrátilová ◽  
Taraka Ramji Moturu ◽  
Jaroslav Koča ◽  
Radka Svobodová ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Cytochromes P450 ◽  
Specific Protein ◽  
Protein Family ◽  
Homologous Proteins ◽  
Functional Relationships ◽  
Biotransformation Enzymes ◽  
The Family ◽  
Family Based ◽  
Typical Length

AbstractMotivationProtein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of homologous structures and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, assigning always the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs and their variability provides an overview of the studied protein family and can be used to enrich the analysis of a particular protein at hand.ResultsWe developed a workflow for analysis of the secondary structure anatomy of a protein family, based on SSE annotation tool SecStrAnnotator. We applied this analysis to the model family of cytochromes P450 (CYPs) – a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, as well as the conservation/variability of these properties. We also suggest a generic residue numbering scheme for the CYP family. The comparison between the bacterial and eukaryotic part of the family highlights the major differences and reveals an anomalous group of bacterial CYPs with some typically eukaryotic features. This hints at possible evolutionary and functional relationships.AvailabilityThe software and data are available at https://webchem.ncbr.muni.cz/Wiki/[email protected], [email protected]

scholarly journals Conserved Motifs and Domains in Members of Pospiviroidae

Cells ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 230
Author(s):  
Kevin-Phil Wüsthoff ◽  
Gerhard Steger
Keyword(s):  
Secondary Structure ◽  
Pairwise Alignment ◽  
Functional Domains ◽  
Alignment Method ◽  
Conserved Motifs ◽  
Fixed Domain ◽  
Original Hypothesis ◽  
The Family

In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family : their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain”; this article is one of the most cited in the field of viroids. Employing the pairwise alignment method used by Keese and Symons and in addition to more recent methods, we tried to reproduce the original results and extent them to further members of which were unknown in 1985. Indeed, individual members of consist of a patchwork of sequence fragments from the family but the lengths of fragments do not point to consistent points of rearrangement, which is in conflict with the original hypothesis of fixed domain borders.

scholarly journals Multigene-Based Analyses of the Phylogenetic Evolution of Oligotrich Ciliates, with Consideration of the Internal Transcribed Spacer 2 Secondary Structure of Three Systematically Ambiguous Genera

2013 ◽  
Vol 12 (3) ◽  
pp. 430-437 ◽  
Author(s):  
Jiamei Li ◽  
Weiwei Liu ◽  
Shan Gao ◽  
Alan Warren ◽  
Weibo Song
Keyword(s):  
Secondary Structure ◽  
Phylogenetic Trees ◽  
Internal Transcribed Spacers ◽  
Morphological Data ◽  
Its2 Region ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Content Type ◽  
Ssu Rrna Gene ◽  
The Family

ABSTRACT Oligotrichs are ciliates of great abundance, but their molecular systematics are rarely studied. In this study, nine species representing three genera ( Strombidium , Novistrombidium , and Omegastrombidium ) of marine oligotrich ciliates were collected from coastal waters of China. The small subunit (SSU) rRNA gene of two species and the internal transcribed spacers and 5.8S region (ITS1-5.8S-ITS2) for all nine species were sequenced for the first time. Phylogenetic trees using both the SSU rRNA gene and ITS1-5.8S-ITS2 region sequences were generated. In addition, the secondary structures of ITS2 RNA transcripts of 11 taxa representing four genera ( Novistrombidium , Strombidium , Omegastrombidium , and Laboea ) were investigated. The phylogenetic analyses show that (i) the family Strombidiidae is polyphyletic, (ii) the genus Novistrombidium is probably paraphyletic, containing at least two subclades, which is consistent with recent cladistic analyses based on morphological data, and (iii) the tail-less genus Laboea is separate from other genera of Strombidiidae, clustering instead with the tontoniids. Comparisons of the secondary structure of ITS2 regions also show that Laboea is clearly different from other strombidiids. These findings cast doubt on the monophyly of the family Strombidiidae.

scholarly journals Uncovering of cytochrome P450 anatomy by SecStrAnnotator

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adam Midlik ◽  
Veronika Navrátilová ◽  
Taraka Ramji Moturu ◽  
Jaroslav Koča ◽  
Radka Svobodová ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Cytochromes P450 ◽  
Substrate Recognition ◽  
Specific Protein ◽  
Homologous Proteins ◽  
Biotransformation Enzymes ◽  
Recognition Sites ◽  
The Family ◽  
Typical Length ◽  
Model Family

AbstractProtein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)—a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz.

STUDIES ON THE MORPHO-ANATOMICAL PARTICULARITIES OF LYSIMACHIA NUMMULARIA L.

2021 ◽  
Author(s):  
Suciu Felicia ◽  
Arcuș Mariana ◽  
Adrian Cosmin ◽  
Bucur Laura ◽  
Popescu Antoanela ◽  
...  
Keyword(s):  
Invasive Species ◽  
Secondary Structure ◽  
North America ◽  
Point Of View ◽  
Left Behind ◽  
Anatomical Analysis ◽  
Anatomical Point ◽  
The Family ◽  
Wet Ground ◽  
Primary Type

"The objective of the study was the histo-anatomical analysis of the root, stem and leaf belonging to the species Lysimachia nummularia L. from the Primulaceae family. The plant is native to Europe, but has been introduced to North America, where it is considered an invasive species in some areas. It aggressively spreads in favourable conditions, such as low wet ground or near ponds. It is moderately difficult to remove by hand pulling. Any tiny piece left behind will regrow. The research results led to the following assessments: root with primary structure and beginning of secondary structure, the presence of calcium oxalate druze in the bark, endoderm and primary type conducting bundles. The results of the study also demonstrated the existence of the stem with four prominent ribs, a meatic-type bark with small secretory channels and a central cylinder with a secondary structure. Another element studied from a histo-anatomical point of view; leaf with dorsi-ventral bifacial structure, with heterogeneous asymmetrical structure, collateral free-woody bundle, without periectors. From the morpho-anatomical data described, it can be concluded that the species Lysimachia nummularia L. belongs to the family Primulaceae and is related to other species of the genus Lysimachia."

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