RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15800
(109 letters)
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. 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.
Length = 309
Score = 74.4 bits (184), Expect = 3e-17
Identities = 27/67 (40%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVG-TVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
A LKVI+ +SVG+DH+ +D K+RGI V T V +DA A+ L +A +RR +G
Sbjct: 62 AAPPLKVIANYSVGYDHIDVDAAKARGIPVTNTPD-VLTDATADLAFALLLAAARRVVEG 120
Query: 64 HNCIASG 70
+ +G
Sbjct: 121 DRFVRAG 127
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family represents
the largest portion of the catalytic domain of
2-hydroxyacid dehydrogenases as the NAD binding domain
is inserted within the structural domain.
Length = 312
Score = 70.8 bits (174), Expect = 6e-16
Identities = 25/66 (37%), Positives = 38/66 (57%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 64
A LKVI+ VG D++ LD RGI V V S+++VAE +GL +A++RR +
Sbjct: 57 AAPGLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALARRIPEAD 116
Query: 65 NCIASG 70
+ +G
Sbjct: 117 ASVRAG 122
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 70.0 bits (172), Expect = 1e-15
Identities = 25/67 (37%), Positives = 39/67 (58%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
LK+I+T S G+D++ L+ K RGI V V S++AVAE + L +A++RR +G
Sbjct: 62 EKLPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEG 121
Query: 64 HNCIASG 70
+ G
Sbjct: 122 DRRVREG 128
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific
2-hydroxyacid-related dehydrogenase.
Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the
NADP-dependent reduction of hydroxyphenylpyruvates,
hydroxypyruvate, or pyruvate to its respective lactate.
HPPR acts as a dimer and is related to D-isomer-specific
2-hydroxyacid dehydrogenases, a superfamily that
includes 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.
Length = 301
Score = 66.3 bits (163), Expect = 2e-14
Identities = 24/63 (38%), Positives = 38/63 (60%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 67
L++I++F VG+D + LD ++RGIRV V +D VA+ +GL +AV RR +
Sbjct: 64 ALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAADRFV 123
Query: 68 ASG 70
+G
Sbjct: 124 RAG 126
>gnl|CDD|240622 cd05198, 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.
Length = 302
Score = 63.4 bits (155), Expect = 3e-13
Identities = 23/67 (34%), Positives = 33/67 (49%)
Query: 7 ENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 66
LK I G D++ LD K RGI V V +++AVAE +GL +A+ RR +
Sbjct: 62 PKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLALLRRLPRADAA 121
Query: 67 IASGTEK 73
+ G
Sbjct: 122 VRRGWGW 128
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as 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. Many, not all, members of this family are
dimeric.
Length = 306
Score = 59.4 bits (145), Expect = 7e-12
Identities = 26/67 (38%), Positives = 40/67 (59%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
A LKVIS + VG+D++ L+ K RGI V +S++VAE IGL +A++R+ Q
Sbjct: 64 AAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALARQIPQA 123
Query: 64 HNCIASG 70
+ +G
Sbjct: 124 DREVRAG 130
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 58.5 bits (142), Expect = 2e-11
Identities = 23/79 (29%), Positives = 34/79 (43%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
A NLK I G D++ L+ RGI V ++ +VAE + L +A++RR
Sbjct: 62 AAAPNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARRIPDA 121
Query: 64 HNCIASGTEKSQQHAITEL 82
G + TEL
Sbjct: 122 DASQRRGEWDRKAFRGTEL 140
>gnl|CDD|240638 cd12161, GDH_like_1, 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,
aka 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.
Length = 315
Score = 57.6 bits (140), Expect = 4e-11
Identities = 29/69 (42%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
A +NLK+IS G DH+ L+ K RGI V S++AVAE IGLAI + R
Sbjct: 65 EACKNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRNIVPC 124
Query: 64 -HNCIASGT 71
A GT
Sbjct: 125 DAAVRAGGT 133
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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.
Length = 317
Score = 54.9 bits (133), Expect = 3e-10
Identities = 21/55 (38%), Positives = 34/55 (61%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRR 59
A +NLK+I+ + G D++ +D K +GI V VS++ AE GL +A++RR
Sbjct: 62 AAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARR 116
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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.
