RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 044647
(93 letters)
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 166 bits (421), Expect = 3e-52
Identities = 67/93 (72%), Positives = 77/93 (82%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G+LLVNI RGGLLDY+ V LESGHLGGL +DVAW++PFDP++PILK V+ITPHV G
Sbjct: 255 GALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPILKHPNVIITPHVAG 314
Query: 61 VTEHSYRSTAKVVGDVALQLHAGTPLRGIEPVN 93
VTE+SYRS K+VGD ALQLHAG PL GIE VN
Sbjct: 315 VTEYSYRSMGKIVGDAALQLHAGRPLTGIEFVN 347
>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 = 104 bits (263), Expect = 6e-29
Identities = 38/86 (44%), Positives = 56/86 (65%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G++L+N RGGL+D E + L SGHL G GLDV W +P P++P+L+ V++TPH+ G
Sbjct: 226 GAILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAG 285
Query: 61 VTEHSYRSTAKVVGDVALQLHAGTPL 86
VT+ SY+ A +V + +L G P
Sbjct: 286 VTDESYQRMAAIVAENIARLLRGEPP 311
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 72.3 bits (178), Expect = 9e-17
Identities = 29/92 (31%), Positives = 53/92 (57%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G++L+N RGG++D + + L+SG + G LDV +P ++P+ V++TPH+GG
Sbjct: 226 GAILINAARGGVVDEDALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGG 285
Query: 61 VTEHSYRSTAKVVGDVALQLHAGTPLRGIEPV 92
T+ + A++V + ++ AG P+ P
Sbjct: 286 STDEAQERVAEIVAENIVRYLAGGPVVNNAPE 317
>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 = 72.2 bits (178), Expect = 1e-16
Identities = 23/73 (31%), Positives = 39/73 (53%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
+ +N R GL+D + + LE G +GG LDV +P ++P+LK V +TPH+ G
Sbjct: 230 TAYFINTARAGLVDEDALIEALEEGKIGGAALDVFPEEPLPADHPLLKLDNVTLTPHIAG 289
Query: 61 VTEHSYRSTAKVV 73
T + +++
Sbjct: 290 ATRDVAERSPEII 302
>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 = 70.8 bits (174), Expect = 4e-16
Identities = 33/77 (42%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G +LVN RG L+D E + L+SG + G GLDV +P ++P+L ++ V+ITPH+G
Sbjct: 231 GVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIGA 290
Query: 61 VT-EHSYRSTAKVVGDV 76
T E Y KVV D+
Sbjct: 291 YTYESLYGMGEKVVDDI 307
>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 = 66.7 bits (164), Expect = 2e-15
Identities = 23/59 (38%), Positives = 39/59 (66%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVG 59
G++L+N RGGL+D + + L+SG + G LDV +P P++P+L+ V++TPH+
Sbjct: 117 GAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>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 = 68.3 bits (168), Expect = 2e-15
Identities = 33/91 (36%), Positives = 46/91 (50%), Gaps = 8/91 (8%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G+ LVN RGGL+D +A L+SG + G LDV +P ++P+L V++TPH
Sbjct: 225 GAFLVNTARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTPHAAW 284
Query: 61 VTEHSY----RSTAKVVGDVALQLHAGTPLR 87
+E S R A+ V V G P R
Sbjct: 285 YSEESLAELRRKAAEEVVRVL----RGEPPR 311
>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 = 67.8 bits (167), Expect = 4e-15
Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 3/82 (3%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G++L+N RGG++D +A L+SG + G LDV +P ++P+L V++TPH+G
Sbjct: 221 GAILINTARGGIVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGA 280
Query: 61 VTEHSYRSTAKVVGDVALQLHA 82
TE + A D A Q+ A
Sbjct: 281 STEEAQERVAV---DAAEQVLA 299
>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 = 65.3 bits (160), Expect = 3e-14
