match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	pfam01768	264	84	95.7	0.0072	[            ---------                            ]	Birna_VP4	Birnavirus VP4 protein. VP4 is a viral protease. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C).
2	TIGR02902	531	77	93.3	0.1	[           --------                              ]	spore_lonB	ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
3	COG1067	647	64	92.8	0.097	[              ------                             ]	LonB	Predicted ATP-dependent protease
4	pfam13541	121	58	92.1	0.3	[             ------                              ]	ChlI	Subunit ChlI of Mg-chelatase.
5	TIGR02903	615	80	88.6	0.99	[           --------                              ]	spore_lon_C	ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
6	pfam05362	205	71	88.0	0.89	[              -------                            ]	Lon_C	Lon protease (S16) C-terminal proteolytic domain. The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.
7	PRK13765	637	92	87.1	1.4	[            ---------                            ]	PRK13765	ATP-dependent protease Lon; Provisional
8	COG1750	579	77	84.1	1.4	[             --------                            ]	COG1750	Predicted archaeal serine protease, S18 family
9	TIGR00764	608	138	83.7	1.7	[     --------------                              ]	lon_rel	lon-related putative ATP-dependent protease. This model represents a set of proteins with extensive C-terminal homology to the ATP-dependent protease La, product of the lon gene of E. coli. The model is based on a seed alignment containing only archaeal members, but several bacterial proteins match the model well. Because several species, including Thermotoga maritima and Treponema pallidum, contain both a close homolog of the lon protease and nearly full-length homolog of the members of this family, we suggest there may also be a functional division between the two families. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
10	TIGR00763	775	54	82.5	1.7	[              -----                              ]	lon	endopeptidase La. This protein, the ATP-dependent serine endopeptidase La, is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.
11	PRK11823	446	75	80.7	3.5	[           --------                              ]	PRK11823	DNA repair protein RadA; Provisional
12	COG0466	782	71	79.1	2.4	[              -------                            ]	Lon	ATP-dependent Lon protease, bacterial type
13	COG1066	456	74	73.8	6.4	[           --------                              ]	Sms	Predicted ATP-dependent serine protease
14	cd06368	324	90	72.0	83	[             ----------                          ]	PBP1_iGluR_non_NMDA_like	N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-d -aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. Non-NMDA receptors have faster kinetics, are most often only weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute several forms of synaptic plasticity and are thought to play an important role in the development of synaptic pathways. Non-NMDA receptors include alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate (AMPA) and kainate receptors.
15	pfam13905	94	78	56.0	77	[                      --------                   ]	Thioredoxin_8	Thioredoxin-like. Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond.
16	TIGR00416	454	94	50.8	22	[         ----------                              ]	sms	DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
17	PRK10787	784	65	41.0	31	[              ------                             ]	PRK10787	DNA-binding ATP-dependent protease La; Provisional
18	COG3480	342	64	40.4	23	[             ------                              ]	SdrC	Predicted secreted protein containing a PDZ domain
19	pfam00926	193	54	35.2	88	[              -------                            ]	DHBP_synthase	3,4-dihydroxy-2-butanone 4-phosphate synthase. 3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesized from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin. Sometimes found as a bifunctional enzyme with pfam00925.
20	pfam02879	103	75	33.9	2.7E+02	[                             --------            ]	PGM_PMM_II	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II.
21	cd05094	287	61	30.6	1.1E+02	[                                    ------       ]	PTKc_TrkC	Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase C. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkC is a receptor PTK (RTK) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkC to its ligand, neurotrophin 3 (NT3), results in receptor oligomerization and activation of the catalytic domain. TrkC is broadly expressed in the nervous system and in some non-neural tissues including the developing heart. NT3/TrkC signaling plays an important role in the innervation of the cardiac conducting system and the development of smooth muscle cells. Mice deficient with NT3 and TrkC have multiple heart defects. NT3/TrkC signaling is also critical for the development and maintenance of enteric neurons that are important for the control of gut peristalsis. The TrkC subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.
