Classification of subfamilies
Group		Subfamily	Entries							Notes
					Plants	Fungi	Nematoda	Insects	Vertebrates
CTER
	CTER-core	CAM	60		yes	yes	yes	yes	yes	The members of five subfamilies in CTER-core are congruent and they are inferred to diverge from a common four-domain precursor.
		TNC	13						yes
		ELC	44			yes	yes	yes	yes
		RLC	40				yes	yes	yes
		TPNV	15				yes	yes
	CTER-plus	CLAT	3		yes					The members of CTER-plus show higher similarity to calmodulin and appear in cluster_1.  These subfamilies share a common ancestor with four domains.
		SQUD	1
		CDC	19		yes	yes			yes
		CAL	3				yes
		CLSP	3						yes
		CML_O	1		yes
		CML_M	2		yes
		CAL8_CE	1				yes
		YT67_CE	1				yes
		SPEC	5
		BCBP	12						yes
		CML_07	11		yes
		CML_11	4		yes
		CDPK	50		yes
		CML_24	2		yes
		CML_T	3		yes
		CML_B	1		yes
		PMAT	2		yes
		CML_17	3		yes
		CML_15	3		yes
	CTER-related
	1	FIMB	10		yes	yes			yes	Fimbrin (FIMB) is an actin filament bundling protein; it has two EF-hands at its N-terminus.
	2	PARV	40						yes	Parvalbumin (PARV) has three EF-hands, the first of which does not bind calcium ions and covers the hydrophobic patch formed by an EF-lobe with 2nd and 3rd EF-hand.
	3	ACTN	10				yes	yes	yes	α-Actinin (ACTN) is an actin filament cross linking protein; it has two EF-hands at its C-terminus.  α-Spectrin (FDRN) reinforces the cell membrane by cross linking ankyrin and protein 4.1.  It has two EF-hands at its C-terminus.
		FDRN	7				yes	yes	yes
	4	BET4	5		yes					Polcalcin (BET4) is a calcium binding pollen allergen and has two EF-hands.  It was put in cluster_12.  SCO5464 protein (CSCD) is a bacterial protein that has four EF-hands.  Probable GTP diphosphokinase CRSH (CRSH_AT) has calcium dependent ppGpp (guanosine 3'-diphosphate 5'-diphosphate) synthetase activity in vitro.  It has two EF-hands.  Calcium binding allergen (CML_16) is a plant allergen as is BET4; however, it has four EF-hands.
		CSCD	1
		CRSH_AT	1		yes
		CML_16	3		yes
	5	GPD	3				yes		yes	Glycerol-3-phosphate dehydrogenase (GPD) is an FAD dependent enzyme located in the outer surface of the inner mitochondrial membrane.  It has two EF-hands at its C-terminus.
	6	CMSE	2							Calerythrin (CMSE) is a bacterial calcium binding protein and has four EF-hands.  Calerythrin is a protein of Saccharopolyspora erythraea.  CMSE has two members.  Another one is the cabA gene product of Streptomyces ambofaciens.  MSV097 putative calcium binding protein (MSV) is a viral protein with four EF-hands.
		MSV	1
	7	AIF1	4						yes	Allograft inflammatory factor 1 (AIF1) is an actin-binding protein that enhances membrane ruffling and activation of RAC, a subfamily of the Rho family of GTPases.  It has two EF-hands.  Swiprosin-1 (EFHD2_DM) is an actin binding protein37,38.  It has four EF-hands.
		EFHD2_DM	1					yes
	8	CBP_DD	3							Calfumirin and its related calcium binding proteins (CBP_DD) are calcium binding proteins from Dictyostelium discoideum.  CBP_DD has four EF-hands.
	9	PLC	16		yes	yes	yes	yes	yes	Phospholipase C (PLC) has two EF-hands at the B-terminal side of its catalytic domain that hydrolyzes phosphatidylinositol-4,5-bisphosphate to inositol-1,4,5-triphophate and diacylglycerol.