Identities = 26/65 (40%), Positives = 42/65 (64%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G++LVN RGGL+D + + L+SG + G LDV +P ++P+L+ V++TPH+ G
Sbjct: 223 GAVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAG 282
Query: 61 VTEHS 65
TE +
Sbjct: 283 YTEEA 287
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 62.6 bits (153), Expect = 3e-13
Identities = 28/76 (36%), Positives = 48/76 (63%), Gaps = 3/76 (3%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILK---FQIVLITPH 57
G++LVN RGGL+D + + L+SG + G GLDV +P ++P+L+ F V++TPH
Sbjct: 229 GAILVNTARGGLVDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPH 288
Query: 58 VGGVTEHSYRSTAKVV 73
+ TE + ++ A++
Sbjct: 289 IASATEEARKAMAELA 304
>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 = 62.1 bits (152), Expect = 5e-13
Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G++L+N RGGL+D E + L+SG + G LDV +P ++P+L+ V++TPH+G
Sbjct: 225 GAILINTARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGA 284
Query: 61 VTEHSYRSTA 70
T+ +
Sbjct: 285 STKEAVLRMG 294
>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 = 61.3 bits (150), Expect = 8e-13
Identities = 26/59 (44%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQI-VLITPHV 58
G++L+N RGGL+D + +A L SG + G GLDV +P +NP+LK ++ITPH+
Sbjct: 226 GAILINTARGGLVDEQALADALNSGKIAGAGLDVLSQEPPRADNPLLKAAPNLIITPHI 284
>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 = 60.6 bits (148), Expect = 1e-12
Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G++++N RGG++D E + L+SG L G LDV +P P + +L+ V +TPH+G
Sbjct: 222 GAIIINTSRGGVIDEEALLEALKSGKLAGAALDVFENEP-PPGSKLLELPNVSLTPHIGA 280
Query: 61 VTEHSYRSTAKVVGD 75
T+ + + + +
Sbjct: 281 STKEAQERIGEELAN 295
>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 = 60.2 bits (147), Expect = 2e-12
Identities = 26/89 (29%), Positives = 47/89 (52%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G++L+N+ RG ++D + + LESG + G LDV +P ++P+ V+ITPH+ G
Sbjct: 218 GAVLINVGRGSVVDEDALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPHISG 277
Query: 61 VTEHSYRSTAKVVGDVALQLHAGTPLRGI 89
+ ++ + + AG PL +
Sbjct: 278 DSPSYPERVVEIFLENLRRYLAGEPLLNV 306
>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 = 58.5 bits (142), Expect = 1e-11
Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 1/88 (1%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G ++VN RGG++D + LE GH+ LDV +P +NP+ V+ TPH+G
Sbjct: 222 GVIIVNCARGGIIDEAALYEALEEGHVRAAALDVFEKEP-PTDNPLFDLDNVIATPHLGA 280
Query: 61 VTEHSYRSTAKVVGDVALQLHAGTPLRG 88
T + + A V + L G P+
Sbjct: 281 STREAQENVATQVAEQVLDALKGLPVPN 308
>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 = 56.8 bits (138), Expect = 4e-11
Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
+LLVN RG L+D + L +G + G LDV +P ++P+ VL+TPH+G
Sbjct: 226 TALLVNTSRGPLVDEGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIGY 285
Query: 61 VTEHSYRS-TAKVVGDVA 77
VTE +Y + V ++A
Sbjct: 286 VTEEAYEGFYGQAVENIA 303
>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 = 54.1 bits (131), Expect = 3e-10
Identities = 23/64 (35%), Positives = 38/64 (59%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G+L +N+ RG +D + + L++ + G LDV +P ++P+ VLITPH+ G
Sbjct: 218 GALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDLDNVLITPHISG 277
Query: 61 VTEH 64
V+EH
Sbjct: 278 VSEH 281
>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 = 53.5 bits (129), Expect = 6e-10
Identities = 26/86 (30%), Positives = 41/86 (47%)
Query: 4 LVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGGVTE 63
L+NI RGGL+D E + L+SG + LDV +P +P+ V ++PH +
