RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 045269
(99 letters)
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 176 bits (449), Expect = 3e-56
Identities = 70/92 (76%), Positives = 79/92 (85%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGV 67
+LLVNI RGGLLDY+AV LESGHLGGL +DVAW+EPFDP+DPILK +V+ITPHV GV
Sbjct: 256 ALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPILKHPNVIITPHVAGV 315
Query: 68 TEHSYRSTAKVVGDVALQLHAGTPLTGIEPVN 99
TE+SYRS K+VGD ALQLHAG PLTGIE VN
Sbjct: 316 TEYSYRSMGKIVGDAALQLHAGRPLTGIEFVN 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 = 113 bits (286), Expect = 3e-32
Identities = 40/86 (46%), Positives = 57/86 (66%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
++L+N RGGL+D EA+ L SGHL G GLDV W EP P+DP+L+ +V++TPH+ G
Sbjct: 226 GAILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAG 285
Query: 67 VTEHSYRSTAKVVGDVALQLHAGTPL 92
VT+ SY+ A +V + +L G P
Sbjct: 286 VTDESYQRMAAIVAENIARLLRGEPP 311
>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 = 80.3 bits (199), Expect = 1e-19
Identities = 25/73 (34%), Positives = 41/73 (56%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
++ +N R GL+D +A+ LE G +GG LDV EP + P+LK +V +TPH+ G
Sbjct: 230 TAYFINTARAGLVDEDALIEALEEGKIGGAALDVFPEEPLPADHPLLKLDNVTLTPHIAG 289
Query: 67 VTEHSYRSTAKVV 79
T + +++
Sbjct: 290 ATRDVAERSPEII 302
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 80.1 bits (198), Expect = 2e-19
Identities = 30/92 (32%), Positives = 53/92 (57%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
++L+N RGG++D +A+ L+SG + G LDV EP + P+ +V++TPH+GG
Sbjct: 226 GAILINAARGGVVDEDALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGG 285
Query: 67 VTEHSYRSTAKVVGDVALQLHAGTPLTGIEPV 98
T+ + A++V + ++ AG P+ P
Sbjct: 286 STDEAQERVAEIVAENIVRYLAGGPVVNNAPE 317
>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 = 75.6 bits (187), Expect = 1e-18
Identities = 24/59 (40%), Positives = 39/59 (66%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVG 65
++L+N RGGL+D +A+ L+SG + G LDV EP P+ P+L+ +V++TPH+
Sbjct: 117 GAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>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 = 77.4 bits (191), Expect = 2e-18
Identities = 38/91 (41%), Positives = 51/91 (56%), Gaps = 2/91 (2%)
Query: 6 TSSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVG 65
+LVN RG L+D EA+ L+SG + G GLDV EP + P+L +++V+ITPH+G
Sbjct: 230 KGVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIG 289
Query: 66 GVT-EHSYRSTAKVVGDVALQLHAGTPLTGI 95
T E Y KVV D+ AG GI
Sbjct: 290 AYTYESLYGMGEKVVDDI-EDFLAGKEPKGI 319
>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 = 75.6 bits (187), Expect = 6e-18
Identities = 31/82 (37%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
+ LVN RGGL+D A+A L+SG + G LDV EP + P+L +V++TPH
Sbjct: 225 GAFLVNTARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTPHAAW 284
Query: 67 VTEHSY----RSTAKVVGDVAL 84
+E S R A+ V V
Sbjct: 285 YSEESLAELRRKAAEEVVRVLR 306
>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 = 74.8 bits (185), Expect = 1e-17
Identities = 31/82 (37%), Positives = 47/82 (57%), Gaps = 3/82 (3%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
++L+N RGG++D A+A L+SG + G LDV EP + P+L +V++TPH+G
Sbjct: 221 GAILINTARGGIVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGA 280
