match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	PRK07233	434	403	100.0	2.4E-59	[-------------------------------------------------]	PRK07233	hypothetical protein; Provisional
2	TIGR02733	492	463	100.0	1.6E-58	[-------------------------------------------------]	desat_CrtD	C-3',4' desaturase CrtD. Members of this family are slr1293, a carotenoid biosynthesis protein which was shown to be the C-3',4' desaturase (CrtD) of myxoxanthophyll biosynthesis in Synechocystis sp. strain PCC 6803, and close homologs (presumed to be functionally equivalent) from other cyanobacteria, where myxoxanthophyll biosynthesis is either known or expected. This enzyme can act on neurosporene and so presumably catalyzes the first step that is committed to myxoxanthophyll.
3	COG1233	487	445	100.0	7E-34	[------------------------------------------------ ]	COG1233	Phytoene dehydrogenase-related protein
4	COG1231	450	401	100.0	2.8E-30	[------------------------------------------------ ]	YobN	Monoamine oxidase
5	COG1232	444	353	99.9	5.7E-26	[------------------------------------------       ]	HemY	Protoporphyrinogen oxidase
6	pfam01593	444	220	99.9	4.3E-27	[                       ------------------------- ]	Amino_oxidase	Flavin containing amine oxidoreductase. This family consists of various amine oxidases, including maze polyamine oxidase (PAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.
7	TIGR02730	493	445	99.9	1.4E-25	[------------------------------------------------ ]	carot_isom	carotene isomerase. Members of this family, including sll0033 (crtH) of Synechocystis sp. PCC 6803, catalyze a cis-trans isomerization of carotenes to the all-trans lycopene, a reaction that can also occur non-enzymatically in light through photoisomerization.
8	TIGR02734	495	424	99.9	3.3E-23	[-----------------------------------------------  ]	crtI_fam	phytoene desaturase. Phytoene is converted to lycopene by desaturation at four (two symmetrical pairs of) sites. This is achieved by two enzymes (crtP and crtQ) in cyanobacteria (Gloeobacter being an exception) and plants, but by a single enzyme in most other bacteria and in fungi. This single enzyme is called the bacterial-type phytoene desaturase, or CrtI. Most members of this family, part of the larger pfam01593, which also contains amino oxidases, are CrtI itself; it is likely that all members act on either phytoene or on related compounds such as dehydrosqualene, for carotenoid biosynthesis.
9	PRK07208	479	354	99.7	2.1E-16	[----------------------------------------         ]	PRK07208	hypothetical protein; Provisional
10	PRK11883	451	400	99.7	1.8E-15	[------------------------------------------------ ]	PRK11883	protoporphyrinogen oxidase; Reviewed
11	COG2907	447	377	99.5	1.6E-13	[------------------------------------------------ ]	COG2907	Predicted NAD/FAD-binding protein
12	pfam13450	67	66	99.5	2.4E-14	[-------                                          ]	NAD_binding_8	NAD(P)-binding Rossmann-like domain.
13	pfam01266	320	52	99.5	9.4E-13	[                       -----                     ]	DAO	FAD dependent oxidoreductase. This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
14	COG3349	485	263	99.4	9.1E-13	[------------------------------                   ]	COG3349	Uncharacterized conserved protein, contains NAD-binding domain and a Fe-S cluster
15	TIGR03467	419	382	99.3	3.1E-10	[ ----------------------------------------------- ]	HpnE	squalene-associated FAD-dependent desaturase. The sequences in this family are members of the pfam01593 superfamily of flavin-containing amine oxidases which include the phytoene desaturases. These sequences also include a FAD-dependent oxidoreductase domain, pfam01266. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of squalene, the condensation product of the polyisoprenoid farnesyl pyrophosphate. This gene and its association with hopene biosynthesis in Zymomonas mobilis has been noted in the literature where the gene symbol hpnE was assigned. This gene is also found in contexts where the downstream conversion of squalene to hopenes is not evidence. The precise nature of the reaction catalyzed by this enzyme is unknown at this time.
16	COG0665	387	56	99.2	3.7E-10	[                       ------                    ]	DadA	Glycine/D-amino acid oxidase (deaminating)
17	PRK00711	416	285	99.2	7.6E-11	[--------------------------------------           ]	PRK00711	D-amino acid dehydrogenase small subunit; Validated
18	PRK01747	662	190	99.0	1.3E-08	[----------------------------                     ]	mnmC	bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed
19	COG0579	429	193	99.0	2.6E-09	[----------------------------                     ]	LhgO	L-2-hydroxyglutarate oxidase LhgO
20	TIGR00562	462	347	99.0	2.8E-08	[-----------------------------------------        ]	proto_IX_ox	protoporphyrinogen oxidase. This enzyme oxidizes protoporphyrinogen IX to protoporphyrin IX, a precursor of heme and chlorophyll. Bacillus subtilis HemY also has coproporphyrinogen III to coproporphyrin III oxidase activity in a heterologous expression system, although the role for this activity in vivo is unclear. This protein is a flavoprotein and has a beta-alpha-beta dinucleotide binding motif near the amino end.
21	TIGR02731	453	396	98.8	1.8E-08	[------------------------------------------------ ]	phytoene_desat	phytoene desaturase. Plants and cyanobacteria (and, supposedly, Chlorobium tepidum) have a conserved pathway from two molecules geranylgeranyl-PP to one of all-trans-lycopene. Members of this family are the enzyme pytoene desaturase (also called phytoene dehydrogenase). This model does not include the region of the chloroplast transit peptide in plants. A closely related family, excluded by this model, is zeta-carotene desaturase, another enzyme in the same pathway.
22	PRK11749	457	39	98.8	2.8E-09	[----                                             ]	PRK11749	dihydropyrimidine dehydrogenase subunit A; Provisional
23	PRK12810	471	39	98.8	5.7E-09	[----                                             ]	gltD	glutamate synthase subunit beta; Reviewed
24	PRK12771	564	53	98.8	5.5E-09	[-----                                            ]	PRK12771	putative glutamate synthase (NADPH) small subunit; Provisional
25	COG3380	331	112	98.7	2.4E-08	[-------------                                    ]	COG3380	Predicted NAD/FAD-dependent oxidoreductase
26	TIGR02732	474	397	98.7	2.5E-07	[------------------------------------------------ ]	zeta_caro_desat	9,9'-di-cis-zeta-carotene desaturase. Carotene 7,8-desaturase, also called zeta-carotene desaturase, catalyzes multiple steps in the pathway from geranylgeranyl-PP to all-trans-lycopene in plants and cyanobacteria. A similar enzyme and pathway is found in the green sulfur bacterium Chlorobium tepidum.
27	PRK12814	652	39	98.7	1.5E-08	[----                                             ]	PRK12814	putative NADPH-dependent glutamate synthase small subunit; Provisional
28	pfam03486	405	84	98.6	2.8E-07	[                       ---------                 ]	HI0933_like	HI0933-like protein.
29	COG0644	396	41	98.6	3.3E-08	[----                                             ]	FixC	Dehydrogenase (flavoprotein)
30	PRK06753	373	35	98.6	4E-08	[---                                              ]	PRK06753	hypothetical protein; Provisional
31	COG2081	408	78	98.5	1.6E-06	[                       --------                  ]	YhiN	Predicted flavoprotein YhiN
32	PRK04176	257	67	98.5	8.6E-08	[--------                                         ]	PRK04176	ribulose-1,5-biphosphate synthetase; Provisional
33	COG0654	387	67	98.5	1.2E-07	[                       -------                   ]	UbiH	2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
34	COG1635	262	68	98.5	7.8E-08	[--------                                         ]	THI4	Archaeal ribulose 1,5-bisphosphate synthetase/yeast thiazole synthase
35	PRK13984	604	66	98.5	8.8E-08	[-------                                          ]	PRK13984	putative oxidoreductase; Provisional
36	PRK09853	1019	67	98.5	1.1E-07	[-------                                          ]	PRK09853	putative selenate reductase subunit YgfK; Provisional
37	TIGR01316	449	70	98.4	9.3E-08	[--------                                         ]	gltA	glutamate synthase (NADPH), homotetrameric. This protein is homologous to the small subunit of NADPH and NADH forms of glutamate synthase as found in eukaryotes and some bacteria. This protein is found in numerous species having no homolog of the glutamate synthase large subunit. The prototype of the family, from Pyrococcus sp. KOD1, was shown to be active as a homotetramer and to require NADPH.
38	TIGR01317	485	39	98.4	1.8E-07	[----                                             ]	GOGAT_sm_gam	glutamate synthases, NADH/NADPH, small subunit. This model represents one of three built for the NADPH-dependent or NADH-dependent glutamate synthase (EC 1.4.1.13 and 1.4.1.14, respectively) small subunit or homologous region. TIGR01316 describes a family in several archaeal and deeply branched bacterial lineages of a homotetrameric form for which there is no large subunit. Another model describes glutamate synthase small subunit from gamma and some alpha subdivision Proteobacteria plus paralogs of unknown function. This model describes the small subunit, or homologous region of longer forms proteins, of eukaryotes, Gram-positive bacteria, cyanobacteria, and some other lineages. All members with known function participate in NADH or NADPH-dependent reactions to interconvert between glutamine plus 2-oxoglutarate and two molecules of glutamate.
39	PRK11728	393	272	98.4	3.3E-06	[---------------------------------------          ]	PRK11728	hydroxyglutarate oxidase; Provisional
40	COG0493	457	40	98.3	2.6E-07	[----                                             ]	GltD	NADPH-dependent glutamate synthase beta chain or related oxidoreductase
41	COG2072	443	120	98.3	1.3E-06	[-------------                                    ]	CzcO	Predicted flavoprotein CzcO associated with the cation diffusion facilitator CzcD
42	PRK12409	410	153	98.3	3.5E-07	[                      --------------------       ]	PRK12409	D-amino acid dehydrogenase small subunit; Provisional
43	PRK12770	352	70	98.3	4.4E-07	[--------                                         ]	PRK12770	putative glutamate synthase subunit beta; Provisional
44	PRK12831	464	85	98.2	5.7E-07	[----------                                       ]	PRK12831	putative oxidoreductase; Provisional
45	PRK06847	375	51	98.2	1.1E-05	[                       -----                     ]	PRK06847	hypothetical protein; Provisional
46	TIGR03315	1012	160	98.1	1.8E-06	[------------------                               ]	Se_ygfK	putative selenate reductase, YgfK subunit. Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase.
47	PRK07588	391	43	97.9	4.8E-06	[----                                             ]	PRK07588	hypothetical protein; Provisional
48	TIGR02032	295	53	97.9	7.9E-06	[                       ------                    ]	GG-red-SF	geranylgeranyl reductase family. This model represents a subfamily which includes geranylgeranyl reductases involved in chlorophyll and bacteriochlorophyll biosynthesis as well as other related enzymes which may also act on geranylgeranyl groups or related substrates.
49	PRK08274	466	64	97.9	2.3E-05	[                      ------                     ]	PRK08274	tricarballylate dehydrogenase; Validated
50	PRK12778	752	39	97.9	5.3E-06	[----                                             ]	PRK12778	putative bifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta; Provisional
51	PRK06185	407	106	97.9	2.1E-05	[-------------                                    ]	PRK06185	hypothetical protein; Provisional
52	COG1148	622	41	97.9	1.1E-05	[----                                             ]	HdrA	Heterodisulfide reductase, subunit A (polyferredoxin)
53	PRK07538	413	34	97.9	1.2E-05	[---                                              ]	PRK07538	hypothetical protein; Provisional
54	pfam01946	229	65	97.8	9.4E-06	[--------                                         ]	Thi4	Thi4 family. This family includes a putative thiamine biosynthetic enzyme.
55	pfam00890	401	48	97.8	2.8E-05	[-----                                            ]	FAD_binding_2	FAD binding domain. This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase.
56	TIGR00292	254	66	97.8	1.2E-05	[--------                                         ]	TIGR00292	thiazole biosynthesis enzyme. This enzyme is involved in the biosynthesis of the thiamine precursor thiazole, and is repressed by thiamine. This family includes c-thi1, a Citrus gene induced during natural and ethylene induced fruit maturation and is highly homologous to plant and yeast thi genes involved in thiamine biosynthesis.
57	TIGR03997	644	43	97.8	2.5E-05	[----                                             ]	mycofact_OYE_2	mycofactocin system FadH/OYE family oxidoreductase 2. The yeast protein called old yellow enzyme and FadH from Escherichia coli (2,4-dienoyl CoA reductase) are enzymes with 4Fe-4S, FMN, and FAD prosthetic groups, and interact with NADPH as well as substrate. Members of this related protein family occur in the vicinity of the putative mycofactocin biosynthesis operon in a number of Actinobacteria such as Frankia sp. and Rhodococcus sp., in Pelotomaculum thermopropionicum SI (Firmicutes), and in Geobacter uraniireducens Rf4 (Deltaproteobacteria). The function of this oxidoreductase is unknown.
58	TIGR03364	365	49	97.7	2.4E-05	[-----                                            ]	HpnW_proposed	FAD dependent oxidoreductase TIGR03364. This clade of FAD dependent oxidoreductases (members of the pfam01266 family) is syntenically associated with a family of proposed phosphonatase-like enzymes (TIGR03351) and is also found (less frequently) in association with phosphonate transporter components. A likely role for this enzyme involves the oxidative deamination of an aminophosphonate differring slightly from 2-aminoethylphosphonate, possibly 1-hydroxy-2-aminoethylphosphonate (see the comments for TIGR03351). Many members of the larger FAD dependent oxidoreductase family act as amino acid oxidative deaminases.
