Table 2 Non-validated functional annotations of non-annotated surface patches. Functional annotated sites have been compared to a collection of surface patches extracted from a non-redundant PDB subset. The reliability of each match was estimated via a series of criteria, as described in the text. The remaining similarities may be new functional annotations of uncharacterized functional sites, or false positive matches, and are shown in this table. Columns:(i) PDB code, chain name and patch number in the annotated query patch; (ii) Description of the protein to which the query patch belongs; (iii) Query patch functional annotation; (iv) Target patch; (v) Description of the protein to which the target patch belongs; (vi) Z-score of the match; (vii) SSM Q score; (viii) SSM P score; (ix) SSM Z score. The SSM Q score takes into account the number of aligned residues, their r.m.s.d. and the size of the proteins; a high Q score means a good similarity. The SSM P score is the log of the pValue (the probability that the match occurred by chance); P scores higher than 3 are considered significant by the authors of the method.
Patch 1 | Protein | Patch 1 Annotation | Patch 2 | Protein | Z-score | SSM Qscore | SSM P-value | SSM Z-score |
|---|---|---|---|---|---|---|---|---|
3mdeA1 | Acyl-CoA dehydrogenase | LIG_CO8 | 1g5bB6 | Bacteriophage lambda S/T Protein Phosphatase | 9.59 | 0.01 | 0 | 0.5 |
1qhaA2 | Hexokinase I | HEXOKINASES | 1i78A5 | Outer Membrane Protease Ompt | 9.44 | 0.01 | 0 | 0.5 |
1qhaA2 | Hexokinase I | HEXOKINASES | 1zdhA2 | Bacteriophage Ms2 Protein Capsid | 9.44 | 0.01 | 0 | 0.1 |
1bp1_1 | Bactericidal permeability-increasing protein | LIG__PC | 1qlwA2 | Bacterial esterase 713 | 9.07 | 0.01 | 0 | 1.5 |
1nah_1 | UDP-galactose 4-epimerase | LIG_NAD | 1im8A1 | YecO methyltransferase | 9.06 | 0.1 | 0 | 4 |
4blcA1 | Beef liver catalase | LIG_NDP | 1io1A5 | Phase 1 Flagellin | 8.86 | 0.01 | 0 | 1.4 |
1dbtA1 | Orotidine 5'-Monophosphate Decarboxylase | OMPDECASE | 1dj8A1 | E. Coli Periplasmic Protein Hdea | 8.76 | 0.03 | 0 | 1.9 |
1fp2A1 | Isoflavone O-Methyltransferase | LIG_SAH | 1nah_1 | UDP-galactose 4-epimerase | 8.6 | 0.05 | 0 | 5.5 |
1fps_1 | Prenyltransferase Trimethylamine | POLYPRENYL_SY NTHET_1 | 1h6gA2 | Alpha-catenin Molybdopterin Biosynthesis Moeb | 8.54 | 0.04 | 0 | 0.3 |
1djnA1 | dehydrogenase | LIG_ADP | 1jwbB1 | Protein | 8.51 | 0.05 | 0 | 5.3 |
19hcA1 | Cytochrome C | LIG_HEM | 1umuB1 | UmuD' protein | 8.44 | 0.03 | 0 | 4.2 |
1qhaA1 | Type I Hexokinase | HEXOKINASES | 1e2uA1 | Hybrid Cluster Protein | 8.34 | 0.01 | 0 | 0.1 |
256bA1 | Cytochrome B562 | LIG_HEM | 1gpjA1 | Glutamyl-tRNA reductase | 8.25 | 0.05 | 0 | 0.4 |
1ep1B1 | Dihydroorotate Dehydrogenase B | LIG_FAD | 1pmi_8 | Phosphomannose Isomerase | 8.18 | 0.02 | 0 | 0.3 |
1tsdA1 | Thymidylate synthase | LIG_U18 | 1prhA1 | Prostaglandin H2 Synthase-1 Formylmethanofuran: Tetrahydromethanopterin | 8.16 | 0.01 | 0 | 0.1 |