Query: 67 VTEHSYRSTAKVVGDVALQLHA 88
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 = 73.0 bits (180), Expect = 6e-17
Identities = 27/64 (42%), Positives = 42/64 (65%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGV 67
++LVN RGGL+D +A+ L+SG + G LDV EP + P+L+ +V++TPH+ G
Sbjct: 224 AVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGY 283
Query: 68 TEHS 71
TE +
Sbjct: 284 TEEA 287
>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 = 71.0 bits (175), Expect = 4e-16
Identities = 26/70 (37%), Positives = 42/70 (60%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
++L+N RGGL+D EA+ L+SG + G LDV EP + P+L+ +V++TPH+G
Sbjct: 225 GAILINTARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGA 284
Query: 67 VTEHSYRSTA 76
T+ +
Sbjct: 285 STKEAVLRMG 294
>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 = 69.9 bits (172), Expect = 1e-15
Identities = 27/91 (29%), Positives = 47/91 (51%)
Query: 5 CTSSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHV 64
++L+N+ RG ++D +A+ LESG + G LDV EP + P+ +V+ITPH+
Sbjct: 216 KPGAVLINVGRGSVVDEDALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPHI 275
Query: 65 GGVTEHSYRSTAKVVGDVALQLHAGTPLTGI 95
G + ++ + + AG PL +
Sbjct: 276 SGDSPSYPERVVEIFLENLRRYLAGEPLLNV 306
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 69.6 bits (171), Expect = 2e-15
Identities = 28/73 (38%), Positives = 45/73 (61%), Gaps = 3/73 (4%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQS---VLITPHVGG 66
LVN RGGL+D +A+ L+SG + G GLDV EP + P+L+ + V++TPH+
Sbjct: 232 LVNTARGGLVDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIAS 291
Query: 67 VTEHSYRSTAKVV 79
TE + ++ A++
Sbjct: 292 ATEEARKAMAELA 304
>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 = 68.3 bits (168), Expect = 3e-15
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVTE 69
++N RGG++D EA+ L+SG L G LDV EP P +L+ +V +TPH+G T+
Sbjct: 225 IINTSRGGVIDEEALLEALKSGKLAGAALDVFENEP-PPGSKLLELPNVSLTPHIGASTK 283
Query: 70 HSYRSTAKVVGD 81
+ + + +
Sbjct: 284 EAQERIGEELAN 295
>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 = 67.9 bits (167), Expect = 5e-15
Identities = 26/59 (44%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQS-VLITPHV 64
++L+N RGGL+D +A+A L SG + G GLDV EP ++P+LK ++ITPH+
Sbjct: 226 GAILINTARGGLVDEQALADALNSGKIAGAGLDVLSQEPPRADNPLLKAAPNLIITPHI 284
>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 = 66.4 bits (163), Expect = 1e-14
Identities = 30/78 (38%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
++LLVN RG L+D A+ L +G + G LDV EP + P+ +VL+TPH+G
Sbjct: 226 TALLVNTSRGPLVDEGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIGY 285
Query: 67 VTEHSYRS-TAKVVGDVA 83
VTE +Y + V ++A
Sbjct: 286 VTEEAYEGFYGQAVENIA 303
>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 = 62.7 bits (153), Expect = 5e-13
Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVTE 69
+VN RGG++D A+ LE GH+ LDV EP ++P+ +V+ TPH+G T
Sbjct: 225 IVNCARGGIIDEAALYEALEEGHVRAAALDVFEKEP-PTDNPLFDLDNVIATPHLGASTR 283
Query: 70 HSYRSTAKVVGDVALQLHAGTPLTG 94
+ + A V + L G P+
Sbjct: 284 EAQENVATQVAEQVLDALKGLPVPN 308
>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 = 62.0 bits (152), Expect = 6e-13
Identities = 23/59 (38%), Positives = 39/59 (66%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVG 65
+++L+N RGG++D +A+ L+SG + G GLDV EP + P+L +V++ PH+G
