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)