Table 4 SSS results for PKCd and PKCe kinases. SSS results for the human kinases PKCd and PKCe (BLAST identity score 40%, similarity 57%). Similar subsequences are shown where BLAST is not able to find appreciable similarity with pure character matching strategies. None of the good alignment detected by BLAST were found to be with high SSS scores. Only the sequences with low SSS scores but low BLAST alignments are shown. Smith-Waterman algorithm application SSearch results are also shown. Figures in the last column are created by Magic Fit using the SPDBV software with real pdb files downloaded from the PDB Databank. F = 16, S z = 8, β = 2.5. PDBids : PKCd = 1BDY, PKCe = 1GMI. 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 | PKCd PKCe | (4) [31–39] (6) [46–54] |
| 2.31 | MKEALSTE DDSRIGQT |
| 1.67 | fig 4a |
2 | PKCd PKCe | (3) [22–30] (4) [33–41] |
| 4.38 | ANQPFCAV QTFLLDPY | ANQPFCA V QTFLLDP Y | 1.17 | fig 4b |
3 | PKCd PKCe | (12) [99–107] (12) [95–103] |
| 3.96 | GKAEFWLD ANCTIQFE | GKAEFWL D ANCTIQF E | 2.08 | fig 4c |
4 | PKCd PKCe | (14) [110–118] (15) [111–119] |
| 3.85 |
|
| 0.83 | fig 4d |
5 | PKCd PKCe | (8) [66–74] (10) [76–84] |
| 1.77 |
|
| 0.66 | fig 4e |
