RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5266
(180 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 = 143 bits (364), Expect = 2e-42
Identities = 50/82 (60%), Positives = 64/82 (78%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SDF+ + C LT +T LI ++ +LMKPTAILINT+RGG++D++ALVE L+ KI GA
Sbjct: 197 AESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGVVDEDALVEALKSGKIAGA 256
Query: 109 GLDVMIPEPLPADHPLVQLDNC 130
GLDV PEPLPADHPL+ L N
Sbjct: 257 GLDVFEPEPLPADHPLLTLPNV 278
>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 = 130 bits (330), Expect = 5e-39
Identities = 43/82 (52%), Positives = 59/82 (71%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD + + LT +T LI ++ +LMKP AILINT+RGGL+D++AL+ L+ +I GA
Sbjct: 87 AESDVVSLHLPLTPETRHLINAERLALMKPGAILINTARGGLVDEDALIAALKSGRIAGA 146
Query: 109 GLDVMIPEPLPADHPLVQLDNC 130
LDV PEPLP DHPL++L N
Sbjct: 147 ALDVFEPEPLPPDHPLLELPNV 168
>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 = 132 bits (334), Expect = 4e-38
Identities = 45/82 (54%), Positives = 61/82 (74%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
+SD + + LT +T +IG ++F+LMKPTA INT+R GL+D++AL+E L + KIGGA
Sbjct: 200 KRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLVDEDALIEALEEGKIGGA 259
Query: 109 GLDVMIPEPLPADHPLVQLDNC 130
LDV EPLPADHPL++LDN
Sbjct: 260 ALDVFPEEPLPADHPLLKLDNV 281
>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 = 124 bits (314), Expect = 4e-35
Identities = 41/81 (50%), Positives = 55/81 (67%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A++DFI + LT +T LI ++ + MKP AILINT+RGG++D+ AL + L+ KI GA
Sbjct: 191 AEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGGIVDEAALADALKSGKIAGA 250
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
LDV EP PAD PL+ L N
Sbjct: 251 ALDVFEQEPPPADSPLLGLPN 271
>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 = 124 bits (313), Expect = 5e-35
Identities = 44/82 (53%), Positives = 56/82 (68%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
+SDFI + LT +T LI + +LMKP AILINT+RGGL+D+EAL E L+ +I GA
Sbjct: 195 KESDFISLHLPLTPETRHLINAAELALMKPGAILINTARGGLVDEEALYEALKSGRIAGA 254
Query: 109 GLDVMIPEPLPADHPLVQLDNC 130
LDV EP PAD PL++L N
Sbjct: 255 ALDVFEEEPPPADSPLLELPNV 276
>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 = 122 bits (308), Expect = 3e-34
Identities = 36/82 (43%), Positives = 51/82 (62%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
++D++ LT +T L ++F+ MKP A+LIN RG ++D++AL+E L +I GA
Sbjct: 188 PEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDALIEALESGRIAGA 247
Query: 109 GLDVMIPEPLPADHPLVQLDNC 130
LDV EPLPAD PL L N
Sbjct: 248 ALDVFEEEPLPADSPLWDLPNV 269
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 122 bits (308), Expect = 3e-34
Identities = 44/84 (52%), Positives = 60/84 (71%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD I + C LT +T LI ++ + MKP AIL+NT+RGGL+D++AL++ L+ KI GA
Sbjct: 199 AESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQALIDALKSGKIAGA 258
Query: 109 GLDVMIPEPLPADHPLVQLDNCGN 132
GLDV EP DHPL++LDN N
Sbjct: 259 GLDVFENEPALFDHPLLRLDNFPN 282
>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 = 122 bits (308), Expect = 3e-34
Identities = 39/82 (47%), Positives = 53/82 (64%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD + + C LT +T LI + +LMKP A L+NT+RGGL+D+ AL L+ +I GA
Sbjct: 195 ARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEAALARALKSGRIAGA 254
Query: 109 GLDVMIPEPLPADHPLVQLDNC 130
LDV+ EP PAD PL+ N
Sbjct: 255 ALDVLEEEPPPADSPLLSAPNV 276
>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 = 121 bits (305), Expect = 7e-34
Identities = 43/83 (51%), Positives = 57/83 (68%), Gaps = 1/83 (1%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
AQSD I + C LT +T LI ++ + MKP AILINT+RGGL+D++AL + L KI GA
Sbjct: 196 AQSDVISLHCPLTPETRNLINAEELAKMKPGAILINTARGGLVDEQALADALNSGKIAGA 255
Query: 109 GLDVMIPEPLPADHPLVQ-LDNC 130
GLDV+ EP AD+PL++ N
Sbjct: 256 GLDVLSQEPPRADNPLLKAAPNL 278
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 303
Score = 118 bits (298), Expect = 8e-33
Identities = 36/82 (43%), Positives = 48/82 (58%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
+D + + LT +T L+ + MKP A L+N +RG L+D +ALV+ LR +I GA
Sbjct: 178 PDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGA 237
Query: 109 GLDVMIPEPLPADHPLVQLDNC 130
LDV PEPLP HPL L N
Sbjct: 238 ALDVTDPEPLPDGHPLWSLPNA 259
>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 = 118 bits (297), Expect = 1e-32
Identities = 44/81 (54%), Positives = 58/81 (71%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD + + LT +T LIG ++ + MKP AILINT+RGGL+D+EAL+ LR + GA