	10	SENS	1							Calsensin (SENS) is a calcium binding protein from Haemopis marmorata (Green horse leech).  It has two EF-hands.  Although we classified SENS as CTER related based on the sequence similarity, its structure is unique.  The main chain trace of SENS is quite different from other EF-hand proteins.  The EF-lobe of SENS looks like an inverted form of other EF-lobes.
	11	RYN	5					yes	yes	Ryanodine receptor (RYN) is a calcium channel that mediates the release of Ca2+ from the sarcoplasmic reticulum into the cytoplasm.  It has two EF-hands at its C-terminus.
	12	RASEF_CE	1				yes			Ras and EF-hand domain containing protein (RASEF_CE) has N-terminal EF-hand domains, a coiled-coil motif, and a C-terminal Rab domain.  It has two EF-hands.  Calcium release activated calcium channel regulator (EF4_HS) plays a role in store operated entry of Ca2+ ions.  It has two EF-hands.
		EF4_HS	2						yes
	13	CAST	1		yes					Calcium binding protein CAST (CAST) is from Solanum tuberosum (potato).  It has four EF-hands.
	14	PFPK	1							Plasmodium falciparum calcium dependent protein kinase (PFPK) has four EF-hands at its C-terminus.
	15	PPTS	4				yes	yes	yes	Serine/threonine-protein phosphatase (PPTS) has four EF-hands at the C-terminal side of the phosphatase domain.
	16	CVP	2							Calcium vector protein (CVP) interacts with CAVPT, whose function remains unknown, in a calcium dependent manner.  It has four EF-hands.
	17	LPS	2							Calcium binding protein LPS (LPS) is involved in larval development and metamorphosis in Lytechinus pictus (painted sea urchin).  It has eight EF-hands.
	18	E631_DM	1					yes		Calcium binding protein E63-1 (E631_DM) is from Drosophila melanogaster (fruit fly).  It has two EF-hands.  It was put in cluster_01.  BTB and MATH domain containing protein (BATH25_CE) is from Caenorhabditis elegans.  It has two EF-hands. Sm20, a 20-kilodalton calcium-binding protein of Schistosoma mansoni (SM20_SM), is associated with the tegumental membrane and inferred to be modified with carbohydrates.  It has four EF-hands.  YNE5_CE contains an uncharacterized calcium-binding protein encoded at the ORF R08D7.5.  It has two EF-hands.  EF3_HS contains EF-hand calcium-binding domain containing protein 3, which is a protein of about 440-amino acid length.  Two EF-hands is located at the N-terminal side.  YLJ5_CE contains an uncharacterized calcium-binding protein, which is encoded at the ORF C50C3.5.  It has a coiled coil domain at the N-terminal side and two EF-hands.   EFHB_HS contains EF-hand domain containing family member B, which is a 833 amino acid proteins encoded by EFHB gene.  Two EF-hands are located at the C-terminal side.  KIC contains two proteins, calcium-binding protein KIC and calcium-binding protein PBP1.  KIC interacts with kinesin motor protein KCBP in a calcium-dependent manner and inhibits KCBP microtubule binding activity and microtubule-stimulated ATPase activity.  PBP1 is a potential calcium sensor.  They have two EF-hands.  TCH3 contains two calcium binding proteins, one from Arabidospsis and the other from Branchiostoma.  Both proteins have six EF-hands.
		BATH25_CE	1				yes
		SM20_SM	1
		YNE5_CE	1				yes
		EF3_HS	1						yes
		YLJ5_CE	1				yes
		EFHB_HS	1						yes
		KIC	2		yes
		TCH3	2		yes
CPV
	CPV-core	CLNB	10			yes		yes	yes	CPV-core includes calcineurin B (CLNB), p22 (P22) and visinin (VIS).  They are congruent and share the same four domain ancestor, which is different from the ancestor of CTER.  There are six other subfamilies in CPV group.  SOS3 is a plant calcium sensor involved in the signaling pathway during growth and development and in response to abiotic stresses.  CIB is a calcium binding protein that plays a role in the regulation of numerous cellular processes, such as cell differentiation, cell migration, thrombosis, angiogenesis and apoptosis.  PCAT_HS has both acyltransferase and acetyltransferase activities.  There are two or four EF-hands at C-terminal side.  KCIP is a regulatory subunit of voltage gated rapidly inactivating A-type potassium channels.  CALS is a calcium-binding protein that interacts with the presenilins and regulates the levels of a presenilin fragment.  DREM is a calcium-dependent transcriptional repressor that binds to the DRE element of genes.