Sbjct: 220 LINIARGGLVDQEALLEALDSGRISLASLDVTDPEPLPEGHPLYTHPRVRLSPHTSAIAP 279
Query: 64 HSYRSTAKVVGDVALQLHAGTPLRGI 89
R+ A + + AG PL +
Sbjct: 280 DGRRNLADRFLENLARYRAGQPLHDL 305
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 53.2 bits (128), Expect = 7e-10
Identities = 33/89 (37%), Positives = 48/89 (53%), Gaps = 2/89 (2%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQI--VLITPHV 58
G+LL+N RGGL+D + +A L SGHLGG DV +P NP+L I +++TPH
Sbjct: 226 GALLINTARGGLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHS 285
Query: 59 GGVTEHSYRSTAKVVGDVALQLHAGTPLR 87
+ + + + + A AG PLR
Sbjct: 286 AWGSREARQRIVGQLAENARAFFAGKPLR 314
>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 = 52.7 bits (127), Expect = 1e-09
Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 4 LVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGGVTE 63
+ NI RG L+D + + LESG + G LDV +P ++P+ V+ITPHV T+
Sbjct: 243 VSNIARGSLVDTDALVAALESGQIRGAALDVTDPEPLPADHPLWSAPNVIITPHVSWQTQ 302
Query: 64 H 64
Sbjct: 303 E 303
>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 = 52.2 bits (126), Expect = 2e-09
Identities = 26/67 (38%), Positives = 42/67 (62%), Gaps = 4/67 (5%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPF---DP-NNPILKFQIVLITP 56
G++L+N RG ++D + +A L SGHL G +DV +P +P ++P+ V++TP
Sbjct: 221 GAILINASRGTVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTP 280
Query: 57 HVGGVTE 63
H+GG TE
Sbjct: 281 HIGGSTE 287
>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 = 52.2 bits (126), Expect = 2e-09
Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPN-NPIL-KFQIVLITPHV 58
G ++VN RG ++D + + LESG + GLDV +P NP L K V + PH+
Sbjct: 238 GVIIVNTARGAVIDEDALVDALESGKVASAGLDV---FENEPEVNPGLLKMPNVTLLPHM 294
Query: 59 GGVTE 63
G +T
Sbjct: 295 GTLTV 299
>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 = 51.9 bits (125), Expect = 2e-09
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKP------FDPNNPILKFQIVLI 54
G++LVN+ RG ++D E + L+ + G +DV W P P + V++
Sbjct: 220 GAILVNVGRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIM 279
Query: 55 TPHVGGVTE 63
+PH G TE
Sbjct: 280 SPHNAGWTE 288
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 52.0 bits (126), Expect = 2e-09
Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G ++N RGG++D +A L+SG + G LDV +P ++P+ + V++TPH+G
Sbjct: 223 GVRIINCARGGIIDEAALAEALKSGKVAGAALDVFEKEP-PTDSPLFELPNVVVTPHLGA 281
Query: 61 VTE 63
T
Sbjct: 282 STA 284
>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 = 51.2 bits (124), Expect = 4e-09
Identities = 21/59 (35%), Positives = 37/59 (62%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVG 59
++L+N RGG++D + + L+SG + G GLDV +P ++P+L V++ PH+G
Sbjct: 227 TAILINTARGGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIG 285
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 50.9 bits (122), Expect = 5e-09
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 2 SLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGGV 61
++LVN RG ++D + + L+ G + G GLDV +P+ N + + V++ PH+G
Sbjct: 234 AILVNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPY-YNEELFSLKNVVLAPHIGSA 292
Query: 62 TEHSYRSTAKVV 73
T + A++V
Sbjct: 293 TFEAREGMAELV 304
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 50.9 bits (123), Expect = 5e-09
Identities = 26/67 (38%), Positives = 42/67 (62%), Gaps = 4/67 (5%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKP---FDP-NNPILKFQIVLITP 56
G++L+N RG ++D + +A L+SGHL G +DV +P DP +P+ V++TP
Sbjct: 232 GAILINASRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTP 291
