SAND, a New Protein Family: From Nucleic Acid to Protein Structure and Function Prediction

As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with experimentally determined function and structure. Thus, there is a considerable attention focused on the accurate prediction of gene function and structure from sequence by using bioinformatics. In the course of our analysis of genomic sequence fromFugu rubripes, we identified a novel gene,SAND, with significant sequence identity to hypothetical proteins predicted inSaccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, aDrosophila melanogastergene, and mouse and human cDNAs. Here we identify a furtherSANDhomologue in human andArabidopsis thalianaby use of standard computational tools. We describe the genomic organisation ofSANDin these evolutionarily divergent species and identify sequence homologues from EST database searches confirming the expression of SAND in over 20 different eukaryotes. We confirm the expression of two different SAND paralogues in mammals and determine expression of one SAND in other vertebrates and eukaryotes. Furthermore, we predict structural properties of SAND, and characterise conserved sequence motifs in this protein family.

Download Full-text

Identification and Analysis of Novel Amino-Acid Sequence Repeats inBacillus anthracisstr.AmesProteome Using Computational Tools

Comparative and Functional Genomics ◽

10.1155/2007/47161 ◽

2007 ◽

Vol 2007 ◽

pp. 1-23 ◽

Cited By ~ 2

Author(s):

G. R. Hemalatha ◽

D. Satyanarayana Rao ◽

L. Guruprasad

Keyword(s):

Amino Acid ◽

Amino Acid Residue ◽

Protein Sequence ◽

Amino Acid Residues ◽

Sequence Motifs ◽

Computational Tools ◽

Conserved Sequence ◽

Conserved Sequence Motifs ◽

Multiple Copies ◽

Domain 3

We have identified four repeats and ten domains that are novel in proteins encoded by theBacillus anthracisstr.Amesproteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residue YEFF domain, (4) 109-amino-acid-residue IMxxH domain, (5) 103-amino-acid-residue VxxT domain, (6) 84-amino-acid-residue ExW domain, (7) 104-amino-acid-residue NTGFIG domain, (8) 36-amino-acid-residue NxGK repeat, (9) 95-amino-acid-residue VYV domain, (10) 75-amino-acid-residue KEWE domain, (11) 59-amino-acid-residue AFL domain, (12) 53-amino-acid-residue RIDVK repeat, (13) (a) 41-amino-acid-residue AGQF repeat and (b) 42-amino-acid-residue GSAL repeat. A repeat or domain type is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure.

Download Full-text

Conserved sequence motifs among bacterial, eukaryotic, and archaeal phosphatases that define a new phosphohydrolase superfamily

Protein Science ◽

10.1002/pro.5560070722 ◽

1998 ◽

Vol 7 (7) ◽

pp. 1647-1652 ◽

Cited By ~ 96

Author(s):

Maria Cristina Thaller ◽

Serena Schippa ◽

Gian Maria Rossolini

Keyword(s):

Sequence Motifs ◽

Conserved Sequence ◽

Conserved Sequence Motifs

Download Full-text

Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA

Molecular Biology and Evolution ◽

10.1093/oxfordjournals.molbev.a025552 ◽

1996 ◽

Vol 13 (1) ◽

pp. 150-169 ◽

Cited By ~ 181

Author(s):

R. E. Hickson ◽

C. Simon ◽

A. Cooper ◽

G. S. Spicer ◽

J. Sullivan ◽

...

Keyword(s):

Secondary Structure ◽

12S Rrna ◽

Sequence Motifs ◽

Conserved Sequence ◽

The Third ◽

Conserved Sequence Motifs

Download Full-text

snRNP Sm proteins share two evolutionarily conserved sequence motifs which are involved in Sm protein-protein interactions.

The EMBO Journal ◽

10.1002/j.1460-2075.1995.tb07199.x ◽

1995 ◽

Vol 14 (9) ◽

pp. 2076-2088 ◽

Cited By ~ 137

Author(s):

H. Hermann ◽

P. Fabrizio ◽

V.A. Raker ◽

K. Foulaki ◽

H. Hornig ◽

...

