Sequence homology

[1] Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity.

Partial homology can occur where a segment of the compared sequences has a shared origin, while the rest does not.

The Chlamydomonas version is more complex: it crosses the membrane twice rather than once, contains additional domains and undergoes alternative splicing.

However, it can fully substitute the much simpler Arabidopsis protein, if transferred from algae to plant genome by means of genetic engineering.

[7] Orthologous sequences provide useful information in taxonomic classification and phylogenetic studies of organisms.

These resources employ approaches that can be generally classified into those that use heuristic analysis of all pairwise sequence comparisons, and those that use phylogenetic methods.

Some tools predict orthologous de novo from the input protein sequences, might not provide any Database.

The descendants' genes A1 and B1 are paralogous to each other because they are homologs that are related via a duplication event in the last common ancestor of the two species.

[1] Additional classifications of paralogs include alloparalogs (out-paralogs) and symparalogs (in-paralogs).

In other words, alloparalogs are paralogs that evolved from duplication events that happened in the LCA of the organisms being compared.

[39] Another example are the globin genes which encode myoglobin and hemoglobin and are considered to be ancient paralogs.

Human angiogenin diverged from ribonuclease, for example, and while the two paralogs remain similar in tertiary structure, their functions within the cell are now quite different.

For instance, Bacillus subtilis encodes two paralogues of glutamate dehydrogenase: GudB is constitutively transcribed whereas RocG is tightly regulated.

However, swaps of enzymes and promoters cause severe fitness losses, thus indicating promoter–enzyme coevolution.

Characterization of the proteins shows that, compared to RocG, GudB's enzymatic activity is highly dependent on glutamate and pH.

Ohnologues are also known to show greater association with cancers, dominant genetic disorders, and pathogenic copy number variations.

[citation needed] Gametology denotes the relationship between homologous genes on non-recombining, opposite sex chromosomes.

Gene phylogeny as red and blue branches within grey species phylogeny. Top: An ancestral gene duplication produces two paralogs ( histone H1.1 and 1.2 ). A speciation event produces orthologs in the two daughter species (human and chimpanzee). Bottom: in a separate species ( E. coli ), a gene has a similar function ( histone-like nucleoid-structuring protein ) but has a separate evolutionary origin and so is an analog .
A sequence alignment of mammalian histone proteins. Sequences are the middle 120-180 amino acid residues of the proteins. Residues that are conserved across all sequences are highlighted in grey. The key below denotes conserved sequence (*), conservative mutations (:), semi-conservative mutations (.), and non-conservative mutations ( ). [ 2 ]
Top: An ancestral gene duplicates to produce two paralogs (Genes A and B). A speciation event produces orthologs in the two daughter species. Bottom: in a separate species, an unrelated gene has a similar function (Gene C) but has a separate evolutionary origin and so is an analog .
Vertebrate Hox genes are organized in sets of paralogs. Each Hox cluster (HoxA, HoxB, etc.) is on a different chromosome. For instance, the human HoxA cluster is on chromosome 7 . The mouse HoxA cluster shown here has 11 paralogous genes (2 are missing). [ 39 ]