Query: 57 HVGGVTE 63
H+GG T+
Sbjct: 292 HIGGSTQ 298
>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 = 50.4 bits (121), Expect = 9e-09
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 20/79 (25%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDV------------AWTKPFDP------ 42
G++L+N RG ++D E + L+ G L G GLDV + + P
Sbjct: 222 GAVLINTARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKL 281
Query: 43 --NNPILKFQIVLITPHVG 59
++ +L+ V+ITPHV
Sbjct: 282 LADHALLRKPNVIITPHVA 300
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 49.6 bits (119), Expect = 1e-08
Identities = 21/61 (34%), Positives = 39/61 (63%), Gaps = 4/61 (6%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQI---VLITPH 57
G++L+N+ RGG+++ + +A L+ + GLDV +P + N+P+L + +LITPH
Sbjct: 225 GAILINVGRGGIVNEKDLAKALDEKDIY-AGLDVLEKEPMEKNHPLLSIKNKEKLLITPH 283
Query: 58 V 58
+
Sbjct: 284 I 284
>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 = 49.6 bits (119), Expect = 1e-08
Identities = 26/68 (38%), Positives = 34/68 (50%), Gaps = 8/68 (11%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDV----AWT---KPFDPNNPILKFQI-V 52
G+LLVN RG ++D VA L+SGHLGG DV W +P +L
Sbjct: 228 GALLVNPCRGSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRT 287
Query: 53 LITPHVGG 60
+ TPH+G
Sbjct: 288 VFTPHIGS 295
>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 = 49.8 bits (120), Expect = 1e-08
Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G+ L+N+ RG L + L+SGHL G LDV +P ++P+ + V +TPH+
Sbjct: 215 GAALINVGRGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPLWRHPRVTVTPHIAA 274
Query: 61 VTEHSYRSTAKVVGDVALQLHAGTPLRG 88
+T S A V + +L AG PL
Sbjct: 275 IT--DPDSAAAQVAENIRRLEAGEPLPN 300
>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 = 49.6 bits (119), Expect = 2e-08
Identities = 28/77 (36%), Positives = 37/77 (48%), Gaps = 14/77 (18%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDV------------AWTKPFDPN-NPIL 47
G++L+N RG L D E + LESG L G G DV K DP +L
Sbjct: 227 GAILINTARGELQDEEAILEALESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKLL 286
Query: 48 K-FQIVLITPHVGGVTE 63
+ VL+TPH+G T+
Sbjct: 287 DLYPRVLLTPHIGSYTD 303
>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 = 48.8 bits (117), Expect = 3e-08
Identities = 28/86 (32%), Positives = 44/86 (51%), Gaps = 1/86 (1%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTK-PFDPNNPILKFQIVLITPHVG 59
++L+N RG ++D E +A L G + G G+DV + P + P+L ++TPHV
Sbjct: 226 SAILINTARGPVVDNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVA 285
Query: 60 GVTEHSYRSTAKVVGDVALQLHAGTP 85
TE + A++V D AG P
Sbjct: 286 FATEEAMEKRAEIVFDNIEAWLAGKP 311
>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 = 48.1 bits (115), Expect = 5e-08
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 13/80 (16%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDV------------AWTKPFDPNNPILK 48
G +++N RG L+D E + L+SG + G GLDV D N +L
Sbjct: 225 GVIIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLG 284
Query: 49 -FQIVLITPHVGGVTEHSYR 67
V+ITPH T+ + +
Sbjct: 285 RRPNVIITPHTAFYTDDALK 304
>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 = 48.0 bits (115), Expect = 6e-08
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 13/82 (15%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVA-----------WTKPFD-PNNPILK 48
G +++N RG L+D E + LESG +GG LDV IL+
Sbjct: 224 GVIIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAILR 283
Query: 49 -FQIVLITPHVGGVTEHSYRST 69
F V++TPH+ T+ +
Sbjct: 284 SFPNVILTPHMAFYTDQAVSDM 305