Sbjct: 196 AESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTARGGLVDEEALLAALRSGHLAGA 255
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
GLDV EPLP D PL++LDN
Sbjct: 256 GLDVFWQEPLPPDDPLLRLDN 276
>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 = 117 bits (296), Expect = 2e-32
Identities = 44/82 (53%), Positives = 60/82 (73%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
AQSD + + LT +T LI ++ +LMKP A+L+NT+RGGL+D++AL+ L+ KI GA
Sbjct: 193 AQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDALLRALKSGKIAGA 252
Query: 109 GLDVMIPEPLPADHPLVQLDNC 130
LDV PEPLPADHPL++L N
Sbjct: 253 ALDVFEPEPLPADHPLLELPNV 274
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 116 bits (293), Expect = 5e-32
Identities = 39/81 (48%), Positives = 53/81 (65%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A++D + + LT +T LI ++ + MKP AILIN +RGG++D++AL+ L KI GA
Sbjct: 196 AEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDALLAALDSGKIAGA 255
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
LDV EPLPAD PL L N
Sbjct: 256 ALDVFEEEPLPADSPLWDLPN 276
>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 = 108 bits (271), Expect = 8e-29
Identities = 42/82 (51%), Positives = 57/82 (69%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD I + LT++T +I K FS MK IL+NT+RG L+D+EAL+E L+ KI GA
Sbjct: 201 AESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTARGELIDEEALIEALKSGKIAGA 260
Query: 109 GLDVMIPEPLPADHPLVQLDNC 130
GLDV+ EP+ ADHPL+ +N
Sbjct: 261 GLDVLEEEPIKADHPLLHYENV 282
>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 = 105 bits (265), Expect = 5e-28
Identities = 42/81 (51%), Positives = 54/81 (66%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A SD + + L+ T L+G + +LMKPTA+L+NTSRG L+D+ AL+ LR +I GA
Sbjct: 196 ATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRGPLVDEGALLAALRAGRIAGA 255
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
LDV EPLPADHPL L N
Sbjct: 256 ALDVFDVEPLPADHPLRGLPN 276
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 106 bits (268), Expect = 2e-27
Identities = 37/81 (45%), Positives = 52/81 (64%), Gaps = 1/81 (1%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A++DFI + LT +T LIG ++ + MKP +IN +RGG++D+ AL E L+ K+ GA
Sbjct: 193 ARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINCARGGIIDEAALAEALKSGKVAGA 252
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
LDV EP P D PL +L N
Sbjct: 253 ALDVFEKEP-PTDSPLFELPN 272
>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 = 103 bits (258), Expect = 6e-27
Identities = 39/80 (48%), Positives = 54/80 (67%), Gaps = 1/80 (1%)
Query: 51 SDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAGL 110
SDFI + LT +T+ +I +K+ LMK AI+INTSRGG++D+EAL+E L+ K+ GA L
Sbjct: 194 SDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVIDEEALLEALKSGKLAGAAL 253
Query: 111 DVMIPEPLPADHPLVQLDNC 130
DV EP P L++L N
Sbjct: 254 DVFENEPPPG-SKLLELPNV 272
>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 = 103 bits (258), Expect = 6e-27
Identities = 41/84 (48%), Positives = 59/84 (70%), Gaps = 3/84 (3%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD + + L +T+ LIG+++ +LMK +AILINT+RG ++D EAL + L + KI GA
Sbjct: 196 AESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVVDNEALADALNEGKIAGA 255
Query: 109 GLDV--MIPEPLPADHPLVQLDNC 130
G+DV M P PLPAD+PL+ N
Sbjct: 256 GIDVFDMEP-PLPADYPLLHAPNT 278
>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 = 96.1 bits (240), Expect = 3e-24
Identities = 35/81 (43%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD + + LT +T +I + +LM+ A INT+RG L+D+ AL+ LR ++ A
Sbjct: 203 ARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEAALLAELRSGRL-RA 261
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
LDV PEPLP D PL L N
Sbjct: 262 ALDVTDPEPLPPDSPLRTLPN 282
>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 = 95.8 bits (239), Expect = 3e-24
Identities = 37/81 (45%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
+SDF+ + T +T LI F LMKPTA LIN +RG L+D++ALV+ L+ +I GA
Sbjct: 198 KESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGPLVDEKALVDALKTGEIAGA 257
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
LDV EP + L +LDN
Sbjct: 258 ALDVFEFEPEVSPE-LKKLDN 277
>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 = 95.7 bits (239), Expect = 3e-24
Identities = 35/81 (43%), Positives = 48/81 (59%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
++D + LT++T L F MK A+ IN RG +D++AL+E L++K+I GA
Sbjct: 188 KEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVGRGPSVDEDALIEALKNKQIRGA 247
