Sequence alignment/structure comparison

To perform sequence alignment/structure comparison of a query pdb file against the CE database,... 

Fig. 1 shows the secondary structure predicted for the cyt b subunit of Rh. sphaeroides, using a "consensus derived from the output of MCF, MPREDICT, amphipathic analysis, and sequence alignment and comparison. The structure has been folded in the membrane to take account of hydropathic and amphipathic analysis, to give the eight trans-membrane helix model previously proposed for the yeast cyt b subunit. Also shown are the locations of residues modified in inhibitor resistant strains, taken from refs. 14-16. To date, all lesions giving resistance to inhibitors at the antimycin site have... 

Three-Dimensional Considerations Discrimination of common protein folds application of protein structure to sequence/structure comparisons, 266, 575 three-dimensional profiles for measuring comparability of amino acid sequence with three-dimensional structure, 266, 598 SSAP sequential structure alignment program for protein structure comparison, 266, 617 understanding protein structure using scop for fold interpretation, 266,... 

The location of the copper with respect to the Greek key fold is interesting when compared to that of the cupredoxins. While the copper in the cupredoxins lies in the interior of the /8 barrel bound by three interior-facing residues of the carboxy-terminal loop in the )8 barrel, and by a histidine in an adjacent strand, the copper in SOD lies on the outside of its jS barrel, bound by one residue from the carhoxy-terminal loop and three from the adjacent strand (cf. Figs. 2c-5c with Fig. 8c.) A structural comparison of plastocyanin and SOD, coupled with sequence alignment of plastocyanin and ceruloplasmin (Ryden, 1988), showed that three of the SOD ligands correspond to putative copper ligands in ceruloplasmin. Why this is so will become more evident after the description of the ascorbate oxidase structure and its relationship to ceruloplasmin. 

Table 1. Comparison of amino acid residues which are involved in the binding of the cofactors ThDP and Mg2+ in PDCS.c. and PDCZ.m., respectively. The corresponding amino acid residues from PDCZ.m. have been deduced from sequence alignments (Figs. 1 and 2) based on the X-ray structure of PDCS.u. [35] and PDCS.c. [51]. Different residues are underlined. Those which have been exchanged by site-directed mutagenesis are marked with (see Tables 4 and 5)...

Very little is known about the structural domains that are responsible for the multiple functions of RNA polymerase. Therefore, comparison of the conserved amino acid sequences of the halobacterial and the eukaryotic enzymes might hint of the possible functional importance of these regions. For instance, the sequence alignment revealed that the zinc-binding motifs suggested for the eukaryotic enzymes are also conserved in the A and B subunits of the H. halobium enzyme, but only the former motif is partially conserved in the P subunit of the E. coli enzyme. Also, the splits of the B and the A subunits of the eukaryotic enzymes into two parts each in the halo-philic enzyme might suggest a division of these subunits into two functional domains. 

Dali Automatic structure comparison program for structural sequence alignments 168 www.ebi.ac.uk/dah/... 

The simplest level of sequence comparison is alignment of the primary structures of homologous molecules. A multiple sequence alignment allows one to look for amino add differences between family members... 

When the sequence of a protein is first determined, comparing it with all previously characterized sequences can be a source of tremendous insight into its evolutionary relatives and, hence, its structure and function. Indeed, an extensive sequence comparison is almost always the first analysis performed on a newly elucidated sequence. The sequence alignment methods heretofore described are used to compare an individual sequence with all members of a database of known sequences. 

Sequence and structure. A comparison of the aligned amino acid sequences of two proteins each consisting of 150 amino acids reveals them to be only 8% identical. However, their three-dimensional structures are very similar. Are these two proteins related evolutionarily Explain. 

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