22	TIGR04003	314	91	30.0	43	[                    -----------                  ]	rSAM_BssD
23	TIGR00368	499	75	29.7	66	[              -------                            ]	TIGR00368	Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
24	PRK13448	135	12	29.1	20	[                -                                ]	atpC	F0F1 ATP synthase subunit epsilon; Provisional
25	pfam09012	69	29	28.9	72	[    ---                                          ]	FeoC	FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a
26	pfam02217	94	57	28.1	1.8E+02	[                                  ------         ]	T_Ag_DNA_bind	Origin of replication binding protein. This domain of large T antigen binds to the SV40 origin of DNA replication.
27	cd08236	343	125	27.5	4.3E+02	[                 --------------                  ]	sugar_DH	NAD(P)-dependent sugar dehydrogenases. This group contains proteins identified as sorbitol dehydrogenases and other sugar dehydrogenases of the medium-chain dehydrogenase/reductase family (MDR), which includes zinc-dependent alcohol dehydrogenase and related proteins. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Related proteins include threonine dehydrogenase, formaldehyde dehydrogenase, and butanediol dehydrogenase. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Horse liver alcohol dehydrogenase is a dimeric enzyme and each subunit has two domains. The NAD binding domain is in a Rossmann fold and the catalytic domain contains a zinc ion to which substrates bind. There is a cleft between the domains that closes upon formation of the ternary complex.
28	COG0108	203	57	26.9	1.2E+02	[              -------                            ]	RibB	3,4-dihydroxy-2-butanone 4-phosphate synthase
29	PRK07670	251	89	26.6	1.2E+02	[ ----------                                      ]	PRK07670	RNA polymerase sigma factor SigD; Validated
30	cd03089	443	120	26.2	1.6E+02	[                           -------------         ]	PMM_PGM	The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a bisphosphorylated sugar intermediate. The reaction involves two phosphoryl transfers, with an intervening 180 degree reorientation of the reaction intermediate during catalysis. Reorientation of the intermediate occurs without dissociation from the active site of the enzyme and is thus, a simple example of processivity, as defined by multiple rounds of catalysis without release of substrate. Glucose-6-phosphate and glucose-1-phosphate are known to be utilized for energy metabolism and cell surface construction, respectively. PMM/PGM belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the phosphoglucomutases (PGM1 and PGM2). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
31	pfam12740	258	88	25.8	2E+02	[                      ---------                  ]	Chlorophyllase2	Chlorophyllase enzyme. This family consists of several chlorophyllase and chlorophyllase-2 (EC:3.1.1.14) enzymes. Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyses the hydrolysis of an ester bond to yield chlorophyllide and phytol. The family includes both plant and Amphioxus members.
32	PRK13696	62	38	24.8	1.8E+02	[   ----                                          ]	PRK13696	hypothetical protein; Provisional
33	pfam01212	288	31	24.1	80	[            ---                                  ]	Beta_elim_lyase	Beta-eliminating lyase.
34	pfam13412	48	36	23.4	2E+02	[    ---                                          ]	HTH_24	Winged helix-turn-helix DNA-binding.
35	PRK08575	326	72	23.2	56	[                       --------                  ]	PRK08575	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional
36	PRK06079	252	77	23.0	2.2E+02	[                              ----------         ]	PRK06079	enoyl-(acyl carrier protein) reductase; Provisional
37	pfam01399	105	39	22.9	4.2E+02	[   ----                                          ]	PCI	PCI domain. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
38	TIGR04548	178	66	22.0	1.9E+02	[ -------                                         ]	DnaD_Mollicutes	DnaD family protein, Mollicutes type. This model describes the full length of a family of proteins in the Mollicutes (Mycoplasma, Spiroplasma, Mesoplasma, etc.) homologous to the N-terminal region of DnaD from Bacillus subtilis.
39	pfam02022	40	25	21.8	1E+02	[     --                                          ]	Integrase_Zn	Integrase Zinc binding domain. Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.
40	COG2153	155	26	21.6	35	[                           ---                   ]	ElaA	Predicted N-acyltransferase, GNAT family