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
LDV EPLP D PL LDN
Sbjct: 248 ALDVFEEEPLPKDSPLWDLDN 268
>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 = 95.4 bits (238), Expect = 6e-24
Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 6/87 (6%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
Q+D + V LTK T LIG + + MKP AIL+N RG ++D+EAL E L+++ I GA
Sbjct: 190 EQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPVVDEEALYEALKERPIAGA 249
Query: 109 GLDVMIPEP------LPADHPLVQLDN 129
+DV P P+ +P +L N
Sbjct: 250 AIDVWWRYPSRGDPVAPSRYPFHELPN 276
>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 = 94.2 bits (235), Expect = 2e-23
Identities = 35/83 (42%), Positives = 49/83 (59%), Gaps = 4/83 (4%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
AQSD + + C LT T LI +K+F+ MK I++NT+RG ++D++ALV+ L K+ A
Sbjct: 208 AQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDALVDALESGKVASA 267
Query: 109 GLDVMIPEPLP----ADHPLVQL 127
GLDV EP P V L
Sbjct: 268 GLDVFENEPEVNPGLLKMPNVTL 290
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 94.0 bits (234), Expect = 2e-23
Identities = 36/81 (44%), Positives = 50/81 (61%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
+SDF+ + LT +T L G +QF+ MK +AI IN RG ++D+ AL+ L+ +I A
Sbjct: 199 QESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVVDENALIAALQKGEIHAA 258
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
GLDV EPL D PL+ L N
Sbjct: 259 GLDVFEQEPLSVDSPLLSLPN 279
>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 = 93.7 bits (234), Expect = 2e-23
Identities = 34/64 (53%), Positives = 44/64 (68%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD I + C LT +T LI + + MK +LINTSRGGL+D +AL+E L+ KIGG
Sbjct: 196 AESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDTKALIEALKSGKIGGL 255
Query: 109 GLDV 112
GLDV
Sbjct: 256 GLDV 259
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 92.9 bits (231), Expect = 5e-23
Identities = 37/80 (46%), Positives = 53/80 (66%), Gaps = 1/80 (1%)
Query: 50 QSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAG 109
+SDF+ + LTK+T +I ++ LMKPTAIL+NT+RG ++D +ALV+ L++ I GAG
Sbjct: 204 ESDFVSLHVPLTKETYHMINEERLKLMKPTAILVNTARGKVVDTKALVKALKEGWIAGAG 263
Query: 110 LDVMIPEPLPADHPLVQLDN 129
LDV EP + L L N
Sbjct: 264 LDVFEEEPYY-NEELFSLKN 282
>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 = 92.8 bits (231), Expect = 2e-22
Identities = 36/81 (44%), Positives = 51/81 (62%), Gaps = 1/81 (1%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A++DFI V LT +T LIG ++ + MK I++N +RGG++D+ AL E L + + A
Sbjct: 192 ARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAALYEALEEGHVRAA 251
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
LDV EP P D+PL LDN
Sbjct: 252 ALDVFEKEP-PTDNPLFDLDN 271
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 91.0 bits (226), Expect = 2e-22
Identities = 38/78 (48%), Positives = 55/78 (70%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
Q+D + + C LT+ T+ LI + +LMKPTA LINT RG L+D++AL++ L + KI GA
Sbjct: 196 KQADIVTLHCPLTETTQNLINAETLALMKPTAFLINTGRGPLVDEQALLDALENGKIAGA 255
Query: 109 GLDVMIPEPLPADHPLVQ 126
LDV++ EP D+PL+Q
Sbjct: 256 ALDVLVKEPPEKDNPLIQ 273
>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 = 88.9 bits (221), Expect = 1e-21
Identities = 37/76 (48%), Positives = 46/76 (60%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD + + LT +T LI + KP LIN +RGGL+DQEAL+E L +I A
Sbjct: 187 ARSDHLVLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLA 246
Query: 109 GLDVMIPEPLPADHPL 124
LDV PEPLP HPL
Sbjct: 247 SLDVTDPEPLPEGHPL 262
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 89.0 bits (221), Expect = 1e-21
Identities = 37/79 (46%), Positives = 53/79 (67%)
Query: 50 QSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAG 109
Q D + + C LT+ T LIG ++ +LMKP A+LINT+RGGL+D++AL + LR +GGA
Sbjct: 197 QVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLVDEQALADALRSGHLGGAA 256
Query: 110 LDVMIPEPLPADHPLVQLD 128
DV+ EP +PL+ D
Sbjct: 257 TDVLSVEPPVNGNPLLAPD 275
>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 = 88.1 bits (219), Expect = 3e-21
Identities = 35/84 (41%), Positives = 48/84 (57%), Gaps = 1/84 (1%)
Query: 48 SAQSDFIFVTCALTKDTEQLIGRKQFSLM-KPTAILINTSRGGLLDQEALVEFLRDKKIG 106
D + V+ LT T+ L+G ++F ++ K + N +RG L+D +ALV L +I
Sbjct: 208 RQDLDLLVVSLPLTPATKHLLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQIR 267
Query: 107 GAGLDVMIPEPLPADHPLVQLDNC 130
GA LDV PEPLPADHPL N
Sbjct: 268 GAALDVTDPEPLPADHPLWSAPNV 291
>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 = 85.4 bits (212), Expect = 3e-20