Sbjct: 227 TAILINTARGGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIG 285
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 60.9 bits (149), Expect = 2e-12
Identities = 23/60 (38%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVTE 69
++N RGG++D A+A L+SG + G LDV EP + P+ + +V++TPH+G T
Sbjct: 226 IINCARGGIIDEAALAEALKSGKVAGAALDVFEKEP-PTDSPLFELPNVVVTPHLGASTA 284
>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 = 60.3 bits (147), Expect = 2e-12
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 9 LLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEP------FDPNDPILKFQSVLITP 62
+LVN+ RG ++D EA+ L+ + G +DV W P P + +V+++P
Sbjct: 222 ILVNVGRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSP 281
Query: 63 HVGGVTE 69
H G TE
Sbjct: 282 HNAGWTE 288
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 60.6 bits (148), Expect = 3e-12
Identities = 26/66 (39%), Positives = 41/66 (62%), Gaps = 4/66 (6%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPND----PILKFQSVLITPH 63
++L+N RG ++D +A+A L+SGHL G +DV EP D P+ +V++TPH
Sbjct: 233 AILINASRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPH 292
Query: 64 VGGVTE 69
+GG T+
Sbjct: 293 IGGSTQ 298
>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 = 60.4 bits (147), Expect = 3e-12
Identities = 25/61 (40%), Positives = 35/61 (57%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVTE 69
+ NI RG L+D +A+ LESG + G LDV EP + P+ +V+ITPHV T+
Sbjct: 243 VSNIARGSLVDTDALVAALESGQIRGAALDVTDPEPLPADHPLWSAPNVIITPHVSWQTQ 302
Query: 70 H 70
Sbjct: 303 E 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 = 59.9 bits (146), Expect = 3e-12
Identities = 24/64 (37%), Positives = 38/64 (59%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
+L +N+ RG +D +A+ L++ + G LDV EP + P+ +VLITPH+ G
Sbjct: 218 GALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDLDNVLITPHISG 277
Query: 67 VTEH 70
V+EH
Sbjct: 278 VSEH 281
>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 = 59.8 bits (146), Expect = 4e-12
Identities = 30/85 (35%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVTE 69
L+N+ RG L + L+SGHL G LDV EP + P+ + V +TPH+ +T
Sbjct: 218 LINVGRGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPLWRHPRVTVTPHIAAIT- 276
Query: 70 HSYRSTAKVVGDVALQLHAGTPLTG 94
S A V + +L AG PL
Sbjct: 277 -DPDSAAAQVAENIRRLEAGEPLPN 300
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 59.4 bits (144), Expect = 5e-12
Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
+++LVN RG ++D +A+ L+ G + G GLDV EP+ N+ + ++V++ PH+G
Sbjct: 233 TAILVNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPY-YNEELFSLKNVVLAPHIGS 291
Query: 67 VTEHSYRSTAKVV 79
T + A++V
Sbjct: 292 ATFEAREGMAELV 304
>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 = 59.3 bits (144), Expect = 6e-12
Identities = 28/86 (32%), Positives = 41/86 (47%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVTE 69
L+NI RGGL+D EA+ L+SG + LDV EP P+ V ++PH +
Sbjct: 220 LINIARGGLVDQEALLEALDSGRISLASLDVTDPEPLPEGHPLYTHPRVRLSPHTSAIAP 279
Query: 70 HSYRSTAKVVGDVALQLHAGTPLTGI 95
R+ A + + AG PL +
Sbjct: 280 DGRRNLADRFLENLARYRAGQPLHDL 305
>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 = 58.7 bits (143), Expect = 1e-11
Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVTE 69
+VN RG ++D +A+ LESG + GLDV EP N +LK +V + PH+G +T