		SOS3	10		yes
		P22	4				yes		yes
		CIB	4						yes
		PCAT_HS	2						yes
		KCIP	3						yes
		VIS	31			yes	yes	yes	yes
		CALS	1						yes
		DREM	1						yes
	CPV-related
	1	DGK	9				yes	yes	yes	CPV-related contains two subfamilies, DGK and DUOX.  The members of both subfamilies are chimeric proteins.
	2	DUOX	4				yes	yes	yes
pairings
	PPTS2A	2AB2E_AT	1		yes					PPTS2A contains regulatory subunit of serine/threonine protein phosphatase 2A from various species.  This protein has four EF-hands at the C-terminal side.  2AB2E_AT contains 2AB2E_ARATH, which is a probable regulatory subunit of serine/threonine protein phosphatase 2A.  This protein has two EF-hands at the C-terminal side.  2AB2D_AT contains 2AB2D_ARATH, which is also a probable regulatory subunit of serine/threonine protein phosphatase 2A.  This protein has three EF-hands at least.
		PPTS2A	7		yes				yes
		2AB2D_AT	1		yes
	CALP	CALP	29					yes	yes	CALP contains catalytic subunits and regulatory subunits of calcium dependent cysteine protease, calpain.  SORC contains sorcin, grancalsin and apoptosis-linked gene 2 protein (ALG-2).  The members of these two subfamilies have five EF-hands.  They are called penta EF-hand proteins (PEF).
		SORC	13		yes	yes	yes		yes
	S100	HYFL	8						yes	S100 has two EF-hands, N-terminal one of which is a S100 specific structure with longer calcium binding loop and C-terminal one of which is a canonical EF-hand.  There are 24 human S100 genes, 19 of which are located within chromosome 1q21.  S100 forms homo- or hetero-dimer.  ICBP has similar structure to S100, but it is a monomeric protein.  HYFL is a chimeric protein with S100 like domain at N-terminal side and a large repeat domain at C-terminal side.  P26 is a frog protein with two S100 like domains.
		ICBP	6						yes
		S100	49						yes
		P26	1						yes
	RTC	RTC	3				yes		yes	RTC has six EF-hands and is inferred to be in the lumen of endoplasmic reticulum (ER) since it has an N-terminal leader sequence and a C-terminal ER retention sequence.  SCF is a supercoiling factor, which generates negative supercoils in DNA in conjunction with eukaryotic topoisomerase II.  SCF has six EF-hands.
		SCF	2					yes
	SCMC	SCMC	2						yes	SCMC is a calcium-dependent mitochondrial solute carrier, which mediates the reversible, electroneutral exchange of Mg-ATP or Mg-ADP against phosphate ions, across the mitochondrial inner membrane.  SCMS2_HS is also a calcium-dependent mitochondrial solute carrier.  SCMS2_HS appeared in a cluster different from SCMC.  CMC1_CE, CMC2_CE, CMC3_CE and CMC_DM are probable calcium-binding mitochondrial carrier by similarity.  Each one appears in different a cluster.
		SCMC2_HS	1						yes
		CMC1_CE	1				yes
		CMC_DM	1					yes
		CMC2_CE	1				yes
		CMC3_CE	1				yes
	BM40	BM40	9				yes		yes	BM40 is an extracellular calcium binding protein and regulates cell growth through interactions with the extracellular matrix and cytokines.  It has two EF-hands, the calcium coordination of the first of which deviates from canonical EF-hand.  QR1 is a extracellular glycoprotein, C-terminal side of which shows the similarity to BM40.
