Structure superposition tools: Difference between revisions
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===Example for Rigid Alignment=== | ===Example for Rigid Alignment=== | ||
[[1fsz]] is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin<ref>PMID: 9628483</ref><ref>PMID: 20459678</ref> found in [[1tub]] chain A, length 440. However, the sequence identity is | [[1fsz]] is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin<ref>PMID: 9628483</ref><ref>PMID: 20459678</ref> found in [[1tub]] chain A, length 440. However, the sequence identity is low. 92/372 residues can be aligned with 19% identity (2 gaps), and another 14 residue stretch with 42% identity (no gaps). | ||
====CE example==== | ====CE example==== | ||
*3.2 Å RMSD for 305 residues. The structural alignment has 96 unaligned "gap" residues: one large gap of ~30 residues, and ten smaller gaps of 8 residues or less. | *3.2 Å RMSD for 305 residues. The structural alignment has 96 unaligned "gap" residues: one large gap of ~30 residues, and ten smaller gaps of 8 residues or less. | ||
*Z-score: 6.5. | *Z-score: 6.5. | ||
*12.5% sequence identity. | *12.5% sequence identity within the structural alignment. | ||
*Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software (see above). | *Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software (see above). | ||