Sbjct: 241 IVNTARGAVIDEDALVDALESGKVASAGLDVFENEPE-VNPGLLKMPNVTLLPHMGTLTV 299
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 315
Score = 57.6 bits (140), Expect = 3e-11
Identities = 33/86 (38%), Positives = 48/86 (55%), Gaps = 1/86 (1%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPND-PILKFQSVLITPHVG 65
S++L+N RG ++D EA+A L G + G G+DV EP P D P+L + ++TPHV
Sbjct: 226 SAILINTARGPVVDNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVA 285
Query: 66 GVTEHSYRSTAKVVGDVALQLHAGTP 91
TE + A++V D AG P
Sbjct: 286 FATEEAMEKRAEIVFDNIEAWLAGKP 311
>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 = 57.1 bits (139), Expect = 4e-11
Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 9 LLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVT 68
+LVN+ RG ++D A+ L+ G + G GLDV EP P +L +V++TPH+ T
Sbjct: 223 VLVNVARGSVVDEAALIAALQEGRIAGAGLDVFENEPNVP-AALLDLDNVVLTPHIASAT 281
Query: 69 EHSYRSTAKVV 79
+ R+ +V
Sbjct: 282 VETRRAMGDLV 292
>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 = 56.8 bits (138), Expect = 5e-11
Identities = 26/66 (39%), Positives = 40/66 (60%), Gaps = 4/66 (6%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPND----PILKFQSVLITPH 63
++L+N RG ++D +A+A L SGHL G +DV EP + P+ +V++TPH
Sbjct: 222 AILINASRGTVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPH 281
Query: 64 VGGVTE 69
+GG TE
Sbjct: 282 IGGSTE 287
>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 = 56.9 bits (138), Expect = 5e-11
Identities = 29/94 (30%), Positives = 48/94 (51%), Gaps = 6/94 (6%)
Query: 6 TSSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVG 65
++ L+N RG L+D +A+ L++G + G LDV EP + + + K +V++TPH+G
Sbjct: 227 PTAYLINAARGPLVDEKALVDALKTGEIAGAALDVFEFEP-EVSPELKKLDNVILTPHIG 285
Query: 66 GVTEHSYRSTAKVVGDVALQLHAGTPLTGIEPVN 99
T + + AK D + L G P N
Sbjct: 286 NATVEARDAMAKEAADNIISF-----LEGKRPKN 314
>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 = 56.1 bits (136), Expect = 9e-11
Identities = 32/89 (35%), Positives = 43/89 (48%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
+ LVN+ RG L+D +A+ L SG + G LDV EP P+ + LITPHV
Sbjct: 208 HAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEPLPDGHPLWSLPNALITPHVAN 267
Query: 67 VTEHSYRSTAKVVGDVALQLHAGTPLTGI 95
E A+ V + AG PL G+
Sbjct: 268 TPEVIRPLLAERVAENVRAFAAGEPLLGV 296
>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 = 55.8 bits (135), Expect = 1e-10
Identities = 26/67 (38%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTE-------PFDPNDPILKFQS-VL 59
+LLVN RG ++D AVA L+SGHLGG DV E P +L +
Sbjct: 229 ALLVNPCRGSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTV 288
Query: 60 ITPHVGG 66
TPH+G
Sbjct: 289 FTPHIGS 295
>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 = 53.4 bits (129), Expect = 7e-10
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 20/78 (25%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDV------------AWTEPFDP------- 48
++L+N RG ++D EA+ L+ G L G GLDV + E P
Sbjct: 223 AVLINTARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLL 282
Query: 49 -NDPILKFQSVLITPHVG 65
+ +L+ +V+ITPHV
Sbjct: 283 ADHALLRKPNVIITPHVA 300
>gnl|CDD|240620 cd01619, LDH_like, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-HicDH is a NAD-dependent member of the
hydroxycarboxylate dehydrogenase family, and shares the
Rossmann fold typical of many NAD binding proteins.