59	pfam00070	80	35	97.7	3.3E-05	[---                                              ]	Pyr_redox	Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
60	COG0492	305	42	97.7	4.4E-05	[----                                             ]	TrxB	Thioredoxin reductase
61	pfam07992	284	39	97.7	4.7E-05	[----                                             ]	Pyr_redox_2	Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
62	PRK05329	422	54	97.6	0.00029	[                      ------                     ]	PRK05329	anaerobic glycerol-3-phosphate dehydrogenase subunit B; Validated
63	PRK12769	654	39	97.6	5E-05	[----                                             ]	PRK12769	putative oxidoreductase Fe-S binding subunit; Reviewed
64	PRK12834	549	53	97.6	0.00013	[------                                           ]	PRK12834	putative FAD-binding dehydrogenase; Reviewed
65	PRK08132	547	42	97.5	6.5E-05	[----                                             ]	PRK08132	FAD-dependent oxidoreductase; Provisional
66	COG0446	415	40	97.5	9.2E-05	[----                                             ]	FadH2	NADPH-dependent 2,4-dienoyl-CoA reductase, sulfur reductase, or a related oxidoreductase
67	COG0562	374	43	97.5	8.2E-05	[----                                             ]	Glf	UDP-galactopyranose mutase
68	TIGR01318	467	39	97.5	7.1E-05	[----                                             ]	gltD_gamma_fam	glutamate synthase small subunit family protein, proteobacterial. This model represents one of three built for the NADPH-dependent or NADH-dependent glutamate synthase (EC 1.4.1.13 and 1.4.1.14, respectively) small subunit and homologs. TIGR01317 describes the small subunit (or equivalent region from longer forms) in eukaryotes, Gram-positive bacteria, and some other lineages, both NADH and NADPH-dependent. TIGR01316 describes a protein of similar length, from Archaea and a number of bacterial lineages, that forms glutamate synthase homotetramers without a large subunit. This model describes both glutatate synthase small subunit and closely related paralogs of unknown function from a number of gamma and alpha subdivision Proteobacteria, including E. coli.
69	TIGR03197	381	92	97.5	0.00083	[                 -----------                     ]	MnmC_Cterm	tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain. In Escherichia coli, the protein previously designated YfcK is now identified as the bifunctional enzyme MnmC. It acts, following the action of the heterotetramer of GidA and MnmE, in the modification of U-34 of certain tRNA to 5-methylaminomethyl-2-thiouridine (mnm5s2U). In other bacterial, the corresponding proteins are usually but always found as a single polypeptide chain, but occasionally as the product of tandem genes. This model represents the C-terminal region of the multifunctional protein.
70	PRK05868	372	43	97.4	0.00018	[----                                             ]	PRK05868	hypothetical protein; Validated
71	PRK06183	538	91	97.3	0.00022	[-----------                                      ]	mhpA	3-(3-hydroxyphenyl)propionate hydroxylase; Validated
72	PRK07236	386	34	97.3	0.00019	[---                                              ]	PRK07236	hypothetical protein; Provisional
73	TIGR01292	299	213	97.3	0.00052	[----------------------------                     ]	TRX_reduct	thioredoxin-disulfide reductase. This model describes thioredoxin-disulfide reductase, a member of the pyridine nucleotide-disulphide oxidoreductases (pfam00070).
74	PRK09126	392	59	97.3	0.00017	[                       ------                    ]	PRK09126	hypothetical protein; Provisional
75	PRK11259	376	71	97.3	0.0018	[                      --------                   ]	solA	N-methyltryptophan oxidase; Provisional
76	PRK08243	392	93	97.3	0.0002	[                       ---------                 ]	PRK08243	4-hydroxybenzoate 3-monooxygenase; Validated
77	PRK10015	429	75	97.3	0.00027	[--------                                         ]	PRK10015	oxidoreductase; Provisional
78	COG2303	542	31	97.3	0.00019	[---                                              ]	BetA	Choline dehydrogenase or related flavoprotein
79	TIGR00275	400	67	97.3	0.0005	[-------                                          ]	TIGR00275	flavoprotein, HI0933 family. The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae.
80	TIGR01813	439	36	97.2	0.00028	[---                                              ]	flavo_cyto_c	flavocytochrome c. This model describes a family of redox proteins related to the succinate dehydrogenases and fumarate reductases of E. coli, mitochondria, and other well-characterized systems. A member of this family from Shewanella frigidimarina NCIMB400 is characterized as a water-soluble periplasmic protein with four heme groups, a non-covalently bound FAD, and essentially unidirectional fumarate reductase activity. At least seven distinct members of this family are found in Shewanella oneidensis, a species able to use a wide variety of pathways for respiraton.
81	PRK07121	492	180	97.2	0.0019	[--------------------------                       ]	PRK07121	hypothetical protein; Validated
82	PRK08163	396	61	97.2	0.0002	[                      ------                     ]	PRK08163	salicylate hydroxylase; Provisional
83	TIGR02023	388	31	97.1	0.00032	[---                                              ]	BchP-ChlP	geranylgeranyl reductase. This model represents a group of geranylgeranyl reductases specific for the biosyntheses of bacteriochlorophyll and chlorophyll. It is unclear whether the processes of isoprenoid ligation to the chlorin ring and reduction of the geranylgeranyl chain to a phytyl chain are necessarily ordered the same way in all species.
84	pfam13738	197	36	97.1	0.0015	[----                                             ]	Pyr_redox_3	Pyridine nucleotide-disulphide oxidoreductase.
85	PRK06522	304	46	97.1	0.00053	[-----                                            ]	PRK06522	2-dehydropantoate 2-reductase; Reviewed
86	PRK07364	415	96	97.1	0.0006	[-----------                                      ]	PRK07364	2-octaprenyl-6-methoxyphenyl hydroxylase; Validated
87	pfam01494	349	52	97.0	0.00051	[                       ------                    ]	FAD_binding_3	FAD binding domain. This domain is involved in FAD binding in a number of enzymes.
88	TIGR04018	316	33	97.0	0.00058	[---                                              ]	Bthiol_YpdA	putative bacillithiol system oxidoreductase, YpdA family. Members of this protein family, including YpdA from Bacillus subtilis, are apparent oxidoreductases present only in species with an active bacillithiol system. They have been suggested actually to be thiol disulfide oxidoreductases (TDOR), although the evidence is incomplete.
89	pfam12831	416	38	97.0	0.00061	[----                                             ]	FAD_oxidored	FAD dependent oxidoreductase. This family of proteins contains FAD dependent oxidoreductases and related proteins.
90	PRK12775	1006	38	97.0	0.00028	[----                                             ]	PRK12775	putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
91	TIGR00031	377	43	97.0	0.0007	[----                                             ]	UDP-GALP_mutase	UDP-galactopyranose mutase. This enzyme is involved in the conversion of UDP-GALP into UDP-GALF through a 2-keto intermediate. It contains FAD as a cofactor. The gene is known as glf, ceoA, and rfbD. It is known experimentally in E. coli, Mycobacterium tuberculosis, and Klebsiella pneumoniae.
92	PRK10157	428	74	96.9	0.00046	[--------                                         ]	PRK10157	putative oxidoreductase FixC; Provisional
93	PRK05335	436	35	96.9	0.00081	[---                                              ]	PRK05335	tRNA (uracil-5-)-methyltransferase Gid; Reviewed
94	TIGR04046	400	43	96.9	0.00075	[----                                             ]	MSMEG_0569_nitr	flavin-dependent oxidoreductase, MSMEG_0569 family. Members of this protein family belong to a conserved seven-gene biosynthetic cluster found sparsely in Cyanobacteria, Proteobacteria, and Actinobacteria. Distant homologies to characterized proteins suggest that members are enzymes dependent on a flavinoid cofactor.
95	PRK08401	466	30	96.9	0.00081	[---                                              ]	PRK08401	L-aspartate oxidase; Provisional
96	COG0029	518	96	96.9	0.002	[----------                                       ]	NadB	Aspartate oxidase
97	COG1053	562	37	96.9	0.0011	[---                                              ]	SdhA	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit
98	COG1249	454	36	96.8	0.0012	[---                                              ]	Lpd	Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component or related enzyme
99	COG3573	552	53	96.8	0.00082	[------                                           ]	COG3573	Predicted oxidoreductase
100	COG0578	532	48	96.8	0.0012	[-----                                            ]	GlpA	Glycerol-3-phosphate dehydrogenase
101	pfam03721	185	32	96.8	0.0011	[---                                              ]	UDPG_MGDP_dh_N	UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain. The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate.
102	PRK07494	388	145	96.8	0.0011	[                       ------------------        ]	PRK07494	2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional
103	PRK06292	460	38	96.7	0.0012	[----                                             ]	PRK06292	dihydrolipoamide dehydrogenase; Validated
104	COG2509	486	338	96.7	0.007	[-------------------------------------------      ]	COG2509	FAD-dependent dehydrogenase
105	COG1893	307	34	96.7	0.0014	[---                                              ]	PanE	Ketopantoate reductase
106	pfam07992	284	36	96.7	0.0016	[---                                              ]	Pyr_redox_2	Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
107	TIGR03026	409	33	96.7	0.0013	[---                                              ]	NDP-sugDHase	nucleotide sugar dehydrogenase. Enzymes in this family catalyze the NAD-dependent alcohol-to-acid oxidation of nucleotide-linked sugars. Examples include UDP-glucose 6-dehydrogenase (1.1.1.22), GDP-mannose 6-dehydrogenase (1.1.1.132), UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136), UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase, and UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase. These enzymes are most often involved in the biosynthesis of polysaccharides and are often found in operons devoted to that purpose. All of these enzymes contain three Pfam domains, pfam03721, pfam00984, and pfam03720 for the N-terminal, central, and C-terminal regions respectively.
108	PRK12921	305	135	96.7	0.0041	[--------------                                   ]	PRK12921	2-dehydropantoate 2-reductase; Provisional
109	COG0569	225	65	96.6	0.0023	[-------                                          ]	TrkA	Trk K+ transport system, NAD-binding component
110	PRK05249	461	35	96.6	0.002	[---                                              ]	PRK05249	soluble pyridine nucleotide transhydrogenase; Provisional
111	PRK06184	502	88	96.5	0.0019	[                       ----------                ]	PRK06184	hypothetical protein; Provisional
112	TIGR01377	380	77	96.4	0.0021	[                      --------                   ]	soxA_mon	sarcosine oxidase, monomeric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms
113	PRK12809	639	38	96.4	0.0021	[----                                             ]	PRK12809	putative oxidoreductase Fe-S binding subunit; Reviewed
114	COG1004	414	32	96.3	0.0036	[---                                              ]	Ugd	UDP-glucose 6-dehydrogenase
115	PRK12843	578	40	96.2	0.004	[----                                             ]	PRK12843	putative FAD-binding dehydrogenase; Reviewed
116	PRK09496	453	34	96.2	0.0045	[---                                              ]	trkA	potassium transporter peripheral membrane component; Reviewed
117	PRK04965	377	82	96.1	0.0093	[----------                                       ]	PRK04965	NADH:flavorubredoxin oxidoreductase; Provisional
118	TIGR02485	432	44	96.1	0.003	[                      ----                       ]	CobZ_N-term	precorrin 3B synthase CobZ. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the N-terminal portion of the R. capsulatus gene which, in other species exists as a separate protein. The C-terminal portion is homologous to the 2-component signal transduction system protein CitB (TIGR02484).
119	TIGR01988	385	146	96.0	0.0057	[                      -----------------          ]	Ubi-OHases	Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family. This model represents a family of FAD-dependent hydroxylases (monooxygenases) which are all believed to act in the aerobic ubiquinone biosynthesis pathway. A separate set of hydroxylases, as yet undiscovered, are believed to be active under anaerobic conditions. In E. coli three enzyme activities have been described, UbiB (which acts first at position 6, see TIGR01982), UbiH (which acts at position 4) and UbiF (which acts at position 5). UbiH and UbiF are similar to one another and form the basis of this subfamily. Interestingly, E. coli contains another hydroxylase gene, called visC, that is highly similar to UbiF, adjacent to UbiH and, when mutated, results in a phenotype similar to that of UbiH (which has also been named visB). Several other species appear to have three homologs in this family, although they assort themselves differently on phylogenetic trees (e.g. Xylella and Mesorhizobium) making it difficult to ascribe a specific activity to each one. Eukaryotes appear to have only a single homolog in this subfamily (COQ6) which complements UbiH, but also possess a non-orthologous gene, COQ7 which complements UbiF.
120	pfam02737	180	31	96.0	0.0056	[---                                              ]	3HCDH_N	3-hydroxyacyl-CoA dehydrogenase, NAD binding domain. This family also includes lambda crystallin.
121	TIGR01372	985	221	96.0	0.0057	[----------------------------                     ]	soxA	sarcosine oxidase, alpha subunit family, heterotetrameric form. This model describes the alpha subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members are share the same function. The model is designated as subfamily rather than equivalog for this reason.Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms
122	TIGR02360	390	59	96.0	0.0064	[-------                                          ]	pbenz_hydroxyl	4-hydroxybenzoate 3-monooxygenase. Members of this family are the enzyme 4-hydroxybenzoate 3-monooxygenase, also called p-hydroxybenzoate hydroxylase. It converts 4-hydroxybenzoate + NADPH + molecular oxygen to protocatechuate + NADPH + water. It contains monooxygenase (pfam01360) and FAD binding (pfam01494) domains. Pathways that contain this enzyme include the protocatechuate 4,5-degradation pathway.
123	PRK12842	574	46	95.9	0.0065	[-----                                            ]	PRK12842	putative succinate dehydrogenase; Reviewed
124	pfam02558	150	31	95.9	0.0069	[---                                              ]	ApbA	Ketopantoate reductase PanE/ApbA. This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway. ApbA and PanE are allelic. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway.
125	PRK06129	308	35	95.9	0.0064	[---                                              ]	PRK06129	3-hydroxyacyl-CoA dehydrogenase; Validated
126	PRK09754	396	42	95.9	0.003	[----                                             ]	PRK09754	phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional
127	PRK06481	506	58	95.9	0.0057	[                       ------                    ]	PRK06481	fumarate reductase flavoprotein subunit; Validated
128	TIGR01350	460	73	95.9	0.007	[                     -------                     ]	lipoamide_DH	dihydrolipoamide dehydrogenase. This model describes dihydrolipoamide dehydrogenase, a flavoprotein that acts in a number of ways. It is the E3 component of dehydrogenase complexes for pyruvate, 2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can also serve as the L protein of the glycine cleavage system. This family includes a few members known to have distinct functions (ferric leghemoglobin reductase and NADH:ferredoxin oxidoreductase) but that may be predicted by homology to act as dihydrolipoamide dehydrogenase as well. The motif GGXCXXXGCXP near the N-terminus contains a redox-active disulfide.
129	pfam04820	457	65	95.8	0.0078	[--------                                         ]	Trp_halogenase	Tryptophan halogenase. Tryptophan halogenase catalyses the chlorination of tryptophan to form 7-chlorotryptophan. This is the first step in the biosynthesis of pyrrolnitrin, an antibiotic with broad-spectrum anti-fungal activity. Tryptophan halogenase is NADH-dependent.