Length = 311
Score = 54.5 bits (132), Expect = 4e-10
Identities = 19/67 (28%), Positives = 35/67 (52%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
A L++I VG D + L+ +RGI V + ++++VAE + L +A+ RR +
Sbjct: 61 AAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRRLPEA 120
Query: 64 HNCIASG 70
+ +G
Sbjct: 121 DRELRAG 127
>gnl|CDD|240628 cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding
and catalytic domains. Phosphoglycerate dehydrogenase
(PGDH) catalyzes the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDH comes in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. 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.
Length = 301
Score = 54.1 bits (131), Expect = 7e-10
Identities = 21/61 (34%), Positives = 38/61 (62%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 64
A +NLK+I+ VG D++ ++ K +GI+V SS++VAE IGL ++++R + +
Sbjct: 60 AAKNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRAN 119
Query: 65 N 65
Sbjct: 120 R 120
>gnl|CDD|240620 cd01619, LDH_like, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase 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.
D-HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. Similar to the structurally
distinct L-HicDH, D-HicDH exhibits low side-chain R
specificity, accepting a wide range of 2-oxocarboxylic
acid side chains. (R)-2-hydroxyglutarate dehydrogenase
(HGDH) catalyzes the NAD-dependent reduction of
2-oxoglutarate to (R)-2-hydroxyglutarate.
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.
Length = 323
Score = 53.8 bits (130), Expect = 7e-10
Identities = 22/52 (42%), Positives = 29/52 (55%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRR 59
LK IS + G+D++ LD K GI V V S +AVAE I L +A+ R
Sbjct: 67 GLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLRN 118
>gnl|CDD|240663 cd12187, LDH_like_1, D-Lactate and related Dehydrogenase like
proteins, NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share 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.
Length = 329
Score = 51.1 bits (123), Expect = 6e-09
Identities = 21/57 (36%), Positives = 31/57 (54%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 64
LK+I+T S G DH+ L+ + RGI V V VAE L +A+SR+ ++
Sbjct: 63 RLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALSRKLREAI 119
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, 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.
Length = 314
Score = 48.0 bits (115), Expect = 9e-08
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRV-GTVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
A + LK+I S G DHL L+++ G+ V G +S AVAE + L +A+++R +
Sbjct: 57 ALKRLKLIQVPSAGVDHLPLERLPE-GVVVANNHG--NSPAVAEHALALILALAKRIVEY 113
Query: 64 HN 65
N
Sbjct: 114 DN 115
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. 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.
Length = 304
Score = 47.4 bits (114), Expect = 1e-07
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 2/80 (2%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVS-SDAVAEFNIGLAIAVSRRFQQ 62
A LKVI VG D++ ++ +RGI V P + + +VAE I L +A++R Q
Sbjct: 58 EAAPRLKVIGRAGVGVDNIDVEAATARGILV-VNAPGANTISVAEHTIALMLALARNIPQ 116
Query: 63 GHNCIASGTEKSQQHAITEL 82
+ +G ++ EL
Sbjct: 117 ADASLRAGKWDRKKFMGVEL 136
>gnl|CDD|240634 cd12157, PTDH, Thermostable Phosphite Dehydrogenase. Phosphite
dehydrogenase (PTDH), a member of the D-specific
2-hydroxyacid dehydrogenase family, catalyzes the
NAD-dependent formation of phosphate from phosphite
(hydrogen phosphonate). PTDH has been suggested as a
potential enzyme for cofactor regeneration systems. 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.
Length = 318
Score = 45.4 bits (108), Expect = 7e-07
Identities = 21/71 (29%), Positives = 33/71 (46%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
A LK+I+ G+D+ ++ +RGI V V + ++ AE IGL I + R G
Sbjct: 62 DACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGRHILAG 121
Query: 64 HNCIASGTEKS 74
+ SG
Sbjct: 122 DRFVRSGKFGG 132
>gnl|CDD|240645 cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-like
dehydrogenases. D-Mandelate dehydrogenase (D-ManDH),
identified as an enzyme that interconverts
benzoylformate and D-mandelate, is a D-2-hydroxyacid
dehydrogenase family member that catalyzes the
conversion of c3-branched 2-ketoacids. D-ManDH exhibits
broad substrate specificities for 2-ketoacids with large
hydrophobic side chains, particularly those with
C3-branched side chains. 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. Glycerate dehydrogenase catalyzes the
reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH
+ H+. 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.