D-HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. Similar to the structurally
distinct L-HicDH, D-HicDH exhibits low side-chain R
specificity, accepting a wide range of 2-oxocarboxylic
acid side chains. (R)-2-hydroxyglutarate dehydrogenase
(HGDH) catalyzes the NAD-dependent reduction of
2-oxoglutarate to (R)-2-hydroxyglutarate.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 323
Score = 53.1 bits (128), Expect = 1e-09
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTE-------------PFDPNDPILKFQ 56
++N RG L+D EA+ L+SG + G GLDV E N + +
Sbjct: 228 IINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRRP 287
Query: 57 SVLITPHVGGVTEHSYR 73
+V+ITPH T+ + +
Sbjct: 288 NVIITPHTAFYTDDALK 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 = 53.0 bits (128), Expect = 1e-09
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 13/80 (16%)
Query: 9 LLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTE--------PFD--PNDPI---LKF 55
+++N RG L+D EA+ LESG +GG LDV E D N + F
Sbjct: 226 IIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAILRSF 285
Query: 56 QSVLITPHVGGVTEHSYRST 75
+V++TPH+ T+ +
Sbjct: 286 PNVILTPHMAFYTDQAVSDM 305
>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 = 52.9 bits (128), Expect = 1e-09
Identities = 30/88 (34%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGV 67
+ +N RG L+D A+ L SG L LDV EP P+ P+ +VL+TPH+ G
Sbjct: 234 ATFINTARGALVDEAALLAELRSGRLRAA-LDVTDPEPLPPDSPLRTLPNVLLTPHIAGS 292
Query: 68 T-EHSYRSTAKVVGDVALQLHAGTPLTG 94
T + R + ++ L AG PL
Sbjct: 293 TGDERRRLGDYALDELERFL-AGEPLLH 319
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 52.4 bits (126), Expect = 2e-09
Identities = 26/60 (43%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPIL--KFQSVLITPHV 64
+LL+N RGGL+D +A+A L SGHLGG DV EP +P+L +++TPH
Sbjct: 226 GALLINTARGGLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHS 285
>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 = 52.3 bits (126), Expect = 2e-09
Identities = 26/77 (33%), Positives = 36/77 (46%), Gaps = 14/77 (18%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDV------------AWTEPFDP--NDPI 52
++L+N RG L D EA+ LESG L G G DV + DP +
Sbjct: 227 GAILINTARGELQDEEAILEALESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKLL 286
Query: 53 LKFQSVLITPHVGGVTE 69
+ VL+TPH+G T+
Sbjct: 287 DLYPRVLLTPHIGSYTD 303
>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 = 51.9 bits (125), Expect = 3e-09
Identities = 24/91 (26%), Positives = 38/91 (41%), Gaps = 3/91 (3%)
Query: 9 LLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVT 68
+ N GG+++ A+ LE G V P N P+L +V++TPH+ G T
Sbjct: 225 AINNARGGGVIEEAALDALLEEGIAAAALDVVEEEPP-PVNSPLLDLPNVILTPHIAGAT 283
Query: 69 EHSYRSTAKVVGDVALQLHAGTPLTGIEPVN 99
E + + A+ + L G VN
Sbjct: 284 EEAQENMAEEAAENLLAFLKGGTPPN--AVN 312
>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 = 51.6 bits (124), Expect = 3e-09
Identities = 24/61 (39%), Positives = 36/61 (59%)
Query: 6 TSSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVG 65
+ +VN+ RG +D +A+ LESG LGG LDV TEP + P+ ++++TPH
Sbjct: 224 KHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLPASSPLWDAPNLILTPHAA 283
Query: 66 G 66
G
Sbjct: 284 G 284
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 51.5 bits (124), Expect = 4e-09
Identities = 21/61 (34%), Positives = 38/61 (62%), Gaps = 4/61 (6%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQS---VLITPH 63
++L+N+ RGG+++ + +A L+ + GLDV EP + N P+L ++ +LITPH
Sbjct: 225 GAILINVGRGGIVNEKDLAKALDEKDIY-AGLDVLEKEPMEKNHPLLSIKNKEKLLITPH 283
Query: 64 V 64
+
Sbjct: 284 I 284
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 50.6 bits (121), Expect = 9e-09