130	PRK13977	576	219	95.8	0.0074	[----------------------------                     ]	PRK13977	myosin-cross-reactive antigen; Provisional
131	TIGR00137	433	33	95.8	0.0069	[---                                              ]	gid_trmFO	tRNA:m(5)U-54 methyltransferase. This model represents an orthologous set of proteins present in relatively few bacteria but very tightly conserved where it occurs. It is closely related to gidA (glucose-inhibited division protein A), which appears to be present in all complete eubacterial genomes so far and in Saccharomyces cerevisiae. It was designated gid but is now recognized as a tRNA:m(5)U-54 methyltransferase and is now designated trmFO.
132	pfam01262	150	32	95.7	0.01	[---                                              ]	AlaDh_PNT_C	Alanine dehydrogenase/PNT, C-terminal domain. This family now also contains the lysine 2-oxoglutarate reductases.
133	TIGR03143	555	73	95.7	0.015	[--------                                         ]	AhpF_homolog	putative alkyl hydroperoxide reductase F subunit. This family of thioredoxin reductase homologs is found adjacent to alkylhydroperoxide reductase C subunit predominantly in cases where there is only one C subunit in the genome and that genome is lacking the F subunit partner (also a thioredcxin reductase homolog) that is usually found (TIGR03140).
134	PRK07843	557	38	95.6	0.012	[----                                             ]	PRK07843	3-ketosteroid-delta-1-dehydrogenase; Reviewed
135	PRK06292	460	38	95.6	0.013	[---                                              ]	PRK06292	dihydrolipoamide dehydrogenase; Validated
136	COG1206	439	37	95.6	0.01	[---                                              ]	TrmFO	Folate-dependent tRNA-U54 methylase TrmFO/GidA
137	PRK06134	581	47	95.5	0.012	[-----                                            ]	PRK06134	putative FAD-binding dehydrogenase; Reviewed
138	pfam01134	391	28	95.5	0.013	[---                                              ]	GIDA	Glucose inhibited division protein A.
139	COG1249	454	35	95.5	0.016	[---                                              ]	Lpd	Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component or related enzyme
140	PRK06834	488	83	95.4	0.01	[----------                                       ]	PRK06834	hypothetical protein; Provisional
141	TIGR03378	419	31	95.4	0.014	[---                                              ]	glycerol3P_GlpB	glycerol-3-phosphate dehydrogenase, anaerobic, B subunit. Members of this protein family are the B subunit, product of the glpB gene, of a three-subunit, membrane-anchored, FAD-dependent anaerobic glycerol-3-phosphate dehydrogenase.
142	TIGR03329	460	191	95.4	0.069	[----------------------------                     ]	Phn_aa_oxid	putative aminophosphonate oxidoreductase. This clade of sequences are members of the pfam01266 family of FAD-dependent oxidoreductases. Characterized proteins within this family include glycerol-3-phosphate dehydrogenase (1.1.99.5), sarcosine oxidase beta subunit (1.5.3.1) and a number of deaminating amino acid oxidases (1.4.-.-). These genes have been consistently observed in a genomic context including genes for the import and catabolism of 2-aminoethylphosphonate (AEP). If the substrate of this oxidoreductase is AEP itself, then it is probably acting in the manner of a deaminating oxidase, resulting in the same product (phosphonoacetaldehyde) as the transaminase PhnW (TIGR02326), but releasing ammonia instead of coupling to pyruvate:alanine. Alternatively, it is reasonable to suppose that the various ABC cassette transporters which are also associated with these loci allow the import of phosphonates closely related to AEP which may not be substrates for PhnW.
143	COG1252	405	34	95.4	0.016	[---                                              ]	Ndh	NADH dehydrogenase, FAD-containing subunit
144	PRK06126	545	30	95.3	0.015	[---                                              ]	PRK06126	hypothetical protein; Provisional
145	PRK05257	494	215	95.3	0.22	[----------------------------                     ]	PRK05257	malate:quinone oxidoreductase; Validated
146	TIGR03996	633	41	95.3	0.015	[----                                             ]	mycofact_OYE_1	mycofactocin system FadH/OYE family oxidoreductase 1. The yeast protein called old yellow enzyme and FadH from Escherichia coli (2,4-dienoyl CoA reductase) are enzymes with 4Fe-4S, FMN, and FAD prosthetic groups, and interact with NADPH as well as substrate. Members of this related protein family occur in the vicinity of the putative mycofactocin biosynthesis operon in a number of Actinobacteria such as Frankia sp. and Rhodococcus sp. The function of this oxidoreductase is unknown.
147	PRK06370	463	39	95.2	0.016	[----                                             ]	PRK06370	mercuric reductase; Validated
148	COG3075	421	46	95.2	0.082	[                      -----                      ]	GlpB	Anaerobic glycerol-3-phosphate dehydrogenase
149	pfam03446	163	32	95.0	0.021	[---                                              ]	NAD_binding_2	NAD binding domain of 6-phosphogluconate dehydrogenase. The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold.
150	pfam05834	374	36	94.9	0.032	[---                                              ]	Lycopene_cycl	Lycopene cyclase protein. This family consists of lycopene beta and epsilon cyclase proteins. Carotenoids with cyclic end groups are essential components of the photosynthetic membranes in all plants, algae, and cyanobacteria. These lipid-soluble compounds protect against photo-oxidation, harvest light for photosynthesis, and dissipate excess light energy absorbed by the antenna pigments. The cyclisation of lycopene (psi, psi-carotene) is a key branch point in the pathway of carotenoid biosynthesis. Two types of cyclic end groups are found in higher plant carotenoids: the beta and epsilon rings. Carotenoids with two beta rings are ubiquitous, and those with one beta and one epsilon ring are common; however, carotenoids with two epsilon rings are rare.
151	COG1748	389	32	94.8	0.026	[---                                              ]	Lys9	Saccharopine dehydrogenase, NADP-dependent
152	PRK12779	944	38	94.8	0.012	[----                                             ]	PRK12779	putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Provisional
153	PRK07804	541	33	94.8	0.025	[---                                              ]	PRK07804	L-aspartate oxidase; Provisional
154	PRK07845	466	39	94.8	0.035	[----                                             ]	PRK07845	flavoprotein disulfide reductase; Reviewed
155	PRK06475	400	32	94.6	0.0072	[---                                              ]	PRK06475	salicylate hydroxylase; Provisional
156	COG2084	286	35	94.6	0.033	[---                                              ]	MmsB	3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase
157	PRK06912	458	76	94.6	0.035	[--------                                         ]	acoL	dihydrolipoamide dehydrogenase; Validated
158	pfam00743	532	38	94.5	0.025	[---                                              ]	FMO-like	Flavin-binding monooxygenase-like. This family includes FMO proteins, cyclohexanone mono-oxygenase and a number of different mono-oxygenases.
159	pfam02254	116	33	94.4	0.045	[---                                              ]	TrkA_N	TrkA-N domain. This domain is found in a wide variety of proteins. These protein include potassium channels, phosphoesterases, and various other transporters. This domain binds to NAD.
160	PRK12844	557	37	94.4	0.039	[---                                              ]	PRK12844	3-ketosteroid-delta-1-dehydrogenase; Reviewed
161	PRK07608	388	135	94.4	0.04	[                       -----------------         ]	PRK07608	ubiquinone biosynthesis hydroxylase family protein; Provisional
162	COG1250	307	32	94.3	0.043	[---                                              ]	FadB	3-hydroxyacyl-CoA dehydrogenase
163	PRK06416	462	37	94.2	0.044	[----                                             ]	PRK06416	dihydrolipoamide dehydrogenase; Reviewed
164	cd01620	317	32	94.1	0.04	[---                                              ]	Ala_dh_like	Alanine dehydrogenase and related dehydrogenases. Alanine dehydrogenase/Transhydrogenase, such as the hexameric L-alanine dehydrogenase of Phormidium lapideum, contain 2 Rossmann fold-like domains linked by an alpha helical region. Related proteins include Saccharopine Dehydrogenase (SDH), bifunctional lysine ketoglutarate reductase /saccharopine dehydrogenase enzyme, N(5)-(carboxyethyl)ornithine synthase, and Rubrum transdehydrogenase. Alanine dehydrogenase (L-AlaDH) catalyzes the NAD-dependent conversion of pyrucate to L-alanine via reductive amination. Transhydrogenases found in bacterial and inner mitochondrial membranes link NAD(P)(H)-dependent redox reactions to proton translocation. The energy of the proton electrochemical gradient (delta-p), generated by the respiratory electron transport chain, is consumed by transhydrogenase in NAD(P)+ reduction. Transhydrogenase is likely involved in the regulation of the citric acid cycle. Rubrum transhydrogenase has 3 components, dI, dII, and dIII. dII spans the membrane while dI and dIII protrude on the cytoplasmic/matirx side. DI contains 2 domains with Rossmann folds, linked by a long alpha helix, and contains a NAD binding site. Two dI polypeptides (represented in this sub-family) spontaneously form a heterotrimer with one dIII in the absence of dII. In the heterotrimer, both dI chains may bind NAD, but only one is well-ordered. dIII also binds a well-ordered NADP, but in a different orientation than classical Rossmann domains.
165	TIGR01790	388	37	94.1	0.04	[----                                             ]	carotene-cycl	lycopene cyclase family protein. This family includes lycopene beta and epsilion cyclases (which form beta and delta carotene, respectively) from bacteria and plants as well as the plant capsanthin/capsorubin and neoxanthin cyclases which appear to have evolved from the plant lycopene cyclases. The plant lycopene epsilon cyclases also transform neurosporene to alpha zeacarotene.
166	pfam13454	154	49	94.1	0.048	[                       -----                     ]	NAD_binding_9	FAD-NAD(P)-binding.
167	PRK08255	765	32	94.0	0.05	[---                                              ]	PRK08255	salicylyl-CoA 5-hydroxylase; Reviewed
168	TIGR00551	489	93	94.0	0.04	[---------                                        ]	nadB	L-aspartate oxidase. L-aspartate oxidase is the B protein, NadB, of the quinolinate synthetase complex. Quinolinate synthetase makes a precursor of the pyridine nucleotide portion of NAD. This model identifies proteins that cluster as L-aspartate oxidase (a flavoprotein difficult to separate from the set of closely related flavoprotein subunits of succinate dehydrogenase and fumarate reductase) by both UPGMA and neighbor-joining trees. The most distant protein accepted as an L-aspartate oxidase (NadB), that from Pyrococcus horikoshii, not only clusters with other NadB but is just one gene away from NadA.
169	PRK06452	566	77	93.9	0.044	[--------                                         ]	sdhA	succinate dehydrogenase flavoprotein subunit; Reviewed
170	PRK05976	472	60	93.8	0.044	[--------                                         ]	PRK05976	dihydrolipoamide dehydrogenase; Validated
171	COG2085	211	30	93.8	0.055	[---                                              ]	COG2085	Predicted dinucleotide-binding enzyme
172	PRK12839	572	72	93.8	0.057	[-------                                          ]	PRK12839	hypothetical protein; Provisional
173	cd08255	277	32	93.7	0.067	[---                                              ]	2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like	2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and other MDR family members. This subgroup of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family has members identified as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase and alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability.
174	PRK02106	560	30	93.6	0.051	[---                                              ]	PRK02106	choline dehydrogenase; Validated
175	PRK08244	493	33	93.4	0.067	[---                                              ]	PRK08244	hypothetical protein; Provisional
176	pfam03807	93	28	93.4	0.085	[---                                              ]	F420_oxidored	NADP oxidoreductase coenzyme F420-dependent.
177	cd05305	359	31	93.3	0.084	[---                                              ]	L-AlaDH	Alanine dehydrogenase NAD-binding and catalytic domains. Alanine dehydrogenase (L-AlaDH) catalyzes the NAD-dependent conversion of pyruvate to L-alanine via reductive amination. Like formate dehydrogenase and related enzymes, L-AlaDH is comprised of 2 domains connected by a long alpha helical stretch, each resembling a Rossmann fold NAD-binding domain. The NAD-binding domain is inserted within the linear sequence of the more divergent catalytic domain. Ligand binding and active site residues are found in the cleft between the subdomains. L-AlaDH is typically hexameric and is critical in carbon and nitrogen metabolism in micro-organisms.
178	pfam13241	103	31	93.2	0.11	[---                                              ]	NAD_binding_7	Putative NAD(P)-binding. This domain is found in fungi, plants, archaea and bacteria.
179	TIGR01812	566	55	93.2	0.075	[-----                                            ]	sdhA_frdA_Gneg	succinate dehydrogenase or fumarate reductase, flavoprotein subunitGram-negative/mitochondrial subgroup. This model represents the succinate dehydrogenase flavoprotein subunit as found in Gram-negative bacteria, mitochondria, and some Archaea. Mitochondrial forms interact with ubiquinone and are designated EC 1.3.5.1, but can be degraded to 1.3.99.1. Some isozymes in E. coli and other species run primarily in the opposite direction and are designated fumarate reductase.
180	PRK07045	388	32	93.2	0.067	[---                                              ]	PRK07045	putative monooxygenase; Reviewed
181	PRK06249	313	35	93.1	0.093	[---                                              ]	PRK06249	2-dehydropantoate 2-reductase; Provisional
182	cd05265	250	36	92.9	0.11	[---                                              ]	SDR_a1	atypical (a) SDRs, subgroup 1. Atypical SDRs in this subgroup are poorly defined and have been identified putatively as isoflavones reductase, sugar dehydratase, mRNA binding protein etc. Atypical SDRs are distinct from classical SDRs. Members of this subgroup retain the canonical active site triad (though not the upstream Asn found in most SDRs) but have an unusual putative glycine-rich NAD(P)-binding motif, GGXXXXG, in the usual location. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
183	PRK08849	384	31	92.8	0.09	[---                                              ]	PRK08849	2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional
184	PRK06327	475	34	92.8	0.047	[---                                              ]	PRK06327	dihydrolipoamide dehydrogenase; Validated
185	TIGR01984	382	33	92.8	0.087	[---                                              ]	UbiH	2-polyprenyl-6-methoxyphenol 4-hydroxylase. This model represents the FAD-dependent monoxygenase responsible for the second hydroxylation step in the aerobic ubiquinone bioynthetic pathway. The scope of this model is limited to the proteobacteria. This family is closely related to the UbiF hydroxylase which catalyzes the final hydroxylation step. The enzyme has also been named VisB due to a mutant VISible light sensitive phenotype.
