RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6351
(168 letters)
>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 = 85.2 bits (212), Expect = 2e-20
Identities = 28/49 (57%), Positives = 35/49 (71%), Gaps = 2/49 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
L+ G GAALDVF +EPP ++ L+ P VI+TPHLGAST+EAQ R
Sbjct: 242 LKSGKIAGAALDVFEQEPPPAD--SPLLGLPNVILTPHLGASTEEAQER 288
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 80.9 bits (201), Expect = 2e-18
Identities = 27/49 (55%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
L+ G GAALDVF +EPP L + P V+VTPHLGAST EAQ
Sbjct: 244 LKSGKVAGAALDVFEKEPPTDS---PLFELPNVVVTPHLGASTAEAQEN 289
Score = 31.2 bits (72), Expect = 0.26
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 69 KNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSS--QNLV 120
++ + LT GLLS +N++N A E G++V S NL+
Sbjct: 360 EDTEPLTAAALKGLLSPVLGERVNYVNAPLLAKERGIEVEESKSEESPDYSNLI 413
>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 = 76.0 bits (188), Expect = 5e-17
Identities = 27/49 (55%), Positives = 33/49 (67%), Gaps = 3/49 (6%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
L+ G GAALDVF EPP +L++ P V +TPH+GASTKEAQ R
Sbjct: 243 LKSGKLAGAALDVFENEPPPGS---KLLELPNVSLTPHIGASTKEAQER 288
>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 = 73.1 bits (180), Expect = 9e-16
Identities = 47/187 (25%), Positives = 64/187 (34%), Gaps = 60/187 (32%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR---QDKQSIFY 61
L GH AALDVF +EPP L VI TPHLGAST+EAQ Q + +
Sbjct: 243 LEEGHVRAAALDVFEKEPPTDNP---LFDLDNVIATPHLGASTREAQENVATQVAEQVLD 299
Query: 62 SLLG-----------------AELK----------------------------------- 69
+L G +LK
Sbjct: 300 ALKGLPVPNAVNAPGIDADVMEKLKPYLDLAEKLGKLAGQLLDGAVQSVEVTYRGELATE 359
Query: 70 NKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSS--QNLVALAFGSN 127
N + LT GLLS + +N +N A E G+ V SS +N +++ +
Sbjct: 360 NSEPLTRAALKGLLSPVLDDEVNMVNAPAVAKERGITVEESKSESSPDYKNYLSVTVTGD 419
Query: 128 VAKHVLT 134
+
Sbjct: 420 SGTVSVA 426
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 68.9 bits (169), Expect = 2e-14
Identities = 26/49 (53%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
L G GAALDVF EEP ++ L P VI+TPH+G ST EAQ R
Sbjct: 247 LDSGKIAGAALDVFEEEPLPADS--PLWDLPNVILTPHIGGSTDEAQER 293
>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 = 68.3 bits (168), Expect = 3e-14
Identities = 28/49 (57%), Positives = 36/49 (73%), Gaps = 2/49 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
L+ G GAALDVF EEPP ++ L++ P VI+TPH+GASTKEA +R
Sbjct: 246 LKSGRIAGAALDVFEEEPPPADS--PLLELPNVILTPHIGASTKEAVLR 292
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 64.4 bits (158), Expect = 9e-13
Identities = 25/49 (51%), Positives = 31/49 (63%), Gaps = 2/49 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFE--LIKHPKVIVTPHLGASTKEAQ 51
L+ GH GAA+DVF EP + FE L VI+TPH+G ST+EAQ
Sbjct: 253 LKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPHIGGSTQEAQ 301
>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 = 61.8 bits (151), Expect = 6e-12
Identities = 27/49 (55%), Positives = 33/49 (67%), Gaps = 2/49 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTF--ELIKHPKVIVTPHLGASTKEAQ 51
LR GH GAA+DVF EEP + + F L P VI+TPH+G ST+EAQ
Sbjct: 242 LRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPHIGGSTEEAQ 290
>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 = 61.5 bits (150), Expect = 7e-12
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 1 MKSELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
+ L+ G GAALDVF EP ++ L++ P VI+TPH+ T+EA+ R