Keyword(s):

Protein Interactions ◽

Sequence Motifs ◽

Protein Protein Interactions ◽

Sm Proteins ◽

Conserved Sequence ◽

Evolutionarily Conserved ◽

Conserved Sequence Motifs ◽

Sm Protein

Download Full-text

Ultraconserved Non-coding DNA Within Diptera and Hymenoptera

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401502 ◽

2020 ◽

Vol 10 (9) ◽

pp. 3015-3024 ◽

Cited By ~ 1

Author(s):

Thomas Brody ◽

Amarendra Yavatkar ◽

Alexander Kuzin ◽

Ward F Odenwald

Keyword(s):

Genomic Sequence ◽

Mosquito Species ◽

Phylogenetic Footprinting ◽

Reference Sequence ◽

Phylogenetic Groups ◽

Developmental Genes ◽

Coding Sequences ◽

Conserved Sequence ◽

Sequence Elements ◽

And Function

Abstract This study has taken advantage of the availability of the assembled genomic sequence of flies, mosquitos, ants and bees to explore the presence of ultraconserved sequence elements in these phylogenetic groups. We compared non-coding sequences found within and flanking Drosophila developmental genes to homologous sequences in Ceratitis capitata and Musca domestica. Many of the conserved sequence blocks (CSBs) that constitute Drosophila cis-regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca. Also conserved is the position but not necessarily the orientation of many of these ultraconserved CSBs (uCSBs) with respect to flanking genes. Using the mosquito EvoPrint algorithm, we have also identified uCSBs shared among distantly related mosquito species. Side by side comparison of bee and ant EvoPrints of selected developmental genes identify uCSBs shared between these two Hymenoptera, as well as less conserved CSBs in either one or the other taxon but not in both. Analysis of uCSBs in these dipterans and Hymenoptera will lead to a greater understanding of their evolutionary origin and function of their conserved non-coding sequences and aid in discovery of core elements of enhancers. This study applies the phylogenetic footprinting program EvoPrinter to detection of ultraconserved non-coding sequence elements in Diptera, including flies and mosquitos, and Hymenoptera, including ants and bees. EvoPrinter outputs an interspecies comparison as a single sequence in terms of the input reference sequence. Ultraconserved sequences flanking known developmental genes were detected in Ceratitis and Musca when compared with Drosophila species, in Aedes and Culex when compared with Anopheles, and between ants and bees. Our methods are useful in detecting and understanding the core evolutionarily hardened sequences required for gene regulation.

Download Full-text

Classification and characterization of multigene family proteins of African swine fever viruses

Briefings in Bioinformatics ◽

10.1093/bib/bbaa380 ◽

2020 ◽

Author(s):

Zhaozhong Zhu ◽

Huiting Chen ◽

Li Liu ◽

Yang Cao ◽

Taijiao Jiang ◽

...

Keyword(s):

Multigene Family ◽

Copy Number ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Copy Number Variations ◽

Network Clustering ◽

Sequence Motifs ◽

Conserved Sequence ◽

Protein Sequence Homology ◽

And Function

Abstract African swine fever virus (ASFV) poses serious threats to the pig industry. The multigene family (MGF) proteins are extensively distributed in ASFVs and are generally classified into five families, including MGF-100, MGF-110, MGF-300, MGF-360 and MGF-505. Most MGF proteins, however, have not been well characterized and classified within each family. To bridge this gap, this study first classified MGF proteins into 31 groups based on protein sequence homology and network clustering. A web server for classifying MGF proteins was established and kept available for free at http://www.computationalbiology.cn/MGF/home.html. Results showed that MGF groups of the same family were most similar to each other and had conserved sequence motifs; the genetic diversity of MGF groups varied widely, mainly due to the occurrence of indels. In addition, the MGF proteins were predicted to have large structural and functional diversity, and MGF proteins of the same MGF family tended to have similar structure, location and function. Reconstruction of the ancestral states of MGF groups along the ASFV phylogeny showed that most MGF groups experienced either the copy number variations or the gain-or-loss changes, and most of these changes happened within strains of the same genotype. It is found that the copy number decrease and the loss of MGF groups were much larger than the copy number increase and the gain of MGF groups, respectively, suggesting the ASFV tended to lose MGF proteins in the evolution. Overall, the work provides a detailed classification for MGF proteins and would facilitate further research on MGF proteins.

Download Full-text