186	PRK08020	391	33	92.6	0.11	[---                                              ]	ubiF	2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed
187	COG4529	474	36	92.6	0.12	[---                                              ]	YdhS	Uncharacterized NAD(P)/FAD-binding protein YdhS
188	pfam06039	489	211	92.6	0.5	[----------------------------                     ]	Mqo	Malate:quinone oxidoreductase (Mqo). This family consists of several bacterial Malate:quinone oxidoreductase (Mqo) proteins (EC:1.1.99.16). Mqo takes part in the citric acid cycle. It oxidizes L-malate to oxaloacetate and donates electrons to ubiquinone-1 and other artificial acceptors or, via the electron transfer chain, to oxygen. NAD is not an acceptor and the natural direct acceptor for the enzyme is most likely a quinone. The enzyme is therefore called malate:quinone oxidoreductase, abbreviated to Mqo. Mqo is a peripheral membrane protein and can be released from the membrane by addition of chelators.
189	PRK14727	479	38	92.2	0.14	[----                                             ]	PRK14727	putative mercuric reductase; Provisional
190	COG0771	448	74	92.1	0.14	[-------                                          ]	MurD	UDP-N-acetylmuramoylalanine-D-glutamate ligase
191	cd05304	363	33	92.0	0.15	[---                                              ]	Rubrum_tdh	Rubrum transdehydrogenase NAD-binding and catalytic domains. Transhydrogenases found in bacterial and inner mitochondrial membranes link NAD(P)(H)-dependent redox reactions to proton translocation. The energy of the proton electrochemical gradient (delta-p), generated by the respiratory electron transport chain, is consumed by transhydrogenase in NAD(P)+ reduction. Transhydrogenase is likely involved in the regulation of the citric acid cycle. Rubrum transhydrogenase has 3 components, dI, dII, and dIII. dII spans the membrane while dI and dIII protrude on the cytoplasmic/matrix side. DI contains 2 domains in Rossmann-like folds, linked by a long alpha helix, and contains a NAD binding site. Two dI polypeptides (represented in this sub-family) spontaneously form a heterotrimer with dIII in the absence of dII. In the heterotrimer, both dI chains may bind NAD, but only one is well-ordered. dIII also binds a well-ordered NADP, but in a different orientation than a classical Rossmann domain.
192	pfam01210	157	31	92.0	0.15	[---                                              ]	NAD_Gly3P_dh_N	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus. NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain.
193	pfam13460	183	31	91.9	0.17	[---                                              ]	NAD_binding_10	NADH(P)-binding.
194	PRK07057	591	150	91.8	0.33	[-----------------                                ]	sdhA	succinate dehydrogenase flavoprotein subunit; Reviewed
195	PRK06467	471	230	91.7	0.16	[-----------------------------                    ]	PRK06467	dihydrolipoamide dehydrogenase; Reviewed
196	COG0451	314	38	91.3	0.29	[---                                              ]	WcaG	Nucleoside-diphosphate-sugar epimerase
197	TIGR03219	414	38	91.0	0.2	[---                                              ]	salicylate_mono	salicylate 1-monooxygenase. Members of this protein family are salicylate 1-monooxygenase, also called salicylate hydroxylase. This enzyme converts salicylate to catechol, which is a common intermediate in the degradation of a number of aromatic compounds (phenol, toluene, benzoate, etc.). The gene for this protein may occur in catechol degradation genes, such as those of the meta-cleavage pathway.
198	cd08231	361	32	91.0	0.23	[---                                              ]	MDR_TM0436_like	Hypothetical enzyme TM0436 resembles the zinc-dependent alcohol dehydrogenases (ADH). This group contains the hypothetical TM0436 alcohol dehydrogenase from Thermotoga maritima, proteins annotated as 5-exo-alcohol dehydrogenase, and other members of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. MDR, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability.
199	PRK12416	463	63	91.0	0.28	[                      -------                    ]	PRK12416	protoporphyrinogen oxidase; Provisional
200	PRK08293	287	33	90.9	0.22	[---                                              ]	PRK08293	3-hydroxybutyryl-CoA dehydrogenase; Validated
201	PRK08641	589	81	90.8	0.51	[--------                                         ]	sdhA	succinate dehydrogenase flavoprotein subunit; Reviewed
202	cd01065	155	32	90.8	0.32	[---                                              ]	NAD_bind_Shikimate_DH	NAD(P) binding domain of Shikimate dehydrogenase. Shikimate dehydrogenase (DH) is an amino acid DH family member. Shikimate pathway links metabolism of carbohydrates to de novo biosynthesis of aromatic amino acids, quinones and folate. It is essential in plants, bacteria, and fungi but absent in mammals, thus making enzymes involved in this pathway ideal targets for broad spectrum antibiotics and herbicides. Shikimate DH catalyzes the reduction of 3-hydroshikimate to shikimate using the cofactor NADH. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DHs, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
203	TIGR01350	460	35	90.8	0.16	[---                                              ]	lipoamide_DH	dihydrolipoamide dehydrogenase. This model describes dihydrolipoamide dehydrogenase, a flavoprotein that acts in a number of ways. It is the E3 component of dehydrogenase complexes for pyruvate, 2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can also serve as the L protein of the glycine cleavage system. This family includes a few members known to have distinct functions (ferric leghemoglobin reductase and NADH:ferredoxin oxidoreductase) but that may be predicted by homology to act as dihydrolipoamide dehydrogenase as well. The motif GGXCXXXGCXP near the N-terminus contains a redox-active disulfide.
204	PRK06327	475	30	90.8	0.21	[---                                              ]	PRK06327	dihydrolipoamide dehydrogenase; Validated
205	cd05244	207	32	90.7	0.25	[---                                              ]	BVR-B_like_SDR_a	biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs. Human BVR-B catalyzes pyridine nucleotide-dependent production of bilirubin-IX beta during fetal development; in the adult BVR-B has flavin and ferric reductase activities. Human BVR-B catalyzes the reduction of FMN, FAD, and riboflavin. Recognition of flavin occurs mostly by hydrophobic interactions, accounting for the broad substrate specificity. Atypical SDRs are distinct from classical SDRs. BVR-B does not share the key catalytic triad, or conserved tyrosine typical of SDRs. The glycine-rich NADP-binding motif of BVR-B is GXXGXXG, which is similar but not identical to the pattern seen in extended SDRs. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
206	cd05292	308	24	90.6	0.18	[--                                               ]	LDH_2	A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed predominantly of bacterial LDHs and a few fungal LDHs. Bacterial LDHs may be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
207	PRK00094	325	32	90.6	0.24	[---                                              ]	gpsA	NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated
208	PRK13339	497	214	90.6	1.1	[----------------------------                     ]	PRK13339	malate:quinone oxidoreductase; Reviewed
209	TIGR02028	398	33	90.5	0.22	[---                                              ]	ChlP	geranylgeranyl reductase. This model represents the reductase which acts reduces the geranylgeranyl group to the phytyl group in the side chain of chlorophyll. It is unclear whether the enzyme has a preference for acting before or after the attachment of the side chain to chlorophyllide a by chlorophyll synthase. This clade is restricted to plants and cyanobacteria to separate it from the homologues which act in the biosynthesis of bacteriochlorophyll.
210	PRK09897	534	36	90.5	0.18	[---                                              ]	PRK09897	hypothetical protein; Provisional
211	PRK06854	608	41	90.4	0.24	[----                                             ]	PRK06854	adenylylsulfate reductase subunit alpha; Validated
212	PRK07190	487	41	90.3	0.29	[----                                             ]	PRK07190	hypothetical protein; Provisional
213	cd05188	271	33	90.3	0.32	[---                                              ]	MDR	Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family. The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc.
214	PRK02705	459	35	90.3	0.26	[---                                              ]	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
215	cd08230	355	37	90.2	0.34	[---                                              ]	glucose_DH	Glucose dehydrogenase. Glucose dehydrogenase (GlcDH), a member of the medium chain dehydrogenase/zinc-dependent alcohol dehydrogenase-like family, catalyzes the NADP(+)-dependent oxidation of glucose to gluconate, the first step in the Entner-Doudoroff pathway, an alternative to or substitute for glycolysis or the pentose phosphate pathway. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossman fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability.
216	PRK08626	657	28	90.0	0.27	[---                                              ]	PRK08626	fumarate reductase flavoprotein subunit; Provisional
217	PRK08071	510	61	89.8	0.27	[------                                           ]	PRK08071	L-aspartate oxidase; Provisional
218	PRK11445	351	127	89.7	0.28	[-----------------                                ]	PRK11445	putative oxidoreductase; Provisional
219	pfam00899	134	24	89.5	0.31	[--                                               ]	ThiF	ThiF family. This family contains a repeated domain in ubiquitin activating enzyme E1 and members of the bacterial ThiF/MoeB/HesA family.
220	COG1087	329	31	89.5	0.37	[---                                              ]	GalE	UDP-glucose 4-epimerase
221	pfam01488	133	30	89.4	0.45	[---                                              ]	Shikimate_DH	Shikimate / quinate 5-dehydrogenase. This family contains both shikimate and quinate dehydrogenases. Shikimate 5-dehydrogenase catalyses the conversion of shikimate to 5-dehydroshikimate. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites 3-dehydroquinate and dehydroshikimate.
222	PRK08850	405	32	89.3	0.33	[---                                              ]	PRK08850	2-octaprenyl-6-methoxyphenol hydroxylase; Validated
223	COG0446	415	71	89.2	0.46	[                     -------                     ]	FadH2	NADPH-dependent 2,4-dienoyl-CoA reductase, sulfur reductase, or a related oxidoreductase
224	COG2072	443	33	89.2	0.4	[---                                              ]	CzcO	Predicted flavoprotein CzcO associated with the cation diffusion facilitator CzcD
225	PRK14106	450	33	88.9	0.32	[---                                              ]	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
226	COG1648	210	29	88.9	0.46	[---                                              ]	CysG2	Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain)
227	PRK11559	296	80	88.7	0.28	[---------                                        ]	garR	tartronate semialdehyde reductase; Provisional
228	PRK05192	618	67	88.4	0.44	[--------                                         ]	PRK05192	tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated
229	cd08261	337	31	88.2	0.49	[---                                              ]	Zn_ADH7	Alcohol dehydrogenases of the MDR family. This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group includes various activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines.
230	PRK13748	561	38	88.1	0.6	[----                                             ]	PRK13748	putative mercuric reductase; Provisional
231	PRK06035	291	32	88.0	0.41	[---                                              ]	PRK06035	3-hydroxyacyl-CoA dehydrogenase; Validated
232	COG0445	621	67	87.9	0.35	[--------                                         ]	MnmG	tRNA U34 5-carboxymethylaminomethyl modifying enzyme MnmG/GidA
233	PRK09291	257	49	87.8	0.4	[-------                                          ]	PRK09291	short chain dehydrogenase; Provisional
234	PRK09496	453	33	87.7	0.6	[---                                              ]	trkA	potassium transporter peripheral membrane component; Reviewed
235	PRK12837	513	37	87.6	0.36	[----                                             ]	PRK12837	3-ketosteroid-delta-1-dehydrogenase; Provisional
236	PRK07251	438	85	87.6	0.39	[----------                                       ]	PRK07251	pyridine nucleotide-disulfide oxidoreductase; Provisional
237	COG5044	434	320	87.4	42	[-----------------------------------------        ]	MRS6	RAB proteins geranylgeranyltransferase component A (RAB escort protein)
238	cd05255	382	30	87.2	0.45	[---                                              ]	SQD1_like_SDR_e	UDP_sulfoquinovose_synthase (Arabidopsis thaliana SQD1 and related proteins), extended (e) SDRs. Arabidopsis thaliana UDP-sulfoquinovose-synthase ( SQD1), an extended SDR, catalyzes the transfer of SO(3)(-) to UDP-glucose in the biosynthesis of plant sulfolipids. Members of this subgroup share the conserved SDR catalytic residues, and a partial match to the characteristic extended-SDR NAD-binding motif. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
239	PRK07688	339	32	87.2	0.41	[---                                              ]	PRK07688	thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
240	TIGR03366	280	29	87.0	0.59	[---                                              ]	HpnZ_proposed	putative phosphonate catabolism associated alcohol dehydrogenase. This clade of zinc-binding alcohol dehydrogenases (members of pfam00107) are repeatedly associated with genes proposed to be involved with the catabolism of phosphonate compounds.
241	PRK07512	513	40	87.0	0.46	[----                                             ]	PRK07512	L-aspartate oxidase; Provisional
242	PRK07573	640	32	86.8	0.56	[---                                              ]	sdhA	succinate dehydrogenase flavoprotein subunit; Reviewed
243	COG0686	371	46	86.7	0.65	[----                                             ]	Ald	Alanine dehydrogenase
244	PRK15317	517	32	86.6	0.56	[---                                              ]	PRK15317	alkyl hydroperoxide reductase subunit F; Provisional
245	COG1063	350	28	86.6	0.78	[---                                              ]	Tdh	Threonine dehydrogenase or related Zn-dependent dehydrogenase
246	cd08269	312	33	86.6	0.73	[---                                              ]	Zn_ADH9	Alcohol dehydrogenases of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability.
247	COG0654	387	32	86.5	8.6	[---                                              ]	UbiH	2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
248	cd05311	226	106	86.5	0.9	[-----------                                      ]	NAD_bind_2_malic_enz	NAD(P) binding domain of malic enzyme (ME), subgroup 2. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists primarily of archaeal and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
249	PRK08773	392	80	86.4	0.69	[                     ---------                   ]	PRK08773	2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Validated
250	TIGR04542	425	41	86.2	0.32	[----                                             ]	GMC_mycofac_2	GMC family mycofactocin-associated oxidreductase. This model describes a set of dehydrogenases belonging to the glucose-methanol-choline oxidoreductase (GMC oxidoreductase) family. Members of the present family are restricted to the bacterial genus Gordonia, and seem to replace the related family TIGR03970, which occurs in Actinobacteria generally but not in the genus Gordonia. Members of both this family and TIGR03970 are associated with the mycofactocin biosynthesis operon in Actinobacteria.
251	COG0287	279	38	86.0	0.85	[---                                              ]	TyrA	Prephenate dehydrogenase
252	PRK06130	311	31	85.7	0.56	[---                                              ]	PRK06130	3-hydroxybutyryl-CoA dehydrogenase; Validated
253	COG0169	283	31	85.7	0.94	[---                                              ]	AroE	Shikimate 5-dehydrogenase
254	PRK09564	444	35	85.7	0.83	[---                                              ]	PRK09564	coenzyme A disulfide reductase; Reviewed
255	COG0240	329	32	85.6	0.85	[---                                              ]	GpsA	Glycerol-3-phosphate dehydrogenase
256	PRK08268	507	32	85.6	0.69	[---                                              ]	PRK08268	3-hydroxy-acyl-CoA dehydrogenase; Validated
257	PRK09260	288	33	85.4	0.43	[---                                              ]	PRK09260	3-hydroxybutyryl-CoA dehydrogenase; Validated
258	PRK07818	466	37	85.3	0.79	[---                                              ]	PRK07818	dihydrolipoamide dehydrogenase; Reviewed
259	TIGR00136	616	67	85.2	0.72	[--------                                         ]	gidA	glucose-inhibited division protein A. GidA, the longer of two forms of GidA-related proteins, appears to be present in all complete eubacterial genomes so far, as well as Saccharomyces cerevisiae. A subset of these organisms have a closely related protein. GidA is absent in the Archaea. It appears to act with MnmE, in an alpha2/beta2 heterotetramer, in the 5-carboxymethylaminomethyl modification of uridine 34 in certain tRNAs. The shorter, related protein, previously called gid or gidA(S), is now called TrmFO (see model TIGR00137).