Sbjct: 240 LLRALKSGKIAGAALDVFEPEPLPADHP--LLELPNVILTPHIAGYTEEARER 290
>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 = 58.5 bits (142), Expect = 9e-11
Identities = 20/43 (46%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 11 GGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
AALDV EEPP L+ P VI+TPH+ +T+EAQ
Sbjct: 249 AAAALDVVEEEPPPVNS--PLLDLPNVILTPHIAGATEEAQEN 289
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 58.0 bits (141), Expect = 1e-10
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTF-ELIKHPKVIVTPHLGASTKEAQIRQDKQSI 59
L+ G GA LDVF EP + L P V++TPH+ ++T+EA+ + ++
Sbjct: 250 LKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAMAELAL 305
>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 = 55.9 bits (136), Expect = 2e-10
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLG 44
L+ G GAALDVF EP + L++ P VI+TPH+
Sbjct: 138 LKSGRIAGAALDVFEPEPLPPDH--PLLELPNVILTPHIA 175
>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 = 57.2 bits (139), Expect = 3e-10
Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQ 51
LR GH GA LDVF +EP + L++ VI+TPH+ T E+
Sbjct: 247 LRSGHLAGAGLDVFWQEPLPPDD--PLLRLDNVILTPHIAGVTDESY 291
>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 = 55.2 bits (134), Expect = 1e-09
Identities = 20/46 (43%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEA 50
L+ G GAALDV EEPP ++ L+ P VI+TPH ++E+
Sbjct: 246 LKSGRIAGAALDVLEEEPPPADS--PLLSAPNVILTPHAAWYSEES 289
>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 = 53.7 bits (130), Expect = 4e-09
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQ 54
L G GGAALDVF EEP ++ L+K V +TPH+ +T++ R
Sbjct: 251 LEEGKIGGAALDVFPEEPLPADH--PLLKLDNVTLTPHIAGATRDVAERS 298
>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 = 53.5 bits (129), Expect = 5e-09
Identities = 20/46 (43%), Positives = 29/46 (63%), Gaps = 2/46 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEA 50
L+ G GA LDV EEP K++ L+ + V++TPH+GA T E+
Sbjct: 252 LKSGKIAGAGLDVLEEEPIKADHP--LLHYENVVITPHIGAYTYES 295
>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 = 52.5 bits (127), Expect = 1e-08
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSI 59
L G A LDVF EP + L+K P V + PH+G T E Q + ++ +
Sbjct: 259 LESGKVASAGLDVFENEPEVNP---GLLKMPNVTLLPHMGTLTVETQEKMEELVL 310
>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 = 51.6 bits (125), Expect = 2e-08
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 5 LRCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
L+ G GA LDVF EP P L+ P V++ PH+G++T E +
Sbjct: 248 LKSGKIAGAGLDVFEPEPLPADH---PLLTLPNVVLLPHIGSATVETRTA 294
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 50.5 bits (121), Expect = 6e-08
Identities = 22/49 (44%), Positives = 28/49 (57%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
LR GH GGAA DV EPP + P++IVTPH ++EA+ R
Sbjct: 247 LRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQR 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 = 50.1 bits (121), Expect = 7e-08
Identities = 20/50 (40%), Positives = 32/50 (64%), Gaps = 3/50 (6%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIK-HPKVIVTPHLGASTKEAQIR 53
L G GA LDV +EPP+++ L+K P +I+TPH+ +++EA+ R
Sbjct: 247 LNSGKIAGAGLDVLSQEPPRADN--PLLKAAPNLIITPHIAWASREARQR 294
>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 = 48.7 bits (117), Expect = 3e-07
Identities = 23/47 (48%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 5 LRCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTKEA 50
LR G GAALDVF EP P L P V++TPH+G T+EA
Sbjct: 247 LRAGRIAGAALDVFDVEPLPADH---PLRGLPNVLLTPHIGYVTEEA 290