		QR1	3						yes
Misc
		TPP	6						yes	This group contains 18 subfamiles, which share at least two members in each of the best three subfamilies of similarity.  TPP is thyroid protein p24 or calcyphosine.  It has four EF-hands.  NUBN is nucleobindin, which has two EF-hands.  The domain including EF-hands showed to interact with necdin, a growth suppressor expressed predominantly in postmitotic neurons.  GRV is groovin (identical to kakapo), which has two EF-hands at the C-terminal side of about 4000 amino-acid long protein.  We included dystrophin in this subfamily.  Dystrophin is about 7000 amino-acid long protein, which acts as an integrator of intermediate filaments, actin and microtubule cytoskeleton networks.  It has two EF-hands at the C-terminal side.  NCAB is a neuronal calcium-binding protein, which has two EF-hands at the N-terminal side of about 300 amino-acid long.  YKT_CE is an uncharacterized calcium-binding protein of C. elegans.  This protein has two EF-hands at the C-terminal side.  EFH5 is an EF-hand protein from Trypanosoma and Leishmania.  It has four EF-hands.   EFCB1_HS is an EF-hand calcium-binding domain containing protein 1 from Human.  It has four EF-hands.  GYP2_SC is a GTPase-activating protein of yeast.  It has a TBC/rab GTPase-activating protein (GAP) domain at the N-terminal side and four EF-hands at the C-terminal side of about 950 residues long.  PSD2_AT is a phosphatidylserine decarboxylase proenzyme from Arabidopsis.  It has two EF-hands at the N-terminal side of about 600-residue long.  AEQ is a calcium-dependent bioluminescence photoprotein.  Calcium ions trigger the intramolecular oxidation of the chromophore, coelenterazine into coelenteramide and CO2 with the concomitant emission of light.  It has four EF-hands.  ANK_HS is a Ankyrin repeat and EF-hand domain containing protein of human.  There are two EF-hands between four Ankyrin repeat at the N-terminal side and another four Ankyrin repeat at the C-terminal side.  EF8_HS is a EF-hand calcium-binding domain containing protein of human.  It has two EF-hands in 144-residues long.  EF7_HS is a EF-hand calcium-binding domain containing protein of human.  It has four EF-hands in 629 residues long.  1F8 is a flagellar calcium-binding protein of Trypanosoma.  It has four EF-hands.  CML_33 is a calcium-binding protein of Arabidopsis.  The 131-residues long protein has four EF-hands.  CML_34 is calcium-binding protein of Arabidopsis.  The 155-residues long protein has four EF-hands.  MIRO is a mitochondrial Rho GTPase.  There are four EF-hands between the N-terminal and the C-terminal nucleotide binding domains.  EP15 is epidermal growth factor receptor substrate 15.  There are six EF-hands in the N-terminus, which are mixed with EH domain, an interaction site for Asn-Pro-Phe (NPF) motifs of target proteins.
