Skip to main content

Table 3 Function prediction for uncharacterized proteins. Functional annotated sites have been used to infer the function(s) of a large set of uncharacterized proteins, using similarity threshold values that have been successfully tested on a training dataset. Columns: (i) PDB code and chain name of structural genomics proteins; (ii) PDB code, chain name and surface patch serial number of the functional annotated patch; (iii) Functional annotation of the matching patch; (iv) Z-score of the match; (v) Number of aligned residues; (vi) Blast2 bitscore; (vii) Sequence similarity evaluated by means of the Needleman-Wunsch global alignment (using the EMBOSS package 59 application needle). (viii) SSM Q score; (ix) SSM P score; (x) SSM Z score.

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

Str.gen SURFACE patch Annotation Z-score Score BLAST2 Seq Sim SSM Q SSM P SSM Z
1rtyC0 1qlaC1 LIG_HEM 14 7 0 0.5 0.06 0 1.5
1mw5A0 1bgyC2 LIG_HEM 13 9 0 0.8 0.04 0 1.8
1vhqA0 1ct9A1 LIG_AMP 13 8 13.9 1.2 0.02 0 1.8
1vhsB0 1cjwA1 LIG_COT 13 9 13.1 0.6 0.45 3.2 5.6
1vhsA0 1qsmD1 LIG_ACO 12 9 11.9 35.3 0.41 2.3 4.7
1j2rC0 19hcA1 LIG_HEM 12 8 12.7 0.4 0.01 0 1.5
1oz9A0 1fy7A1 LIG_COA 11 7 14.6 1.5 0.04 0 0.4
1vimA0 1dqrA1 LIG_6PG 10 7 15.4 1.1 0.07 0 3.1
1vj1A0 1tsdA1 LIG_UMP 10 6 13.9 3.2 0.01 0 0.2
1rtyA0 1fps_1 POLYPRENYL_SYNTHET_2 10 7 16.2 15 0.05 0 3.6
1vhnA0 2dorA1 DHODEHASE_2 10 8 13.5 0.7 0.23 0 5.7
1vhkA0 1grj_1 GREAB_1 10 7 0 2.5 0.02 0 2.2
1k7kA0 1qd1B1 LIG_FON 10 6 12.7 1 0.03 0 0.5
1vhkC0 1qd1B1 LIG_FON 10 6 13.5 2.1 0.04 0 2.5
1vhcA0 1bmtA2 LIG_COB 10 8 15 3.7 0.06 0 2
1uf9A0 1esmA1 LIG_COA 10 8 13.9 0.4 0.11 0 4.2
1h2hA0 1ezfA1 SQUALEN_PHYTOEN_SYN_1 10 7 13.1 1.3 0.02 0 0.4
1j5pA0 1ezfA1 SQUALEN_PHYTOEN_SYN_1 10 7 13.1 1.5 0.02 0 1
1rcuB0 2tpsB1 LIG_TPS 10 7 13.9 4.2 0.08 0 1.8
1vhcA0 2tpsB1 LIG_TPS 10 7 16.2 7.9 0.32 0.1 4.2
1jriC0 1atiA1 AA_TRNA_LIGASE_II_1 10 6 14.2 6.6 0.02 0 2.2
1j9jA0 1ft1A6 PPTA 10 7 14.2 1.9 0.02 0 0.6
1j9kB0 1ft1A6 PPTA 10 7 14.2 1.9 0.01 0 0.7
1i36A0 1eluA5 LIG_PDA 9 6 13.9 0.5 0.04 0 1.2
1j6pA0 1bxoA1 ASP_PROTEASE 9 6 13.9 2.7 0.02 0 0.3