>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 = 48.3 bits (116), Expect = 3e-07
Identities = 17/42 (40%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 12 GAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
G + F EP P VI TPHLGAST+EA+
Sbjct: 248 GGYVTDF-PEPALLG------HLPNVIATPHLGASTEEAEEN 282
>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 = 47.6 bits (114), Expect = 5e-07
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEA-QIRQD 55
L G GA +DVF EPP + L+ P I+TPH+ +T+EA + R +
Sbjct: 247 LNEGKIAGAGIDVFDMEPPLPAD-YPLLHAPNTILTPHVAFATEEAMEKRAE 297
>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 = 47.5 bits (114), Expect = 5e-07
Identities = 20/43 (46%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGAST 47
L GH GA LDVF +EP ++ +HP+V VTPH+ A T
Sbjct: 236 LDSGHLSGAVLDVFEQEPLPADHPL--WRHPRVTVTPHIAAIT 276
>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 = 47.3 bits (113), Expect = 7e-07
Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 20/70 (28%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQ------------------TFELIKHPKVIVTPHLGAS 46
L+ G GA LDV +E E+ L++ P VI+TPH+ +
Sbjct: 243 LKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHALLRKPNVIITPHVAYN 302
Query: 47 TKEA--QIRQ 54
TKEA +I
Sbjct: 303 TKEALERILD 312
>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 = 47.1 bits (113), Expect = 8e-07
Identities = 20/46 (43%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 5 LRCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTKE 49
L G GAALDVF EEP P L P VI+TPH+ +
Sbjct: 239 LESGRIAGAALDVFEEEPLPADS---PLWDLPNVIITPHISGDSPS 281
>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 = 46.7 bits (112), Expect = 1e-06
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 5 LRCGHCGGAALDVFCEEP--PKSEQTFELIKHPKVIVTPHLGASTKEA 50
L+ G GA LDVF EP P L+ V++TPH+ ++T E
Sbjct: 242 LQEGRIAGAGLDVFENEPNVPA-----ALLDLDNVVLTPHIASATVET 284
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 45.2 bits (107), Expect = 4e-06
Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQ 51
L G GA LDVF EP E L +HP+V +TPH+ A T+ A+
Sbjct: 240 LDSGKVKGAMLDVFSREPLPPESP--LWQHPRVAITPHVAAVTRPAE 284
>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 = 44.1 bits (105), Expect = 8e-06
Identities = 24/48 (50%), Positives = 29/48 (60%), Gaps = 3/48 (6%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQI 52
L+ G GAALDVF EP S EL K VI+TPH+G +T EA+
Sbjct: 249 LKTGEIAGAALDVFEFEPEVSP---ELKKLDNVILTPHIGNATVEARD 293
>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 = 44.1 bits (105), Expect = 1e-05
Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 8 GHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYSLLGA 66
GAALDVF EEP PK L V++TPH+ ++ R IFY L +
Sbjct: 242 KQIRGAALDVFEEEPLPKDS---PLWDLDNVLITPHISGVSEHFNERL--FDIFYENLKS 296
Query: 67 ELKNKQFLT 75
L++ + L
Sbjct: 297 FLEDGELLK 305
>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 = 43.0 bits (102), Expect = 2e-05
Identities = 20/46 (43%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 5 LRCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTKE 49
L G GAALDV EP P L P VI+TPH+ T+E
Sbjct: 261 LESGQIRGAALDVTDPEPLPADH---PLWSAPNVIITPHVSWQTQE 303
>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 = 42.9 bits (102), Expect = 2e-05
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 3 SELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGAST 47
+ELR G AALDV EP + L P V++TPH+ ST
Sbjct: 252 AELRSGR-LRAALDVTDPEPLPPDS--PLRTLPNVLLTPHIAGST 293
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 42.9 bits (101), Expect = 3e-05
Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 3/49 (6%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
L+ G GA LDVF EEP +E EL V++ PH+G++T EA+
Sbjct: 254 LKEGWIAGAGLDVFEEEPYYNE---ELFSLKNVVLAPHIGSATFEAREG 299
>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 = 42.5 bits (101), Expect = 3e-05
Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 11/57 (19%)
Query: 5 LRCGHCGGAALDVF-CEEP--PK--SEQTF------ELIKHPKVIVTPHLGASTKEA 50
L G GAALD + E K S + ELI P V++TPH+ T A
Sbjct: 248 LDSGKIAGAALDTYENETGYFNKDWSGKEIEDEVLKELIAMPNVLITPHIAFYTDTA 304
>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 = 39.6 bits (93), Expect = 3e-04
Identities = 22/52 (42%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTF-------ELIKHPKVIVTPHLGASTKE 49
L+ G GA LDV E E F LIK PKVI+TPH+ T E
Sbjct: 239 LKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGWTFE 290
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 39.7 bits (93), Expect = 3e-04
Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGAST 47
L GH GG A+DV EP + ++KHP VI+TPH+ T
Sbjct: 276 LESGHLGGLAIDVAWSEPFDPDD--PILKHPNVIITPHVAGVT 316
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 39.7 bits (93), Expect = 3e-04
Identities = 19/54 (35%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 8 GHCGGAALDVFCEEPP-----KSEQTF------ELIKHPKVIVTPHLGASTKEA 50
G GAALD + E P + QT LI VI+TPH+ T A
Sbjct: 253 GLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHIAFYTDAA 306
>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 = 39.2 bits (92), Expect = 4e-04
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 9/70 (12%)
Query: 5 LRCGHCGGAALDVFCEEP------PKSEQTFELIKHPKVIVTPHLGASTKEAQI---RQD 55
L+ GH GG A DVF E P+S L +H + + TPH+G++ E ++ +
Sbjct: 249 LKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGSAVDEVRLEIELEA 308
Query: 56 KQSIFYSLLG 65
+I +L G
Sbjct: 309 ALNILQALQG 318
>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 = 39.3 bits (92), Expect = 4e-04
Identities = 19/39 (48%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 5 LRCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPH 42
L G GGAALDV EP P S L P +I+TPH
Sbjct: 246 LESGRLGGAALDVTATEPLPASSP---LWDAPNLILTPH 281
>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 = 39.2 bits (92), Expect = 4e-04
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 12/58 (20%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTF-----------ELIK-HPKVIVTPHLGASTKEA 50
L G G DV E + F +L+ +P+V++TPH+G+ T EA
Sbjct: 248 LESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKLLDLYPRVLLTPHIGSYTDEA 305
>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 = 37.8 bits (89), Expect = 0.001
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 11/57 (19%)
Query: 5 LRCGHCGGAALDVFCEEPP-----KSEQ-----TFE-LIKHPKVIVTPHLGASTKEA 50
L+ G GG LDV+ EE S++ L+ P V++T H TKEA
Sbjct: 247 LKSGKIGGLGLDVYEEEAGLFFEDHSDEIIQDDVLARLLSFPNVLITGHQAFFTKEA 303
>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 = 37.6 bits (88), Expect = 0.001
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 5 LRCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTKEAQIRQ 54
LR G GAALDV EP P + L P ++TPH+ A+T E
Sbjct: 229 LRSGEIAGAALDVTDPEPLPDGHPLWSL---PNALITPHV-ANTPEVIRPL 275
>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 = 37.3 bits (87), Expect = 0.002
Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 8 GHCGGAALDVFCEEPP-----KSEQTF------ELIKHPKVIVTPHLGASTKEA 50
G GA LDV +E P + F L + P VI+TPH T +A
Sbjct: 249 GKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRRPNVIITPHTAFYTDDA 302
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 37.1 bits (86), Expect = 0.002
