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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.

From: Functional annotation by identification of local surface similarities: a novel tool for structural genomics

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