		NUBN	4				yes		yes
		GRV	3					yes	yes
		NCAB	3						yes
		YKT_CE	1				yes
		EFH5	4
		EFCB1_HS	1						yes
		GYP2_SC	1			yes
		PSD2_AT	1		yes
		AEQ	6
		ANK_HS	1						yes
		EF8_HS	1						yes
		EF7_HS	1						yes
		1F8	2
		CML_33	1		yes
		CML_34	1		yes
		MIRO	5		yes	yes		yes	yes
		EP15	13		yes	yes			yes
Low-similarity
		PFS	1							There are 23 subfamiles in this group.  PFS is a membrane-associated calcium-binding protein of Plasmodium.  It has six EF-hands.  MICU is a regulator of mitochondrial calcium uniporter (MCU).  It has four EF-hands at the C-rerminal side of abou 500 residues long.  UEBP is a URE3-BP sequence specific DNA binding protein.  It has five EF-hands.  TCBP is a calcium binding protein from Tetrahymena.  It has four EF-hands.  CLBN is Calbindin, a vitamin D-dependent calcium-binding protein, which is a calcium buffer and inferred to activate a membrane Ca2+-ATPase and a 3',5'-cyclic nucleotide phosphodiesterase.  It has six EF-hands.  SM16_SM is a 16 kDa calcium-binding protein, which is expressed in eggs of Schistosoma.  It has four EF-hands.  H10E_CE is an uncharacterized protein of C. elegans.  It has at least four EF-hands.  CMC1_SC is a truncated non-functional calcium-binding mitochondrial carrier SAL1-1, which has tree EF-hands at the N-terminal side.  KCO_AT is a Two pore potassium channel from Arabidopsis.  It has two EF-hands at The C-terminla side.  SARC is a Sarcoplasmic calcium-binding protein.  It has four EF-hands.  FSTL4_HS is a follistatin-related protein 4 of Human.  It has two EF-hands in the N-terminal side of about 800 residue long.  RBOH is a calcium-dependent NADPH oxidase that generates superoxide.  It is inferred to have six transmembrane helices and has two EF-hands at the N-terminal cytoplasmic domain.  STIM is a stromal interaction molecule, which acts as Ca2+ sensor in the endoplasmic reticulum with its EF-hand domain.  It has two EF-hands at the N-terminal domain in the endoplasmic reticulum.  GRP is a cation- and diacylglycerol (DAG)-regulated nucleotide exchange factor activating Ras through the exchange of bound GDP for GTP.  It has two EF-hands at the C-terminal side.  FKBP is a peptidyl-prolyl cis-trans isomerase, which is inhibited by FK506.  It has two EF-hands at the C-terminal side.  LAV is a plasmodial-specific protein.  It has four EF-hands.  CCH1_AT is a voltage gated inward-rectifying Ca2+ channel (VDCC) across the vacuole membrane.  It has two EF-hands between the N-terminal and the C-terminal transmembrane domain with six helices.  EF9_HS is EF-hand calcium-binding domain containing protein 9 from Human.  It has four EF-hands.  STAT is a signal transducer and transcription activator that mediates cellular responses to interferons (IFNs), cytokine KITLG/SCF and other cytokines and other growth factors.  It has two EF-hand-like structures at the middle of about 800 residue long.  H32 is a hypersensitive reaction associated Ca2+-binding protein from kidney bean.  It has four EF-hands.  RFIP3_HS is Rab11 family-interacting protein 3 of human.  It has four EF-hands at the middle of about 750 residue long.  TPR_AT is an uncharacterized TPR repeat-containing protein of Arabidopsis.  It has two EF-hands at the N-terminus of about 800 residue long.  CMPK is a calcium and calcium/calmodulin-dependent serine/threonine-protein kinase of trumpet lily.  It has four EF-hands at the C-terminus of about 500 residue long.
