Table 1.
Sequence profile search and fold recognition analysis
| A. Sequence Profile Search | |||||
| Method | GenPept | SwissProt | PDB | ||
| PSI-BLAST | Acid SMascb | 1 × 10−133 | NOc | NO | |
| PAP | 3 × 10−51 | ||||
| 5′ Nucleotidase | 1 × 10−2 | ||||
| HMMa | Acid SMaseb | 1 × 10−202 | Acid SMase | 1 × 10−202 | NO |
| PAP | 2.8 × 10−5 | PAP | 3.0 × 10−5 | ||
| Ser/Thr Phosphatase 1 | 1.2 × 10−4 | Exonuclease sbcd | 2.1 × 10−3 | ||
| 5′ Nucleotidase | 4.5 × 10−4 | Bis(5′-nucleosyl)-tetraphosphatase | 2.3 × 10−3 | ||
| Exonuclease sbcd | 2.1 × 10−3 | 2′ ,3′-cyclic-nucleotide 2′ Phosphodiesterase | 3.4 × 10−3 | ||
| Bis(5′-nucleosyl)-tetraphosphatase | 2.3 × 10−3 | 5′ Nucleotidase | 7.3 × 10−3 | ||
| 2′, 3′-cyclic-nucleotide 2′ Phosphodiesterase | 3.4 × 10−3 | Ser/Thr Phosphatase 2B | 9.0 × 10−3 | ||
| B. Fold Recognition Analysis | |||||
| Method | Fold Library | PDB ID | Rank | E-value | |
| a HMM built from a protein family that have ASM or ASM-like annotations only. | |||||
| b E-value or P-score from PSI-BLAST and HMM, respectively, corresponds to the first occurrence of the protein (independent of source) present in the motif alignment from the study of Klabunde et al. (1996). PSI-BLAST identified templates after five iterations using an E-value of 0.001 for the inclusion of the next pass. | |||||
| c Method was not able to identify a structural template with significant sequence homology (E-value or P score < 1). | |||||
| d E-values from 3D-PSSM below 0.05 are highly confident. | |||||
| 3D-PSSM | Pig PAP | (1UTE) | 1 | 0.02d | 95% confidence level |
| Kidney Bean PAP | (4KBP) | 2 | 1.03 | ||
| Kidney Bean PAP | (1KBP) | 3 | 2.06 | ||
| 5′ Nucleotidase | (1USH) | 15 | 6.32 | ||
| Z-score | |||||
| 123D+ | Phenol Hydrolase | 1 | 5.34 | ||
| Pig PAP | (1UTE) | 2 | 4.34 | ||
| Kidney Bean PAP | (4KBP) | 9 | 3.39 | ||