Length = 321
Score = 44.1 bits (105), Expect = 2e-06
Identities = 15/58 (25%), Positives = 28/58 (48%)
Query: 7 ENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 64
+LK+I+ G+D + +D + RGI+V +A A+ + L + R F +
Sbjct: 75 PSLKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAE 132
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.
Phosphoglycerate dehydrogenases (PGDHs) catalyze the
initial step in the biosynthesis of L-serine from
D-3-phosphoglycerate. PGDHs come in 3 distinct
structural forms, with this first group being related to
2-hydroxy acid dehydrogenases, sharing structural
similarity to formate and glycerate dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily,
which also include groups such as 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. Many, not all,
members of this family are dimeric.
Length = 308
Score = 44.0 bits (105), Expect = 2e-06
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRV-GTVGPVSSDAVAEFNIGLAIAVSRRFQQ 62
NLK++ T + + + L K RGI V GT G A AE L +A++R +
Sbjct: 69 NLKLLVTTGMRNASIDLAAAKERGIVVCGTGG--GPTATAELTWALILALARNLPE 122
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 43.7 bits (104), Expect = 3e-06
Identities = 18/65 (27%), Positives = 32/65 (49%)
Query: 7 ENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 66
LKVI + VG D++ + RGI V V ++ VA+ + L +A++R+
Sbjct: 64 PRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALARKLPFLDRA 123
Query: 67 IASGT 71
+ +G
Sbjct: 124 VRAGG 128
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 43.6 bits (103), Expect = 3e-06
Identities = 20/69 (28%), Positives = 40/69 (57%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 64
A L++++ ++VG+D++ +++ RGI V V ++A A+F L +A +RR +
Sbjct: 64 AAPRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRLVEAD 123
Query: 65 NCIASGTEK 73
+ + SG K
Sbjct: 124 HFVRSGEWK 132
>gnl|CDD|240661 cd12185, HGDH_LDH_like, Putative Lactate dehydrogenase and
(R)-2-Hydroxyglutarate Dehydrogenase-like proteins,
NAD-binding and catalytic domains. This group contains
various putative dehydrogenases related to D-lactate
dehydrogenase (LDH), (R)-2-hydroxyglutarate
dehydrogenase (HGDH), and related enzymes, members of
the 2-hydroxyacid dehydrogenases family. LDH catalyzes
the interconversion of pyruvate and lactate, and HGDH
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. Despite often low sequence
identity within this 2-hydroxyacid dehydrogenase family,
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.
Length = 322
Score = 43.4 bits (103), Expect = 4e-06
Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 10 KVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRR 59
K IST S+G+DH+ LD K GI+V V S ++VA++ + L + R+
Sbjct: 70 KYISTRSIGYDHIDLDAAKELGIKVSNV-TYSPNSVADYTVMLMLMALRK 118
>gnl|CDD|240654 cd12177, 2-Hacid_dh_12, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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.
Length = 321
Score = 41.5 bits (98), Expect = 2e-05
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTV-GPVSSDAVAEFNIGLAIAVSRRFQQGHNC 66
LK+I+ +G+D++ L G+ V V G V DAVAE + L + V R+ Q
Sbjct: 69 GLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVLRKINQASEA 128
Query: 67 IASG 70
+ G
Sbjct: 129 VKEG 132
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, 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.
Length = 310
Score = 41.0 bits (97), Expect = 2e-05
Identities = 20/67 (29%), Positives = 34/67 (50%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
A LK+I G +++ ++ RGI V +++AVAEF +GL +A +R +
Sbjct: 63 EAAPKLKLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLAETRNIARA 122
Query: 64 HNCIASG 70
H + G
Sbjct: 123 HAALKDG 129
>gnl|CDD|240659 cd12183, LDH_like_2, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2-domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share 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.
Length = 328
Score = 40.5 bits (96), Expect = 4e-05
Identities = 18/56 (32%), Positives = 30/56 (53%)
Query: 10 KVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHN 65
K+I+ G +++ L K GI V V S AVAE + L +A++R+ + +N
Sbjct: 70 KLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLALNRKIHRAYN 125
>gnl|CDD|240662 cd12186, 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.