Identities = 22/62 (35%), Positives = 39/62 (62%), Gaps = 4/62 (6%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPIL----KFQSVLITP 62
++ L+N RG L+D +A+ LE+G + G LDV EP + ++P++ + ++LITP
Sbjct: 226 TAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNLLITP 285
Query: 63 HV 64
H+
Sbjct: 286 HI 287
>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 = 50.4 bits (121), Expect = 9e-09
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 9/81 (11%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPF----DPNDP-----ILKFQSVLI 60
+N RG ++ + + L+SG + G LDV E N P ++K V++
Sbjct: 221 FINTARGKVVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVIL 280
Query: 61 TPHVGGVTEHSYRSTAKVVGD 81
TPH+ G T SY A+V+ D
Sbjct: 281 TPHIAGWTFESYEKIAEVLVD 301
>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 = 49.9 bits (120), Expect = 2e-08
Identities = 34/84 (40%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 9 LLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVT 68
LLVN+ RG ++D +A+ L SG L LDV EP P P+ VLITPHVGG T
Sbjct: 214 LLVNVARGPVVDTDALVAELASGRLR-AALDVTDPEPLPPGHPLWSAPGVLITPHVGGAT 272
Query: 69 EHSYRSTAKVVGDVALQLHAGTPL 92
+V + AG PL
Sbjct: 273 PAFLPRAYALVRRQLRRYAAGEPL 296
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 49.5 bits (118), Expect = 2e-08
Identities = 24/60 (40%), Positives = 35/60 (58%)
Query: 9 LLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVT 68
L+VN RG ++D +AVA SGH+GG G DV + +P + P + +TPH+ G T
Sbjct: 286 LIVNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYMPNHAMTPHISGTT 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 = 48.9 bits (117), Expect = 4e-08
Identities = 26/61 (42%), Positives = 34/61 (55%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGV 67
+ LVN RG + D EAVA LESGHL G DV + +P + P + +TPH+ G
Sbjct: 248 AYLVNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMPNNAMTPHISGT 307
Query: 68 T 68
T
Sbjct: 308 T 308
>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 = 46.7 bits (112), Expect = 2e-07
Identities = 29/67 (43%), Positives = 37/67 (55%), Gaps = 13/67 (19%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPF----DPNDPI---------LKFQ 56
L+N RGGL+D +A+ L+SG +GGLGLDV E D +D I L F
Sbjct: 229 LINTSRGGLIDTKALIEALKSGKIGGLGLDVYEEEAGLFFEDHSDEIIQDDVLARLLSFP 288
Query: 57 SVLITPH 63
+VLIT H
Sbjct: 289 NVLITGH 295
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 45.5 bits (108), Expect = 5e-07
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
S++ +N RG ++D A+ L+ G + GLDV EP + P+L +V+ PH+G
Sbjct: 229 SAIFINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGS 288
Query: 67 VTEHSYR 73
T H R
Sbjct: 289 AT-HETR 294
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 45.0 bits (107), Expect = 8e-07
Identities = 25/61 (40%), Positives = 33/61 (54%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGV 67
S LVN RG ++D +AV LESGHL G DV + +P + P +TPH+ G
Sbjct: 278 SYLVNTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISGT 337
Query: 68 T 68
T
Sbjct: 338 T 338
>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 = 44.8 bits (107), Expect = 1e-06
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 13/78 (16%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTE-PFDPN--------DPILK--- 54
++LVN RGGL+D +A+ L+SG + G LD E + D +LK
Sbjct: 227 GAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEVLKELI 286
Query: 55 -FQSVLITPHVGGVTEHS 71
+VLITPH+ T+ +
Sbjct: 287 AMPNVLITPHIAFYTDTA 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 = 43.7 bits (104), Expect = 2e-06
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGVTE 69
L+N RG ++D EA+ L+ G LGG D F + +V+ TPH+G TE
Sbjct: 224 LLNFARGEIVDEEALLEALDEGKLGGYVTD------FPEPALLGHLPNVIATPHLGASTE 277
Query: 70 HSYRSTAKVVGD 81
+ + A +
