Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures

Table 2 Protein domain hierarchies generated automatically either from a single curated alignment or from non-aligned sequences

identifier	Protein superfamily name	# seqs	# nodes amcBPPS	LLR	Run time^§
Started from curated alignments:
cd00075	Histidine kinase-like ATPase c	87,258	95(62)	518062	119.27
cd00130	PAS	50,200	117(115)	416375	103.95
cd00174	SH3	13,890	44(35)	26971	3.83
cd00590	RRM	107,488	63(56)	557782	63.75
cd01427	HAD-like hydrolases	41,818	85(73)	324699	59.77
cd02440	AdoMet_MTases	150,872	112(99)	1417985	250.27
cd04301	NAT-SF	43,486	71	244420	23.30
cl02566	SET (pfam00856)	8,946	21	54230	2.58
cl10444	P-loop GTPases^‡	198,624	115 (109)	3826672	464.67
none	AAA + ATPases^‡	84,695	86(85)	1779227	173.73
Started from unaligned sequences:
none	α,β- hydrolase fold	50,811	109(104)	752259	139.82
none	Helicases	86,287	117 (111)	1935380	342.10

^‡ For these non-CDD curated alignments were used as input.
^§ The time (in minutes) is for Steps 2 and 3 of the algorithm only.
Unaligned sequences were aligned using the multiple alignment procedures cited in Methods to generate an input alignment for the amcBPPS program.

ISSN: 1471-2105