260	TIGR00507	270	32	85.0	0.93	[---                                              ]	aroE	shikimate dehydrogenase. This model finds proteins from prokaryotes and functionally equivalent domains from larger, multifunctional proteins of fungi and plants. Below the trusted cutoff of 180, but above the noise cutoff of 20, are the putative shikimate dehydrogenases of Thermotoga maritima and Mycobacterium tuberculosis, and uncharacterized paralogs of shikimate dehydrogenase from E. coli and H. influenzae. The related enzyme quinate 5-dehydrogenase scores below the noise cutoff. A neighbor-joining tree, constructed with quinate 5-dehydrogenases as the outgroup, shows the Clamydial homolog as clustering among the shikimate dehydrogenases, although the sequence is unusual in the degree of sequence divergence and the presence of an additional N-terminal domain.
261	PRK08294	634	34	84.9	0.93	[---                                              ]	PRK08294	phenol 2-monooxygenase; Provisional
262	PRK06223	307	31	84.9	0.95	[---                                              ]	PRK06223	malate dehydrogenase; Reviewed
263	PRK09564	444	50	84.6	0.81	[                       ------                    ]	PRK09564	coenzyme A disulfide reductase; Reviewed
264	TIGR00275	400	115	84.4	2.4	[                  -------------                  ]	TIGR00275	flavoprotein, HI0933 family. The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae.
265	PRK06370	463	35	84.4	1.1	[---                                              ]	PRK06370	mercuric reductase; Validated
266	COG3640	255	34	84.2	1.3	[---                                              ]	CooC	CO dehydrogenase nickel-insertion accessory protein CooC1
267	PRK07803	626	29	84.1	0.95	[---                                              ]	sdhA	succinate dehydrogenase flavoprotein subunit; Reviewed
268	PRK05976	472	37	83.9	0.54	[---                                              ]	PRK05976	dihydrolipoamide dehydrogenase; Validated
269	PRK12835	584	51	83.8	0.96	[-----                                            ]	PRK12835	3-ketosteroid-delta-1-dehydrogenase; Reviewed
270	TIGR01438	484	31	83.8	0.9	[---                                              ]	TGR	thioredoxin and glutathione reductase selenoprotein. This homodimeric, FAD-containing member of the pyridine nucleotide disulfide oxidoreductase family contains a C-terminal motif Cys-SeCys-Gly, where SeCys is selenocysteine encoded by TGA (in some sequence reports interpreted as a stop codon). In some members of this subfamily, Cys-SeCys-Gly is replaced by Cys-Cys-Gly. The reach of the selenium atom at the C-term arm of the protein is proposed to allow broad substrate specificity.
271	COG2910	211	32	83.7	1.3	[---                                              ]	YwnB	Putative NADH-flavin reductase
272	TIGR02053	463	40	83.6	1.5	[----                                             ]	MerA	mercury(II) reductase. This model represents the mercuric reductase found in the mer operon for the detoxification of mercury compounds. MerA is a FAD-containing flavoprotein which reduces Hg(II) to Hg(0) utilizing NADPH.
273	PRK12266	508	48	83.6	0.87	[-----                                            ]	glpD	glycerol-3-phosphate dehydrogenase; Reviewed
274	TIGR03911	266	33	83.1	0.74	[---                                              ]	pyrrolys_PylD	pyrrolysine biosynthesis protein PylD. This protein is PylD, part of a three-gene cassette that is sufficient to direct the biosynthesis of pyrrolysine, the twenty-second amino acid, incorporated in some species at a UAG canonical stop codon.
275	COG0039	313	32	83.1	1.2	[---                                              ]	Mdh	Malate/lactate dehydrogenase
276	TIGR03140	515	30	83.0	0.93	[---                                              ]	AhpF	alkyl hydroperoxide reductase subunit F. This enzyme is the partner of the peroxiredoxin (alkyl hydroperoxide reductase) AhpC which contains the peroxide-reactive cysteine. AhpF contains the reductant (NAD(P)H) binding domain (pfam00070) and presumably acts to resolve the disulfide which forms after oxidation of the active site cysteine in AphC. This proteins contains two paired conserved cysteine motifs, CxxCP and CxHCDGP.
277	COG3634	520	31	82.4	0.93	[---                                              ]	AhpF	Alkyl hydroperoxide reductase subunit AhpF
278	pfam06100	500	43	82.2	0.52	[----                                             ]	Strep_67kDa_ant	Streptococcal 67 kDa myosin-cross-reactive antigen like family. Members of this family are thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis.
279	PRK05732	395	32	82.1	1.4	[---                                              ]	PRK05732	2-octaprenyl-6-methoxyphenyl hydroxylase; Validated
280	TIGR03385	427	35	82.0	1.2	[---                                              ]	CoA_CoA_reduc	CoA-disulfide reductase. Members of this protein family are CoA-disulfide reductase (EC 1.8.1.14), as characterized in Staphylococcus aureus, Pyrococcus horikoshii, and Borrelia burgdorferi, and inferred in several other species on the basis of high levels of CoA and an absence of glutathione as a protective thiol.
281	cd05191	86	31	82.0	1.7	[---                                              ]	NAD_bind_amino_acid_DH	NAD(P) binding domain of amino acid dehydrogenase-like proteins. Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
282	COG0677	436	33	81.7	1.3	[---                                              ]	WecC	UDP-N-acetyl-D-mannosaminuronate dehydrogenase
283	cd05247	323	30	81.6	1.2	[---                                              ]	UDP_G4E_1_SDR_e	UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs. UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
284	pfam13478	137	31	81.1	1.5	[---                                              ]	XdhC_C	XdhC Rossmann domain. This entry is the rossmann domain found in the Xanthine dehydrogenase accessory protein.
285	pfam00056	140	40	80.7	1.5	[----                                             ]	Ldh_1_N	lactate/malate dehydrogenase, NAD binding domain. L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. N-terminus (this family) is a Rossmann NAD-binding fold. C-terminus is an unusual alpha+beta fold.
286	PRK06069	577	78	80.3	1.4	[--------                                         ]	sdhA	succinate dehydrogenase flavoprotein subunit; Reviewed
287	TIGR02279	503	32	80.1	1.3	[---                                              ]	PaaC-3OHAcCoADH	3-hydroxyacyl-CoA dehydrogenase PaaC. This 3-hydroxyacyl-CoA dehydrogenase is involved in the degradation of phenylacetic acid, presumably in steps following the opening of the phenyl ring. The sequences included in this model are all found in aparrent operons with other related genes such as paaA, paaB, paaD, paaE, paaF and paaN. Some genomes contain these other genes without an apparent paaC in the same operon - possibly in these cases a different dehydrogenase involved in fatty acid degradation may fill in the needed activity. This enzyme has domains which are members of the pfam02737 and pfam00725 families.
288	PRK12557	342	32	79.7	1.6	[---                                              ]	PRK12557	H(2)-dependent methylenetetrahydromethanopterin dehydrogenase-related protein; Provisional
289	cd08236	343	31	79.6	2.1	[---                                              ]	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.
290	PRK07819	286	31	79.5	1.6	[---                                              ]	PRK07819	3-hydroxybutyryl-CoA dehydrogenase; Validated
291	cd01483	143	23	79.3	1.7	[--                                               ]	E1_enzyme_family	Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS.
292	PRK06416	462	29	79.1	1.3	[                       ---                       ]	PRK06416	dihydrolipoamide dehydrogenase; Reviewed
293	PRK11880	267	33	79.0	2.1	[---                                              ]	PRK11880	pyrroline-5-carboxylate reductase; Reviewed
294	cd12154	310	33	78.9	1.8	[---                                              ]	FDH_GDH_like	Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases. The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases.
295	PRK01372	304	74	78.8	4.7	[--------                                         ]	ddl	D-alanine--D-alanine ligase; Reviewed
296	PRK00683	418	53	78.8	1.4	[-----                                            ]	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
297	TIGR01373	407	51	78.7	1.9	[-----                                            ]	soxB	sarcosine oxidase, beta subunit family, heterotetrameric form. This model describes the beta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members are share the same function. The model is designated as subfamily rather than equivalog for this reason. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms.
298	TIGR02053	463	32	78.2	2.3	[---                                              ]	MerA	mercury(II) reductase. This model represents the mercuric reductase found in the mer operon for the detoxification of mercury compounds. MerA is a FAD-containing flavoprotein which reduces Hg(II) to Hg(0) utilizing NADPH.
299	TIGR01811	603	31	78.1	1.6	[---                                              ]	sdhA_Bsu	succinate dehydrogenase or fumarate reductase, flavoprotein subunit, Bacillus subtilis subgroup. This model represents the succinate dehydrogenase flavoprotein subunit as found in the low-GC Gram-positive bacteria and a few other lineages. This enzyme may act in a complete or partial TCA cycle, or act in the opposite direction as fumarate reductase. In some but not all species, succinate dehydrogenase and fumarate reductase may be encoded as separate isozymes.
300	TIGR01202	308	109	78.0	5	[-------------                                    ]	bchC	2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase.
301	cd05291	306	24	77.8	1.8	[--                                               ]	HicDH_like	L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases. L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. This subfamily is composed of HicDHs and some bacterial L-lactate dehydrogenases (LDH). LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Bacterial LDHs can be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. Members of this subfamily with known structures such as the HicDH of Lactobacillus confusus, the non-allosteric LDH of Lactobacillus pentosus, and the allosteric LDH of Bacillus stearothermophilus, show that they exist as homotetramers. The HicDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
302	PRK06720	169	33	77.8	2	[---                                              ]	PRK06720	hypothetical protein; Provisional
303	PRK05714	405	32	77.5	1.9	[---                                              ]	PRK05714	2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional
304	PRK08013	400	33	77.4	1.4	[---                                              ]	PRK08013	oxidoreductase; Provisional
305	PRK06115	466	31	77.1	0.98	[---                                              ]	PRK06115	dihydrolipoamide dehydrogenase; Reviewed
306	COG1028	251	36	77.0	3.5	[---                                              ]	FabG	NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
307	TIGR04018	316	36	76.7	3	[---                                              ]	Bthiol_YpdA	putative bacillithiol system oxidoreductase, YpdA family. Members of this protein family, including YpdA from Bacillus subtilis, are apparent oxidoreductases present only in species with an active bacillithiol system. They have been suggested actually to be thiol disulfide oxidoreductases (TDOR), although the evidence is incomplete.
308	TIGR03169	364	35	76.6	2.8	[---                                              ]	Nterm_to_SelD	pyridine nucleotide-disulfide oxidoreductase family protein. Members of this protein family include N-terminal sequence regions of (probable) bifunctional proteins whose C-terminal sequences are SelD, or selenide,water dikinase, the selenium donor protein necessary for selenium incorporation into protein (as selenocysteine), tRNA (as 2-selenouridine), or both. However, some members of this family occur in species that do not show selenium incorporation, and the function of this protein family is unknown.
309	PRK00258	278	31	76.5	3.2	[---                                              ]	aroE	shikimate 5-dehydrogenase; Reviewed
310	PRK08243	392	59	76.1	6	[-------                                          ]	PRK08243	4-hydroxybenzoate 3-monooxygenase; Validated
311	PRK00066	315	24	75.8	2	[--                                               ]	ldh	L-lactate dehydrogenase; Reviewed
312	cd05226	176	34	75.5	3	[---                                              ]	SDR_e_a	Extended (e) and atypical (a) SDRs. Extended or atypical short-chain dehydrogenases/reductases (SDRs, aka tyrosine-dependent oxidoreductases) are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
313	PRK15317	517	35	75.3	2.6	[----                                             ]	PRK15317	alkyl hydroperoxide reductase subunit F; Provisional
314	PRK07818	466	31	75.3	1.2	[---                                              ]	PRK07818	dihydrolipoamide dehydrogenase; Reviewed
315	PRK10309	347	33	75.2	3.2	[---                                              ]	PRK10309	galactitol-1-phosphate dehydrogenase; Provisional
316	PRK08229	341	32	75.2	2.3	[---                                              ]	PRK08229	2-dehydropantoate 2-reductase; Provisional
317	PRK11101	546	48	75.1	2.8	[-----                                            ]	glpA	sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional
318	COG0281	432	31	75.0	3.3	[---                                              ]	SfcA	Malic enzyme
319	cd08234	334	30	75.0	3.2	[---                                              ]	threonine_DH_like	L-threonine dehydrogenase. L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine, via NAD(H)-dependent oxidation. THD is a member of the zinc-requiring, medium chain NAD(H)-dependent alcohol dehydrogenase family (MDR). MDRs have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. 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. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose.
320	TIGR03970	487	33	74.9	2.1	[---                                              ]	Rv0697	dehydrogenase, Rv0697 family. This model describes a set of dehydrogenases belonging to the glucose-methanol-choline oxidoreductase (GMC oxidoreductase) family. Members of the present family are restricted to Actinobacterial genome contexts containing also members of families TIGR03962 and TIGR03969 (the mycofactocin system), and are proposed to be uniform in function.
321	TIGR03140	515	36	74.6	2.5	[----                                             ]	AhpF	alkyl hydroperoxide reductase subunit F. This enzyme is the partner of the peroxiredoxin (alkyl hydroperoxide reductase) AhpC which contains the peroxide-reactive cysteine. AhpF contains the reductant (NAD(P)H) binding domain (pfam00070) and presumably acts to resolve the disulfide which forms after oxidation of the active site cysteine in AphC. This proteins contains two paired conserved cysteine motifs, CxxCP and CxHCDGP.
