scholarly journals InterPro (The Integrated Resource of Protein Domains and Functional Sites)

Yeast ◽  
2000 ◽  
Vol 1 (4) ◽  
pp. 327-334
Author(s):  
Christopher Southan
Keyword(s):  
Comparative Genomics ◽  
Protein Domains ◽  
Protein Family ◽  
European Bioinformatics Institute ◽  
Protein Families ◽  
Functional Sites ◽  
The Family ◽  
Graphic Displays

The family and motif databases, PROSITE, PRINTS, Pfam and ProDom, have been integrated into a powerful resource for protein secondary annotation. As of June 2000, InterPro had processed 384 572 proteins in SWISS-PROT and TrEMBL. Because the contributing databases have different clustering principles and scoring sensitivities, the combined assignments compliment each other for grouping protein families and delineating domains. The graphic displays of all matches above the scoring thresholds enables judgements to be made on the concordances or differences between the assignments. The website links can be used to analyse novel sequences and for queries across the proteomes of 32 organisms, including the partial human set, by domain and/or protein family. An analysis of selected HtrA/DegQ proteases demonstrates the utility of this website for detailed comparative genomics. Further information on the project can be found at the European Bioinformatics Institute at http://www.ebi.ac.uk/interpro/.

scholarly journals Origins of coevolution between residues distant in protein 3D structures

2017 ◽  
Vol 114 (34) ◽  
pp. 9122-9127 ◽  
Author(s):  
Ivan Anishchenko ◽  
Sergey Ovchinnikov ◽  
Hetunandan Kamisetty ◽  
David Baker
Keyword(s):  
Structure Prediction ◽  
Structural Variation ◽  
Protein Structures ◽  
Direct Coupling ◽  
Protein Families ◽  
Oligomeric State ◽  
3D Structures ◽  
Functional Sites ◽  
Repeat Proteins ◽  
The Family

Residue pairs that directly coevolve in protein families are generally close in protein 3D structures. Here we study the exceptions to this general trend—directly coevolving residue pairs that are distant in protein structures—to determine the origins of evolutionary pressure on spatially distant residues and to understand the sources of error in contact-based structure prediction. Over a set of 4,000 protein families, we find that 25% of directly coevolving residue pairs are separated by more than 5 Å in protein structures and 3% by more than 15 Å. The majority (91%) of directly coevolving residue pairs in the 5–15 Å range are found to be in contact in at least one homologous structure—these exceptions arise from structural variation in the family in the region containing the residues. Thirty-five percent of the exceptions greater than 15 Å are at homo-oligomeric interfaces, 19% arise from family structural variation, and 27% are in repeat proteins likely reflecting alignment errors. Of the remaining long-range exceptions (<1% of the total number of coupled pairs), many can be attributed to close interactions in an oligomeric state. Overall, the results suggest that directly coevolving residue pairs not in repeat proteins are spatially proximal in at least one biologically relevant protein conformation within the family; we find little evidence for direct coupling between residues at spatially separated allosteric and functional sites or for increased direct coupling between residue pairs on putative allosteric pathways connecting them.

scholarly journals Comparative Genomics of Trace Element Dependence in Biology

2011 ◽  
Vol 286 (27) ◽  
pp. 23623-23629 ◽  
Author(s):  
Yan Zhang ◽  
Vadim N. Gladyshev
Keyword(s):  
Trace Elements ◽  
Comparative Genomics ◽  
Trace Element ◽  
Evolutionary Dynamics ◽  
Protein Families ◽  
Fundamental Properties ◽  
Recent Advances ◽  
Living Organisms ◽  
Zinc Protein

Biological trace elements are needed in small quantities but are used by all living organisms. A growing list of trace element-dependent proteins and trace element utilization pathways highlights the importance of these elements for life. In this minireview, we focus on recent advances in comparative genomics of trace elements and explore the evolutionary dynamics of the dependence of user proteins on these elements. Many zinc protein families evolved representatives that lack this metal, whereas selenocysteine in proteins is dynamically exchanged with cysteine. Several other elements, such as molybdenum and nickel, have a limited number of user protein families, but they are strictly dependent on these metals. Comparative genomics of trace elements provides a foundation for investigating the fundamental properties, functions, and evolutionary dynamics of trace element dependence in biology.

Comparative genomics: tracking chromosome evolution in the family Ursidae using reciprocal chromosome painting

1998 ◽  
Vol 83 (3-4) ◽  
pp. 182-192 ◽  
Author(s):  
W.G. Nash ◽  
J. Wienberg ◽  
M.A. Ferguson-Smith ◽  
J.C. Menninger ◽  
S.J. O’Brien
Keyword(s):  
Comparative Genomics ◽  
Chromosome Painting ◽  
Chromosome Evolution ◽  
Reciprocal Chromosome Painting ◽  
The Family

scholarly journals The distinction of CPR bacteria from other bacteria based on protein family content

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Raphaël Méheust ◽  
David Burstein ◽  
Cindy J. Castelle ◽  
Jillian F. Banfield
Keyword(s):  
Protein Family ◽  
Cell Interactions ◽  
Genome Reduction ◽  
Protein Families ◽  
Phylogenetic Structure ◽  
Family Presence ◽  
Core Sets ◽  
Lineage Divergence ◽  
Candidate Phyla Radiation ◽  
Cell Cell

Abstract Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. Here, we leveraged sequences from thousands of uncultivated organisms and identified protein families that co-occur in genomes, thus are likely foundational for lineage capacities. Protein family presence/absence patterns cluster CPR bacteria together, and away from all other bacteria and archaea, partly due to proteins without recognizable homology to proteins in other bacteria. Some are likely involved in cell-cell interactions and potentially important for episymbiotic lifestyles. The diversity of protein family combinations in CPR may exceed that of all other bacteria. Over the bacterial tree, protein family presence/absence patterns broadly recapitulate phylogenetic structure, suggesting persistence of core sets of proteins since lineage divergence. The CPR could have arisen in an episode of dramatic but heterogeneous genome reduction or from a protogenote community and co-evolved with other bacteria.

Bovine parotid secretory protein: structure, expression and relatedness to other BPI (bactericidal/permeability-increasing protein)-like proteins

2003 ◽  
Vol 31 (4) ◽  
pp. 781-784 ◽  
Author(s):  
T.T. Wheeler ◽  
K. Hood ◽  
K. Oden ◽  
J. McCracken ◽  
C.A. Morris
Keyword(s):  
Minor Salivary Gland ◽  
Secretory Protein ◽  
Protein Family ◽  
Sequence Information ◽  
The Family ◽  
Salivary Gland Protein ◽  
Full Length Sequence ◽  
Parotid Secretory Protein ◽  
Restricted Pattern

Members of the family of BPI (bactericidal/permeability-increasing protein)-like proteins are as yet incompletely characterized, particularly in cattle, where full-length sequence information is available for only three of the 13 family members known from other species. Structural bioinformatic analyses incorporating bovine homologues of several members of the BPI-like protein family, including two forms of bovine parotid secretory protein (PSP), showed that this family is also present in cattle. Expression analyses of several members of the BPI-like protein family in cattle, including PSP (Bsp30), von Ebner's minor salivary gland protein (VEMSGP) and lung-specific X protein (LUNX), showed a restricted pattern of expression, consistent with earlier hypotheses that these proteins function in the innate immune response to bacteria. The possible role of bovine PSP in susceptibility to pasture bloat in cattle is discussed.

Sign in / Sign up

Export Citation Format

Share Document