Identities = 40/101 (39%), Positives = 54/101 (53%), Gaps = 20/101 (19%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
+SD I + T T LI R+ F+LMKP A+LINT+RG ++D EALV L++ K+ GA
Sbjct: 192 QESDIISLHVPYTPQTHHLINRENFALMKPGAVLINTARGAVVDTEALVRALKEGKLAGA 251
Query: 109 GLDV------MIPE--------------PLPADHPLVQLDN 129
GLDV + E L ADH L++ N
Sbjct: 252 GLDVLEQEEVLREEAELFREDVSPEDLKKLLADHALLRKPN 292
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 84.3 bits (209), Expect = 6e-20
Identities = 34/86 (39%), Positives = 52/86 (60%), Gaps = 1/86 (1%)
Query: 50 QSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAG 109
SD I + L + T+ LI K+ L+K AILIN RGG+++++ L + L +K I AG
Sbjct: 196 TSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVGRGGIVNEKDLAKALDEKDI-YAG 254
Query: 110 LDVMIPEPLPADHPLVQLDNCGNGLL 135
LDV+ EP+ +HPL+ + N L+
Sbjct: 255 LDVLEKEPMEKNHPLLSIKNKEKLLI 280
>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 = 80.3 bits (199), Expect = 1e-18
Identities = 31/77 (40%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A +D+I + LT +T LI + + MKP AIL+N +RG ++D+EAL+E L + K+GG
Sbjct: 191 ATADYITLHVPLTDETRGLINAELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLGGY 250
Query: 109 GLDVMIPEPLPADHPLV 125
D P L P V
Sbjct: 251 VTDFPEPALLGH-LPNV 266
>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 = 79.8 bits (198), Expect = 2e-18
Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A+SD + V C T L+ + + P +L+N +RG ++D+ AL+ L++ +I GA
Sbjct: 191 AESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGSVVDEAALIAALQEGRIAGA 250
Query: 109 GLDVMIPEPLPADHPLVQLDN 129
GLDV EP L+ LDN
Sbjct: 251 GLDVFENEPNVPA-ALLDLDN 270
>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 = 79.9 bits (198), Expect = 3e-18
Identities = 29/65 (44%), Positives = 40/65 (61%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
Q+D I + LTK+ LI + F+ MK AIL+N +RGGL+D +AL++ L KI GA
Sbjct: 197 KQADIISLHVPLTKENHHLINAEAFAKMKDGAILVNAARGGLVDTKALIDALDSGKIAGA 256
Query: 109 GLDVM 113
LD
Sbjct: 257 ALDTY 261
>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 = 79.2 bits (196), Expect = 5e-18
Identities = 31/64 (48%), Positives = 42/64 (65%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
+SD I + LT++T LI ++ + MK I+INT+RG L+D EAL+E L KIGGA
Sbjct: 194 KESDIITLHTPLTEETYHLINKESIAKMKDGVIIINTARGELIDTEALIEGLESGKIGGA 253
Query: 109 GLDV 112
LDV
Sbjct: 254 ALDV 257
>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 = 78.8 bits (195), Expect = 6e-18
Identities = 34/85 (40%), Positives = 48/85 (56%), Gaps = 4/85 (4%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
A++DF+ + T T+ +IG ++ + MK AILIN SRG ++D +AL E LR + GA
Sbjct: 191 AEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRGTVVDIDALAEALRSGHLAGA 250
Query: 109 GLDVMIPEPL----PADHPLVQLDN 129
+DV EP P PL L N
Sbjct: 251 AVDVFPEEPASNGEPFSSPLQGLPN 275
>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 = 78.0 bits (193), Expect = 1e-17
Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 50 QSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAG 109
++D + + LT +T L+ + + M A+L+N +RG ++D +ALV L ++ A
Sbjct: 183 EADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDALVAELASGRL-RAA 241
Query: 110 LDVMIPEPLPADHPLVQLDNC 130
LDV PEPLP HPL
Sbjct: 242 LDVTDPEPLPPGHPLWSAPGV 262
>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 = 77.8 bits (192), Expect = 2e-17
Identities = 29/75 (38%), Positives = 43/75 (57%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
++ D + + C L +TE L ++ S MK A L+NT+RG + D+EA+ E L + G
Sbjct: 217 SKCDVVTINCPLHPETEGLFNKELLSKMKKGAYLVNTARGKICDREAVAEALESGHLAGY 276
Query: 109 GLDVMIPEPLPADHP 123
DV P+P P DHP
Sbjct: 277 AGDVWFPQPAPKDHP 291
>gnl|CDD|240641 cd12164, GDH_like_2, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
also known as hydroxypyruvate reductase) and other
enzymes of the 2-hydroxyacid dehydrogenase family. GDH
catalyzes the reversible reaction of (R)-glycerate +
NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 306
Score = 77.2 bits (191), Expect = 2e-17
Identities = 29/76 (38%), Positives = 40/76 (52%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
AQ+D + LT +T ++ + + + A LIN RG L + L+ L + GA
Sbjct: 185 AQTDILVCLLPLTPETRGILNAELLARLPRGAALINVGRGPHLVEADLLAALDSGHLSGA 244
Query: 109 GLDVMIPEPLPADHPL 124
LDV EPLPADHPL
Sbjct: 245 VLDVFEQEPLPADHPL 260
>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 = 77.3 bits (191), Expect = 2e-17
Identities = 31/64 (48%), Positives = 39/64 (60%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