Length = 329
Score = 39.8 bits (94), Expect = 6e-05
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRF 60
+K I+ S G D + LD K G+++ V S A+AEF + A+ + R
Sbjct: 68 GIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRAIAEFAVTQALNLLRNT 120
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 39.7 bits (93), Expect = 7e-05
Identities = 20/63 (31%), Positives = 31/63 (49%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 67
NLK+ T +G DH+ L GI V V +S +VAE + + +A+ R ++ H
Sbjct: 114 NLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRNYEPSHRQA 173
Query: 68 ASG 70
G
Sbjct: 174 VEG 176
>gnl|CDD|240632 cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2-hydroxyacid
dehydrogenase family. Phosphoglycerate Dehydrogenase
(PGDH) catalyzes the NAD-dependent conversion of
3-phosphoglycerate into 3-phosphohydroxypyruvate, which
is the first step in serine biosynthesis.
Over-expression of PGDH has been implicated as
supporting proliferation of certain breast cancers,
while PGDH deficiency is linked to defects in mammalian
central nervous system development. PGDH is a member of
the 2-hydroxyacid dehydrogenase family, 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/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.
Length = 314
Score = 37.9 bits (89), Expect = 3e-04
Identities = 17/55 (30%), Positives = 31/55 (56%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQ 62
NLK I +S G D+L L+ IK +GI + + S +AE+ +G + + + ++
Sbjct: 60 NLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLKK 114
>gnl|CDD|240660 cd12184, HGDH_like, (R)-2-Hydroxyglutarate Dehydrogenase and
related dehydrogenases, NAD-binding and catalytic
domains. (R)-2-hydroxyglutarate dehydrogenase (HGDH)
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. HGDH is a member of the
D-2-hydroxyacid NAD(+)-dependent dehydrogenase family;
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.
Length = 330
Score = 38.0 bits (89), Expect = 3e-04
Identities = 17/54 (31%), Positives = 29/54 (53%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQ 61
+K + T +VG +H+ L+ K G ++ V S +A+AE LA+ +SR
Sbjct: 68 GIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAIAELAFTLAMTLSRHTA 121
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, 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 yydrolase. 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.
Length = 307
Score = 37.8 bits (89), Expect = 4e-04
Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 67
NLK+I + G++++ L K RGI V V S+D+VA+ L +A++R ++ +
Sbjct: 65 NLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHNDVV 124
Query: 68 ASGT-EKSQQ-----HAITEL 82
+G +KS + I EL
Sbjct: 125 KAGEWQKSPDFCFWDYPIIEL 145
>gnl|CDD|240651 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as 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. Many, not all, members of this family are
dimeric.
Length = 305
Score = 37.2 bits (87), Expect = 5e-04
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRV-GTVGPVSSDAVAEFNIGLAIAVSRRFQQG 63
+LK I+ G +++ +D RGI V T G +++AVAE I + +A+SR Q
Sbjct: 47 FAPSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGA-NANAVAELVIAMMLALSRNIIQA 105
Query: 64 HNCIASG 70
+ +G
Sbjct: 106 IKWVTNG 112
>gnl|CDD|240627 cd05302, FDH, NAD-dependent Formate Dehydrogenase (FDH).
NAD-dependent formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of a formate anion to carbon
dioxide coupled with the reduction of NAD+ to NADH.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxy acid dehydrogenase family have 2
highly similar subdomains of the alpha/beta form, with
NAD binding occurring in the cleft between subdomains.
NAD contacts are primarily to the Rossmann-fold
NAD-binding domain which is inserted within the linear
sequence of the more diverse flavodoxin-like catalytic
subdomain. Some related proteins have similar structural
subdomain but with a tandem arrangement of the catalytic
and NAD-binding subdomains in the linear sequence. FDHs
of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
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 from C1 compounds such as methanol,
and in the stress responses of plants. NAD-dependent FDH
is useful in cofactor regeneration in asymmetrical
biocatalytic reduction processes, where FDH irreversibly
oxidizes formate to carbon dioxide, while reducing the
oxidized form of the cofactor to the reduced form.
