Table 6 SSS results for xyna-psefl and xynz-clotm. SSS results for the F/10 xylanases xyna-psefl and xynz-clotm (BLAST identity score 33%, similarity 52%). Similar subsequences are shown where BLAST is not able to find appreciable similarity with pure character matching strategies. Interestingly the second subsequence does not find alignment in BLAST and is not sequentially similar but produces good alignment. SSearch alignment results are based on Smith-Waterman algorithm. SSearch also did not align the presented subsequences, though it is more sensitive to local and detailed alignments of sequences. Smith-Waterman score was 510 while similarity score in SSearch was 32.984%. Referenced figures show the fit obtained using SPDBV Magic Fit. F = 16, S z = 8, β = 2.5, SSS = 0.783. PDBids : xyna-psefl = 1CLX, xynz-clotm = 1XYZ. The assignments for secondary structure are: h = helix; b = residue in isolated beta bridge; e = extended beta strand; g = 310 helix; i = pi helix; t = hydrogen bonded turn; s = bend [37].
From: Detailed protein sequence alignment based on Spectral Similarity Score (SSS)
| Â | Seq | Segment | Subseq | msd | Blast Result | SSearch Results | rms | Image |
|---|---|---|---|---|---|---|---|---|
1 | x-clotm x-psefl | (37) [297–305] (37) [297–305] |
| 2.10 |
|
| 1.29 | fig 6a |
2 | x-clotm x-psefl | (16) [124–132] (23) [184–192] |
| 2.51 | RDSLLAVMR ENGAKTTAE | DSLLAVM NGAKTTA | 1.96 | fig 6b |
3 | x-clotm x-psefl | (07) [054–062] (18) [145–153] |
| 2.59 | YNSILQREY RQSVFYRQR | NSILQRE QSVFYRQ | 2.58 | fig 6c |