SD I + LT + +I + F LMK I+INT+RG L+D EAL+E L KI GA
Sbjct: 195 KNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTARGSLVDTEALIEALDSGKIFGA 254
Query: 109 GLDV 112
GLDV
Sbjct: 255 GLDV 258
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 74.4 bits (184), Expect = 4e-16
Identities = 35/85 (41%), Positives = 49/85 (57%), Gaps = 4/85 (4%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
AQSD + + T T+ +IG ++ +LMKP AILIN SRG ++D +AL + L+ + GA
Sbjct: 202 AQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASRGTVVDIDALADALKSGHLAGA 261
Query: 109 GLDVMIPEPLPADH----PLVQLDN 129
+DV EP PL LDN
Sbjct: 262 AIDVFPVEPKSNGDPFESPLRGLDN 286
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 74.3 bits (183), Expect = 5e-16
Identities = 28/73 (38%), Positives = 41/73 (56%)
Query: 51 SDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAGL 110
D + + C L +TE L S MK + L+NT+RG ++D++A+V L + G
Sbjct: 249 CDVVTIHCPLHPETEHLFDADVLSRMKRGSYLVNTARGKIVDRDAVVRALESGHLAGYAG 308
Query: 111 DVMIPEPLPADHP 123
DV P+P PADHP
Sbjct: 309 DVWFPQPAPADHP 321
>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 = 70.4 bits (173), Expect = 8e-15
Identities = 27/91 (29%), Positives = 44/91 (48%)
Query: 40 LILVIRTRSAQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEF 99
L+ ++ +SD + T I + M A+ IN +RGG + +EA ++
Sbjct: 183 LLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEEAALDA 242
Query: 100 LRDKKIGGAGLDVMIPEPLPADHPLVQLDNC 130
L ++ I A LDV+ EP P + PL+ L N
Sbjct: 243 LLEEGIAAAALDVVEEEPPPVNSPLLDLPNV 273
>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 = 69.2 bits (170), Expect = 2e-14
Identities = 32/91 (35%), Positives = 45/91 (49%), Gaps = 5/91 (5%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
SDF+ + LT DT LI + + MKP A+L+N RG ++D+ A+ E L+ +GG
Sbjct: 198 ESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCRGSVVDEAAVAEALKSGHLGGY 257
Query: 109 GLDVMIPEPLP-ADHPLVQLDNCGNGLLDQE 138
DV E D P + LLDQ
Sbjct: 258 AADVFEMEDWARPDRP----RSIPQELLDQH 284
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 67.4 bits (165), Expect = 9e-14
Identities = 34/101 (33%), Positives = 55/101 (54%), Gaps = 6/101 (5%)
Query: 29 VDLTGGSKQVYLILVIRTRSAQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRG 88
VD GG + +Y ++D + + C LTK+T ++ + S MK A+L+N +RG
Sbjct: 211 VDEKGGHEDIYEFA------GEADIVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIARG 264
Query: 89 GLLDQEALVEFLRDKKIGGAGLDVMIPEPLPADHPLVQLDN 129
GLLD +A++ L +GG +DV EP D P+++ N
Sbjct: 265 GLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPILKHPN 305
>gnl|CDD|240637 cd12160, 2-Hacid_dh_3, 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 = 65.1 bits (159), Expect = 5e-13
Identities = 24/64 (37%), Positives = 35/64 (54%)
Query: 61 TKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAGLDVMIPEPLPA 120
T T + + + + A ++N RG +D++ALV L ++GGA LDV EPLPA
Sbjct: 207 TPSTAHALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLPA 266
Query: 121 DHPL 124
PL
Sbjct: 267 SSPL 270
Score = 47.0 bits (112), Expect = 1e-06
Identities = 20/41 (48%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 129 NCGNG-LLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPL 168
N G G +D++ALV L ++GGA LDV EP+PA PL
Sbjct: 230 NVGRGATVDEDALVAALESGRLGGAALDVTATEPLPASSPL 270
>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 = 62.9 bits (154), Expect = 4e-12
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 49 AQSDFIFVTCALTKD----TEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKK 104
A++D I + LT+D T L+ + +KP ILIN SRG ++D +AL+ L+ K
Sbjct: 165 AEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGAVIDNQALLALLQRGK 224
Query: 105 IGGAGLDVMIPEP 117
LDV EP
Sbjct: 225 DLRVVLDVWENEP 237
>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 = 60.4 bits (147), Expect = 3e-11
Identities = 29/69 (42%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 49 AQSDFIFVTCALTK-DTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGG 107
+SD I + K ++LI ++ S MK AILINT+RG L D+EA++E L K+ G
Sbjct: 196 KKSDIISLHVPYIKGKNDKLINKEFISKMKDGAILINTARGELQDEEAILEALESGKLAG 255
Query: 108 AGLDVMIPE 116
G DV+ E
Sbjct: 256 FGTDVLNNE 264
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 58.3 bits (141), Expect = 2e-10
Identities = 28/68 (41%), Positives = 42/68 (61%)
Query: 50 QSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAG 109
++D I + L K T LI +++ +LMK A+L+N SRG ++D+ ALVE L+ + G
Sbjct: 236 EADVISLHPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEVALVEHLKANPMFRVG 295
Query: 110 LDVMIPEP 117
LDV EP
Sbjct: 296 LDVFEDEP 303