Length = 348
Score = 35.8 bits (83), Expect = 0.002
Identities = 20/63 (31%), Positives = 30/63 (47%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 67
NLK+ T +G DH+ L RGI V V + +VAE + + + + R + GH
Sbjct: 84 NLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRNYVPGHEQA 143
Query: 68 ASG 70
G
Sbjct: 144 IEG 146
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase. This model
represents a long form of D-3-phosphoglycerate
dehydrogenase, the serA gene of one pathway of serine
biosynthesis. Shorter forms, scoring between trusted and
noise cutoff, include SerA from E. coli [Amino acid
biosynthesis, Serine family].
Length = 525
Score = 35.0 bits (81), Expect = 0.003
Identities = 21/78 (26%), Positives = 35/78 (44%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 64
A LKVI VG D++ ++ +RGI V ++ + AE + + +A +R Q
Sbjct: 59 AAPKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAARNIPQAD 118
Query: 65 NCIASGTEKSQQHAITEL 82
+ G + TEL
Sbjct: 119 ASLKEGEWDRKAFMGTEL 136
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 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 subdomains 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. 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 the
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.
Length = 313
Score = 34.8 bits (81), Expect = 0.003
Identities = 13/57 (22%), Positives = 26/57 (45%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRF 60
A L+ I + S G D L ++ R + + + +AE+ +G +A +R+
Sbjct: 55 PAAPRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKL 111
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 34.1 bits (78), Expect = 0.006
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 9 LKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQ------Q 62
+K I+ + G D LD K I + V S + +AE+++ +A+ + RRF Q
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQ 129
Query: 63 GHN 65
H+
Sbjct: 130 AHD 132
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 34.1 bits (78), Expect = 0.008
Identities = 18/64 (28%), Positives = 34/64 (53%)
Query: 7 ENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 66
+NL+++ T +G DH+ L + G+ V V + +VAE + + + R F G++
Sbjct: 120 KNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPGYHQ 179
Query: 67 IASG 70
+ SG
Sbjct: 180 VVSG 183
>gnl|CDD|240644 cd12167, 2-Hacid_dh_8, 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.
Length = 330
Score = 33.7 bits (78), Expect = 0.010
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 25 DQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRR 59
D + RGI V + +++ VAEF + + RR
Sbjct: 89 DAVWERGILVTSAADANAEPVAEFTLAAILLALRR 123
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 33.7 bits (77), Expect = 0.010
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 3 SRAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRR 59
S+AG K S +VG++++ ++ GI VG V ++ AE L++A +RR
Sbjct: 83 SKAGG--KAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARR 137
>gnl|CDD|240643 cd12166, 2-Hacid_dh_7, 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.
Length = 300
Score = 33.7 bits (78), Expect = 0.010
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRF 60
L+V+ T S G+D + L + G+ + V + AE + L +A R
Sbjct: 60 RLRVVQTLSAGYDGV-LPLLP-EGVTLCNARGVHDASTAELAVALILASLRGL 110
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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.
Length = 306
Score = 33.4 bits (77), Expect = 0.012
Identities = 16/66 (24%), Positives = 32/66 (48%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 64
NLK I+ G +++ L+ K +GI + + DAV E +G+ +A+ + +
Sbjct: 59 KATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRAD 118
Query: 65 NCIASG 70
+ +G
Sbjct: 119 QEVRNG 124
>gnl|CDD|240653 cd12176, PGDH_3, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. 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.
Length = 304
Score = 32.9 bits (76), Expect = 0.018
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 4 RAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVS-SDAVAEFNIGLAIAVSRR 59
A L I F +G + + LD RGI V P S + +VAE IG I ++RR
Sbjct: 60 EAAPKLLAIGCFCIGTNQVDLDAAAKRGIPVFN-APFSNTRSVAELVIGEIIMLARR 115
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 32.0 bits (73), Expect = 0.040
Identities = 16/52 (30%), Positives = 30/52 (57%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRR 59
L+ ST SVG+D+ +D + +R I + V ++ VA+ + L ++ +RR
Sbjct: 66 KLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARR 117
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 31.6 bits (72), Expect = 0.050
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 64
A LK+I + G +++ L + RGI V + +VA+ + L +A++ R
Sbjct: 63 AAPQLKLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQ 122
Query: 65 NCIASGT-EKSQQ-----HAITEL 82
+A+G ++S Q I EL
Sbjct: 123 QAVAAGRWQQSSQFCLLDFPIVEL 146
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, 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.