Sbjct: 278 EAEENCAVMAAR 289
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 42.1 bits (99), Expect = 8e-06
Identities = 23/62 (37%), Positives = 33/62 (53%)
Query: 7 SSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
+ L+N+ RG + + + L+SG + G LDV EP P P+ + V ITPHV
Sbjct: 219 GAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPPESPLWQHPRVAITPHVAA 278
Query: 67 VT 68
VT
Sbjct: 279 VT 280
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 37.4 bits (87), Expect = 3e-04
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 13/75 (17%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTE-PFDP--------NDPILK---- 54
++ VN RG L+D +A+ L++G + G LD E P P NDP+L+
Sbjct: 230 AVFVNCARGSLVDTKALLDALDNGLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLIN 289
Query: 55 FQSVLITPHVGGVTE 69
+ V++TPH+ T+
Sbjct: 290 REDVILTPHIAFYTD 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 = 36.0 bits (84), Expect = 0.001
Identities = 29/99 (29%), Positives = 46/99 (46%), Gaps = 15/99 (15%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAW-TEPFDPNDPILKFQSVLI-TPHVG 65
+L+N RG ++D +A+ L+ G + LDV W EP + + +L V I TPH+
Sbjct: 200 QILINASRGAVIDNQALLALLQRGKDLRVVLDV-WENEP-EIDLELLDK--VDIATPHIA 255
Query: 66 GVTEHSY----RSTAKVVGDVA--LQLHAGTPLTGIEPV 98
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 = 32.6 bits (74), Expect = 0.020
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 15/87 (17%)
Query: 2 SDVCTSSLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDV----------AWTEPFDPNDP 51
V ++LVN RG +++ + + G L G +D WT D +D
Sbjct: 222 DHVKKGAILVNAARGAVINTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNK-DIDDK 280
Query: 52 IL----KFQSVLITPHVGGVTEHSYRS 74
L + + +L+TPH+ ++ + ++
Sbjct: 281 TLLELIEHERILVTPHIAFFSDEAVQN 307
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 30.6 bits (69), Expect = 0.080
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGGV 67
++L+N RG ++D A+ L G + LDV EP + N +LK + TPH+ G
Sbjct: 201 AILINACRGAVVDNTALLTCLNEGQKLSVVLDVWEGEP-ELNVELLKKVDI-GTPHIAGY 258
Query: 68 T-EHSYRSTAKV 78
T E R T +V
Sbjct: 259 TLEGKARGTTQV 270
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 27.5 bits (61), Expect = 1.3
Identities = 14/39 (35%), Positives = 25/39 (64%)
Query: 8 SLLVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPF 46
++LVN RG ++D A+ +L++ + +GLDV EP+
Sbjct: 266 AVLVNASRGPVIDEVALVEHLKANPMFRVGLDVFEDEPY 304
>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 = 27.4 bits (61), Expect = 1.4
Identities = 7/31 (22%), Positives = 12/31 (38%)
Query: 11 VNIVRGGLLDYEAVAHYLESGHLGGLGLDVA 41
+ E + YL S + G+G +A
Sbjct: 67 ERMELEAPTSKEGIVAYLSSRSIKGVGKKLA 97
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 26.9 bits (60), Expect = 1.5
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 10 LVNIVRGGLLDYEAVAHYLESGHLGGLGLDVAWTEPFDPNDPILKFQSVLITPHVGG 66
L+N RG ++D +A+ L SG LDV EP D L + TPH+ G
Sbjct: 203 LINASRGAVVDNQALREALLSGEDLDAVLDVWEGEP--QIDLELADLCTIATPHIAG 257
>gnl|CDD|147305 pfam05054, DUF673, Protein of unknown function (DUF673). Family
of uncharacterized viral proteins.
Length = 354
Score = 26.4 bits (59), Expect = 2.5
Identities = 6/26 (23%), Positives = 9/26 (34%)
Query: 54 KFQSVLITPHVGGVTEHSYRSTAKVV 79
F+SVL+ H + A
Sbjct: 57 TFKSVLVYKHESNFESRDPKKNANAT 82
>gnl|CDD|130336 TIGR01269, Tyr_3_monoox, tyrosine 3-monooxygenase, tetrameric.
This model describes tyrosine 3-monooxygenase, a member
of the family of tetrameric, biopterin-dependent
aromatic amino acid hydroxylases found in metazoans. It
is closely related to tetrameric
phenylalanine-4-hydroxylase and tryptophan
5-monooxygenase, and more distantly related to the
monomeric phenylalanine-4-hydroxylase found in some
Gram-negative bacteria.
