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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