Length = 334
Score = 31.1 bits (71), Expect = 0.085
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 8 NLKVISTFSVGHDH-LHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQ 62
NL+++ FS G DH L K + + T + +AE+ IG + +S F Q
Sbjct: 54 NLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIGTWLVLSHHFLQ 109
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 30.5 bits (69), Expect = 0.14
Identities = 16/48 (33%), Positives = 25/48 (52%)
Query: 9 LKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAV 56
LK+I+ + G +++ L K GI V V SS V E +G+ A+
Sbjct: 66 LKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFAL 113
>gnl|CDD|183721 PRK12749, PRK12749, quinate/shikimate dehydrogenase; Reviewed.
Length = 288
Score = 29.6 bits (66), Expect = 0.23
Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 53 AIAVSRRFQQGHNCIASGTEKSQQHAITELITQSD--TNHTQ 92
A+A ++R + +C+ + T+ + Q A E + +D TN T+
Sbjct: 164 ALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTK 205
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 29.3 bits (66), Expect = 0.34
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 9 LKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQ 62
+K I+ S G D L+ + + V S +++AEF + AI + R F Q
Sbjct: 70 IKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQ 123
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 29.1 bits (65), Expect = 0.39
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 6 GENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRR 59
G+ K+I + S G DH+ + I + G S +VAE L +A ++
Sbjct: 47 GKKTKMIQSLSAGVDHIDVSGIPENVVLCSNAGAYSI-SVAEHAFALLLAWAKN 99
>gnl|CDD|239170 cd02769, MopB_DMSOR-BSOR-TMAOR, The MopB_DMSOR-BSOR-TMAOR CD
contains dimethylsulfoxide reductase (DMSOR), biotin
sulfoxide reductase (BSOR), trimethylamine N-oxide
reductase (TMAOR) and other related proteins. DMSOR
always catalyzes the reduction of DMSO to
dimethylsulfide, but its cellular location and
oligomerization state are organism-dependent. For
example, in Rhodobacter sphaeriodes and Rhodobacter
capsulatus, it is an 82-kDa monomeric soluble protein
found in the periplasmic space; in E. coli, it is
membrane-bound and exists as a heterotrimer. BSOR
catalyzes the reduction of biotin sulfixode to biotin,
and is unique among Mo enzymes because no additional
auxiliary proteins or cofactors are required. TMAOR is
similar to DMSOR, but its only natural substrate is
TMAO. Members of this CD belong to the
molybdopterin_binding (MopB) superfamily of proteins.
Length = 609
Score = 28.8 bits (65), Expect = 0.50
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 24 LDQIKSRGIRVGTVGPVSSDAVAEFN 49
L +K RGIR ++ P+ D AE
Sbjct: 201 LKALKDRGIRFISISPLRDDTAAELG 226
>gnl|CDD|235899 PRK06975, PRK06975, bifunctional uroporphyrinogen-III
synthetase/uroporphyrin-III C-methyltransferase;
Reviewed.
Length = 656
Score = 27.8 bits (62), Expect = 1.2
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 23 HLDQIKSRGIRVGTVGPVSSDAVAEFNI 50
LD I + V VGP S A+A I
Sbjct: 73 RLDAIWPHALPVAVVGPGSVAALARHGI 100
>gnl|CDD|173544 PTZ00351, PTZ00351, adenylosuccinate synthetase; Provisional.
Length = 710
Score = 27.7 bits (61), Expect = 1.4
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 35 GTVGPVS-SDAVAEFNIGLAIAVSRRFQQGHNCIASGTEKSQQHAITELITQSDTNHTQ 92
G + PV SD ++NIG+A+A++ Q H + T+K + + + Q + N Q
Sbjct: 530 GIMAPVEYSDETGDYNIGVAMAIAS--AQHHGECGAVTKKPRVCGFFDCVLQHEVNSIQ 586
>gnl|CDD|240635 cd12158, ErythrP_dh, D-Erythronate-4-Phosphate Dehydrogenase
NAD-binding and catalytic domains.