Length = 457
Score = 26.0 bits (57), Expect = 3.9
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 54 KFQSVLITPHVGGVTEHSYRSTAKVVGDVALQLHAGTPLTGIE 96
KFQ L T H G + YR + + ++A Q G P+ +E
Sbjct: 142 KFQPDLDTDH-PGFHDKVYRQRREAIAEIAFQYKYGDPIPEVE 183
>gnl|CDD|215110 PLN00412, PLN00412, NADP-dependent glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 496
Score = 25.9 bits (57), Expect = 4.3
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 40 VAWTEPFDPNDPILKFQSV 58
+AW EPF P P+++ SV
Sbjct: 387 IAWEEPFGPVLPVIRINSV 405
>gnl|CDD|222736 pfam14399, BtrH, A predicted NlpC/p60-like peptidase. Members of
this family are often found in the gene neighborhood, or
fused to, non-ribosomal peptide synthetases. They are
predicted to function as trans-peptidases in peptide
metabolite biosynthesis.
Length = 329
Score = 25.8 bits (57), Expect = 4.3
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 22 EAVAHYLESGHLGGLGLDVAWTEPFDPND 50
E + L++G L LD+ + P+ PN+
Sbjct: 91 EELKELLDAGRPVILQLDMYYL-PYFPNE 118
>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 = 25.9 bits (57), Expect = 4.3
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 52 ILKFQSVLITPHVGGVTEHSYRSTAKVVGDVALQLHAGTPLTGIE 96
+LK+ L H G + YR K D+A G P+ +E
Sbjct: 17 VLKYGPELDADH-PGFKDPVYRQRRKYFADIAFNYKHGDPIPHVE 60
>gnl|CDD|143401 cd07082, ALDH_F11_NP-GAPDH, NADP+-dependent non-phosphorylating
glyceraldehyde 3-phosphate dehydrogenase and ALDH family
11. NADP+-dependent non-phosphorylating glyceraldehyde
3-phosphate dehydrogenase (NP-GAPDH, EC=1.2.1.9)
catalyzes the irreversible oxidation of glyceraldehyde
3-phosphate to 3-phosphoglycerate generating NADPH for
biosynthetic reactions. This CD also includes the
Arabidopsis thaliana osmotic-stress-inducible ALDH
family 11, ALDH11A3 and similar sequences. In
autotrophic eukaryotes, NP-GAPDH generates NADPH for
biosynthetic processes from photosynthetic
glyceraldehyde-3-phosphate exported from the chloroplast
and catalyzes one of the classic glycolytic bypass
reactions unique to plants.
Length = 473
Score = 25.6 bits (57), Expect = 4.4
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 38 LDVAWTEPFDPNDPILKFQSV 58
+ +AW EPF P PI++ +
Sbjct: 371 MRLAWEEPFGPVLPIIRVNDI 391
>gnl|CDD|222842 PHA01972, PHA01972, structural protein.
Length = 828
Score = 25.6 bits (56), Expect = 5.7
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 31 GHLGGLGLDVAWTEPFDPNDPILKFQSVL 59
GHL G+ D+ E F P DP F ++L
Sbjct: 328 GHLDGMSRDIGLVETFGP-DPDRNFNTLL 355
>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 = 6.5
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 20 DY--EAVAHYLESGHLGGLGLDVAWTEPFD 47
DY + V ++E + GL LD A+ D
Sbjct: 123 DYLFDVVRFWIEEFDIDGLRLDAAYCLDPD 152
>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 = 25.3 bits (56), Expect = 6.8
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 23 AVAHYLESGHLGGLGLDVA 41
A YL +G LGGLGL VA
Sbjct: 148 PDATYLITGGLGGLGLLVA 166
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
0.317 0.138 0.416
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,043,873
Number of extensions: 418063
Number of successful extensions: 451
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 77
Length of query: 99
Length of database: 10,937,602
Length adjustment: 65
Effective length of query: 34
Effective length of database: 8,054,592
Effective search space: 273856128
Effective search space used: 273856128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.3 bits)