2nlrA1 | Endoglucanase | LIG_G2F | 1ftrA1 | Formyltransferase | 8.05 | 0.02 | 0 | 0.5 |
1ej0A1 | RNA Methyltransferase | LIG_SAM | 2cmd_1 | Malate Dehydrogenase | 8.01 | 0.12 | 0 | 3.9 |
1ecmB1 | Chorismate mutase | LIG_TSA | 1b3qB1 | Histidine Kinase Chea | 7.96 | 0.02 | 0 | 2.8 |
1av6A3 | Vaccinia Methyltransferase Vp39 | LIG_SAH | 1b3mA1 | Sarcosine oxidase | 7.95 | 0.02 | 0 | 2.8 |
1av6A3 | Vaccinia Methyltransferase Vp39 | LIG_SAH | 1b4vA1 | Cholesterole oxidase | 7.95 | 0.02 | 0 | 0.9 |
1qrrA1 | Sulfolipid Biosynthesis (Sqd1) Protein | LIG_NAD | 1g6q12 | Arginine methyltransferase HMT1 | 7.85 | 0.04 | 0 | 1.9 |
1qrrA1 | Sulfolipid Biosynthesis (Sqd1) Protein | LIG_NAD | 1im8A1 | YecO methyltransferase | 7.85 | 0.09 | 0 | 2.4 |
1qrrA1 | Sulfolipid Biosynthesis (Sqd1) Protein | LIG_NAD | 1khhA1 | Guanidinoacetate methyltransferase | 7.85 | 0.1 | 0 | 2.9 |
6reqA1 | Methylmalonyl-Coa Mutase | LIG_3CP | 1fepA2 | Ferric Enterobactin Receptor | 7.79 | 0.01 | 0 | 0 |
6reqA1 | Methylmalonyl-Coa Mutase | LIG_3CP | 1jihB10 | Yeast DNA Polymerase Eta | 7.79 | 0.01 | 0 | 1 |
1bgyC1 | Cytochrome BC1 | LIG_HEM | 1dc1B2 | Bsobi Restriction Endonuclease | 7.62 | 0.01 | 0 | 0.4 |
1bgyC2 | Cytochrome BC1 | LIG_HEM | 1k92A4 | Argininosuccinate Synthetase | 7.62 | 0.01 | 0 | 0.2 |
1bgyC2 | Cytochrome BC1 | LIG_HEM | 5r1rA2 | Ribonucleotide Reductase R1 | 7.62 | 0.01 | 0 | 0.9 |
1qanA1 | Rrna Methyltransferase Ermc' | RRNA_A_DIMETH | 1b37B1 | Flavin-dependent polyamine oxidase | 7.54 | 0.04 | 0 | 5.3 |
1qanA1 | Rrna Methyltransferase Ermc' | RRNA_A_DIMETH | 1b3mA1 | Sarcosine oxidase | 7.54 | 0.04 | 0 | 4.3 |
1qanA1 | Rrna Methyltransferase Ermc' | RRNA_A_DIMETH | 1gpeA1 | Glucose oxidase | 7.54 | 0.03 | 0 | 3.2 |
1qanA1 | Rrna Methyltransferase Ermc' | RRNA_A_DIMETH | 1i8tA1 | UDP-galactopyranose mutase | 7.54 | 0.04 | 0 | 4.1 |
2cut_1 | Serine esterase | LIG_DEP | 1jfrA1 | Exfoliatus Lipase | 7.43 | 0.17 | 0 | 5.3 |
1bp1_2 | Bactericidal Permeability-increasing protein | LIG__PC | 1fuoA10 | Fumarase C | 7.42 | 0.01 | 0 | 0.1 |
1hcy_4 | Hexameric haemocyanin | LIG_NAG | 2kinA2 | Kinesin | 7.42 | 0.01 | 0 | 2.2 |
1cpq_1 | Cytochrome C | LIG_HEM | 1wpoB1 | Human Cytomegalovirus Protease | 7.41 | 0.01 | 0 | 1.3 |
1inp_1 | Inositol polyphosphate 1-phosphatase | IMP_2 | 1bgxT6 | TAQ polymerase | 7.38 | 0 | 0 | 0 |
1ksaA1 | Bacteriochlorophyll A Protein | LIG_BCL | 1xvaA1 | Glycine N-Methyltransferase | 7.27 | 0.02 | 0 | 1.3 |
1b63A1 | MutL DNA mismatch repair protein | LIG_ANP | 1wpoB1 | Human Cytomegalovirus Protease | 7.22 | 0.03 | 0 | 0.6 |
1e7uA1 | Phosphoinositide 3-Kinase Inhibition | PI3_4_KINASE_1 | 1qi9B1 | Vanadium Bromoperoxidase Soluble Quinoprotein Glucose | 7.15 | 0.01 | 0 | 0.6 |
1a12A1 | Regulator Of Chromosome Condensation (Rcc1) | RCC1_2 | 1cruB1 | Dehydrogenase | 7.06 | 0.08 | 0 | 0.4 |