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 47.9 bits (114), Expect = 7e-08
Identities = 24/62 (38%), Positives = 35/62 (56%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G L+VN RG ++D + VA SGH+GG G DV + +P ++P +TPH+ G
Sbjct: 284 GVLIVNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYMPNHAMTPHISG 343
Query: 61 VT 62
T
Sbjct: 344 TT 345
>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 = 47.7 bits (114), Expect = 8e-08
Identities = 26/62 (41%), Positives = 34/62 (54%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G+ LVN RG + D E VA LESGHL G DV + +P ++P +TPH+ G
Sbjct: 247 GAYLVNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMPNNAMTPHISG 306
Query: 61 VT 62
T
Sbjct: 307 TT 308
>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 = 47.3 bits (113), Expect = 8e-08
Identities = 30/88 (34%), Positives = 42/88 (47%)
Query: 2 SLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGGV 61
+ LVN+ RG L+D + + L SG + G LDV +P +P+ LITPHV
Sbjct: 209 AWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEPLPDGHPLWSLPNALITPHVANT 268
Query: 62 TEHSYRSTAKVVGDVALQLHAGTPLRGI 89
E A+ V + AG PL G+
Sbjct: 269 PEVIRPLLAERVAENVRAFAAGEPLLGV 296
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 47.5 bits (113), Expect = 9e-08
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPIL----KFQIVLITP 56
+ L+N RG L+D + + LE+G + G LDV +P + +NP++ + +LITP
Sbjct: 226 TAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNLLITP 285
Query: 57 HV 58
H+
Sbjct: 286 HI 287
>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 = 47.1 bits (113), Expect = 1e-07
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 3 LLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGGVT 62
+LVN+ RG ++D + L+ G + G GLDV +P P +L V++TPH+ T
Sbjct: 223 VLVNVARGSVVDEAALIAALQEGRIAGAGLDVFENEPNVP-AALLDLDNVVLTPHIASAT 281
Query: 63 EHSYRSTAKVV 73
+ R+ +V
Sbjct: 282 VETRRAMGDLV 292
>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 = 46.5 bits (111), Expect = 2e-07
Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
+ L+N RG L+D + + L++G + G LDV +P + + + K V++TPH+G
Sbjct: 228 TAYLINAARGPLVDEKALVDALKTGEIAGAALDVFEFEP-EVSPELKKLDNVILTPHIGN 286
Query: 61 VTEHSYRSTAKVVGDVALQLHAGTPLRGIEPVN 93
T + + AK D + L G P N
Sbjct: 287 ATVEARDAMAKEAADNIISF-----LEGKRPKN 314
>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 = 46.4 bits (111), Expect = 2e-07
Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G+ +N RG L+D + L SG L LDV +P P++P+ VL+TPH+ G
Sbjct: 233 GATFINTARGALVDEAALLAELRSGRLRAA-LDVTDPEPLPPDSPLRTLPNVLLTPHIAG 291
Query: 61 VT-EHSYRSTAKVVGDVALQLHAGTPLRG 88
T + R + ++ L AG PL
Sbjct: 292 STGDERRRLGDYALDELERFL-AGEPLLH 319
>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 = 46.1 bits (110), Expect = 3e-07
Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 3/91 (3%)
Query: 3 LLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGGVT 62
+ N GG+++ + LE G V P N+P+L V++TPH+ G T
Sbjct: 225 AINNARGGGVIEEAALDALLEEGIAAAALDVVEEEPP-PVNSPLLDLPNVILTPHIAGAT 283
Query: 63 EHSYRSTAKVVGDVALQLHAGTPLRGIEPVN 93
E + + A+ + L G VN
Sbjct: 284 EEAQENMAEEAAENLLAFLKGGTPPN--AVN 312
>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 = 44.1 bits (105), Expect = 1e-06
Identities = 33/86 (38%), Positives = 44/86 (51%), Gaps = 1/86 (1%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G+LLVN+ RG ++D + + L SG L LDV +P P +P+ VLITPHVGG
Sbjct: 212 GALLVNVARGPVVDTDALVAELASGRLR-AALDVTDPEPLPPGHPLWSAPGVLITPHVGG 270
Query: 61 VTEHSYRSTAKVVGDVALQLHAGTPL 86