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 6/43 (13%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELI----KHPKVIVTPHL 43
L G GAALDV +EPP+ + LI + P +++TPH+
Sbjct: 247 LENGKIAGAALDVLVKEPPEKDNP--LIQAAKRLPNLLITPHI 287
>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 = 36.1 bits (84), Expect = 0.004
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFE----LIKHPKVIVTPHLGASTKEA-QIRQD 55
L+ GAA+DV+ P + + + P VI++PH T+E + R D
Sbjct: 241 LKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEETFRRRID 296
>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 = 35.3 bits (82), Expect = 0.008
Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 8 GHCGGAALDVFCEE-----------PPKSEQTFELIKHPKVIVTPHLGASTKEA 50
G GGAALDV E + + L P VI+TPH+ T +A
Sbjct: 248 GKIGGAALDVIEGEDGIYYNDRKGDILSNRELAILRSFPNVILTPHMAFYTDQA 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 = 34.9 bits (81), Expect = 0.013
Identities = 19/46 (41%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 4 ELRCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTK 48
EL G AALDV EP P L P V++TPH+G +T
Sbjct: 232 ELASGRLR-AALDVTDPEPLPPGH---PLWSAPGVLITPHVGGATP 273
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 34.3 bits (79), Expect = 0.016
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 5 LRCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTKE 49
L+ G A LDVF +EP L+ P V+ PH+G++T E
Sbjct: 250 LQKGEIHAAGLDVFEQEPLSVDS---PLLSLPNVVAVPHIGSATHE 292
>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 = 32.7 bits (75), Expect = 0.071
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 8 GHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
G A+LDV EP HP+V ++PH A + +
Sbjct: 241 GRISLASLDVTDPEPLPEGHPL--YTHPRVRLSPHTSAIAPDGRRN 284
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 31.5 bits (72), Expect = 0.15
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 12 GAALDVFCEEPPKSEQTFELIK-HPKVIVTPHLGASTKEA 50
A LDV +EP + IK K+++TPH+ ++KEA
Sbjct: 252 YAGLDVLEKEPMEKNHPLLSIKNKEKLLITPHIAWASKEA 291
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 31.0 bits (70), Expect = 0.23
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 11/54 (20%)
Query: 8 GHCGGAALDVFCEEPP-----------KSEQTFELIKHPKVIVTPHLGASTKEA 50
G GAA+D + E + ELI+H +++VTPH+ + EA
Sbjct: 251 GTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIAFFSDEA 304
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 31.0 bits (70), Expect = 0.27
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 8 GHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
GH GG DV+ +P + + + P +TPH+ +T +AQ+R
Sbjct: 308 GHIGGYGGDVWYPQPAPKDHPWRYM--PNHAMTPHISGTTIDAQLR 351
>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 = 30.4 bits (69), Expect = 0.35
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
L GH G A DV+ +P + + + P +TPH+ +T +AQ R
Sbjct: 268 LESGHLAGYAGDVWFPQPAPKDHPWRTM--PNNAMTPHISGTTLDAQAR 314
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 28.3 bits (64), Expect = 2.0
Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 12/51 (23%)
Query: 11 GGAALDVFCEEPPKSEQTFELIKH------------PKVIVTPHLGASTKE 49
GG L +F E P E +L+K P + G E
Sbjct: 449 GGTILHLFLGESPDPEALKKLVKKAAKTGLPYFTITPTFSICNDCGYIDGE 499
>gnl|CDD|150760 pfam10122, Mu-like_Com, Mu-like prophage protein Com. Members of
this family of proteins comprise the translational
regulator of mom.
Length = 51
Score = 25.9 bits (57), Expect = 2.7
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 1 MKSELRCGHCG 11
M +RCGHC
Sbjct: 1 MLKNIRCGHCN 11
>gnl|CDD|182035 PRK09699, PRK09699, D-allose transporter subunit; Provisional.