D-Erythronate-4-phosphate Dehydrogenase (E. coli gene
PdxB), a D-specific 2-hydroxyacid dehydrogenase family
member, catalyzes the NAD-dependent oxidation of
erythronate-4-phosphate, which is followed by
transamination to form
4-hydroxy-L-threonine-4-phosphate within the de novo
biosynthesis pathway of vitamin B6.
D-Erythronate-4-phosphate dehydrogenase has the common
architecture shared with D-isomer specific
2-hydroxyacid dehydrogenases but contains an additional
C-terminal dimerization domain in addition to an
NAD-binding domain and the "lid" domain. The lid domain
corresponds to the catalytic domain of phosphoglycerate
dehydrogenase and other proteins of the D-isomer
specific 2-hydroxyacid dehydrogenase family, which
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.
Length = 343
Score = 27.1 bits (61), Expect = 1.6
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEF 48
G +K + T ++G DH+ D +K RGI ++++VAE+
Sbjct: 54 EGSKVKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVAEY 97
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 27.3 bits (61), Expect = 1.7
Identities = 13/48 (27%), Positives = 28/48 (58%)
Query: 8 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIA 55
NLK+I + G +++ ++ K +GI V V S+++VA+ + ++
Sbjct: 63 NLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLS 110
>gnl|CDD|197711 smart00414, H2A, Histone 2A.
Length = 106
Score = 26.5 bits (59), Expect = 1.8
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 7/47 (14%)
Query: 2 SSRAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEF 48
S+RAG F VG H L + + RVG PV AV E+
Sbjct: 3 SARAG------LQFPVGRIHRLLRK-GTYAKRVGAGAPVYLAAVLEY 42
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 26.9 bits (60), Expect = 1.9
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGI 32
G ++ + T ++G DHL LD GI
Sbjct: 55 EGSRVRFVGTCTIGTDHLDLDYFAEAGI 82
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 27.0 bits (61), Expect = 2.0
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRV------GTVGPVSSDAVAEFNIGLAIAVSR 58
A +NLKVI VG D++ + RGI V T+ + AE I L +A++R
Sbjct: 61 AAKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTI------SAAEHTIALMLALAR 114
Query: 59 RFQQGHNCIASGT-EKS 74
Q H + +G E+
Sbjct: 115 NIPQAHASLKAGKWERK 131
>gnl|CDD|217244 pfam02826, 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.
Length = 175
Score = 25.9 bits (58), Expect = 3.7
Identities = 7/33 (21%), Positives = 15/33 (45%)
Query: 50 IGLAIAVSRRFQQGHNCIASGTEKSQQHAITEL 82
+ L +A++RR + + +G + EL
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGREL 33
>gnl|CDD|177756 PLN00154, PLN00154, histone H2A; Provisional.
Length = 136
Score = 25.7 bits (56), Expect = 4.2
Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 2 SSRAGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEF 48
SSRAG F VG H L Q S RVG V + A+ E+
Sbjct: 32 SSRAGLQ------FPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEY 72
>gnl|CDD|182747 PRK10807, PRK10807, paraquat-inducible protein B; Provisional.
Length = 547
Score = 25.8 bits (57), Expect = 5.1
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 30 RGIRVGTVGPV 40
RGIR+GTV V
Sbjct: 309 RGIRLGTVSKV 319
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 25.6 bits (56), Expect = 5.6
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 5 AGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEF 48
AG+ +K + T + G DH+ +K GI ++ AV E+
Sbjct: 55 AGKPIKFVGTATAGTDHVDEAWLKQAGIGFSAAPGCNAIAVVEY 98
>gnl|CDD|240657 cd12180, 2-Hacid_dh_15, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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.
Length = 308
Score = 25.4 bits (56), Expect = 6.8
Identities = 7/23 (30%), Positives = 16/23 (69%)
Query: 40 VSSDAVAEFNIGLAIAVSRRFQQ 62
V+++A+AEF + +A ++R +
Sbjct: 94 VAAEAIAEFVLAAILAAAKRLPE 116
>gnl|CDD|197227 cd09129, PLDc_unchar2_1, Putative catalytic domain, repeat 1, of
uncharacterized phospholipase D-like proteins.
Putative catalytic domain, repeat 1, of uncharacterized
phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD
enzymes hydrolyze phospholipid phosphodiester bonds to
yield phosphatidic acid and a free polar head group.