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 57.6 bits (139), Expect = 3e-10
Identities = 23/75 (30%), Positives = 42/75 (56%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
+ D + + LT+ T + +++ + MK +++N +RG ++D +A+ + IGG
Sbjct: 254 PKCDVVVINTPLTEKTRGMFNKERIAKMKKGVLIVNNARGAIMDTQAVADACSSGHIGGY 313
Query: 109 GLDVMIPEPLPADHP 123
G DV P+P P DHP
Sbjct: 314 GGDVWYPQPAPKDHP 328
>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 = 51.5 bits (124), Expect = 3e-08
Identities = 21/65 (32%), Positives = 37/65 (56%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
++D + + LT +T ++ ++ S K INT+RG ++ + LV+ L+ KI GA
Sbjct: 188 KEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTKDLVKALKSGKILGA 247
Query: 109 GLDVM 113
LDV+
Sbjct: 248 CLDVL 252
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 48.0 bits (114), Expect = 5e-07
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 50 QSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDK 103
+SDF+ ++ LT +T +I K SL + +IN +R ++D+ ++ FLR+
Sbjct: 173 KSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLNFLRNH 226
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 48.1 bits (115), Expect = 6e-07
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 49 AQSDFIFVTCALTKD----TEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKK 104
+ D I + LTK+ T L+ + ++P A LIN SRG ++D +AL E L +
Sbjct: 166 EECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQALREALLSGE 225
Query: 105 IGGAGLDVMIPEP 117
A LDV EP
Sbjct: 226 DLDAVLDVWEGEP 238
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 46.8 bits (111), Expect = 1e-06
Identities = 24/101 (23%), Positives = 45/101 (44%), Gaps = 6/101 (5%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGA 108
+D I + K++ L + F +K AIL+N +RG +++ L+ + D + GA
Sbjct: 197 KDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIAAVNDGTLLGA 256
Query: 109 GLDVMIPEPLPADHPLVQLDNCGNGLLDQEALVEFLRDKKI 149
+D E D N +D + L+E + ++I
Sbjct: 257 AIDTYENEA-----AYFTND-WTNKDIDDKTLLELIEHERI 291
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 43.2 bits (102), Expect = 3e-05
Identities = 20/62 (32%), Positives = 31/62 (50%)
Query: 50 QSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAG 109
+D + + TK L F K A+ +N +RG L+D +AL++ L + I GA
Sbjct: 200 GADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDNGLIKGAA 259
Query: 110 LD 111
LD
Sbjct: 260 LD 261
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 41.3 bits (97), Expect = 1e-04
Identities = 22/64 (34%), Positives = 35/64 (54%)
Query: 61 TKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAGLDVMIPEPLPA 120
T +T +I ++ + A L+N +RG + ++ L+ L K+ GA LDV EPLP
Sbjct: 201 TPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPP 260
Query: 121 DHPL 124
+ PL
Sbjct: 261 ESPL 264
Score = 30.9 bits (70), Expect = 0.26
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 135 LDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPL 168
+ ++ L+ L K+ GA LDV EP+P + PL
Sbjct: 231 VVEDDLLAALDSGKVKGAMLDVFSREPLPPESPL 264
Score = 29.4 bits (66), Expect = 1.0
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 11/56 (19%)
Query: 97 VEFLRDKKIG-----GAGLDVMI------PEPLPADHPLVQLDNCGNGLLDQEALV 141
VE L + + GAG+D ++ PE L PL +L++ G G QE V
Sbjct: 49 VEMLAGRDLKAVFALGAGVDSILSKLQAHPEMLDPSVPLFRLEDTGMGEQMQEYAV 104
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 37.2 bits (86), Expect = 0.003
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 5/53 (9%)
Query: 65 EQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAGLDVMIPEP 117
E+LI +KP AILIN RG ++D AL+ L + + LDV EP
Sbjct: 191 EKLIRS-----LKPGAILINACRGAVVDNTALLTCLNEGQKLSVVLDVWEGEP 238
>gnl|CDD|240647 cd12170, 2-Hacid_dh_9, 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 = 294
Score = 34.6 bits (80), Expect = 0.018
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 50 QSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKK 104
D I TC L K+ L+G ++F L+ IL NTS G + EAL ++L+
Sbjct: 191 TVDVIC-TC-LPKNV-ILLGEEEFELLGDGKILFNTSLGPSFEVEALKKWLKASG 242
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 31.4 bits (71), Expect = 0.21
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 3/91 (3%)
Query: 49 AQSDFIFVTCALTKDTE-QLIGRKQFSLMKPTAILINTSRGGLLDQEALVEF-LRDKKIG 106
A++D I T L L+ + MKP ++++N + G + +AL L +
Sbjct: 215 AEADVIVTTTLLPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEEGHGV 274
Query: 107 GAGLDVMIPEPLPA-DHPLVQLDNCGNGLLD 136
DV +P P A P L
Sbjct: 275 VHYGDVNMPGPGCAMGVPWDATLRLAANTLP 305
>gnl|CDD|216092 pfam00742, Homoserine_dh, Homoserine dehydrogenase.