322	TIGR00518	370	46	74.6	2.1	[----                                             ]	alaDH	alanine dehydrogenase. The family of known L-alanine dehydrogenases (EC 1.4.1.1) includes representatives from the Proteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria, all with about 50 % identity or better. An outlier to this group in both sequence and gap pattern is the homolog from Helicobacter pylori, an epsilon division Proteobacteria, which must be considered a putative alanine dehydrogenase. In Mycobacterium smegmatis and M. tuberculosis, the enzyme doubles as a glycine dehydrogenase (1.4.1.10), running in the reverse direction (glyoxylate amination to glycine, with conversion of NADH to NAD+). Related proteins include saccharopine dehydrogenase and the N-terminal half of the NAD(P) transhydrogenase alpha subunit. All of these related proteins bind NAD and/or NADP.
323	TIGR01915	219	29	74.5	2.1	[---                                              ]	npdG	NADPH-dependent F420 reductase. This model represents a subset of a parent family described by pfam03807. Unlike the parent family, members of this family are found only in species with evidence of coenzyme F420. All members of this family are believed to act as NADPH-dependent F420 reductase.
324	PRK05562	223	29	74.2	1.6	[---                                              ]	PRK05562	precorrin-2 dehydrogenase; Provisional
325	PRK09424	509	15	74.1	1.8	[-                                                ]	pntA	NAD(P) transhydrogenase subunit alpha; Provisional
326	PRK09599	301	34	74.0	2.4	[---                                              ]	PRK09599	6-phosphogluconate dehydrogenase-like protein; Reviewed
327	PRK05808	282	31	74.0	2.9	[---                                              ]	PRK05808	3-hydroxybutyryl-CoA dehydrogenase; Validated
328	TIGR01810	532	30	73.8	1.5	[---                                              ]	betA	choline dehydrogenase. Choline dehydrogenase catalyzes the conversion of exogenously supplied choline into the intermediate glycine betaine aldehyde, as part of a two-step oxidative reaction leading to the formation of osmoprotectant betaine. This enzymatic system can be found in both gram-positive and gram-negative bacteria. As in Escherichia coli, Staphylococcus xylosus, and Sinorhizobium meliloti, this enzyme is found associated in a transciptionally co-induced gene cluster with betaine aldehyde dehydrogenase, the second catalytic enzyme in this reaction. Other gram-positive organisms have been shown to employ a different enzymatic system, utlizing a soluable choline oxidase or type III alcohol dehydrogenase instead of choline dehydrogenase. This enzyme is a member of the GMC oxidoreductase family (pfam00732 and pfam05199), sharing a common evoluntionary origin and enzymatic reaction with alcohol dehydrogenase. Outgrouping from this model, Caulobacter crescentus shares sequence homology with choline dehydrogenase, yet other genes participating in this enzymatic reaction have not currently been identified.
329	cd05271	273	33	73.6	5.3	[---                                              ]	NDUFA9_like_SDR_a	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs. This subgroup of extended SDR-like proteins are atypical SDRs. They have a glycine-rich NAD(P)-binding motif similar to the typical SDRs, GXXGXXG, and have the YXXXK active site motif (though not the other residues of the SDR tetrad). Members identified include NDUFA9 (mitochondrial) and putative nucleoside-diphosphate-sugar epimerase. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
330	PRK05249	461	35	73.5	2.6	[---                                              ]	PRK05249	soluble pyridine nucleotide transhydrogenase; Provisional
331	PRK06115	466	76	73.3	2.2	[                     -------                     ]	PRK06115	dihydrolipoamide dehydrogenase; Reviewed
332	PRK14694	468	40	73.2	3.8	[----                                             ]	PRK14694	putative mercuric reductase; Provisional
333	PRK13369	502	39	73.0	2.6	[----                                             ]	PRK13369	glycerol-3-phosphate dehydrogenase; Provisional
334	PRK02472	447	90	72.8	3.1	[---------                                        ]	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
335	COG1252	405	34	72.6	2.5	[---                                              ]	Ndh	NADH dehydrogenase, FAD-containing subunit
336	PRK07578	199	28	72.6	3	[---                                              ]	PRK07578	short chain dehydrogenase; Provisional
337	cd05233	234	31	72.5	3.6	[---                                              ]	SDR_c	classical (c) SDRs. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
338	TIGR01763	305	22	72.4	2.6	[--                                               ]	MalateDH_bact	malate dehydrogenase, NAD-dependent. This enzyme converts malate into oxaloacetate in the citric acid cycle. The critical residues which discriminate malate dehydrogenase from lactate dehydrogenase have been characterized, and have been used to set the cutoffs for this model. Sequences showing
339	PRK13800	897	33	72.4	3.3	[---                                              ]	PRK13800	putative oxidoreductase/HEAT repeat-containing protein; Provisional
340	PRK09077	536	80	72.3	3.2	[--------                                         ]	PRK09077	L-aspartate oxidase; Provisional
341	TIGR01989	437	34	72.0	3.6	[---                                              ]	COQ6	ubiquinone biosynthesis monooxygenase COQ6. This model represents the monooxygenase responsible for the 4-hydroxylateion of the phenol ring in the aerobic biosynthesis of ubiquinone
342	PRK08277	278	32	72.0	4.1	[---                                              ]	PRK08277	D-mannonate oxidoreductase; Provisional
343	PRK08010	441	135	71.9	3	[                       ----------------          ]	PRK08010	pyridine nucleotide-disulfide oxidoreductase; Provisional
344	cd08262	341	28	71.7	3.9	[---                                              ]	Zn_ADH8	Alcohol dehydrogenases of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines.
345	cd00757	228	26	71.6	4.2	[--                                               ]	ThiF_MoeB_HesA_family	ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1).
346	COG4007	340	31	71.2	3.6	[---                                              ]	COG4007	Predicted dehydrogenase related to H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase
347	cd08235	343	30	71.0	4.7	[---                                              ]	iditol_2_DH_like	L-iditol 2-dehydrogenase. Putative L-iditol 2-dehydrogenase based on annotation of some members in this subgroup. L-iditol 2-dehydrogenase catalyzes the NAD+-dependent conversion of L-iditol to L-sorbose in fructose and mannose metabolism. This enzyme is related to sorbitol dehydrogenase, alcohol dehydrogenase, and other medium chain dehydrogenase/reductases. The zinc-dependent alcohol dehydrogenase (ADH-Zn)-like family of proteins is a diverse group of proteins related to the first identified member, class I mammalian ADH. This group is also called the medium chain dehydrogenases/reductase family (MDR) to highlight its broad range of activities and to distinguish from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal GroES-like catalytic domain. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines.
348	cd08233	351	29	70.6	4.5	[---                                              ]	butanediol_DH_like	(2R,3R)-2,3-butanediol dehydrogenase. (2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent medium chain alcohol dehydrogenase, catalyzes the NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and meso-butanediol to acetoin. BDH functions as a homodimer. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. The medium chain alcohol dehydrogenase family (MDR) have 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. 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.
349	cd03784	401	29	70.1	4.2	[---                                              ]	GT1_Gtf_like	This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the oxidatively cross-linked heptapeptide core of vancomycin group antibiotics. The core structure is important for the bioactivity of the antibiotics.
350	COG0373	414	44	70.0	4.8	[----                                             ]	HemA	Glutamyl-tRNA reductase
351	PRK03806	438	75	70.0	4.7	[-------                                          ]	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
352	PRK07530	292	32	69.8	3.1	[---                                              ]	PRK07530	3-hydroxybutyryl-CoA dehydrogenase; Validated
353	TIGR03371	246	67	69.6	5.4	[-----------                                      ]	cellulose_yhjQ	cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
354	PRK07531	495	36	69.3	3	[---                                              ]	PRK07531	bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase; Validated
355	cd12186	329	37	69.2	5.1	[---                                              ]	LDH	D-Lactate dehydrogenase and D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH), NAD-binding and catalytic domains. D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenases family. LDH is homologous to D-2-hydroxyisocaproic acid dehydrogenase(D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-HicDH is a NAD-dependent member of the hydroxycarboxylate dehydrogenase family, and shares the Rossmann fold typical of many NAD binding proteins. HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. D-HicDH, like the structurally distinct L-HicDH, exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain.
356	PRK08644	212	28	68.8	5.1	[---                                              ]	PRK08644	thiamine biosynthesis protein ThiF; Provisional
357	PRK04308	445	35	68.8	4.8	[---                                              ]	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
358	pfam03949	255	32	68.8	6	[---                                              ]	Malic_M	Malic enzyme, NAD binding domain.
359	PRK00045	423	30	68.7	5.2	[---                                              ]	hemA	glutamyl-tRNA reductase; Reviewed
360	PRK00143	346	66	68.7	9.6	[--------                                         ]	mnmA	tRNA-specific 2-thiouridylase MnmA; Reviewed
361	cd05285	343	30	68.5	5.9	[---                                              ]	sorbitol_DH	Sorbitol dehydrogenase. 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. Aldose reductase catalyzes the NADP(H)-dependent conversion of glucose to sorbital, and SDH uses NAD(H) in the conversion of sorbitol to fructose. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. The medium chain alcohol dehydrogenase family (MDR) have 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.
362	cd12159	303	35	68.2	6.1	[---                                              ]	2-Hacid_dh_2	Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric.
363	COG0702	275	33	68.0	7.3	[---                                              ]	YbjT	Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains
364	PRK06116	450	145	67.9	6.9	[                       ----------------          ]	PRK06116	glutathione reductase; Validated
365	PRK08205	583	78	67.7	4.3	[--------                                         ]	sdhA	succinate dehydrogenase flavoprotein subunit; Reviewed
366	cd05327	269	32	67.5	5.4	[---                                              ]	retinol-DH_like_SDR_c_like	retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs. Classical SDR subgroup containing retinol-DHs, LPORs, and related proteins. Retinol is processed by a medium chain alcohol dehydrogenase followed by retinol-DHs. Pchlide reductases act in chlorophyll biosynthesis. There are distinct enzymes that catalyze Pchlide reduction in light or dark conditions. Light-dependent reduction is via an NADP-dependent SDR, LPOR. Proteins in this subfamily share the glycine-rich NAD-binding motif of the classical SDRs, have a partial match to the canonical active site tetrad, but lack the typical active site Ser. This subgroup includes the human proteins: retinol dehydrogenase -12, -13 ,and -14, dehydrogenase/reductase SDR family member (DHRS)-12 , -13 and -X (a DHRS on chromosome X), and WWOX (WW domain-containing oxidoreductase), as well as a Neurospora crassa SDR encoded by the blue light inducible bli-4 gene. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
367	PRK09310	477	31	67.0	5.9	[---                                              ]	aroDE	bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase protein; Reviewed
368	PRK14694	468	33	66.9	5.5	[---                                              ]	PRK14694	putative mercuric reductase; Provisional
369	PRK06467	471	33	66.8	2.3	[---                                              ]	PRK06467	dihydrolipoamide dehydrogenase; Reviewed
370	cd08239	339	30	66.8	5.5	[---                                              ]	THR_DH_like	L-threonine dehydrogenase (TDH)-like. MDR/AHD-like proteins, including a protein annotated as a threonine dehydrogenase. L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine via NAD(H)-dependent oxidation. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Zinc-dependent ADHs are medium chain dehydrogenase/reductase type proteins (MDRs) and have a NAD(P)(H)-binding domain in a Rossmann fold of an beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. In addition to alcohol dehydrogenases, this group includes quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines.
371	PRK06996	398	35	66.8	5.8	[---                                              ]	PRK06996	hypothetical protein; Provisional
372	cd05323	244	34	66.8	7	[---                                              ]	ADH_SDR_c_like	insect type alcohol dehydrogenase (ADH)-like, classical (c) SDRs. This subgroup contains insect type ADH, and 15-hydroxyprostaglandin dehydrogenase (15-PGDH) type I; these proteins are classical SDRs. ADH catalyzes the NAD+-dependent oxidation of alcohols to aldehydes/ketones. This subgroup is distinct from the zinc-dependent alcohol dehydrogenases of the medium chain dehydrogenase/reductase family, and evolved in fruit flies to allow the digestion of fermenting fruit. 15-PGDH catalyzes the NAD-dependent interconversion of (5Z,13E)-(15S)-11alpha,15-dihydroxy-9-oxoprost-13-enoate and (5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate, and has a typical SDR glycine-rich NAD-binding motif, which is not fully present in ADH. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
373	PRK14619	308	33	66.6	6.4	[---                                              ]	PRK14619	NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Provisional
374	COG4716	587	41	65.9	2.4	[----                                             ]	COG4716	Myosin-crossreactive antigen (function unknown)
375	COG0300	265	32	65.5	7.9	[---                                              ]	DltE	Short-chain dehydrogenase
376	PRK12845	564	38	65.5	6.2	[----                                             ]	PRK12845	3-ketosteroid-delta-1-dehydrogenase; Reviewed
377	pfam03435	384	30	65.2	5.2	[---                                              ]	Saccharop_dh	Saccharopine dehydrogenase. This family comprised of three structural domains that can not be separated in the linear sequence. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase.
378	pfam11293	55	24	64.9	4.8	[                                      ---        ]	DUF3094	Protein of unknown function (DUF3094). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
379	pfam00996	439	42	64.7	6.1	[----                                             ]	GDI	GDP dissociation inhibitor.
380	pfam03054	354	64	64.4	14	[--------                                         ]	tRNA_Me_trans	tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs.
381	PRK06019	372	69	64.1	9.8	[--------                                         ]	PRK06019	phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed
382	PRK05565	247	29	63.7	7.1	[---                                              ]	fabG	3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
383	pfam13454	154	30	63.7	11	[---                                              ]	NAD_binding_9	FAD-NAD(P)-binding.
384	pfam05047	52	40	63.6	11	[                                        ----     ]	L51_S25_CI-B8	Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain. The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.
385	COG0190	283	33	63.3	7.1	[---                                              ]	FolD	5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase
386	PRK01438	480	33	63.2	6.2	[---                                              ]	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
387	TIGR01505	291	70	63.0	3.7	[--------                                         ]	tartro_sem_red	2-hydroxy-3-oxopropionate reductase. This model represents 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60), also called tartronate semialdehyde reductase. It follows glyoxylate carboligase and precedes glycerate kinase in D-glycerate pathway of glyoxylate degradation. The eventual product, 3-phosphoglycerate, is an intermediate of glycolysis and is readily metabolized. Tartronic semialdehyde, the substrate of this enzyme, may also come from other pathways, such as D-glucarate catabolism.