T +V + AG PL
Sbjct: 271 ATPAFLPRAYALVRRQLRRYAAGEPL 296
>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 = 43.9 bits (104), Expect = 1e-06
Identities = 22/60 (36%), Positives = 35/60 (58%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
+ +VN+ RG +D + + LESG LGG LDV T+P ++P+ +++TPH G
Sbjct: 225 HAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLPASSPLWDAPNLILTPHAAG 284
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 43.9 bits (104), Expect = 2e-06
Identities = 25/62 (40%), Positives = 34/62 (54%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
GS LVN RG ++D + V LESGHL G DV + +P ++P +TPH+ G
Sbjct: 277 GSYLVNTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISG 336
Query: 61 VT 62
T
Sbjct: 337 TT 338
>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 = 43.4 bits (103), Expect = 2e-06
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 9/81 (11%)
Query: 4 LVNIVRGGLLDYEVVAHYLESGHLGGLGLDV-----AWTKPFDPNNPILKFQI----VLI 54
+N RG ++ + + L+SG + G LDV A + ++ I V++
Sbjct: 221 FINTARGKVVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVIL 280
Query: 55 TPHVGGVTEHSYRSTAKVVGD 75
TPH+ G T SY A+V+ D
Sbjct: 281 TPHIAGWTFESYEKIAEVLVD 301
>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 = 42.0 bits (100), Expect = 7e-06
Identities = 18/34 (52%), Positives = 25/34 (73%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDV 34
G +L+N RGGL+D + + L+SG +GGLGLDV
Sbjct: 226 GVMLINTSRGGLIDTKALIEALKSGKIGGLGLDV 259
>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 = 41.8 bits (99), Expect = 9e-06
Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 17/80 (21%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDV----------AWT-KPFDPNNPILKF 49
G++LVN RGGL+D + + L+SG + G LD W+ K + +LK
Sbjct: 227 GAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIED--EVLKE 284
Query: 50 QI----VLITPHVGGVTEHS 65
I VLITPH+ T+ +
Sbjct: 285 LIAMPNVLITPHIAFYTDTA 304
>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 = 39.9 bits (94), Expect = 4e-05
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 10/77 (12%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQI--VLITPHV 58
G++L+N RG ++D E + L+ G LGG D P L + V+ TPH+
Sbjct: 221 GAILLNFARGEIVDEEALLEALDEGKLGGYVTDFP--------EPALLGHLPNVIATPHL 272
Query: 59 GGVTEHSYRSTAKVVGD 75
G TE + + A +
Sbjct: 273 GASTEEAEENCAVMAAR 289
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 39.4 bits (92), Expect = 6e-05
Identities = 23/62 (37%), Positives = 35/62 (56%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G+ L+N+ RG + + + L+SG + G LDV +P P +P+ + V ITPHV
Sbjct: 219 GAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPPESPLWQHPRVAITPHVAA 278
Query: 61 VT 62
VT
Sbjct: 279 VT 280
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 37.8 bits (88), Expect = 2e-04
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
++ +N RG ++D + L+ G + GLDV +P ++P+L V+ PH+G
Sbjct: 229 SAIFINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGS 288
Query: 61 VTEHSYR 67
T H R
Sbjct: 289 AT-HETR 294
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 37.0 bits (86), Expect = 4e-04
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 13/76 (17%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDV-AWTKPFDP--------NNPILKFQI 51
G++ VN RG L+D + + L++G + G LD + +P P N+P+L+ I
Sbjct: 229 GAVFVNCARGSLVDTKALLDALDNGLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLI 288
Query: 52 ----VLITPHVGGVTE 63
V++TPH+ T+
Sbjct: 289 NREDVILTPHIAFYTD 304
