Table 1.

Functionally important SSRs selected by Zebra3D analysis of the case-studies.

#	Query		# of PDBs in aln.	# of SSRs	SSR
	Title	PDB			Region	Rank	Z	P	Functional role	Interpretation of subfamily classification
1	H1N1 Neuraminidase	3B7E:A	29	19 (17)	427–440	3 (1)	6.00	9.6e−10	Flexible loop-430 that drives formation of the cavity-430	Neuraminidases from influenza strains/types with different pathogenicity
					136–156	10 (8)	2.32	1.0e−02	Flexible loop-150 that drives formation of the cavity-150	Neuraminidases from influenza strains/types with different pathogenicity
2	Ornithine Decarboxylase from Trypanosoma brucei	1F3T:A	31	23 (21)	322–336	8 (6)	2.37	8.8e−03	The 310-helix shaping the binding cavity to discriminate substrate preference	β/α-barrel-fold basic amino acid decarboxylases with different substrate specificity
3	Human Aldose Reductase	2ACQ:A	62	14 (12)	112–135	1 (1)	10.11	2.5e−24	Dynamic region involved in substrate binding	Aldo-keto reductases with different substrate specificity
4	Common ancestor of Haloalkane Dehalogenases and Renilla Luciferase	6G75:A	41	14 (13)	146–176	3 (3)	3.64	1.4e−04	Region that includes L9-α4 loop-helix fragment involved in substrate binding	α/β-hydrolases with different catalytic activity
					222–239	5 (4)	2.53	5.7e−03	Region that includes L14 loop involved in substrate binding	α/β-hydrolases with different catalytic activity
5	Polyester Hydrolase from Pseudomonas aestusnigri	6SBN:A	20	13 (11)	127–134	5 (3)	3.84	6.1e−05	Substrate binding element of the active site	PET-hydrolases and closely related cutinases versus non-PET-hydrolase enzymes
					97–103	8 (6)	1.66	4.8e−02	Substrate binding element of the active site	PET-hydrolases and closely related cutinases versus non-PET-hydrolase enzymes
6	Human Guanine Deaminase	2UZ9:A	23	22 (20)	215–222	7 (5)	3.32	4.5e−04	Substrate-recognition element	Metal-dependent hydrolases with different substrate specificity
7	Human p38α MAP Kinase	1R3C:A	61	11 (10)	169–185	3 (2)	9.90	2.1e−23	Kinase DFG motif and activation loop	PDB entries capturing different structural states of the activation loop
8	Human HSP90	1YET:A	19	9 (7)	107–136	3 (2)	2.52	5.8e−03	Flexible lid segment	PDB entries capturing different structural states of the lid segment
9	Malate Dehydrogenase from Sus scrofa	5MDH:A	60	21 (21)	89–100	2 (2)	3.83	6.5e−05	Mobile region hosting residues involved in catalytic and binding functions	PDB entries capturing different structural states of the mobile region
10	Zinc Metallo-Beta-Lactamase from Bacillus cereus	1BVT:A	40	13 (12)	30–39	3 (3)	8.13	2.2e−16	Functionally important L1 loop of the active site	Different classes/types of metallo-beta-lactamases
					181–184	4 (4)	7.75	4.5e−15	Part of functionally important L3 loop of the active site	Different classes/types of metallo-beta-lactamases
					170–179	5 (5)	6.42	6.8e−11	Part of functionally important L3 loop of the active site	Different classes/types of metallo-beta-lactamases

“Query PDB” indicates PDB code and chain ID that was submitted as a query to the Mustguseal web-server to automatically collect and align a non-redundant set of 3D-structures of homologs. “# of PDBs in aln.” indicates the total number of finally selected 3D-entries in such alignment. “# of SSRs” indicates the total number of subfamily-specific regions identified by Zebra3D with default settings. “Region”, “Rank”, “Z”, and “P” indicate the first and last amino acid residues in SSR (according to numbering of query PDB record), its rank, statistical significance Z-score and P-value, respectively. The total number of SSRs and the ranking after excluding SSRs with N-/C-terminal regions (i.e. by running with the “exclude_ncterm = 5” parameter, see section “Algorithm”) is shown in parenthesis in the fields “# of SSRs” and “Rank”.