388	cd05242	296	106	63.0	8.7	[--------------                                   ]	SDR_a8	atypical (a) SDRs, subgroup 8. This subgroup contains atypical SDRs of unknown function. Proteins in this subgroup have a glycine-rich NAD(P)-binding motif consensus that resembles that of the extended SDRs, (GXXGXXG or GGXGXXG), but lacks the characteristic active site residues of the SDRs. A Cys often replaces the usual Lys of the YXXXK active site motif, while the upstream Ser is generally present and Arg replaces the usual Asn. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
389	pfam01820	110	25	62.7	5.1	[     ---                                         ]	Dala_Dala_lig_N	D-ala D-ala ligase N-terminus. This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF).
390	PRK14571	299	74	62.4	15	[--------                                         ]	PRK14571	D-alanyl-alanine synthetase A; Provisional
391	cd01983	99	28	62.1	8.9	[---                                              ]	Fer4_NifH	The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
392	PRK07251	438	47	62.0	8.4	[                       -----                     ]	PRK07251	pyridine nucleotide-disulfide oxidoreductase; Provisional
393	TIGR02352	337	140	61.6	22	[                       -------------------       ]	thiamin_ThiO	glycine oxidase ThiO. This family consists of the homotetrameric, FAD-dependent glycine oxidase ThiO, from species such as Bacillus subtilis that use glycine in thiamine biosynthesis. In general, members of this family will not be found in species such as E. coli that instead use tyrosine and the ThiH protein.
394	cd05230	305	72	61.5	8.6	[----------                                       ]	UGD_SDR_e	UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs. UGD catalyzes the formation of UDP-xylose from UDP-glucuronate; it is an extended-SDR, and has the characteristic glycine-rich NAD-binding pattern, TGXXGXXG, and active site tetrad. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
395	COG0476	254	24	61.5	6.7	[--                                               ]	ThiF	Molybdopterin or thiamine biosynthesis adenylyltransferase
396	TIGR02462	547	32	61.4	7.4	[---                                              ]	pyranose_ox	pyranose oxidase. Pyranose oxidase (also called glucose 2-oxidase) converts D-glucose and molecular oxygen to 2-dehydro-D-glucose and hydrogen peroxide. Peroxide production is believed to be important to the wood rot fungi in which this enzyme is found for lignin degradation.
397	COG0345	266	32	61.4	8.8	[---                                              ]	ProC	Pyrroline-5-carboxylate reductase
398	COG0026	375	30	61.3	8.7	[---                                              ]	PurK	Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase)
399	pfam02826	176	35	60.5	12	[---                                              ]	2-Hacid_dh_C	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain. This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389.
400	cd05266	251	33	60.5	8.6	[---                                              ]	SDR_a4	atypical (a) SDRs, subgroup 4. Atypical SDRs in this subgroup are poorly defined, one member is identified as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif that is related to, but is different from, the archetypical SDRs, GXGXXG. This subgroup also lacks most of the characteristic active site residues of the SDRs; however, the upstream Ser is present at the usual place, and some potential catalytic residues are present in place of the usual YXXXK active site motif. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
401	cd05278	347	32	60.3	7.6	[---                                              ]	FDH_like	Formaldehyde dehydrogenases. Formaldehyde dehydrogenase (FDH) is a member of the zinc-dependent/medium chain alcohol dehydrogenase family. Formaldehyde dehydrogenase (aka ADH3) may be the ancestral form of alcohol dehydrogenase, which evolved to detoxify formaldehyde. This CD contains glutathione dependant FDH, glutathione independent FDH, and related alcohol dehydrogenases. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. Unlike typical FDH, Pseudomonas putida aldehyde-dismutating FDH (PFDH) is glutathione-independent. The medium chain alcohol dehydrogenase family (MDR) have 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.
402	TIGR00561	512	14	60.2	4.9	[-                                                ]	pntA	NAD(P) transhydrogenase, alpha subunit. This integral membrane protein is the alpha subunit of alpha 2 beta 2 tetramer that couples the proton transport across the membrane to the reversible transfer of hydride ion equivalents between NAD and NADP. An alternate name is pyridine nucleotide transhydrogenase alpha subunit. The N-terminal region is homologous to alanine dehydrogenase. In some species, such as Rhodospirillum rubrum, the alpha chain is replaced by two shorter chains, both with some homology to the full-length alpha chain modeled here. These score below the trusted cutoff.
403	pfam07991	165	28	60.0	8.5	[--                                               ]	IlvN	Acetohydroxy acid isomeroreductase, catalytic domain. Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine.
404	TIGR01087	433	33	60.0	7.3	[---                                              ]	murD	UDP-N-acetylmuramoylalanine--D-glutamate ligase.
405	cd02440	107	32	59.6	10	[---                                              ]	AdoMet_MTases	S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
406	cd05371	252	36	59.5	9.8	[---                                              ]	HSD10-like_SDR_c	17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs. HSD10, also known as amyloid-peptide-binding alcohol dehydrogenase (ABAD), was previously identified as a L-3-hydroxyacyl-CoA dehydrogenase, HADH2. In fatty acid metabolism, HADH2 catalyzes the third step of beta-oxidation, the conversion of a hydroxyl to a keto group in the NAD-dependent oxidation of L-3-hydroxyacyl CoA. In addition to alcohol dehydrogenase and HADH2 activites, HSD10 has steroid dehydrogenase activity. Although the mechanism is unclear, HSD10 is implicated in the formation of amyloid beta-petide in the brain (which is linked to the development of Alzheimer's disease). Although HSD10 is normally concentrated in the mitochondria, in the presence of amyloid beta-peptide it translocates into the plasma membrane, where it's action may generate cytotoxic aldehydes and may lower estrogen levels through its use of 17-beta-estradiol as a substrate. HSD10 is a member of the SRD family, but differs from other SDRs by the presence of two insertions of unknown function. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
407	cd05258	337	36	59.2	11	[---                                              ]	CDP_TE_SDR_e	CDP-tyvelose 2-epimerase, extended (e) SDRs. CDP-tyvelose 2-epimerase is a tetrameric SDR that catalyzes the conversion of CDP-D-paratose to CDP-D-tyvelose, the last step in tyvelose biosynthesis. This subgroup is a member of the extended SDR subfamily, with a characteristic active site tetrad and NAD-binding motif. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
408	PRK11749	457	34	59.1	11	[---                                              ]	PRK11749	dihydropyrimidine dehydrogenase subunit A; Provisional
409	cd02034	116	32	59.0	10	[---                                              ]	CooC	The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.
410	cd05253	332	31	58.8	9.6	[---                                              ]	UDP_GE_SDE_e	UDP glucuronic acid epimerase, extended (e) SDRs. This subgroup contains UDP-D-glucuronic acid 4-epimerase, an extended SDR, which catalyzes the conversion of UDP-alpha-D-glucuronic acid to UDP-alpha-D-galacturonic acid. This group has the SDR's canonical catalytic tetrad and the TGxxGxxG NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
411	TIGR02356	202	30	58.7	8.7	[---                                              ]	adenyl_thiF	thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with the Escherichia. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the more widely distributed clade of ThiF proteins such found in E. coli.
412	PRK06567	1028	29	58.1	3.3	[---                                              ]	PRK06567	putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated
413	PRK06175	433	29	57.8	4.9	[---                                              ]	PRK06175	L-aspartate oxidase; Provisional
414	TIGR01421	450	56	57.3	11	[                       -----                     ]	gluta_reduc_1	glutathione-disulfide reductase, animal/bacterial. The tripeptide glutathione is an important reductant, e.g., for maintaining the cellular thiol/disulfide status and for protecting against reactive oxygen species such as hydrogen peroxide. Glutathione-disulfide reductase regenerates reduced glutathione from oxidized glutathione (glutathione disulfide) + NADPH. This model represents one of two closely related subfamilies of glutathione-disulfide reductase. Both are closely related to trypanothione reductase, and separate models are built so each of the three can describe proteins with conserved function. This model describes glutathione-disulfide reductases of animals, yeast, and a number of animal-resident bacteria.
415	COG0492	305	33	57.1	14	[---                                              ]	TrxB	Thioredoxin reductase
416	pfam07942	268	72	57.0	6.1	[----------                                       ]	N2227	N2227-like protein. This family features sequences that are similar to a region of hypothetical yeast gene product N2227. This is thought to be expressed during meiosis and may be involved in the defence response to stressful conditions.
417	cd05259	282	32	56.8	12	[---                                              ]	PCBER_SDR_a	phenylcoumaran benzylic ether reductase (PCBER) like, atypical (a) SDRs. PCBER and pinoresinol-lariciresinol reductases are NADPH-dependent aromatic alcohol reductases, and are atypical members of the SDR family. Other proteins in this subgroup are identified as eugenol synthase. These proteins contain an N-terminus characteristic of NAD(P)-binding proteins and a small C-terminal domain presumed to be involved in substrate binding, but they do not have the conserved active site Tyr residue typically found in SDRs. Numerous other members have unknown functions. The glycine rich NADP-binding motif in this subgroup is of 2 forms: GXGXXG and G
418	PRK08958	588	86	56.8	8.6	[----------                                       ]	sdhA	succinate dehydrogenase flavoprotein subunit; Reviewed
419	TIGR03909	374	34	56.7	8.5	[---                                              ]	pyrrolys_PylC	pyrrolysine biosynthesis protein PylC. This protein is PylC, part of a three-gene cassette that is sufficient to direct the biosynthesis of pyrrolysine, the twenty-second amino acid, incorporated in some species at a UAG canonical stop codon.
420	PRK06718	202	29	56.1	9.6	[---                                              ]	PRK06718	precorrin-2 dehydrogenase; Reviewed
421	PRK07333	403	137	55.9	12	[                       -----------------         ]	PRK07333	2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional
422	PRK08244	493	34	55.8	11	[                       ----                      ]	PRK08244	hypothetical protein; Provisional
423	TIGR01424	446	135	55.5	9.9	[                        ---------------          ]	gluta_reduc_2	glutathione-disulfide reductase, plant. The tripeptide glutathione is an important reductant, e.g., for maintaining the cellular thiol/disulfide status and for protecting against reactive oxygen species such as hydrogen peroxide. Glutathione-disulfide reductase regenerates reduced glutathione from oxidized glutathione (glutathione disulfide) + NADPH. This model represents one of two closely related subfamilies of glutathione-disulfide reductase. Both are closely related to trypanothione reductase, and separate models are built so each of the three can describe proteins with conserved function. This model describes glutathione-disulfide reductases of plants and some bacteria, including cyanobacteria.
424	cd05213	311	43	54.9	16	[----                                             ]	NAD_bind_Glutamyl_tRNA_reduct	NADP-binding domain of glutamyl-tRNA reductase. Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
425	TIGR01789	370	37	54.9	8.8	[----                                             ]	lycopene_cycl	lycopene cyclase. This model represents a family of bacterial lycopene cyclases catalyzing the transformation of lycopene to carotene. These enzymes are found in a limited spectrum of alpha and gamma proteobacteria as well as Flavobacterium.
426	PRK12825	249	28	54.8	12	[--                                               ]	fabG	3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
427	cd06259	150	54	54.7	31	[-------                                          ]	YdcF-like	YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis.
428	PRK05786	238	32	54.4	12	[---                                              ]	fabG	3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
429	PRK09231	582	85	54.3	12	[                           ---------             ]	PRK09231	fumarate reductase flavoprotein subunit; Validated
430	pfam00185	152	95	54.2	35	[                      ----------                 ]	OTCace	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain.
431	TIGR01470	205	30	54.2	15	[---                                              ]	cysG_Nterm	siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
432	pfam04016	147	34	54.1	16	[---                                              ]	DUF364	Domain of unknown function (DUF364). This domain of unknown function has a PLP-dependent transferase-like fold. Its genomic context suggests that it may have a role in anaerobic vitamin B12 biosynthesis. This domain is often found at the C-terminus of proteins containing DUF4213, pfam13938.
433	PRK06912	458	33	53.9	7.6	[---                                              ]	acoL	dihydrolipoamide dehydrogenase; Validated
434	cd01487	174	28	53.5	12	[---                                              ]	E1_ThiF_like	E1_ThiF_like. Member of superfamily of activating enzymes (E1) of the ubiquitin-like proteins. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of the substrate. The exact function of this family is unknown.
435	PRK12475	338	31	53.4	11	[---                                              ]	PRK12475	thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
436	pfam02780	124	33	53.2	21	[---                                              ]	Transketolase_C	Transketolase, C-terminal domain. The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site.
437	TIGR02032	295	39	52.9	14	[----                                             ]	GG-red-SF	geranylgeranyl reductase family. This model represents a subfamily which includes geranylgeranyl reductases involved in chlorophyll and bacteriochlorophyll biosynthesis as well as other related enzymes which may also act on geranylgeranyl groups or related substrates.
438	PRK06617	374	33	52.2	16	[---                                              ]	PRK06617	2-octaprenyl-6-methoxyphenyl hydroxylase; Validated
439	pfam09851	31	16	51.8	8.9	[                                      --         ]	SHOCT	Short C-terminal domain.
440	TIGR01179	328	30	51.7	14	[---                                              ]	galE	UDP-glucose-4-epimerase GalE. Alternate name: UDPgalactose 4-epimerase This enzyme interconverts UDP-glucose and UDP-galactose. A set of related proteins, some of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are excluded from this model and described by a separate model.
441	PRK00141	473	73	51.7	11	[-------                                          ]	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
442	PRK03803	448	37	51.4	15	[----                                             ]	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
443	cd05246	315	51	51.2	17	[-----                                            ]	dTDP_GD_SDR_e	dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs. This subgroup contains dTDP-D-glucose 4,6-dehydratase and related proteins, members of the extended-SDR family, with the characteristic Rossmann fold core region, active site tetrad and NAD(P)-binding motif. dTDP-D-glucose 4,6-dehydratase is closely related to other sugar epimerases of the SDR family. dTDP-D-dlucose 4,6,-dehydratase catalyzes the second of four steps in the dTDP-L-rhamnose pathway (the dehydration of dTDP-D-glucose to dTDP-4-keto-6-deoxy-D-glucose) in the synthesis of L-rhamnose, a cell wall component of some pathogenic bacteria. In many gram negative bacteria, L-rhamnose is an important constituent of lipopoylsaccharide O-antigen. The larger N-terminal portion of dTDP-D-Glucose 4,6-dehydratase forms a Rossmann fold NAD-binding domain, while the C-terminus binds the sugar substrate. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
444	TIGR01035	417	97	51.1	16	[-----------                                      ]	hemA	glutamyl-tRNA reductase. This enzyme, together with glutamate-1-semialdehyde-2,1-aminomutase (TIGR00713), leads to the production of delta-amino-levulinic acid from Glu-tRNA.