They can also catalyze transphosphatidylation of
phospholipids to acceptor alcohols. Members of this
subfamily contain two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the PLD superfamily. The two motifs may be part of the
active site and may be involved in phosphatidyl group
transfer.
Length = 196
Score = 25.3 bits (56), Expect = 6.8
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 12 ISTFSVGHDHLHLDQIKSRGIRVGTV 37
I+TF HD+ HL ++K GI V
Sbjct: 64 INTFYGSHDNPHLKKLKEAGIEVVET 89
>gnl|CDD|233001 TIGR00509, bisC_fam, molybdopterin guanine dinucleotide-containing
S/N-oxide reductases. This enzyme family shares
sequence similarity and a requirement for a molydenum
cofactor as the only prosthetic group. The form of the
cofactor is a single molybdenum atom coordinated by two
molybdopterin guanine dinucleotide molecules. Members of
the family include biotin sulfoxide reductase,
dimethylsulfoxide reductase, and trimethylamine-N-oxide
reductase, although a single member may show all those
activities and related activities; it may not be
possible to resolve the primary function for members of
this family by sequence comparison alone. A number of
similar molybdoproteins in which the N-terminal region
contains a CXXXC motif and may bind an iron-sulfur
cluster are excluded from this set, including formate
dehydrogenases and nitrate reductases. Also excluded is
the A chain of a heteromeric, anaerobic DMSO reductase,
which also contains the CXXXC motif.
Length = 770
Score = 25.5 bits (56), Expect = 7.3
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 19 HDHLHLDQIKSRGIRVGTVGPVSSDAVAEFN 49
+ +L+++K++G RV ++ PV ++ F
Sbjct: 192 GGYEYLERLKAKGKRVISIDPVRTETAEFFG 222
>gnl|CDD|239152 cd02751, MopB_DMSOR-like, The MopB_DMSOR-like CD contains
dimethylsulfoxide reductase (DMSOR), biotin sulfoxide
reductase (BSOR), trimethylamine N-oxide reductase
(TMAOR) and other related proteins. DMSOR catalyzes the
reduction of DMSO to dimethylsulfide, but its cellular
location and oligomerization state are
organism-dependent. For example, in Rhodobacter
sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa
monomeric soluble protein found in the periplasmic
space; in E. coli, it is membrane-bound and exists as a
heterotrimer. BSOR catalyzes the reduction of biotin
sulfixode to biotin, and is unique among Mo enzymes
because no additional auxiliary proteins or cofactors
are required. TMAOR is similar to DMSOR, but its only
natural substrate is TMAO. Also included in this group
is the pyrogallol-phloroglucinol transhydroxylase from
Pelobacter acidigallici. Members of the MopB_DMSOR-like
CD belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 609
Score = 25.3 bits (56), Expect = 7.4
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 16 SVGHDHL---HLDQIKSRGIRVGTVGPVSSDAVAEFN 49
G DH +L Q K G+R + P +D A
Sbjct: 188 GGGPDHGSYYYLKQAKDAGVRFICIDPRYTDTAAVLA 224
>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH. A sigma
factor is a DNA-binding protein protein that binds to
the DNA-directed RNA polymerase core to produce the
holoenzyme capable of initiating transcription at
specific sites. Different sigma factors act in
vegetative growth, heat shock, extracytoplasmic
functions (ECF), etc. This model represents the clade
of sigma factors called RpoH and further restricted to
the Proteobacteria. This protein may be called
sigma-32, sigma factor H, heat shock sigma factor, and
alternative sigma factor RpoH. Note that in some
species the single locus rpoH may be replaced by two or
more differentially regulated stress response sigma
factors [Cellular processes, Adaptations to atypical
conditions, Transcription, Transcription factors].
Length = 270
Score = 25.3 bits (56), Expect = 7.8
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 42 SDAVAEFNIGLAIAVSRRF 60
+D + E NIGL AV +RF
Sbjct: 63 ADLIQEGNIGLMKAV-KRF 80
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.129 0.365
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,928,775
Number of extensions: 388742
Number of successful extensions: 442
Number of sequences better than 10.0: 1
Number of HSP's gapped: 430
Number of HSP's successfully gapped: 72
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.2 bits)