RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= 537021.9.peg.33_1 (100 letters) >gnl|CDD|153174 cd04902, ACT_3PGDH-xct, C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between identical domains in the asymmetric unit. How this asymmetry influences the mechanism of effector inhibition is still unknown. Members of this CD belong to the superfamily of ACT regulatory domains. Length = 73 Score = 62.5 bits (153), Expect = 2e-11 Identities = 27/73 (36%), Positives = 38/73 (52%) Query: 25 MICIVNADILGIVVFVGNILGEYGINIAHFHLGRSQSTEHAISFLCIDGSILNSVLEKLS 84 M+ + N D G++ VG ILGE GINIA +GR + A+ L +D + + VLE+L Sbjct: 1 MLVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDEPVPDEVLEELR 60 Query: 85 VNVTIRFVKQFEF 97 I K E Sbjct: 61 ALPGILSAKVVEL 73 >gnl|CDD|153151 cd04879, ACT_3PGDH-like, ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-exposed active site cleft. This CD also includes the C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillus, and Treponema species. LSD enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in E. coli, and other Enterobacteriales, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains. Length = 71 Score = 56.3 bits (137), Expect = 2e-09 Identities = 24/59 (40%), Positives = 35/59 (59%) Query: 25 MICIVNADILGIVVFVGNILGEYGINIAHFHLGRSQSTEHAISFLCIDGSILNSVLEKL 83 + IV+ D+ G++ VG ILGE+GINIA +GR + A L +D + VLE+L Sbjct: 1 RLLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDSPVPEEVLEEL 59 >gnl|CDD|153175 cd04903, ACT_LSD, C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains. Length = 71 Score = 42.1 bits (100), Expect = 3e-05 Identities = 15/56 (26%), Positives = 31/56 (55%) Query: 28 IVNADILGIVVFVGNILGEYGINIAHFHLGRSQSTEHAISFLCIDGSILNSVLEKL 83 +V+ D G + V ++L ++ INIA + R + + A+ + +D I V+E++ Sbjct: 4 VVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEVDQPIDEEVIEEI 59 >gnl|CDD|153139 cd02116, ACT, ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times. Length = 60 Score = 31.5 bits (72), Expect = 0.046 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 1/59 (1%) Query: 26 ICIVNADILGIVVFVGNILGEYGINIAHFHLGRSQSTEHAISFLCIDGS-ILNSVLEKL 83 + + D G++ V ++L E GINI S A F+ +DG L +LE L Sbjct: 1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVVDGDGDLEKLLEAL 59 >gnl|CDD|153173 cd04901, ACT_3PGDH, C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-exposed active site cleft. Members of this CD belong to the superfamily of ACT regulatory domains. Length = 69 Score = 27.1 bits (61), Expect = 1.2 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 7/68 (10%) Query: 26 ICIVNADILGIVVFVGNILGEYGINIAHFHLGRSQSTEHAISFLCID--GSILNSVLEKL 83 I ++ ++ G++ + IL E+ INIA +L T I ++ ID + +LE L Sbjct: 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYL----QTRGEIGYVVIDIDSEVSEELLEAL 57 Query: 84 -SVNVTIR 90 ++ TIR Sbjct: 58 RAIPGTIR 65 >gnl|CDD|177049 CHL00127, rpl11, ribosomal protein L11; Validated. Length = 140 Score = 27.0 bits (60), Expect = 1.3 Identities = 8/15 (53%), Positives = 11/15 (73%) Query: 40 VGNILGEYGINIAHF 54 VG LG++G+NI F Sbjct: 24 VGPALGQHGVNINLF 38 >gnl|CDD|145157 pfam01842, ACT, ACT domain. This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95, which is inhibited by serine. Aspartokinase EC:2.7.2.4, which is regulated by lysine. Acetolactate synthase small regulatory subunit, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51. formyltetrahydrofolate deformylase EC:3.5.1.10, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5. Length = 66 Score = 26.5 bits (59), Expect = 1.6 Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 1/57 (1%) Query: 28 IVNADILGIVVFVGNILGEYGINIAHFHLGRSQSTEHAISFLCI-DGSILNSVLEKL 83 + D G++ V L + GINI S + + + D L + LE L Sbjct: 5 VGVPDRPGLLARVFGALADRGINIESISQSTSGDKAGIVFIVVVVDEEDLEAALEAL 61 >gnl|CDD|153144 cd04872, ACT_1ZPV, ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein. This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains. Length = 88 Score = 26.0 bits (58), Expect = 2.1 Identities = 11/29 (37%), Positives = 16/29 (55%) Query: 23 RLMICIVNADILGIVVFVGNILGEYGINI 51 + +I +V D +GIV V L E +NI Sbjct: 1 KAVITVVGKDRVGIVAGVSTKLAELNVNI 29 >gnl|CDD|37481 KOG2270, KOG2270, KOG2270, Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms, Cell cycle control, cell division, chromosome partitioning]. Length = 520 Score = 25.7 bits (56), Expect = 2.6 Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 7/47 (14%) Query: 59 SQSTE----HAISFLCIDGSILNSVLEKLSVNV-TIRFVKQFEFNVD 100 SQS E HA+ FL +D + +N +L V V T+R + FEF D Sbjct: 309 SQSVEHDHPHALDFLRMDCNNVNDFFRRLGVAVMTVREL--FEFITD 353 >gnl|CDD|31346 COG1152, CdhA, CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]. Length = 772 Score = 24.9 bits (54), Expect = 4.6 Identities = 9/24 (37%), Positives = 14/24 (58%) Query: 18 DVDIGRLMICIVNADILGIVVFVG 41 DV+I + + IV I GI+ +G Sbjct: 484 DVEIRNVGVPIVMGTIPGIIAVIG 507 >gnl|CDD|32333 COG2150, COG2150, Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]. Length = 167 Score = 24.8 bits (54), Expect = 5.3 Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 1/84 (1%) Query: 1 VFSDGKPRFIKIQEINFDVDIGRLMICIVNADILGIVVFVGNILGEYGINIAHFHLGRSQ 60 +F + +P + ++ + +G + I +A GI+ V +++ + GI+I + Sbjct: 74 IFENLEPV-ASLADVAPLLGLGVIEIYPEDARYPGILAGVASLIAKRGISIRQIISEDPE 132 Query: 61 STEHAISFLCIDGSILNSVLEKLS 84 E + + I ++++L Sbjct: 133 LQEEPKLTIVTERPIPGDLIDELK 156 >gnl|CDD|31131 COG0788, PurU, Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]. Length = 287 Score = 24.8 bits (54), Expect = 5.5 Identities = 14/78 (17%), Positives = 24/78 (30%), Gaps = 11/78 (14%) Query: 28 IVNADILGIVVFVGNILGEYGINIAHFHLGRSQSTEH---AISFLCIDGSI--------L 76 + D GIV + L E+G NI T + F G + Sbjct: 12 VSCPDQPGIVAAISGFLAEHGCNIVDSDQFDDPETGRFFMRVEFEGEGGPLDREALRAAF 71 Query: 77 NSVLEKLSVNVTIRFVKQ 94 + E+ ++ + Q Sbjct: 72 APLAEEFGMDWRLHDAAQ 89 >gnl|CDD|32505 COG2358, Imp, TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]. Length = 321 Score = 24.5 bits (53), Expect = 5.8 Identities = 17/82 (20%), Positives = 25/82 (30%), Gaps = 19/82 (23%) Query: 31 ADILGIVVFVGN-----------ILGEYGINIAHFHLGRSQSTEHAISFLC---IDGSIL 76 AD+ G V +G IL GI + L + L ID + Sbjct: 133 ADLKGKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAESADALKNGTIDAAFY 192 Query: 77 -----NSVLEKLSVNVTIRFVK 93 N + +L+ I V Sbjct: 193 VAGVPNPAISELATTCDIVLVP 214 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.329 0.147 0.428 Gapped Lambda K H 0.267 0.0739 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,198,447 Number of extensions: 57594 Number of successful extensions: 198 Number of sequences better than 10.0: 1 Number of HSP's gapped: 198 Number of HSP's successfully gapped: 19 Length of query: 100 Length of database: 6,263,737 Length adjustment: 68 Effective length of query: 32 Effective length of database: 4,794,325 Effective search space: 153418400 Effective search space used: 153418400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (23.4 bits)