>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 = 32.1 bits (74), Expect = 0.021
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 13/99 (13%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPN-NPILKFQIVLITPHVG 59
G +L+N RG ++D + + L+ G + LDV W +P + L ++ + TPH+
Sbjct: 199 GQILINASRGAVIDNQALLALLQRGKDLRVVLDV-W--ENEPEIDLELLDKVDIATPHIA 255
Query: 60 GVTEHSY----RSTAKVVGDVA--LQLHAGTPLRGIEPV 92
G +S R T + + L L A L + P
Sbjct: 256 G---YSLEGKARGTEMIYEALCQFLGLKARKSLSDLLPA 291
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 31.8 bits (72), Expect = 0.030
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 15/82 (18%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDV----------AWTKPFDPNNPILKFQ 50
G++LVN RG +++ + + G L G +D WT D ++ L
Sbjct: 227 GAILVNAARGAVINTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNK-DIDDKTLLEL 285
Query: 51 I----VLITPHVGGVTEHSYRS 68
I +L+TPH+ ++ + ++
Sbjct: 286 IEHERILVTPHIAFFSDEAVQN 307
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 31.8 bits (72), Expect = 0.031
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLGLDVAWTKPFDPNNPILKFQIVLITPHVGG 60
G++L+N RG ++D + L G + LDV W + N +LK ++ + TPH+ G
Sbjct: 200 GAILINACRGAVVDNTALLTCLNEGQKLSVVLDV-WEGEPELNVELLK-KVDIGTPHIAG 257
Query: 61 VT-EHSYRSTAKV 72
T E R T +V
Sbjct: 258 YTLEGKARGTTQV 270
>gnl|CDD|202599 pfam03340, Pox_Rif, Poxvirus rifampicin resistance protein.
Length = 541
Score = 26.2 bits (58), Expect = 2.5
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 30 LGLDVAWTKPFDPNNPILKF--QIVLITPHVGGVTEHSYRSTAKVVG 74
L + V + K DPNNPI Q+V++ + ++ + K+
Sbjct: 496 LSVRVVY-KSMDPNNPISYVNKQLVVVCTDLYKISYDNNIIVVKITE 541
>gnl|CDD|200476 cd11337, AmyAc_CMD_like, Alpha amylase catalytic domain found in
cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase
(NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC
3.2.1.133) catalyze the hydrolysis of alpha-(1,4)
glycosidic linkages on a number of substrates including
cyclomaltodextrins (CDs), pullulan, and starch. These
enzymes hydrolyze CDs and starch to maltose and pullulan
to panose by cleavage of alpha-1,4 glycosidic bonds
whereas alpha-amylases essentially lack activity on CDs
and pullulan. They also catalyze transglycosylation of
oligosaccharides to the C3-, C4- or C6-hydroxyl groups
of various acceptor sugar molecules. Since these
proteins are nearly indistinguishable from each other,
they are referred to as cyclomaltodextrinases (CMDs).
This group of CMDs is mainly bacterial. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 328
Score = 25.2 bits (56), Expect = 5.2
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 14 DY--EVVAHYLESGHLGGLGLDVAWTKPFD 41
DY +VV ++E + GL LD A+ D
Sbjct: 123 DYLFDVVRFWIEEFDIDGLRLDAAYCLDPD 152
>gnl|CDD|200477 cd11338, AmyAc_CMD, Alpha amylase catalytic domain found in
cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase
(NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC
3.2.1.133) catalyze the hydrolysis of alpha-(1,4)
glycosidic linkages on a number of substrates including
cyclomaltodextrins (CDs), pullulan, and starch. These
enzymes hydrolyze CDs and starch to maltose and pullulan
to panose by cleavage of alpha-1,4 glycosidic bonds
whereas alpha-amylases essentially lack activity on CDs
and pullulan. They also catalyze transglycosylation of
oligosaccharides to the C3-, C4- or C6-hydroxyl groups
of various acceptor sugar molecules. Since these
proteins are nearly indistinguishable from each other,
they are referred to as cyclomaltodextrinases (CMDs).