445	COG0059	338	28	51.0	14	[--                                               ]	IlvC	Ketol-acid reductoisomerase
446	pfam13434	335	23	50.8	18	[--                                               ]	K_oxygenase	L-lysine 6-monooxygenase (NADPH-requiring). This is family of Rossmann fold oxidoreductases that catalyses the NADPH-dependent hydroxylation of lysine at the N6 position, EC:1.14.13.59.
447	COG1192	259	42	50.6	16	[----                                             ]	BcsQ	Cellulose biosynthesis protein BcsQ
448	cd08282	375	30	50.6	17	[---                                              ]	PFDH_like	Pseudomonas putida aldehyde-dismutating formaldehyde dehydrogenase (PFDH). Formaldehyde dehydrogenase (FDH) is a member of the zinc-dependent/medium chain alcohol dehydrogenase family. Unlike typical FDH, Pseudomonas putida aldehyde-dismutating FDH (PFDH) is glutathione-independent. PFDH converts 2 molecules of aldehydes to corresponding carboxylic acid and alcohol. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Like the zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these tetrameric FDHs have a catalytic zinc that resides between the catalytic and NAD(H)binding domains and a structural zinc in a lobe of the catalytic domain. Unlike ADH, where NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly bound redox cofactor (similar to nicotinamide proteins). The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of an 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.
449	pfam02698	154	54	49.8	33	[-------                                          ]	DUF218	DUF218 domain. This large family of proteins contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The family includes SanA, which is involved in Vancomycin resistance. This protein may be involved in murein synthesis.
450	TIGR01724	341	31	49.3	13	[---                                              ]	hmd_rel	H2-forming N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase-related protein. This model represents a sister clade to the authenticated coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase (HMD) of TIGR01723. Two members, designated HmdII and HmdIII, are found. Members are restricted to methanogens, but the function is unknown.
451	PRK07395	553	150	49.3	9.1	[-----------------                                ]	PRK07395	L-aspartate oxidase; Provisional
452	PRK15461	296	32	49.0	13	[---                                              ]	PRK15461	NADH-dependent gamma-hydroxybutyrate dehydrogenase; Provisional
453	TIGR03736	244	35	49.0	16	[---                                              ]	PRTRC_ThiF	PRTRC system ThiF family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. This family is the PRTRC system ThiF family protein.
454	cd05257	316	32	49.0	18	[---                                              ]	Arna_like_SDR_e	Arna decarboxylase_like, extended (e) SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme involved in the modification of outer membrane protein lipid A of gram-negative bacteria. It is a bifunctional enzyme that catalyzes the NAD-dependent decarboxylation of UDP-glucuronic acid and N-10-formyltetrahydrofolate-dependent formylation of UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent decaboxylating activity is in the C-terminal 360 residues. This subgroup belongs to the extended SDR family, however the NAD binding motif is not a perfect match and the upstream Asn of the canonical active site tetrad is not conserved. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
455	TIGR02374	785	125	48.9	10	[-------------                                    ]	nitri_red_nirB	nitrite reductase
456	cd01339	300	30	48.8	16	[---                                              ]	LDH-like_MDH	L-lactate dehydrogenase-like malate dehydrogenase proteins. Members of this subfamily have an LDH-like structure and an MDH enzymatic activity. Some members, like MJ0490 from Methanococcus jannaschii, exhibit both MDH and LDH activities. Tetrameric MDHs, including those from phototrophic bacteria, are more similar to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
457	cd00300	300	29	48.7	12	[---                                              ]	LDH_like	L-lactate dehydrogenase-like enzymes. Members of this subfamily are tetrameric NAD-dependent 2-hydroxycarboxylate dehydrogenases including LDHs, L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and LDH-like malate dehydrogenases (MDH). Dehydrogenases catalyze the conversion of carbonyl compounds to alcohols or amino acids. LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. L-HicDH catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
458	PRK09078	598	86	48.2	12	[----------                                       ]	sdhA	succinate dehydrogenase flavoprotein subunit; Reviewed
459	PRK12490	299	33	48.1	13	[---                                              ]	PRK12490	6-phosphogluconate dehydrogenase-like protein; Reviewed
460	cd05198	302	37	48.1	25	[---                                              ]	formate_dh_like	Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family. Formate dehydrogenase, D-specific 2-hydroxy acid dehydrogenase, Phosphoglycerate Dehydrogenase, Lactate dehydrogenase, Thermostable Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate reductase, among others, share a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production and in the stress responses of plants. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase, among others. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric.
461	cd05229	302	33	47.8	21	[---                                              ]	SDR_a3	atypical (a) SDRs, subgroup 3. These atypical SDR family members of unknown function have a glycine-rich NAD(P)-binding motif consensus that is very similar to the extended SDRs, GXXGXXG. Generally, this group has poor conservation of the active site tetrad, However, individual sequences do contain matches to the YXXXK active site motif, and generally Tyr or Asn in place of the upstream Ser found in most SDRs. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
462	PRK09754	396	25	47.7	16	[--                                               ]	PRK09754	phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional
463	TIGR01176	580	43	47.3	13	[                                ----             ]	fum_red_Fp	fumarate reductase (quinol), flavoprotein subunit. The terms succinate dehydrogenase and fumarate reductase may be used interchangeably in certain systems. However, a number of species have distinct complexes, with the fumarate reductase active under anaerobic conditions. This model represents the fumarate reductase flavoprotein subunit from several such species in which a distinct succinate dehydrogenase is also found. Not all bona fide fumarate reductases will be found by this model.
464	pfam08659	181	61	47.3	32	[                      ----------                 ]	KR	KR domain. This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group.
465	COG0673	342	25	47.2	22	[--                                               ]	MviM	Predicted dehydrogenase
466	PRK05396	341	27	47.1	22	[--                                               ]	tdh	L-threonine 3-dehydrogenase; Validated
467	pfam10727	111	28	46.9	15	[---                                              ]	Rossmann-like	Rossmann-like domain. This family of proteins contain a Rossmann-like domain.
468	TIGR02352	337	24	46.5	8.4	[ ---                                             ]	thiamin_ThiO	glycine oxidase ThiO. This family consists of the homotetrameric, FAD-dependent glycine oxidase ThiO, from species such as Bacillus subtilis that use glycine in thiamine biosynthesis. In general, members of this family will not be found in species such as E. coli that instead use tyrosine and the ThiH protein.
469	cd05281	341	28	46.1	22	[--                                               ]	TDH	Threonine dehydrogenase. L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine via NAD(H)- dependent oxidation. THD is a member of the zinc-requiring, medium chain NAD(H)-dependent alcohol dehydrogenase family (MDR). MDRs have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. 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. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose.
470	TIGR01316	449	36	45.8	20	[---                                              ]	gltA	glutamate synthase (NADPH), homotetrameric. This protein is homologous to the small subunit of NADPH and NADH forms of glutamate synthase as found in eukaryotes and some bacteria. This protein is found in numerous species having no homolog of the glutamate synthase large subunit. The prototype of the family, from Pyrococcus sp. KOD1, was shown to be active as a homotetramer and to require NADPH.
471	PRK00811	283	28	45.7	13	[---                                              ]	PRK00811	spermidine synthase; Provisional
472	cd08935	271	40	45.5	22	[----                                             ]	mannonate_red_SDR_c	putative D-mannonate oxidoreductase, classical (c) SDR. D-mannonate oxidoreductase catalyzes the NAD-dependent interconversion of D-mannonate and D-fructuronate. This subgroup includes Bacillus subtitils UxuB/YjmF, a putative D-mannonate oxidoreductase; the B. subtilis UxuB gene is part of a putative ten-gene operon (the Yjm operon) involved in hexuronate catabolism. Escherichia coli UxuB does not belong to this subgroup. This subgroup has a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
473	COG0644	396	61	44.7	40	[                      ------                     ]	FixC	Dehydrogenase (flavoprotein)
474	PRK10262	321	92	44.3	31	[----------                                       ]	PRK10262	thioredoxin reductase; Provisional
475	cd04955	363	35	44.0	23	[---                                              ]	GT1_like_6	This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found in certain bacteria and Archaea.
476	COG0111	324	31	43.7	27	[---                                              ]	SerA	Phosphoglycerate dehydrogenase or related dehydrogenase
477	PRK08275	554	65	43.7	19	[                       -------                   ]	PRK08275	putative oxidoreductase; Provisional
478	cd08232	339	72	43.6	26	[-------                                          ]	idonate-5-DH	L-idonate 5-dehydrogenase. L-idonate 5-dehydrogenase (L-ido 5-DH ) catalyzes the conversion of L-lodonate to 5-ketogluconate in the metabolism of L-Idonate to 6-P-gluconate. In E. coli, this GntII pathway is a subsidiary pathway to the canonical GntI system, which also phosphorylates and transports gluconate. L-ido 5-DH is found in an operon with a regulator indR, transporter idnT, 5-keto-D-gluconate 5-reductase, and Gnt kinase. L-ido 5-DH is a zinc-dependent alcohol dehydrogenase-like protein. The alcohol dehydrogenase ADH-like family of proteins is a diverse group of proteins related to the first identified member, class I mammalian ADH. This group is also called the medium chain dehydrogenases/reductase family (MDR) which displays a broad range of activities and are distinguished from the smaller short chain dehydrogenases(~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal GroES-like catalytic domain. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines.
479	PRK10675	338	31	43.4	21	[---                                              ]	PRK10675	UDP-galactose-4-epimerase; Provisional
480	cd05294	309	24	43.3	18	[--                                               ]	LDH-like_MDH_nadp	A lactate dehydrogenases-like structure with malate dehydrogenase enzymatic activity. The LDH-like MDH proteins have a lactate dehyhydrogenase-like (LDH-like) structure and malate dehydrogenase (MDH) enzymatic activity. This subgroup is composed of some archaeal LDH-like MDHs that prefer NADP(H) rather than NAD(H) as a cofactor. One member, MJ0490 from Methanococcus jannaschii, has been observed to form dimers and tetramers during crystalization, although it is believed to exist primarilly as a tetramer in solution. In addition to its MDH activity, MJ0490 also possesses fructose-1,6-bisphosphate-activated LDH activity. Members of this subgroup have a higher sequence similarity to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)- binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenase, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
481	PRK08605	332	30	43.2	21	[---                                              ]	PRK08605	D-lactate dehydrogenase; Validated
482	TIGR00692	340	32	43.2	26	[---                                              ]	tdh	L-threonine 3-dehydrogenase. This protein is a tetrameric, zinc-binding, NAD-dependent enzyme of threonine catabolism. Closely related proteins include sorbitol dehydrogenase, xylitol dehydrogenase, and benzyl alcohol dehydrogenase. Eukaryotic examples of this enzyme have been demonstrated experimentally but do not appear in database search results.E. coli His-90 modulates substrate specificity and is believed part of the active site.
483	cd08946	200	30	43.2	21	[---                                              ]	SDR_e	extended (e) SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
484	cd12164	306	35	43.0	25	[---                                              ]	GDH_like_2	Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family. This group contains a variety of proteins variously identified as glycerate dehydrogenase (GDH, also known as hydroxypyruvate reductase) and other enzymes of the 2-hydroxyacid dehydrogenase family. GDH catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric.
485	cd01076	227	29	42.8	25	[---                                              ]	NAD_bind_1_Glu_DH	NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha -beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
486	PRK12831	464	34	42.6	29	[---                                              ]	PRK12831	putative oxidoreductase; Provisional
487	PRK06914	280	28	42.5	21	[--                                               ]	PRK06914	short chain dehydrogenase; Provisional
488	PRK06483	236	35	42.3	31	[---                                              ]	PRK06483	dihydromonapterin reductase; Provisional
489	pfam02882	160	33	42.2	27	[---                                              ]	THF_DHG_CYH_C	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain.
490	TIGR01423	486	152	41.9	1.1E+02	[                      ------------------         ]	trypano_reduc	trypanothione-disulfide reductase. Trypanothione, a glutathione-modified derivative of spermidine, is (in its reduced form) an important antioxidant found in trypanosomatids (Crithidia, Leishmania, Trypanosoma). This model describes trypanothione reductase, a possible antitrypanosomal drug target closely related to some forms of glutathione reductase.
491	pfam03853	164	26	41.8	27	[--                                               ]	YjeF_N	YjeF-related protein N-terminus. YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128), where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions.
492	cd12181	295	34	41.6	31	[---                                              ]	ceo_syn	N(5)-(carboxyethyl)ornithine synthase. N(5)-(carboxyethyl)ornithine synthase (ceo_syn) catalyzes the NADP-dependent conversion of N5-(L-1-carboxyethyl)-L-ornithine to L-ornithine + pyruvate. Ornithine plays a key role in the urea cycle, which in mammals is used in arginine biosynthesis, and is a precursor in polyamine synthesis. ceo_syn is related to the NAD-dependent L-alanine dehydrogenases. Like formate dehydrogenase and related enzymes, ceo_syn is comprised of 2 domains connected by a long alpha helical stretch, each resembling a Rossmann fold NAD-binding domain. The NAD-binding domain is inserted within the linear sequence of the more divergent catalytic domain. These ceo_syn proteins have a partially conserved NAD-binding motif and active site residues that are characteristic of related enzymes such as Saccharopine Dehydrogenase.
493	COG1251	793	32	41.4	23	[---                                              ]	NirB	NAD(P)H-nitrite reductase, large subunit
494	cd08957	307	36	41.3	29	[---                                              ]	WbmH_like_SDR_e	Bordetella bronchiseptica enzymes WbmH and WbmG-like, extended (e) SDRs. Bordetella bronchiseptica enzymes WbmH and WbmG, and related proteins. This subgroup exhibits the active site tetrad and NAD-binding motif of the extended SDR family. It has been proposed that the active site in Bordetella WbmG and WbmH cannot function as an epimerase, and that it plays a role in O-antigen synthesis pathway from UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
495	COG0421	282	30	41.1	27	[---                                              ]	SpeE	Spermidine synthase
496	COG1251	793	37	40.9	25	[---                                              ]	NirB	NAD(P)H-nitrite reductase, large subunit
497	COG4221	246	30	40.6	34	[---                                              ]	YdfG	NADP-dependent 3-hydroxy acid dehydrogenase YdfG
498	pfam00106	167	32	40.5	46	[---                                              ]	adh_short	short chain dehydrogenase. This family contains a wide variety of dehydrogenases.
499	pfam12847	106	30	39.9	35	[---                                              ]	Methyltransf_18	Methyltransferase domain. Protein in this family function as methyltransferases.
500	PRK08655	437	36	39.7	30	[---                                              ]	PRK08655	prephenate dehydrogenase; Provisional