1p5fA0 1eyrA1 LIG_CDP 9 6 21.6 33.2 0.06 0 1.9
1kytA0 1drmA1 LIG_HEM 9 6 12.3 0.9 0.02 0 1.6
1l6rB0 1drmA1 LIG_HEM 9 6 0 0.9 0.02 0 0.8
1j6rA0 1pprM1 LIG_DGD 9 6 0 3.7 0.01 0 1.4
1p99A0 1dik_1 LIG_SO4 9 6 14.2 1.7 0.07 0 0.7
1j2rD0 1dbtA1 OMPDECASE 9 6 15 2.5 0.07 0 1.6
1ni9A0 1pkp_1 RIBOSOMAL_S5 9 6 15.4 18.8 0.03 0 2.6
1lxnA0 1eg7A4 FTHFS_1 9 6 13.5 3.4 0.02 0 2.1
1rtyA0 1cpcB2 LIG_CYC 8 6 0 3.3 0.06 0 0.9
1vhnA0 1rblA1 LIG_CAP 8 6 14.2 1.5 0.09 0 2.9
1rtyA0 2cmd_1 MDH 8 6 13.9 19.8 0.02 0 0.9
1vj1A0 1hdoA1 LIG_NAP 8 6 14.6 3.2 0.07 0 3.3
1nc5A0 1aorA1 LIG_PTE 8 6 14.6 0.5 0.01 0 0.5
1rtwA0 1ft1A2 PPTA 8 6 13.1 11.7 0.03 0 1.7
1pg6A0 1qs0A1 LIG_TDP 8 6 13.5 0.2 0.02 0 0.9
1vizA0 1ho4B1 LIG_PXP 8 6 13.9 0.2 0.02 0 4.4
1l5xA0 1knyA1 LIG_APC 8 5 0 9.7 0.03 0 1.5
1vh6B0 1b72B1 HOMEOBOX_1 8 5 0 21.6 0.06 0.4 2.9
1mwqB0 19hcA1 CYTOCHROME_C 8 6 0 3.5 0.02 0 0.8
1s0uA0 1tplA1 BETA_ELIM_LYASE 8 6 15 0.6 0.02 0 2.6
1ixlA0 1ksaA1 LIG_BCL 8 6 0 2.2 0.04 0 1.9
1ufaA0 1nstA1 LIG_A3P 8 6 15.8 2.3 0.02 0 0.7
1rvkA0 2mnr_1 LIG__MN 8 6 14.2 39.5 0.05 9.3 9.8
1rvkA0 2mnr_1 MR_MLE_2 8 6 14.2 39.5 0.05 9.3 9.8
1vh6A0 1rdzA2 LIG_AMP 8 6 13.1 1.7 0.02 0 1
1ns5A0 1qjbB4 LIG_SEP 8 5 0 0.8 0.02 0 1.6
1rtyA0 1bcfA1 BACTERIOFERRITIN 8 6 16.2 7.3 0.14 0 0.9
1vi3A0 1a44_2 PBP 8 6 38.9 31.7 0.24 1 4.7
1j74A0 1dat_1 FERRITIN_1 8 6 15.8 5 0.00 0 0
1j7dA0 1dat_1 FERRITIN_1 8 6 15.8 0.7 0.00 0 0
1pc6A0 1qq8A1 HEME_OXYGENASE 8 6 0 0.9 0.03 0 1
1htwA0 1a4sA1 ALDEHYDE_DEHYDR_GLU 7 6 15 1.7 0.04 0 2
1vhmA0 1f5mB1 UPF0067 7 6 120 52.7 0.64 10 9.3
1vhmB0 1f5mB1 UPF0067 7 6 121 53.3 0.63 11.6 10.1
1rvkA0 2mnr_4 MR_MLE_1 7 6 14.2 39.5 0.05 9.3 9.8
1j6oA0 1e5dA4 LIG_FEO 7 6 14.2 0.3 0.03 0 0.1
1vhmA0 9icwA8 DNA_POLYMERASE_X 7 6 0 0.8 0.03 0 1.5
1qyiA0 2scpA1 EF_HAND 7 6 0 5.7 0.02 0 1.1
1nkvA0 1dhs_2 LIG_NAD 7 6 0 2 0.04 0 0.3
1nigA0 1c8zA1 TUB_2 7 6 0 0.7 0.01 0 4
1gpqB0 1bif_1 ATP_GTP_A 7 6 0 2.5 0.03 0 1
1p9vA0 1cjcA1 LIG_FAD 7 6 14.2 3.5 0.01 0 0.6
1vhmA0 1cjcA1 LIG_FAD 7 6 14.6 0.5 0.02 0 1
1vhmB0 1cjcA1 LIG_FAD 7 6 14.6 0.7 0.01 0 0.2
1lqlA0 1i78A5 OMPTIN_2 7 7 0 2.2 0.03 0 0