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 389
Score = 25.1 bits (56), Expect = 5.9
Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 12 LLDYE--VVAHYLESGHLGGLGLDVA 35
+ +Y V ++L+ G + G LDVA
Sbjct: 186 VREYLDSVARYWLKEGDIDGWRLDVA 211
>gnl|CDD|201173 pfam00351, Biopterin_H, Biopterin-dependent aromatic amino acid
hydroxylase. This family includes
phenylalanine-4-hydroxylase, the phenylketonuria
disease protein.
Length = 306
Score = 25.2 bits (55), Expect = 6.0
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 43 NNPILKFQIVLITPHVGGVTEHSYRSTAKVVGDVALQLHAGTPLRGIE 90
N +LK+ L H G + YR K D+A G P+ +E
Sbjct: 14 ANLVLKYGPELDADH-PGFKDPVYRQRRKYFADIAFNYKHGDPIPHVE 60
>gnl|CDD|233351 TIGR01304, IMP_DH_rel_2, IMP dehydrogenase family protein. This
model represents a family of proteins, often annotated
as a putative IMP dehydrogenase, related to IMP
dehydrogenase and GMP reductase. Most species with a
member of this family belong to the high GC
Gram-positive bacteria, and these also have the IMP
dehydrogenase described by TIGRFAMs equivalog model
TIGR01302 [Unknown function, General].
Length = 369
Score = 24.8 bits (54), Expect = 7.7
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 1 GSLLVNIVRGGLLDYEVVAHYLESGHLGGLG 31
G L V ++ GG+ DY H + +G G +
Sbjct: 185 GELDVPVIAGGVNDYTTALHLMRTGAAGVIV 215
>gnl|CDD|187658 cd08955, KR_2_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 2, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase, has 2 subdomains, each corresponding to a
short-chain dehydrogenases/reductase (SDR) family
monomer. The C-terminal subdomain catalyzes the
NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerizes but is composed of 2
subdomains, each resembling an SDR monomer. In some
instances, as in porcine FAS, an enoyl reductase (a
Rossman fold NAD binding domain of the MDR family)
module is inserted between the sub-domains. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic asparagine and tyrosine
are swapped, so that the canonical YXXXK motif changes
to YXXXN. Modular polyketide synthases are
multifunctional structures in which the makeup
recapitulates that found in (and may have evolved from)
fatty acid synthase. In some instances, such as
porcine FAS , an enoyl reductase module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER).
Polyketide syntheses also proceeds via the addition of
2-carbon units as in fatty acid synthesis. The complex
SDR NADP binding motif, GGXGXXG, is often present, but
is not strictly conserved in each instance of the
module. This subfamily includes the KR domain of the
Lyngbya majuscule Jam J, -K, and #L which are encoded
on the jam gene cluster and are involved in the
synthesis of the Jamaicamides (neurotoxins); Lyngbya
majuscule Jam P belongs to a different KR_FAS_SDR_x
subfamily. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
PGDH numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 376
Score = 24.6 bits (54), Expect = 8.7
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 19 AHYLESGHLGGLGLDVA 35
A YL +G LGGLGL VA
Sbjct: 150 ATYLITGGLGGLGLLVA 166
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447.
Members of this family, however, are not found in a
context of RecB and RecC and are longer by about 200
amino acids at the amino end. Chlamydia muridarum has
both a member of this family and a RecD [Unknown
function, Enzymes of unknown specificity].
Length = 720
Score = 24.7 bits (54), Expect = 9.6
Identities = 7/31 (22%), Positives = 12/31 (38%)
Query: 5 VNIVRGGLLDYEVVAHYLESGHLGGLGLDVA 35
+ E + YL S + G+G +A
Sbjct: 67 ERMELEAPTSKEGIVAYLSSRSIKGVGKKLA 97
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
0.319 0.142 0.433
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,854,829
Number of extensions: 402505
Number of successful extensions: 418
Number of sequences better than 10.0: 1
Number of HSP's gapped: 389
Number of HSP's successfully gapped: 71
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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 (21.7 bits)
S2: 53 (24.1 bits)