		MICU	3				yes	yes	yes
		UEBP	1
		TCBP	2
		CLBN	11					yes	yes
		SM16_SM	1
		H10E_CE	1				yes
		CMC1_SC	1			yes
		KCO_AT	3		yes
		SARC	8
		FSTL4_HS	1						yes
		RBOH	9		yes
		STIM	4				yes	yes	yes
		GRP	2						yes
		FKBP	5						yes
		LAV	1
		CCH1_AT	1		yes
		EF9_HS	1						yes
		STAT	17					yes	yes
		H32	1		yes
		RFIP3_HS	1						yes
		TPR_AT	1		yes
		CMPK	1		yes
Isolated
		EF11_HS	1						yes	This group contains 27 subfamilies.  EF11_HS is EF-hand calcium-binding domain containing protein 11 of human.  It has four EF-hands.  EF2_HS is EF-hand domain containing family member C2 of human.  It has four EF-hands at the C-terminal side of about 750 residue long.  PCAT_DM is a lysophosphatidylcholine acyltransferase of fruit fly.  It is a memebrane protein at endoplasmic reticulum.  There are two EF-hands at the C-terminus of luminal domain.  EFC1_HS is a EF-hand and coiled-coil domain containing protein 1 of human.  It has two EF-hands at the N-terminus followed by two coiled-coil domains.  CLSM is Calsymin, a bacterial protein with six EF-hands.  CGRE_HS is a cell growth regulator with EF hand domain protein of human.  It has two EF-hands.  CRGP is multiple coagulation factor deficiency protein 2 of human.  It has two EF-hands.  LPCT_AT is a Lysophospholipid acyltransferase from Arabidopsis.  It shows acyl-CoA-dependent lysophospholipid acyltransferase activity and has two EF-hands at the C-terminal side.  UBP_HS is a ubiquitin carboxyl-terminal hydrolase of human.  It has four EF-hands at the N-terminal side of 1600 residue long.  ARP_EG is a calcium-binding acidic-repeat protein from Euglena.  It has at least 15 EF-hand-like repeats.  EF12_HS is a EF-hand calcium-binding domain containing protein of human.  It has two EF-hands in the middle of about 750 residue long.  MICU3_HS is a calcium uptake protein from human mitochondria.  It has four EF-hands at the C-terminal side.  CEX_CE is calexcitin of C. elegans.  It has three EF-hands.  SS120_SC is Protein SSP120 of yeast.  It has two EF-hands.  CMSO is a calcium binding protein of Streptomyces.  This bacterial protein has four EF-hands.  CSCJ is also a calcium binding protein of Streptomyces.  This bacterial protein has four EF-hands.  EF10_HS is a EF-hand calcium-binding domain containing protein of human.  It has two EF-hands.  CBCC is a bacterial EF hand protein from Caulobacter.  It has two EF-hands.  CBL is a E3 ubiquitin-protein ligase and functions as a negative regulator of many signaling pathways that are triggered by activation of cell surface receptors.  It has a pair of EF-hand-like structure at the N-terminal side of about 900 residue long.  ACHE is a acetylcholinesterase.  It has two EF-hand-like structures at the C-terminal side of about 600 residue long.  EF14_HS is a EF-hand calcium-binding domain containing protein of human.  It has two EF-hands at the C-terminus of about 500 residue long.  PKD is a polycystin of mouse, which functions as a calcium permeable cation channel involved in fluid-flow mechanosensation by the primary cilium.  It is a transmembrane protein and has two EF-hands at the C-terminal side of about 970 residue long.  PXG_AT is a peroxygenase of Arabidopsis.  It has four EF-hands at the N-terminal side.  NBD_AT is a mitochondrial NADH-ubiquinone oxidoreductase of Arabidopsis.  It has two EF-hands at the middle of about 600 residue long.  EF12 is a calcium binding protein from nematode.  It has 12 EF-hands.  FSTL1_HS is a follistatin-related protein of human.  It has two EF-hands in the middle of the chain.  TBC8_HS is a TBC1 domain family member of human, which is inferred to act as a GTPase-activating protein for Rab family protein(s).  It has two EF-hands at the C-terminal side of about 1100 residue long.
		EF2_HS	1						yes
		PCAT_DM	1					yes
		EFC1_HS	1						yes
		CLSM	1
		CGRE_HS	1						yes
		CRGP	1						yes
		LPCT_AT	1		yes
		UBP_HS	1						yes
		ARP_EG	1
		EF12_HS	1						yes
		MICU3_HS	1						yes
		CEX_CE	2				yes
		SS120_SC	1			yes
		CMSO	2
		CSCJ	1
		EF10_HS	1						yes
		CBCC	1
		CBL	5				yes	yes	yes
		ACHE	1						yes
		EF14_HS	1						yes
		PKD	3						yes
		PXG_AT	3		yes
		NBD_AT	3		yes
		EF12	3				yes
		FSTL1_HS	1						yes
		TBC8_HS	1						yes