Length = 312
Score = 27.8 bits (62), Expect = 2.8
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 37 VIVTPHLGASTKEAQIRQDKQSIFYSLLGAE--LKNKQFLTTPVQIGLLSGRTSNGLNFI 94
V+ T LGA+ A + + +I +++G K + + V GL+ G +NGLN +
Sbjct: 226 VVSTARLGAAEPLAGMGFETYAIASAIIGGTSFFGGKGRIFSVVIGGLIIGTINNGLNIL 285
Query: 95 NVNTYASE---GGLKVA 108
V TY GGL +A
Sbjct: 286 QVQTYYQLVVMGGLIIA 302
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 26.5 bits (58), Expect = 2.9
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 55 DKQSIFYSLLGAELKNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLK----VAYE 110
D +IF LG ++ + QIG++ G IN+ T G LK V+++
Sbjct: 1 DNNTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 60
Query: 111 HDPSS 115
PS+
Sbjct: 61 DPPSA 65
>gnl|CDD|197662 smart00336, BBOX, B-Box-type zinc finger.
Length = 42
Score = 25.0 bits (55), Expect = 4.6
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 2 KSELRCGHCGGAALDVFCEE 21
+ +C G + FCEE
Sbjct: 1 QRAPKCDSHGDEPAEFFCEE 20
>gnl|CDD|140322 PTZ00301, PTZ00301, uridine kinase; Provisional.
Length = 210
Score = 26.9 bits (59), Expect = 5.7
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 9/42 (21%)
Query: 3 SELRCGHCGGAALDVFCEE--------PPKSEQTFELIKHPK 36
SEL HCG ++ V CE+ P+SE+ + HPK
Sbjct: 25 SELMA-HCGPVSIGVICEDFYYRDQSNIPESERAYTNYDHPK 65
>gnl|CDD|132900 cd06845, Bcl-2_like, Apoptosis regulator proteins of the Bcl-2
family, named after B-cell lymphoma 2. This alignment
model spans what have been described as Bcl-2 homology
regions BH1, BH2, BH3, and BH4. Many members of this
family have an additional C-terminal transmembrane
segment. Some homologous proteins, which are not
included in this model, may miss either the BH4 (Bax,
Bak) or the BH2 (Bcl-X(S)) region, and some appear to
only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1).
This family is involved in the regulation of the outer
mitochondrial membrane's permeability and in promoting
or preventing the release of apoptogenic factors, which
in turn may trigger apoptosis by activating caspases.
Bcl-2 and the closely related Bcl-X(L) are
anti-apoptotic key regulators of programmed cell death.
They are assumed to function via heterodimeric
protein-protein interactions, binding pro-apoptotic
proteins such as Bad (BCL2-antagonist of cell death),
Bid, and Bim, by specifically interacting with their BH3
regions. Interfering with this heterodimeric interaction
via small-molecule inhibitors may prove effective in
targeting various cancers. This family also includes the
Caenorhabditis elegans Bcl-2 homolog CED-9, which binds
to CED-4, the C. Elegans homolog of mammalian Apaf-1.
Apaf-1, however, does not seem to be inhibited by Bcl-2
directly.
Length = 144
Score = 26.1 bits (58), Expect = 7.3
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 119 LVAL-AFGSNVAKHVLTVKQGLFTELLSYSLILVLQEDTAQW 159
+VAL AFG +A + ++ L+E+ A W
Sbjct: 90 IVALFAFGGRLAVKCVEQGLPELVRSIAEWTSDFLEENLADW 131
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 26.6 bits (59), Expect = 7.9
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
L GH G A DV+ +P ++ + + + TPH+ +T AQ R
Sbjct: 298 LESGHLAGYAGDVWFPQPAPADHPWRTMPRNGM--TPHISGTTLSAQAR 344
>gnl|CDD|237838 PRK14862, rimO, ribosomal protein S12 methylthiotransferase;
Provisional.
Length = 440
Score = 26.4 bits (59), Expect = 9.2
Identities = 13/19 (68%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 36 KVIVTPHLGASTKEAQIRQ 54
KVIVT LGA KE QIR+
Sbjct: 76 KVIVTGCLGA--KEDQIRE 92
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
0.316 0.132 0.379
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,100,762
Number of extensions: 699158
Number of successful extensions: 618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 573
Number of HSP's successfully gapped: 67
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
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: 55 (25.0 bits)