Homology remote

Alkylidenes (alkylidene carbenes) are valence isomers of alkynes. They have been prepared by alkyne pyrolysis, by homologation of ketones, and by generation of alkenyl anions bearing oc-leaving groups. Generated by any of these means, an alkylidene will insert intramolecularly into a remote C- H bond to form a new C—C bond and thus a cyclopentene. A concerted two-electron process, this reaction proceeds with retention of absolute configuration at the C - H site. 

In this series the 150 values for the system pseudo-ChE-ACh are practically identical with those of the monoquaternary compounds with an equal number of carbon atoms in the side chain. Therefore, it appears that the second positive charge does not contribute materially to the over-all binding force, because of the lack of a second anionic site , serving as anchor. This proves the absence of important dispersion forces acting on tetra-methylammonium. The situation is, however, different with higher homologs, since free rotation in longer alkyl chains makes contact with remote parts of the protein surface possible (see VII, 6). 

The expedient and regioselective metalation of unprotected biphenyl-2-, -3-, and -4-carboxylic acids has been reported.59 Unprotected biphenyl-2-carboxylic acid has been cleanly metalated with. sex-butyllithium at the position adjacent to the carboxylate and can then be subjected to site-selective electrophilic substitution (Scheme 8). The remote C(2 )-position has been attacked by the superbasic mixture of n-BuLi and t-BuOK (LICKOR) in THF or benzene. The resulting dianion cyclizes to give the fluorenone skeleton. The mechanism of the metalation of homologous compounds, 2-(pyridin-3-yl)benzoic acid derivatives, with strong bases has also been discussed.60... 

A second goal of these new methods is the detection of structural homologies in the twilight zone" of sequence similarity (less than 25% identity), e.g., the structural similarity between carboxypeptidases A and N (sequence identity 18%). None of the sequence-structuie-aligmnent methods has been proven to conristentlv and eenerallv detect remote structural homoloeies with a hi eh score... 

Recognition of Nontrivial Remote Homology Relationships Involving Proteins of Helicobacter pylori Implications for Function Recognition... 

Key words Helicobacter pylori, Proteins, Remote homology detection, Function assignment... 

A protein (HP1075 from strain 26695) that shows remote homology to the AstE AspA family is reported in the present study. The H. pylori protein sequence shares sequence identity of 17% with the profile of the AstE AspA domain family with an E-value of 10 7 and profile coverage of 81%. Also, the H. pylori protein sequence fits on the crystal structure of aspartoacylase protein from Mcsorhizobium loti with an E-value of 10 15 (estimated precision 100%). 

The KEGG database provides information on different pathways that are responsible for various cell processes. The aspartate metabolism pathway in H. pylori as reported in the KEGG database (60) has been studied. A remote homology relationship between the H. pylori protein sequence and the aspartoacylase protein fills the gap in this metabolic pathway. 

In some proteins, only a part of the H. pylori protein is assigned a functional domain by Pfam and the rest of the protein is not assigned any function. Remote homology detection methods employed in the current analysis have established relationships between these unassigned regions and Pfam domain families. 

The effect of PSI-BLAST is to attune the scoring scheme to the query, and in practice this may or may not be desirable. On one hand, PSI-BLAST can be very sensitive to remote homology on the other hand, spurious sequences may be included and their scores may become inflated. Previously we used NP 000764 as a BLAST query to identify CYP2E1 homologs now we use NP 000764 to initiate a PSI-BLAST search. The first round of PSI-BLAST yields the same BLAST results... 

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