Length = 178
Score = 28.6 bits (65), Expect = 1.3
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 115 PEPLPADHPLVQLDNCGNGLL 135
P +P DHPL +D N +L
Sbjct: 129 PTLVPKDHPLASVDGVDNAVL 149
>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2. It is vital for
effective cell-replication that replication is not
stalled at any point by, for instance, damaged bases.
Rtf2 stabilizes the replication fork stalled at the
site-specific replication barrier RTS1 by preventing
replication restart until completion of DNA synthesis by
a converging replication fork initiated at a flanking
origin. The RTS1 element terminates replication forks
that are moving in the cen2-distal direction while
allowing forks moving in the cen2-proximal direction to
pass through the region. Rtf2 contains a C2HC2 motif
related to the C3HC4 RING-finger motif, and would appear
to fold up, creating a RING finger-like structure but
forming only one functional Zn2+ ion-binding site.
Length = 254
Score = 28.9 bits (65), Expect = 1.3
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 13/57 (22%)
Query: 49 AQSDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRDKKI 105
+ + TCAL+++ L KP G L +++A++E L DK
Sbjct: 28 EERLARWFTCALSQEP----------LKKPIVA---DRLGNLYNKDAVLEALLDKSK 71
>gnl|CDD|224055 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
permease components [Defense mechanisms].
Length = 567
Score = 28.5 bits (64), Expect = 2.0
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 29 VDLTGGSKQVYLILVIRTRSAQSDFIFV---TCALTKDTEQLIGRKQFSLMK-PTAILI 83
V+L+GG +Q I R + + T AL +TE LI L+K T ++I
Sbjct: 464 VNLSGGQRQRLAI--ARALLRNPPILILDEATSALDTETEALIQDALKKLLKGRTTLII 520
>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1) and similar
proteins. This subfamily corresponds to the RRM3 of
hnRNP H proteins and GRSF-1. The hnRNP H protein family
includes hnRNP H (also termed mcs94-1), hnRNP H2 (also
termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also
termed hnRNP 2H9), which represent a group of nuclear
RNA binding proteins that are involved in pre-mRNA
processing. These proteins have similar RNA binding
affinities and specifically recognize the sequence
GGGA. They can either stimulate or repress splicing
upon binding to a GGG motif. hnRNP H binds to the RNA
substrate in the presence or absence of these proteins,
whereas hnRNP F binds to the nuclear mRNA only in the
presence of cap-binding proteins. hnRNP H and hnRNP H2
are almost identical; both have been found to bind
nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements
downstream of the 5' splice site in the transcripts of
c-src, human immunodeficiency virus type 1 (HIV-1),
Bcl-X, GRIN1, and myelin. It silences exons when bound
to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
hnRNP H3 may be involved in the splicing arrest induced
by heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
except for hnRNP H3, in which the RRM1 is absent. RRM1
and RRM2 are responsible for the binding to the RNA at
DGGGD motifs, and they play an important role in
efficiently silencing the exon. For instance, members
in this family can regulate the alternative splicing of
the fibroblast growth factor receptor 2 (FGFR2)
transcripts, and function as silencers of FGFR2 exon
IIIc through an interaction with the exonic GGG motifs.
The lack of RRM1 could account for the reduced
silencing activity within hnRNP H3. In addition, the
family members have an extensive glycine-rich region
near the C-terminus, which may allow them to homo- or
heterodimerize. The family also includes a cytoplasmic
poly(A)+ mRNA binding protein, GRSF-1, which interacts
with RNA in a G-rich element-dependent manner. It may
function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. GRSF-1 also contains three potential RRMs
responsible for the RNA binding, and two auxiliary
domains (an acidic alpha-helical domain and an
N-terminal alanine-rich region) that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 26.5 bits (59), Expect = 2.3
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 64 TEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEF 99
TE I + FS + P + I + G EA VEF
Sbjct: 13 TENDI-FEFFSPLNPVNVRIEYNADGRATGEADVEF 47
>gnl|CDD|240619 cd00401, SAHH, S-Adenosylhomocysteine Hydrolase, NAD-binding and
catalytic domains. S-adenosyl-L-homocysteine hydrolase
(SAHH, AdoHycase) catalyzes the hydrolysis of
S-adenosyl-L-homocysteine (AdoHyc) to form adenosine
(Ado) and homocysteine (Hcy). The equilibrium lies far
on the side of AdoHyc synthesis, but in nature the
removal of Ado and Hyc is sufficiently fast, so that the
net reaction is in the direction of hydrolysis. Since
AdoHyc is a potent inhibitor of S-adenosyl-L-methionine
dependent methyltransferases, AdoHycase plays a critical
role in the modulation of the activity of various
methyltransferases. The enzyme forms homotetramers, with
each monomer binding one molecule of NAD+.
Length = 402
Score = 27.4 bits (62), Expect = 4.5
Identities = 19/49 (38%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 54 IFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRD 102
IFVT KD +I + F MK AIL N G D E V L +
Sbjct: 253 IFVTATGNKD---VIRGEHFEKMKDGAILCNA---GHFDVEIDVAALEE 295
>gnl|CDD|225823 COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA
replication, recombination, and repair].
Length = 299
Score = 27.4 bits (61), Expect = 4.9
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 6/52 (11%)
Query: 72 QFSLMKPTAILINTSRGGLLDQEALVEFLRDKKIGGAGLDVMIPEPLPADHP 123
F+ + A+ + LLD+ LV F K GG GL V +P A
Sbjct: 139 AFAEVVEAALELR----DLLDELGLVSFP--KTSGGKGLHVYVPLAPKATWE 184
Score = 27.0 bits (60), Expect = 6.7
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 133 GLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHP 167
LLD+ LV F K GG GL V +P A
Sbjct: 152 DLLDELGLVSFP--KTSGGKGLHVYVPLAPKATWE 184
>gnl|CDD|236144 PRK08057, PRK08057, cobalt-precorrin-6x reductase; Reviewed.
Length = 248
Score = 27.1 bits (61), Expect = 5.5
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 77 KPTAILINTSRGGLLDQEALVEFLRDKKIG 106
P + GG E L +LR++ I
Sbjct: 38 GPADLPGPVRVGGFGGAEGLAAYLREEGID 67
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 26.8 bits (60), Expect = 6.2
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 115 PEPLPADHPLVQLDNCGNGL 134
P +P DHPL ++ N +
Sbjct: 274 PTLVPKDHPLASVNGVMNAV 293
>gnl|CDD|233632 TIGR01910, DapE-ArgE, acetylornithine deacetylase or
succinyl-diaminopimelate desuccinylase. This group of
sequences contains annotations for both acetylornithine
deacetylase and succinyl-diaminopimelate desuccinylase,
but does not contain any members with experimental
characterization. Bacillus, Staphylococcus and
Sulfolobus species contain multiple hits to this
subfamily and each may have a separate activity.
Determining which is which must await further laboratory
research [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 375
Score = 27.0 bits (60), Expect = 7.1
Identities = 17/81 (20%), Positives = 22/81 (27%), Gaps = 17/81 (20%)
Query: 79 TAILINTSRGGLLDQEALVEFLRDKKIGGAGLDVMIPEPLPADHPLV-QLDNCGNGLLDQ 137
I+ + + L E K G P P D LV L+ +
Sbjct: 271 KQIIEDVVKALSKSDGWLYENEPVVKWSG-------PNETPPDSRLVKALEAIIKKVRGI 323
Query: 138 EALVE---------FLRDKKI 149
E V FLR I
Sbjct: 324 EPEVLVSTGGTDARFLRKAGI 344
>gnl|CDD|238983 cd02025, PanK, Pantothenate kinase (PanK) catalyzes the
phosphorylation of pantothenic acid to form
4'-phosphopantothenic, which is the first of five steps
in coenzyme A (CoA) biosynthetic pathway. The reaction
carried out by this enzyme is a key regulatory point in
CoA biosynthesis.
Length = 220
Score = 26.5 bits (59), Expect = 7.8
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 76 MKPTAILIN---TSRGGL---LDQEALVEFLRDKKIGGAGLDVMIPE 116
+ P LI R G D EAL++FL+D K G +V IP
Sbjct: 41 LYPNKELIERGLMDRKGFPESYDMEALLKFLKDIKSG--KKNVKIPV 85
>gnl|CDD|197258 cd09161, PLDc_PaCLS_like_2, Putative catalytic domain, repeat 2, of
Pseudomonas aeruginosa cardiolipin synthase and similar
proteins. Putative catalytic domain, repeat 2, of
Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS)
and similar proteins. Although PaCLS and similar
proteins have not been functionally characterized,
members in this subfamily show high sequence homology to
bacterial CL synthases, which catalyze the reversible
phosphatidyl group transfer between two
phosphatidylglycerol molecules to form CL and glycerol.
Moreover, PaCLS and other members of this subfamily
contain two HKD motifs (H-x-K-x(4)-D, where x represents
any amino acid residue) that characterizes the
phospholipase D (PLD) superfamily. The two motifs may be
part of the active site and may be involved in
phosphatidyl group transfer.
Length = 176
Score = 26.1 bits (58), Expect = 8.0
Identities = 17/61 (27%), Positives = 22/61 (36%), Gaps = 19/61 (31%)
Query: 109 GLDVMIPEPLPADHPLV---------QLDNCG-------NGLLDQEALVEFLRDKKIGGA 152
G+DV I P DH LV +L G G L Q+ L D ++
Sbjct: 51 GVDVRILIPERPDHLLVYLASFSYLPELIRAGVKVYRYQPGFLHQKV---VLVDDELAAV 107
Query: 153 G 153
G
Sbjct: 108 G 108
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 26.6 bits (60), Expect = 8.5
Identities = 18/49 (36%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 54 IFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLRD 102
IFVT KD I + MK AIL N G D E V L +
Sbjct: 270 IFVTATGNKDV---ITAEHMEAMKDGAILANI---GHFDNEIDVAALEE 312
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
0.322 0.142 0.420
Gapped
Lambda K H
0.267 0.0864 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,470,788
Number of extensions: 899980
Number of successful extensions: 928
Number of sequences better than 10.0: 1
Number of HSP's gapped: 913
Number of HSP's successfully gapped: 138
Length of query: 180
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 89
Effective length of database: 6,901,388
Effective search space: 614223532
Effective search space used: 614223532
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.1 bits)